@article{Helton2018,
abstract = {Streams and rivers can be highly reactive sites for nitrogen (N) transformation and removal. Empirical and model-based research show how location in a stream network affects rates of N removal. Because the structure of stream networks can vary widely and N cycling in headwater streams may affect N cycling in downstream reaches, we hypothesised that network structure may affect whole stream network processing of N. We generated three stream networks with the same catchment area but differing shapes, based on optimal channel network theory. We applied a model of nitrate ((Formula presented.)) transport and denitrification, and implemented model scenarios to examine how network shape affects (Formula presented.) removal with (1) increased (Formula presented.) loading from the catchment, (2) altered spatial distributions of (Formula presented.) loading and (3) decreased drainage density (i.e. loss of headwater streams). For all stream networks, the fraction of total (Formula presented.) removed decreased with increasing (Formula presented.) loading from the catchment. Stream networks in narrow catchments removed a higher fraction of (Formula presented.), particularly at intermediate (Formula presented.) loading rates. Network shape also controlled the distribution of removal in small versus large streams, with larger streams removing a higher fraction of the total (Formula presented.) load in narrower networks. The effects of network shape on (Formula presented.) removal when the spatial distribution of (Formula presented.) loading was altered varied with the magnitude of (Formula presented.) loading. At low loads, (Formula presented.) was entirely removed when added to distal parts of the stream network, and about 50{\%} removed when added near the outlet; there was no effect of network shape. At intermediate and high loads, the fraction of total (Formula presented.) load removed by the narrow stream network was 1.5× higher than the rectangular and square networks when (Formula presented.) was added to distal parts of the networks. Network shape did not have an effect when (Formula presented.) load occurred near the outlet, regardless of the magnitude of the (Formula presented.) load. The fraction of total (Formula presented.) removed by the stream network was up to 5{\%} lower when drainage density was reduced from 1.0 to 0.74 km−1, with the least change for the narrow network. Reducing the drainage density also altered the role of small relative to large streams, with the net effect of moving the location of (Formula presented.) removal downstream. Overall, effects of network shape contributed up to 20{\%} of the variation in the fraction of (Formula presented.) removed by stream networks. Network shape was most important at intermediate to high (Formula presented.) loads and when (Formula presented.) was loaded to distal parts of the catchment. The narrow network removed more (Formula presented.) across model scenarios, with elevated removal in larger streams explaining most of the difference. We suggest the shape of the catchment may modulate the degree to which large streams contribute to whole network (Formula presented.) removal.},
author = {Helton, <NAME>. and Hall, <NAME>. and <NAME>},
doi = {10.1111/fwb.12990},
file = {:Users/mtalluto/work/Mendeley/Helton, Hall, Bertuzzo{\_}2018.pdf:pdf},
issn = {13652427},
journal = {Freshwater Biology},
keywords = {drainage density,nitrate loading,nitrate uptake,stream network,watershed},
mendeley-groups = {FLUFLUX Model},
number = {1},
pages = {128--140},
title = {{How network structure can affect nitrogen removal by streams}},
volume = {63},
year = {2018}
}
@article{BENDA2004,
abstract = {Abstract Hierarchical and branching river networks interact with dynamic watershed disturbances, such as fires, storms, and floods, to impose a spatial and temporal organization on the nonuniform distribution of riverine habitats, with consequences for ...},
author = {<NAME> <NAME> and <NAME> <NAME>, <NAME> <NAME>},
doi = {10.1641/0006-3568(2004)054[0413:tndhhc]2.0.co;2},
file = {:Users/mtalluto/work/Mendeley/Benda et al.{\_}2004.pdf:pdf},
issn = {0006-3568},
journal = {BioScience},
keywords = {disturbance,fluvial geomorphology,landscape ecology,river ecology,river networks},
mendeley-groups = {FLUFLUX Model},
number = {5},
pages = {413},
title = {{The Network Dynamics Hypothesis: How Channel Networks Structure Riverine Habitats}},
volume = {54},
year = {2004}
}
@article{Heino2015,
abstract = {Metacommunity ecology addresses the situation where sets of local communities are connected by the dispersal of a number of potentially interacting species. Aquatic systems (e.g. lentic versus lotic versus marine) differ from each other in connectivity and environmental heterogeneity, suggesting that metacommunity organisation also differs between major aquatic systems. Here, we review findings from observational field studies on metacommunity organisation in aquatic systems. Species sorting (i.e. species are 'filtered' by environmental factors and occur only at environmentally suitable sites) prevails in aquatic systems, particularly in streams and lakes, but the degree to which dispersal limitation interacts with such environmental control varies among different systems and spatial scales. For example, mainstem rivers and marine coastal systems may be strongly affected by 'mass effects' (i.e. where high dispersal rates homogenise communities to some degree at neighbouring localities, irrespective of their abiotic and biotic environmental conditions), whereas isolated lakes and ponds may be structured by dispersal limitation (i.e. some species do not occur at otherwise-suitable localities simply because sites with potential colonists are too far away). Flow directionality in running waters also differs from water movements in other systems, and this difference may also have effects on the role of dispersal in different aquatic systems. Dispersal limitation typically increases with increasing spatial distance between sites, mass effects potentially increase in importance with decreasing distance between sites, and the dispersal ability of organisms may determine the spatial extents at which species sorting and dispersal processes are most important. A better understanding of the relative roles of species sorting, mass effects and dispersal limitation in affecting aquatic metacommunities requires the following: (i) characterising dispersal rates more directly or adopting better proxies than have been used previously; (ii) considering the nature of aquatic networks; (iii) combining correlative and experimental approaches; (iv) exploring temporal aspects of metacommunity organisation and (v) applying past approaches and statistical methods innovatively for increasing our understanding of metacommunity organisation.},
author = {<NAME>. and <NAME>},
doi = {10.1111/fwb.12533},
file = {:Users/mtalluto/work/Mendeley/Heino et al.{\_}2015.pdf:pdf},
issn = {13652427},
journal = {Freshwater Biology},
keywords = {Dispersal limitation,Dispersal rates,Environmental heterogeneity,Mass effects,Spatial processes,Species sorting},
mendeley-groups = {FLUFLUX Model},
number = {5},
pages = {845--869},
title = {{Metacommunity organisation, spatial extent and dispersal in aquatic systems: Patterns, processes and prospects}},
volume = {60},
year = {2015}
}

@article{Gounand2018,
abstract = {The meta-ecosystem framework demonstrates the significance of among-ecosystem spatial flows for ecosystem dynamics and has fostered a rich body of theory. The high level of abstraction of the models, however, impedes applications to empirical systems. We argue that further understanding of spatial dynamics in natural systems strongly depends on dense exchanges between field and theory. From empiricists, more and specific quantifications of spatial flows are needed, defined by the major categories of organismal movement (dispersal, foraging, life-cycle, and migration). In parallel, the theoretical framework must account for the distinct spatial scales at which these naturally common spatial flows occur. Integrating all levels of spatial connections among landscape elements will upgrade and unify landscape and meta-ecosystem ecology into a single framework for spatial ecology. Cross-ecosystem movements drive landscape dynamics. Among-ecosystem couplings are either dispersal- or resource-dominated. Dispersal-based couplings occur at the regional scale between similar habitat types. Resource-based couplings occur at the local scale between different habitat types.},
author = {<NAME> <NAME>, <NAME>. and Altermatt, Florian},
doi = {10.1016/j.tree.2017.10.006},
file = {:Users/mtalluto/work/Mendeley/Gounand et al.{\_}2018.pdf:pdf},
issn = {01695347},
journal = {Trends in Ecology and Evolution},
keywords = {animal movement,landscape,meta-ecosystem,metacommunity,resource flow,subsidy},
mendeley-groups = {FLUFLUX Model},
number = {1},
pages = {36--46},
publisher = {Elsevier Ltd},
title = {{Meta-Ecosystems 2.0: Rooting the Theory into the Field}},
url = {http://dx.doi.org/10.1016/j.tree.2017.10.006},
volume = {33},
year = {2018}
}

@article{Altermatt2020,
abstract = {Uncovering biodiversity as an inherent feature of ecosystems and understanding its effects on ecosystem processes is one of the most central goals of ecology. Studying organisms' occurrence and biodiversity patterns in natural ecosystems has spurred the discovery of foundational ecological rules, such as the species–area relationship, and is of general scientific interest. Recent global changes add relevance and urgency to understanding the occurrence and diversity of organisms, and their respective roles in ecosystem processes. While information on ecosystem properties and abiotic environmental conditions are now available at unprecedented, highly-resolved spatial and temporal scales, the most fundamental variable – biodiversity itself – is still often studied in a local perspective, and generally not available at a wide taxonomic breadth, high temporal scale and spatial coverage. This is limiting the capacity and impact of ecology as a field of science. In this forum article, we propose that complete biodiversity assessments should be inclusive across taxonomic and functional groups, across space, and across time to better understand emergent properties, such as ecosystem functioning. We use riverine ecosystems as a case example because they are among the most biodiverse ecosystems worldwide, but are also highly threatened, such that an in-depth understanding of these systems is critically needed. Furthermore, their inherent spatial structure requires a multiscale perspective and consideration of spatial autocorrelation structures commonly ignored in biodiversity–ecosystem functioning studies. We show how recent methodological advances in environmental DNA (eDNA) provide novel opportunities to uncover broad biodiversity and link it to ecosystem processes, with the potential to revolutionize ecology and biodiversity sciences. We then outline a roadmap for using this technique to assess biodiversity in a complete and inclusive manner. Our proposed approach will help to get an understanding of biodiversity and associated ecosystem processes at spatial scales relevant for landscape ecology and environmental managers.},
author = {Altermatt, <NAME> Little, <NAME> M{\"{a}}chler, <NAME> Wang, <NAME> Zhang, <NAME>.},
doi = {10.1111/oik.06806},
file = {:Users/mtalluto/work/Mendeley/Altermatt et al.{\_}2020.pdf:pdf},
isbn = {0000000248},
issn = {16000706},
journal = {Oikos},
keywords = {biomonitoring,dendritic networks,eDNA,ecosystem function,environmental DNA,spatial ecology},
mendeley-groups = {FLUFLUX Model},
number = {December 2019},
pages = {1--12},
title = {{Uncovering the complete biodiversity structure in spatial networks: the example of riverine systems}},
year = {2020}
}

@article{Terui2018,
abstract = {Intraspecific population diversity (specifically, spatial asynchrony of population dynamics) is an essential component of metapopulation stability and persistence in nature. In 2D systems, theory predicts that metapopulation stability should increase with ecosystem size (or habitat network size): Larger ecosystems will harbor more diverse subpopulations with more stable aggregate dynamics. However, current theories developed in simplified landscapes may be inadequate to predict emergent properties of branching ecosystems, an overlooked but widespread habitat geometry. Here, we combine theory and analyses of a unique long-term dataset to show that a scale-invariant characteristic of fractal river networks, branching complexity (measured as branching probability), stabilizes watershed metapopulations. In riverine systems, each branch (i.e., tributary) exhibits distinctive ecological dynamics, and confluences serve as “merging” points of those branches. Hence, increased levels of branching complexity should confer a greater likelihood of integrating asynchronous dynamics over the landscape. We theoretically revealed that the stabilizing effect of branching complexity is a consequence of purely probabilistic processes in natural conditions, where within-branch synchrony exceeds among-branch synchrony. Contrary to current theories developed in 2D systems, metapopulation size (a variable closely related to ecosystem size) had vague effects on metapopulation stability. These theoretical predictions were supported by 18-y observations of fish populations across 31 watersheds: Our cross-watershed comparisons revealed consistent stabilizing effects of branching complexity on metapopulations of very different riverine fishes. A strong association between branching complexity and metapopulation stability is likely to be a pervasive feature of branching networks that strongly affects species persistence during rapid environmental changes.},
author = {<NAME>, Nobuo and Urabe, Hirokazu and Ono, Satoru and Finlay, <NAME>. and <NAME>},
doi = {10.1073/pnas.1800060115},
file = {:Users/mtalluto/work/Mendeley/Terui et al.{\_}2018(2).pdf:pdf},
issn = {10916490},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
keywords = {Dendritic ecological network,Dispersal,Portfolio effect,Spatially structured population,Stream},
number = {26},
pages = {E5963--E5969},
title = {{Metapopulation stability in branching river networks}},
volume = {115},
year = {2018}
}
@article{Mouillot:2014cj,
author = {<NAME>{\'{<NAME>{\'{e}}<NAME> Arias-Gonz{\'{a}}lez, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>},
file = {:Users/mtalluto/work/Mendeley/Relevance, Functional, Fish{\_}2008.pdf:pdf},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
month = {sep},
number = {38},
pages = {13757--13762},
title = {{Functional over-redundancy and high functional vulnerability in global fish faunas on tropical reefs.}},
volume = {111},
year = {2014}
}
@article{Mazel2018,
abstract = {In the face of the biodiversity crisis, it is argued that we should prioritize species in order to capture high functional diversity (FD). Because species traits often reflect shared evolutionary history, many researchers have assumed that maximizing phylogenetic diversity (PD) should indirectly capture FD, a hypothesis that we name the “phylogenetic gambit”. Here, we empirically test this gambit using data on ecologically relevant traits from {\textgreater}15,000 vertebrate species. Specifically, we estimate a measure of surrogacy of PD for FD. We find that maximizing PD results in an average gain of 18{\%} of FD relative to random choice. However, this average gain obscures the fact that in over one-third of the comparisons, maximum PD sets contain less FD than randomly chosen sets of species. These results suggest that, while maximizing PD protection can help to protect FD, it represents a risky conservation strategy.},
author = {<NAME>, <NAME>. and Cadotte, <NAME>. and <NAME> and {<NAME>}, <NAME> and <NAME>, <NAME> Mouillot, <NAME>, <NAME>, <NAME>.},
doi = {10.1038/s41467-018-05126-3},
file = {:Users/mtalluto/work/Mendeley/Mazel et al.{\_}2018.pdf:pdf},
isbn = {4146701805},
issn = {20411723},
journal = {Nature Communications},
number = {1},
publisher = {Springer US},
title = {{Prioritizing phylogenetic diversity captures functional diversity unreliably}},
url = {http://dx.doi.org/10.1038/s41467-018-05126-3},
volume = {9},
year = {2018}
}
@article{Relevance2008,
author = {Relevance, Ecological and Functional, Fish and Fish, Traits},
file = {:Users/mtalluto/work/Mendeley/Relevance, Functional, Fish{\_}2008.pdf:pdf},
number = {1},
pages = {1--4},
title = {{Mouillot et al 2011 Supporting Info}},
volume = {105},
year = {2008}
}
@article{Rosauer:2017fx,
author = {Rosauer, <NAME> and Pollock, <NAME> and <NAME> and Jetz, Walter},
journal = {Proceedings. Biological sciences},
month = {oct},
number = {1865},
pages = {20170627},
title = {{Phylogenetically informed spatial planning is required to conserve the mammalian tree of life.}},
volume = {284},
year = {2017}
}
@article{Pavoine2014,
abstract = {Ecological studies often rely on coefficients of intercommunity (dis)similarity to decipher effects of ecological, evolutionary and human-driven mechanisms on the composition of communities. Yet, two main criticisms have been levelled at (dis)similarity coefficients. First, few developments include information on species' abundances, and either phylogeny or functional traits. Secondly, some (dis)similarity coefficients fail to always provide maximum dissimilarity between two completely distinct communities, that is, communities without common species and with zero similarities among their species. Here, we introduce a new family of similarity coefficients responding to these criticisms. Within this family, we concentrate on four coefficients and compare them to Rao's dissimilarity on macroinvertebrate communities, and simulated data. Our new coefficients correctly treat maximally dissimilar communities: similarities are always zero between two completely distinct communities. The originality of these new coefficients is even more profound as the existence of maximally dissimilar communities was not a requirement for the new coefficients to behave differently than Rao's dissimilarity coefficient. Our new family of similarity coefficients relies on the abundances or occurrences of species within communities and on phylogenetic, taxonomic or functional similarities among species. We demonstrate that this new family embeds many of the recent developments in both functional and phylogenetic diversity. It provides a unique framework for comparing traditional compositional turnover with functional or phylogenetic similarities among communities. {\textcopyright} 2014 British Ecological Society.},
author = {<NAME> and <NAME>},
doi = {10.1111/2041-210X.12193},
file = {:Users/mtalluto/work/Mendeley/Pavoine, Ricotta{\_}2014.pdf:pdf},
issn = {2041210X},
journal = {Methods in Ecology and Evolution},
keywords = {Beta diversity,Biodiversity,Choice of coefficient,Community ecology,Community phylogenetics,Compositional turnover,Principle of maximum dissimilarity,Quadratic entropy},
number = {7},
pages = {666--675},
title = {{Functional and phylogenetic similarity among communities}},
volume = {5},
year = {2014}
}
@article{Maire2015,
abstract = {Aim: Functional diversity is a key facet of biodiversity that is increasingly being measured to quantify its changes following disturbance and to understand its effects on ecosystem functioning. Assessing the functional diversity of assemblages based on species traits requires the building of a functional space (dendrogram or multidimensional space) where indices will be computed. However, there is still no consensus on the best method for measuring the quality of functional spaces. Innovation: Here we propose a framework for evaluating the quality of a functional space (i.e. the extent to which it is a faithful representation of the initial functional trait values). Using simulated datasets, we analysed the influence of the number and type of functional traits used and of the number of species studied on the identity and quality of the best functional space. We also tested whether the quality of the functional space affects functional diversity patterns in local assemblages, using simulated datasets and a real study case. Main conclusions: The quality of functional space strongly varied between situations. Spaces having at least four dimensions had the highest quality, while functional dendrograms and two-dimensional functional spaces always had a low quality. Importantly, we showed that using a poor-quality functional space could led to a biased assessment of functional diversity and false ecological conclusions. Therefore, we advise a pragmatic approach consisting of computing all the possible functional spaces and selecting the most parsimonious one.},
author = {<NAME>{\"{e}}<NAME>{\'{e}}<NAME>{\'{<NAME>{\'{e}}bastien},
doi = {10.1111/geb.12299},
file = {:Users/mtalluto/work/Mendeley/Maire et al.{\_}2015.pdf:pdf},
issn = {14668238},
journal = {Global Ecology and Biogeography},
keywords = {Diversity indices,Functional dendrogram,Functional dissimilarity,Functional ecology,Functional traits,Multidimensional space},
number = {6},
pages = {728--740},
title = {{How many dimensions are needed to accurately assess functional diversity? A pragmatic approach for assessing the quality of functional spaces}},
volume = {24},
year = {2015}
}
@article{Pollock2017,
abstract = {Different facets of biodiversity other than species numbers are increasingly appreciated as critical for maintaining the function of ecosystems and their services to humans. While new international policy and assessment processes such as the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES) recognize the importance of an increasingly global, quantitative and comprehensive approach to biodiversity protection, most insights are still focused on a single facet of biodiversity - species. Here we broaden the focus and provide an evaluation of how much of the world's species, functional and phylogenetic diversity of birds and mammals is currently protected and the scope for improvement. We show that the large existing gaps in the coverage for each facet of diversity could be remedied by a slight expansion of protected areas: an additional 5{\%} of the land has the potential to more than triple the protected range of species or phylogenetic or functional units. Further, the same areas are often priorities for multiple diversity facets and for both taxa. However, we find that the choice of conservation strategy has a fundamental effect on outcomes. It is more difficult (that is, requires more land) to maximize basic representation of the global biodiversity pool than to maximize local diversity. Overall, species and phylogenetic priorities are more similar to each other than they are to functional priorities, and priorities for the different bird biodiversity facets are more similar than those of mammals. Our work shows that large gains in biodiversity protection are possible, while also highlighting the need to explicitly link desired conservation objectives and biodiversity metrics. We provide a framework and quantitative tools to advance these goals for multi-faceted biodiversity conservation.},
author = {Pollock, <NAME>. and <NAME>},
doi = {10.1038/nature22368},
file = {:Users/mtalluto/work/Mendeley/Pollock, Thuiller, Jetz{\_}2017.pdf:pdf},
issn = {14764687},
journal = {Nature},
number = {7656},
pages = {141--144},
publisher = {Nature Publishing Group},
title = {{Large conservation gains possible for global biodiversity facets}},
url = {http://dx.doi.org/10.1038/nature22368},
volume = {546},
year = {2017}
}
@article{Petchey2002,
abstract = {Functional diversity is an important component of biodiversity, yet in comparison to taxonomic diversity, methods of quantifying functional diversity are less well developed. Here, we propose a means for quantifying functional diversity that may be particularly useful for determining how functional diversity is related to ecosystem functioning. This measure of functional diversity "FD" is defined as the total branch length of a functional dendrogram. Various characteristics of FD make it preferable to other measures of functional diversity, such as the number of functional groups in a community. Simulating species' trait values illustrates how the relative importance of richness and composition for FD depends on the effective dimensionality of the trait space in which species separate. Fewer dimensions increase the importance of community composition and functional redundancy. More dimensions increase the importance of species richness and decreases functional redundancy. Clumping of species in trait space increases the relative importance of community composition. Five natural communities show remarkably similar relationships between FD and species richness.},
author = {Petchey, <NAME>. and Gaston, <NAME>.},
doi = {10.1046/j.1461-0248.2002.00339.x},
file = {:Users/mtalluto/work/Mendeley/Petchey, Gaston{\_}2002.pdf:pdf},
issn = {1461023X},
journal = {Ecology Letters},
keywords = {Clustering,Community composition,FD,Functional dendrogram,Functional diversity,Functional groups,Functional redundancy,Species identity,Species richness,Traits},
number = {3},
pages = {402--411},
title = {{Functional diversity (FD), species richness and community composition}},
volume = {5},
year = {2002}
}
@article{Pellissier:2014jn,
author = {Pellissier, Lo$\backslash$"$\backslash$ic and Leprieur, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME> and Bellwood, <NAME> and Mouillot, David},
file = {:Users/mtalluto/work/Mendeley/Pellissier et al.{\_}2014.pdf:pdf},
journal = {Science},
month = {may},
number = {6187},
pages = {1016--1019},
title = {{Quaternary coral reef refugia preserved fish diversity.}},
volume = {344},
year = {2014}
}
@article{Leprieur2012,
abstract = {The evolutionary dissimilarity between communities (phylogenetic beta diversity PBD) has been increasingly explored by ecologists and biogeographers to assess the relative roles of ecological and evolutionary processes in structuring natural communities. Among PBD measures, the PhyloSor and UniFrac indices have been widely used to assess the level of turnover of lineages over geographical and environmental gradients. However, these indices can be considered as 'broad-sense' measures of phylogenetic turnover as they incorporate different aspects of differences in evolutionary history between communities that may be attributable to phylogenetic diversity gradients. In the present study, we extend an additive partitioning framework proposed for compositional beta diversity to PBD. Specifically, we decomposed the PhyloSor and UniFrac indices into two separate components accounting for 'true' phylogenetic turnover and phylogenetic diversity gradients, respectively. We illustrated the relevance of this framework using simple theoretical and archetypal examples, as well as an empirical study based on coral reef fish communities. Overall, our results suggest that using PhyloSor and UniFrac may greatly over-estimate the level of spatial turnover of lineages if the two compared communities show contrasting levels of phylogenetic diversity. We therefore recommend that future studies use the 'true' phylogenetic turnover component of these indices when the studied communities encompass a large phylogenetic diversity gradient. {\textcopyright} 2012 Leprieur et al.},
author = {Leprieur, <NAME> Albouy, <NAME> <NAME>, <NAME> Cowman, <NAME>. and Bellwood, <NAME>. and Mouillot, David},
doi = {10.1371/journal.pone.0042760},
file = {:Users/mtalluto/work/Mendeley/Leprieur et al.{\_}2012.PDF:PDF},
issn = {19326203},
journal = {PLoS ONE},
number = {8},
title = {{Quantifying phylogenetic beta diversity: Distinguishing between 'true' turnover of lineages and phylogenetic diversity gradients}},
volume = {7},
year = {2012}
}
@incollection{UNEPWCMC:2015tw,
address = {Cambridge, UK},
author = {UNEP-WCMC},
booktitle = {World Vector Shoreline, 3rd edition, National Geospatial-Intelligence Agency},
title = {{Dataset combining Exclusive Economic Zones (EEZ; VLIZ 2014) and terrestrial country boundaries}},
year = {2015}
}
@article{Cook2014,
author = {Cook, <NAME> and Bonar, F and Harcourt, P and Astrom, M and Archer, <NAME> and Viney, C and Kaplan, D and Lombardi, S and Kariuki, <NAME> and Harris, <NAME> and Collins, <NAME> and Collins, <NAME> and Grenier, S and Tolentino, <NAME> and Santis, <NAME> and Kariuki, <NAME> and Harris, <NAME> and Collins, <NAME> and Laundy, D and Kariuki, <NAME> and Harris, <NAME> and Zaffora, A and Constantino, <NAME> and Pandolfi, A and Moggridge, <NAME>},
file = {:Users/mtalluto/work/Mendeley/Pellissier et al.{\_}2014.pdf:pdf},
number = {6187},
pages = {1016--1020},
title = {{R es e a rc h | r e po r ts 9.}},
volume = {344},
year = {2014}
}
@article{Taylor2012,
abstract = {CMIP5, as in earlier CMIP phases, calls for integrated sets of experiments that offer a multimodel perspective of simulated climate change and climate variability. Most modeling groups worldwide are participating in CMIP5, and their simulations are expected not only to be useful to research scientists in a variety of climate-related disciplines but also of relevance to national and international assessments of climate science (e.g., the IPCC AR5). {\textcopyright} 2012 American Meteorological Society.},
author = {Taylor, <NAME>. and Stouffer, <NAME>. and Meehl, <NAME>.},
doi = {10.1175/BAMS-D-11-00094.1},
file = {:Users/mtalluto/work/Mendeley/Taylor, Stouffer, Meehl{\_}2012.pdf:pdf},
issn = {00030007},
journal = {Bulletin of the American Meteorological Society},
number = {4},
pages = {485--498},
title = {{An overview of CMIP5 and the experiment design}},
volume = {93},
year = {2012}
}
@book{Rasmussen:2005:GPM:1162254,
author = {Rasmussen, <NAME> and Williams, <NAME>},
publisher = {The MIT Press},
title = {{Gaussian Processes for Machine Learning (Adaptive Computation and Machine Learning)}},
year = {2005}
}
@article{Hughes2018,
abstract = {Tropical reef systems are transitioning to a new era in which the interval between recurrent bouts of coral bleaching is too short for a full recovery of mature assemblages. We analyzed bleaching records at 100 globally distributed reef locations from 1980 to 2016. The median return time between pairs of severe bleaching events has diminished steadily since 1980 and is now only 6 years. As global warming has progressed, tropical sea surface temperatures are warmer now during current La Ni{\~{n}}a conditions than they were during El Ni{\~{n}}o events three decades ago. Consequently, as we transition to the Anthropocene, coral bleaching is occurring more frequently in all El Ni{\~{n}}o-Southern Oscillation phases, increasing the likelihood of annual bleaching in the coming decades.},
author = {Hughes, <NAME> Anderson, <NAME>. and Connolly, <NAME>. and Heron, <NAME>. and Kerry, <NAME>. and Lough, <NAME>. and Baird, <NAME>. and Baum, <NAME>. and Berumen, <NAME>. and Bridge, <NAME>. and Claar, <NAME>. and <NAME>, <NAME>. and Graham, <NAME>. and <NAME> and Hobbs, <NAME>. and Hoey, <NAME>. and Hoogenboom, Mia and Lowe, <NAME>. and McCulloch, <NAME>. and Pandolfi, <NAME>. and Pratchett, Morgan and Schoepf, Verena and Torda, Gergely and Wilson, <NAME>.},
doi = {10.1126/science.aan8048},
file = {:Users/mtalluto/work/Mendeley/Hughes et al.{\_}2018.pdf:pdf},
issn = {10959203},
journal = {Science},
pmid = {29302011},
title = {{Spatial and temporal patterns of mass bleaching of corals in the Anthropocene}},
year = {2018}
}
@article{Talluto2018,
abstract = {Aim: Modelling the response of $\beta$-diversity (i.e., the turnover in species composition among sites) to environmental variation has wide-ranging applications, including informing conservation planning, understanding community assembly and forecasting the impacts of climate change. However, modelling $\beta$-diversity is challenging, especially for multiple diversity facets (i.e., taxonomic, functional and phylogenetic diversity), and current methods have important limitations. Here, we present a new approach for predicting the response of multifaceted $\beta$-diversity to the environment, called Multifaceted Biodiversity Modelling (MBM). We illustrate the approach using both a plant diversity dataset from the French Alps and a set of simulated data. We also provide an implementation via an R package. Location: French Alps. Methods: For both the French Alps and the simulated communities, we compute $\beta$-diversity indices (e.g., S{\o}rensen dissimilarity, mean functional/phylogenetic pairwise distance) among site pairs. We then apply Gaussian process regression, a flexible nonlinear modelling technique, to predict $\beta$-diversity in response to environmental distance among site pairs. For comparison, we also perform similar analyses using Generalized Dissimilarity Modelling (GDM), a well-established method for modelling $\beta$-diversity in response to environmental distance. Results: In the Alps, we observed a general increase in taxonomic (TD) and functional (FD) $\beta$-diversity (i.e., site pairs were more different from each other) as the climatic distance between site pairs increased. GDM performed better for TD and FD when fitting to calibration data, whereas MBM performed better for both when predicting to a validation dataset. For phylogenetic $\beta$-diversity, MBM outperformed GDM in predicting the observed decrease in phylogenetic $\beta$-diversity with increasing climatic distance. Main conclusions: Multifaceted Biodiversity Modelling provides a flexible new approach that expands our capacity to model multiple facets of $\beta$-diversity. Advantages of MBM over existing methods include simpler assumptions, more flexible modelling, potential to consider multiple facets of diversity across a range of diversity indices, and robust uncertainty estimation.},
author = {Talluto, <NAME>. and Mokany, Karel and Pollock, <NAME>. and Thuiller, Wilfried},
doi = {10.1111/ddi.12781},
file = {:Users/mtalluto/work/Mendeley/Talluto et al.{\_}2018.pdf:pdf},
issn = {14724642},
journal = {Diversity and Distributions},
keywords = {Gaussian processes,beta diversity,biodiversity modelling,functional diversity,macroecology,phylogenetic diversity},
number = {10},
pages = {1492--1502},
title = {{Multifaceted biodiversity modelling at macroecological scales using Gaussian processes}},
volume = {24},
year = {2018}
}
@inproceedings{Hemsman:2013tn,
author = {<NAME>, Nicol{\`{o}} and Lawrence, <NAME>},
booktitle = {Proceedings of the 29th Conference on Uncertainty in Artificial Intelligence},
file = {:Users/mtalluto/work/Mendeley/H{\"{u}}bner, Jans, Drenckhahn{\_}2001.pdf:pdf},
month = {may},
title = {{Gaussian Processes for Big Data}},
year = {2013}
}
@article{Hughes2018a,
abstract = {Tropical reef systems are transitioning to a new era in which the interval between recurrent bouts of coral bleaching is too short for a full recovery of mature assemblages. We analyzed bleaching records at 100 globally distributed reef locations from 1980 to 2016. The median return time between pairs of severe bleaching events has diminished steadily since 1980 and is now only 6 years. As global warming has progressed, tropical sea surface temperatures are warmer now during current La Ni{\~{n}}a conditions than they were during El Ni{\~{n}}o events three decades ago. Consequently, as we transition to the Anthropocene, coral bleaching is occurring more frequently in all El Ni{\~{n}}o-Southern Oscillation phases, increasing the likelihood of annual bleaching in the coming decades.},
author = {Hughes, <NAME>. and Anderson, <NAME>. and Connolly, <NAME>. and Heron, <NAME>. and Kerry, <NAME>. and Lough, <NAME>. and Baird, <NAME>. and Baum, <NAME>. and Berumen, <NAME>. and Bridge, <NAME>. and Claar, <NAME>. and <NAME> Gilmour, <NAME>. and Graham, <NAME>. and Harrison, <NAME>, <NAME>. and Hoey, <NAME>. and Hoogenboom, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>.},
doi = {10.1126/science.aan8048},
issn = {10959203},
journal = {Science},
pmid = {29302011},
title = {{Spatial and temporal patterns of mass bleaching of corals in the Anthropocene}},
year = {2018}
}
@article{Hubner2001,
abstract = {Cytoplasmic junctional plaque proteins play an important role at intercellular junctions. They link transmembrane cell adhesion molecules to components of the cytoskeleton, thereby playing an important role in the control of many cellular processes. Recent studies on the subcellular distribution of some plaque proteins have revealed that a number of these proteins are able to localize in the nucleus. This dual location indicates that in addition to promoting adhesive interactions, plaque proteins may also play a direct role in nuclear processes, and in particular in the transfer of signals from the membrane to the nucleus. Therefore, translocation of plaque proteins into the nucleus in response to extracellular signals could represent a novel and direct mechanism by which signals can be transmitted from the plasma membrane to the nucleus. This could allow cells to respond to changing environmental conditions in a rapid and efficient way. In addition, conditional sequestration of karyophilic proteins at the sites of cell-cell and cell-substratum adhesion may represent a general mechanism for the regulation of nucleocytoplasmic transport. {\textcopyright} 2001 Academic Press.},
author = {H{\"{<NAME>. and <NAME>. and <NAME>.},
doi = {10.1016/S0074-7696(01)08005-6},
file = {:Users/mtalluto/work/Mendeley/H{\"{u}}bner, Jans, Drenckhahn{\_}2001.pdf:pdf},
issn = {00747696},
journal = {International Review of Cytology},
keywords = {Cell junctions,Cytoskeleton,Nuclear localization sequence,Nuclear protein import,Nuclear signaling,Plaque proteins},
pages = {207--265},
title = {{Roles of cytoskeletal and junctional plaque proteins in nuclear signaling}},
volume = {208},
year = {2001}
}
@article{Pandolfi2011,
abstract = {Many physiological responses in present-day coral reefs to climate change are interpreted as consistent with the imminent disappearance of modern reefs globally because of annual mass bleaching events, carbonate dissolution, and insufficient time for substantial evolutionary responses. Emerging evidence for variability in the coral calcification response to acidification, geographical variation in bleaching susceptibility and recovery, responses to past climate change, and potential rates of adaptation to rapid warming supports an alternative scenario in which reef degradation occurs with greater temporal and spatial heterogeneity than current projections suggest. Reducing uncertainty in projecting coral reef futures requires improved understanding of past responses to rapid climate change; physiological responses to interacting factors, such as temperature, acidification, and nutrients; and the costs and constraints imposed by acclimation and adaptation.},
author = {Pandolfi, <NAME>. and Connolly, <NAME>. and Marshall, <NAME>. and Cohen, <NAME>.},
doi = {10.1126/science.1204794},
file = {:Users/mtalluto/work/Mendeley/Pandolfi et al.{\_}2011.pdf:pdf},
issn = {00368075},
journal = {Science},
number = {6041},
pages = {418--422},
title = {{Projecting coral reef futures under global warming and ocean acidification}},
volume = {333},
year = {2011}
}
@article{Moss2010,
abstract = {Advances in the science and observation of climate change are providing a clearer understanding of the inherent variability of Earths climate system and its likely response to human and natural influences. The implications of climate change for the environment and society will depend not only on the response of the Earth system to changes in radiative forcings, but also on how humankind responds through changes in technology, economies, lifestyle and policy. Extensive uncertainties exist in future forcings of and responses to climate change, necessitating the use of scenarios of the future to explore the potential consequences of different response options. To date, such scenarios have not adequately examined crucial possibilities, such as climate change mitigation and adaptation, and have relied on research processes that slowed the exchange of information among physical, biological and social scientists. Here we describe a new process for creating plausible scenarios to investigate some of the most challenging and important questions about climate change confronting the global community. {\textcopyright} 2010 Macmillan Publishers Limited. All rights reserved.},
author = {Moss, <NAME>. and Edmonds, <NAME> Hibbard, <NAME> Manning, <NAME> Rose, <NAME>. and {<NAME>}, <NAME>. and Carter, <NAME>. and Emori, Seita and Kainuma, Mikiko and Kram, Tom and Meehl, <NAME>. and Mitchell, <NAME>. and Nakicenovic, Nebojsa and <NAME> and Smith, <NAME>. and Stouffer, <NAME>. and Thomson, <NAME>. and Weyant, <NAME>. and Wilbanks, <NAME>.},
doi = {10.1038/nature08823},
file = {:Users/mtalluto/work/Mendeley/Moss et al.{\_}2010.pdf:pdf},
issn = {00280836},
journal = {Nature},
number = {7282},
pages = {747--756},
publisher = {Nature Publishing Group},
title = {{The next generation of scenarios for climate change research and assessment}},
url = {http://dx.doi.org/10.1038/nature08823},
volume = {463},
year = {2010}
}
@article{Ottimofiore2017,
abstract = {Coral reefs and their associated fauna are largely impacted by ongoing climate change. Unravelling species responses to past climatic variations might provide clues on the consequence of ongoing changes. Here, we tested the relationship between changes in sea surface temperature and sea levels during the Quaternary and present-day distributions of coral reef fish species. We investigated whether species-specific responses are associated with life-history traits. We collected a database of coral reef fish distribution together with life-history traits for the Indo-Pacific Ocean. We ran species distribution models (SDMs) on 3,725 tropical reef fish species using contemporary environmental factors together with a variable describing isolation from stable coral reef areas during the Quaternary. We quantified the variance explained independently by isolation from stable areas in the SDMs and related it to a set of species traits including body size and mobility. The variance purely explained by isolation from stable coral reef areas on the distribution of extant coral reef fish species largely varied across species. We observed a triangular relationship between the contribution of isolation from stable areas in the SDMs and body size. Species, whose distribution is more associated with historical changes, occurred predominantly in the Indo-Australian archipelago, where the mean size of fish assemblages is the lowest. Our results suggest that the legacy of habitat changes of the Quaternary is still detectable in the extant distribution of many fish species, especially those with small body size and the most sedentary. Because they were the least able to colonize distant habitats in the past, fish species with smaller body size might have the most pronounced lags in tracking ongoing climate change.},
author = {Ottimofiore, <NAME>, <NAME>, <NAME> Descombes, <NAME>, <NAME>, <NAME>, <NAME>{\"{i}}c},
doi = {10.1002/ece3.2800},
file = {:Users/mtalluto/work/Mendeley/Ottimofiore et al.{\_}2017.pdf:pdf},
issn = {20457758},
journal = {Ecology and Evolution},
keywords = {Indo-Pacific Ocean,climate change,dispersal,species distribution models},
number = {6},
pages = {1996--2005},
title = {{Responses of coral reef fishes to past climate changes are related to life-history traits}},
volume = {7},
year = {2017}
}
@article{Jacquet2017,
abstract = {The Theory of Island Biogeography (TIB) predicts how area and isolation influence species richness equilibrium on insular habitats. However, the TIB remains silent about functional trait composition and provides no information on the scaling of functional diversity with area, an observation that is now documented in many systems. To fill this gap, we develop a probabilistic approach to predict the distribution of a trait as a function of habitat area and isolation, extending the TIB beyond the traditional species–area relationship. We compare model predictions to the body-size distribution of piscivorous and herbivorous fishes found on tropical reefs worldwide. We find that small and isolated reefs have a higher proportion of large-sized species than large and connected reefs. We also find that knowledge of species body-size and trophic position improves the predictions of fish occupancy on tropical reefs, supporting both the allometric and trophic theory of island biogeography. The integration of functional ecology to island biogeography is broadly applicable to any functional traits and provides a general probabilistic approach to study the scaling of trait distribution with habitat area and isolation.},
author = {<NAME>, <NAME>, <NAME>, Dominique},
doi = {10.1111/ele.12716},
file = {:Users/mtalluto/work/Mendeley/Jacquet et al.{\_}2017.pdf:pdf},
issn = {14610248},
journal = {Ecology Letters},
keywords = {Allometric theory,body-size,food web,island biogeography,tropical reefs},
number = {2},
pages = {135--146},
title = {{Extensions of Island Biogeography Theory predict the scaling of functional trait composition with habitat area and isolation}},
volume = {20},
year = {2017}
}
@article{Weinstein2014,
abstract = {Comparison of the taxonomic, phylogenetic, and trait dimensions of beta diversity may uncover the mechanisms that generate and maintain biodiversity, such as geographic isolation, environmental filtering, and convergent adaptation. We developed an approach to predict the relationship between environmental and geographic distance and the dimensions of beta diversity. We tested these predictions using hummingbird assemblages in the northern Andes. We expected taxonomic beta diversity to result from recent geographic barriers limiting dispersal, and we found that cost distance, which includes barriers, was a better predictor than Euclidean distance. We expected phylogenetic beta diversity to result from historical connectivity and found that differences in elevation were the best predictors of phylogenetic beta diversity. We expected high trait beta diversity to result from local adaptation to differing environments and found that differences in elevation were correlated with trait beta diversity. When combining beta diversity dimensions, we observe that high beta diversity in all dimensions results from adaption to different environments between isolated assemblages. Comparisons with high taxonomic, low phylogenetic, and low trait beta diversity occurred among lowland assemblages separated by the Andes, suggesting that geographic barriers have recently isolated lineages in similar environments. We provide insight into mechanisms governing hummingbird biodiversity patterns and provide a framework that is broadly applicable to other taxonomic groups. {\textcopyright} 2014 by The University of Chicago.},
author = {Weinstein, <NAME>. and Tinoco, Boris and Parra, <NAME> and Brown, <NAME>. and McGuire, <NAME>. and {<NAME>}, F. and Graham, <NAME>.},
doi = {10.1086/676991},
file = {:Users/mtalluto/work/Mendeley/Weinstein et al.{\_}2014.pdf:pdf},
issn = {00030147},
journal = {American Naturalist},
keywords = {Clade turnover,Elevation,Environment,Gradients,Isolation},
number = {2},
pages = {211--224},
title = {{Taxonomic, phylogenetic, and trait beta diversity in south American hummingbirds}},
volume = {184},
year = {2014}
}
@article{Wang2016,
abstract = {Although diversity-stability relationships have been extensively studied in local ecosystems, the global biodiversity crisis calls for an improved understanding of these relationships in a spatial context. Here, we use a dynamical model of competitive metacommunities to study the relationships between species diversity and ecosystem variability across scales. We derive analytic relationships under a limiting case; these results are extended to more general cases with numerical simulations. Our model shows that, while alpha diversity decreases local ecosystem variability, beta diversity generally contributes to increasing spatial asynchrony among local ecosystems. Consequently, both alpha and beta diversity provide stabilising effects for regional ecosystems, through local and spatial insurance effects respectively. We further show that at the regional scale, the stabilising effect of biodiversity increases as spatial environmental correlation increases. Our findings have important implications for understanding the interactive effects of global environmental changes (e.g. environmental homogenisation) and biodiversity loss on ecosystem sustainability at large scales.},
author = {<NAME> and <NAME>},
doi = {10.1111/ele.12582},
file = {:Users/mtalluto/work/Mendeley/Wang, Loreau{\_}2016.pdf:pdf},
issn = {14610248},
journal = {Ecology Letters},
keywords = {Biodiversity loss,Biotic homogenisation,Diversity-stability relationship,Effective number of species,Environmental homogenisation,Metacommunity,Scale,Variability},
number = {5},
pages = {510--518},
pmid = {26918536},
title = {{Biodiversity and ecosystem stability across scales in metacommunities}},
volume = {19},
year = {2016}
}
@article{Bellwood:2004ku,
author = {Bellwood, <NAME> and Hughes, <NAME> and Folke, <NAME>{\"{o}}m, M},
file = {:Users/mtalluto/work/Mendeley//Englund, Hell, Johansson{\_}2004.pdf:pdf},
journal = {Nature},
month = {jun},
number = {6994},
pages = {827--833},
title = {{Confronting the coral reef crisis.}},
volume = {429},
year = {2004}
}
@article{Parravicini2013,
abstract = {In the marine realm, the tropics host an extraordinary diversity of taxa but the drivers underlying the global distribution of marine organisms are still under scrutiny and we still lack an accurate global predictive model. Using a spatial database for 6336 tropical reef fishes, we attempted to predict species richness according to geometric, biogeographical and environmental explanatory variables. In particular, we aimed to evaluate and disentangle the predictive performances of temperature, habitat area, connectivity, mid-domain effect and biogeographical region on reef fish species richness. We used boosted regression trees, a flexible machine-learning technique, to build our predictive model and structural equation modeling to test for potential 'mediation effects' among predictors. Our model proved to be accurate, explaining 80{\%} of the total deviance in fish richness using a cross-validated procedure. Coral reef area and biogeographical region were the primary predictors of reef fish species richness, followed by coast length, connectivity, mid-domain effect and sea surface temperature, with interactions between the region and other predictors. Important indirect effects of water temperature on reef fish richness, mediated by coral reef area, were also identified. The relationship between environmental predictors and species richness varied markedly among biogeographical regions. Our analysis revealed that a few easily accessible variables can accurately predict reef fish species richness. They also highlight concerns regarding ongoing environmental declines, with region-specific responses to variation in environmental conditions predicting a variable response to anthropogenic impacts. {\textcopyright} 2013 The Authors.},
author = {<NAME> <NAME> <NAME> <NAME>.},
doi = {10.1111/j.1600-0587.2013.00291.x},
file = {:Users/mtalluto/work/Mendeley/Parravicini et al.{\_}2013.pdf:pdf},
issn = {09067590},
journal = {Ecography},
number = {12},
pages = {1254--1262},
title = {{Global patterns and predictors of tropical reef fish species richness}},
volume = {36},
year = {2013}
}
@article{Mazel2017a,
abstract = {Convergent adaptive evolution of species' ecological niches—i.e., the appearance of similar niches in independent lineages—is the result of natural selection acting on niche-related species traits (“traits” hereafter) and contrasts with neutral evolution [1–4]. Although trait convergences are recognized as being of importance at the species scale, we still know little about the impact of species convergence on the overall trait and niche structure of entire biotas at large spatial scales [5]. Here, we map the convergent evolution of four traits (diet, body mass, activity cycle, and foraging strata) for mammal species and assemblages (defined at 200 × 200 km resolution) at a global scale. Using data on the geographic distributions, traits, and phylogenetic relationships of species and by comparing observed patterns of trait $\beta$-diversity to evolutionary neutral expectations, we show that trait convergence is not restricted to particular lineages but scales up to entire assemblages (i.e., whole species communities). We find region-wide biota convergence in traits between regions with similar climates, particularly between Australia and other continents. Pairs of assemblages that show trait divergence often involves Arctic regions where rapid evolutionary changes occurred in response to extreme climatic constraints. By integrating both macroecological and macroevolutionary approaches into a single framework, our study quantifies the crucial role of evolutionary processes such as natural selection in the spatial distribution and structure of large-scale species assemblages.},
author = {<NAME>{\"{u}}est, <NAME> Gueguen, <NAME> Renaud, <NAME>, <NAME>, S{\'{e}}<NAME>},
doi = {10.1016/j.cub.2017.03.046},
file = {:Users/mtalluto/work/Mendeley/Mazel et al.{\_}2017(2).pdf:pdf},
issn = {09609822},
journal = {Current Biology},
keywords = {Brownian motion,biogeography,community convergence,community divergence,convergence,functional $\beta$-diversity,marsupials,neutral evolution,phylogenetic $\beta$-diversity,trait $\beta$-diversity},
number = {9},
pages = {1369--1374},
title = {{The Geography of Ecological Niche Evolution in Mammals}},
volume = {27},
year = {2017}
}
@article{Englund2004,
abstract = {In 1985 Siegenthaler introduced the concept of correlation attacks on LFSR based stream ciphers. A few years later Meier and Staffelbach demonstrated a special technique, usually referred to as fast correlation attacks, that is very effective if the feedback polynomial has a special form, namely, if its weight is very low. Due to this seminal result, it is a well known fact that one avoids low weight feedback polynomials in the design of LFSR based stream ciphers. This paper identifies a new class of such weak feedback polynomials, polynomials of the form f(x) = g 1 (x)+g 2 (x)x M1 + ... + g t (x)x Mt-1 , where g 1 ,g 2 ,...,g t are all polynomials of low degree. For such feedback polynomials, we identify an efficient correlation attack in the form of a distinguishing attack. {\textcopyright} International Association for Cryptologic Research 2004.},
author = {<NAME> <NAME> and <NAME>},
doi = {10.1007/978-3-540-25937-4_9},
file = {:Users/mtalluto/work/Mendeley//Englund, Hell, Johansson{\_}2004.pdf:pdf},
issn = {03029743},
journal = {Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)},
number = {June},
pages = {127--142},
title = {{Correlation attacks using a new class of weak feedback polynomials}},
volume = {3017},
year = {2004}
}
@book{Legendre:2003uq,
address = {Amsterdam},
author = {<NAME> and <NAME>},
edition = {2nd},
file = {:Users/mtalluto/work/Mendeley/Legendre, Legendre{\_}2003.pdf:pdf},
publisher = {Elsevier},
title = {{Numerical Ecology}},
year = {2003}
}
@article{Bellwood2005,
abstract = {The Indo-Australian Archipelago supports the world's richest coral reef biodiversity hotspot. Traditional hypotheses that account for such exceptional biodiversity have highlighted the importance of environmental variables such as habitat area and energy input. Recently, however, an additional explanation has been proposed based on geometric constraints in the placement of geographical ranges within a bounded domain, which cause a mid-domain peak in species richness; the mid-domain effect (MDE). Here, for the first time, we examine the relative importance of area, energy and MDE jointly on species richness patterns. Model selection indicates that the best model incorporates MDE and reef area, but no energy effect; moreover, this best-fit model captures all major features of reef fish and coral species richness patterns. Habitat area is the major environmental factor influencing species richness. The prevention of further fragmentation and loss of habitat area is of critical importance for the conservation of coral reef biodiversity. {\textcopyright}2005 Blackwell Publishing Ltd/CNRS.},
author = {<NAME>. and <NAME>. and <NAME>. and <NAME>.},
doi = {10.1111/j.1461-0248.2005.00763.x},
file = {:Users/mtalluto/work/Mendeley/Bellwood et al.{\_}2005.pdf:pdf},
issn = {1461023X},
journal = {Ecology Letters},
keywords = {Biodiversity,Coral reefs,Fishes,Hot spots,Mid-domain effect,Spatial models},
number = {6},
pages = {643--651},
title = {{Environmental and geometric constraints on Indo-Pacific coral reef biodiversity}},
volume = {8},
year = {2005}
}
@article{Graham2014,
abstract = {The composition and functions of many ecosystems are changing, giving rise to the concept of novel ecosystems. Although some coral reefs are becoming non-coral systems, others are becoming novel coral-dominated ecosystems driven principally by differential species responses to climate change and other drivers, but also due to species range shifts at higher latitudes, and in some cases introduced species. Returning many coral reefs to pristine baselines is unrealistic, whereas embracing novel futures enables more pragmatic approaches to maintaining or re-building the dominance of corals. Coral reefs are changing in unprecedented ways, providing the impetus to improve our understanding of reef compositions that may dominate in the future, explore new management approaches, assess changes in ecosystem services, and investigate how human societies can adapt and respond to novel futures. {\textcopyright} 2013 Elsevier B.V.},
author = {Graham, <NAME>. and Cinner, <NAME>. and Norstr{\"{o}}m, <NAME>. and Nystr{\"{o}}m, Magnus},
doi = {10.1016/j.cosust.2013.11.023},
file = {:Users/mtalluto/work/Mendeley/Graham et al.{\_}2014.pdf:pdf},
issn = {18773435},
journal = {Current Opinion in Environmental Sustainability},
pages = {9--14},
title = {{Coral reefs as novel ecosystems: embracing new futures}},
volume = {7},
year = {2014}
}
@article{Pavoine2009,
abstract = {Functional diversity is at the heart of current research in the field of conservation biology. Most of the indices that measure diversity depend on variables that have various statistical types (e.g. circular, fuzzy, ordinal) and that go through a matrix of distances among species. We show how to compute such distances from a generalization of Gower's distance, which is dedicated to the treatment of mixed data. We prove Gower's distance can be extended to include new types of data. The impact of this generalization is illustrated on a real data set containing 80 plant species and 13 various traits. Gower's distance allows an efficient treatment of missing data and the inclusion of variable weights. An evaluation of the real contribution of each variable to the mixed distance is proposed. We conclude that such a generalized index will be crucial for analyzing functional diversity at small and large scales.},
author = {<NAME>{\'{e}}<NAME> <NAME> and <NAME>{\'{e}}},
doi = {10.1111/j.1600-0706.2009.16668.x},
file = {:Users/mtalluto/work/Mendeley/Pavoine et al.{\_}2009.pdf:pdf},
issn = {00301299},
journal = {Oikos},
number = {3},
pages = {391--402},
title = {{On the challenge of treating various types of variables: application for improving the measurement of functional diversity}},
volume = {118},
year = {2009}
}
@article{Ferrier2007,
abstract = {Generalized dissimilarity modelling (GDM) is a statistical technique for analysing and predicting spatial patterns of turnover in community composition (beta diversity) across large regions. The approach is an extension of matrix regression, designed specifically to accommodate two types of nonlinearity commonly encountered in large-scaled ecological data sets: (1) the curvilinear relationship between increasing ecological distance, and observed compositional dissimilarity, between sites; and (2) the variation in the rate of compositional turnover at different positions along environmental gradients. GDM can be further adapted to accommodate special types of biological and environmental data including, for example, information on phylogenetic relationships between species and information on barriers to dispersal between geographical locations. The approach can be applied to a wide range of assessment activities including visualization of spatial patterns in community composition, constrained environmental classification, distributional modelling of species or community types, survey gap analysis, conservation assessment, and climate-change impact assessment. {\textcopyright} 2007 The Authors.},
author = {<NAME> <NAME> and <NAME> and <NAME>},
doi = {10.1111/j.1472-4642.2007.00341.x},
file = {:Users/mtalluto/work/Mendeley/Ferrier et al.{\_}2007.pdf:pdf},
issn = {13669516},
journal = {Diversity and Distributions},
keywords = {Beta diversity,Biodiversity,Compositional turnover,Conservation assessment,Generalized dissimilarity modelling},
number = {3},
pages = {252--264},
title = {{Using generalized dissimilarity modelling to analyse and predict patterns of beta diversity in regional biodiversity assessment}},
volume = {13},
year = {2007}
}
@article{Dray2007,
abstract = {Multivariate analyses are well known and widely used to identify and understand structures of ecological communities. The ade4 package for the R statistical environment proposes a great number of multivariate methods. Its implementation follows the tradition of the French school of "Analyse des Donn{\'{e}}es" and is based on the use of the duality diagram. We present the theory of the duality diagram and discuss its implementation in ade4. Classes and main functions are presented. An example is given to illustrate the ade4 philosophy.},
author = {<NAME>{\'{e}}phane and Dufour, <NAME>{\'{e}}atrice},
doi = {10.18637/jss.v022.i04},
file = {:Users/mtalluto/work/Mendeley/Dray, Dufour{\_}2007.pdf:pdf},
issn = {15487660},
journal = {Journal of Statistical Software},
keywords = {Ade4,Duality diagram,Ecological data,Multivariate analysis,Ordination},
number = {4},
pages = {1--20},
title = {{The ade4 package: Implementing the duality diagram for ecologists}},
volume = {22},
year = {2007}
}
@article{Ellis2012,
abstract = {In ecological analyses of species and community distributions there is interest in the nature of their responses to environmental gradients and in identifying the most important environmental variables, which may be used for predicting patterns of biodiversity. Methods such as random forests already exist to assess predictor importance for individual species and to indicate where along gradients abundance changes. However, there is a need to extend these methods to whole assemblages, to establish where along the range of these gradients the important compositional changes occur, and to identify any important thresholds or change points. We develop such a method, called "gradient forest", which is an extension of the random forest approach. By synthesizing the cross-validated R2 and accuracy importance measures from univariate random forest analyses across multiple species, sampling devices, and surveys, gradient forest obtains a monotonic function of each predictor that represents the compositional turnover along the gradient of the predictor. When applied to a synthetic data set, the method correctly identified the important predictors and delineated where the compositional change points occurred along these gradients. Application of gradient forest to a real data set from part of the Great Barrier Reef identified mud fraction of the sediment as the most important predictor, with highest compositional turnover occurring at mud fraction values around 25{\%}, and provided similar information for other predictors. Such refined information allows for more accurate capturing of biodiversity patterns for the purposes of bioregionalization, delineation of protected areas, or designing of biodiversity surveys. {\textcopyright} 2012 by the Ecological Society of America.},
author = {<NAME> Smith, <NAME>. and {<NAME>}, C.},
doi = {10.1890/11-0252.1},
file = {:Users/mtalluto/work/Mendeley/Ellis, Smith, Roland Pitcher{\_}2012.pdf:pdf},
issn = {00129658},
journal = {Ecology},
keywords = {Biodiversity,Community data,Compositional turnover,Great Barrier Reef,Random forests,Variable importance},
number = {1},
pages = {156--168},
pmid = {22486096},
title = {{Gradient forests: Calculating importance gradients on physical predictors}},
volume = {93},
year = {2012}
}
@book{Dufresne2013,
abstract = {We present the global general circulation model IPSL-CM5 developed to study the long-term response of the climate system to natural and anthropogenic forcings as part of the 5th Phase of the Coupled Model Intercomparison Project (CMIP5). This model includes an interactive carbon cycle, a representation of tropospheric and stratospheric chemistry, and a comprehensive representation of aerosols. As it represents the principal dynamical, physical, and bio-geochemical processes relevant to the climate system, it may be referred to as an Earth System Model. However, the IPSL-CM5 model may be used in a multitude of configurations associated with different boundary conditions and with a range of complexities in terms of processes and interactions. This paper presents an overview of the different model components and explains how they were coupled and used to simulate historical climate changes over the past 150 years and different scenarios of future climate change. A single version of the IPSL-CM5 model (IPSL-CM5A-LR) was used to provide climate projections associated with different socio-economic scenarios, including the different Representative Concentration Pathways considered by CMIP5 and several scenarios from the Special Report on Emission Scenarios considered by CMIP3. Results suggest that the magnitude of global warming projections primarily depends on the socio-economic scenario considered, that there is potential for an aggressive mitigation policy to limit global warming to about two degrees, and that the behavior of some components of the climate system such as the Arctic sea ice and the Atlantic Meridional Overturning Circulation may change drastically by the end of the twenty-first century in the case of a no climate policy scenario. Although the magnitude of regional temperature and precipitation changes depends fairly linearly on the magnitude of the projected global warming (and thus on the scenario considered), the geographical pattern of these changes is strikingly similar for the different scenarios. The representation of atmospheric physical processes in the model is shown to strongly influence the simulated climate variability and both the magnitude and pattern of the projected climate changes. {\textcopyright} 2013 The Author(s).},
author = {<NAME>. and Eth{\'{e}}, C. and <NAME> <NAME>. and <NAME>. and <NAME>. and <NAME>. and <NAME>. and <NAME>. and <NAME>. and <NAME>. and <NAME>. and <NAME>. and <NAME>. and <NAME>. and <NAME>. and Lott, F. and <NAME> <NAME>. and <NAME>. and Rio, C. and <NAME>.},
booktitle = {Climate Dynamics},
doi = {10.1007/s00382-012-1636-1},
file = {:Users/mtalluto/work/Mendeley/Dufresne et al.{\_}2013.pdf:pdf},
isbn = {0038201216},
issn = {09307575},
keywords = {Aerosols,Allowable emissions,CMIP3,CMIP5,Carbon cycle,Climate,Climate change,Climate projections,Earth System Model,Greenhouse gases,Land use changes,RCP scenarios},
number = {9-10},
pages = {2123--2165},
title = {{Climate change projections using the IPSL-CM5 Earth System Model: From CMIP3 to CMIP5}},
volume = {40},
year = {2013}
}
@article{Leprieur2016a,
abstract = {The Cretaceous breakup of Gondwana strongly modified the global distribution of shallow tropical seas reshaping the geographic configuration of marine basins. However, the links between tropical reef availability, plate tectonic processes and marine biodiversity distribution patterns are still unknown. Here, we show that a spatial diversification model constrained by absolute plate motions for the past 140 million years predicts the emergence and movement of diversity hotspots on tropical reefs. The spatial dynamics of tropical reefs explains marine fauna diversification in the Tethyan Ocean during the Cretaceous and early Cenozoic, and identifies an eastward movement of ancestral marine lineages towards the Indo-Australian Archipelago in the Miocene. A mechanistic model based only on habitat-driven diversification and dispersal yields realistic predictions of current biodiversity patterns for both corals and fishes. As in terrestrial systems, we demonstrate that plate tectonics played a major role in driving tropical marine shallow reef biodiversity dynamics.},
author = {Leprieur, <NAME>, Patrice and Gaboriau, Theo and Cowman, <NAME>. and Parravicini, Valeriano and Kulbicki, Michel and Melian, <NAME>. and {De Santana}, <NAME>. and Heine, Christian and Mouillot, David and Bellwood, <NAME>. and Pellissier, Loic},
doi = {10.1038/ncomms11461},
file = {:Users/mtalluto/work/Mendeley/Leprieur et al.{\_}2016(2).pdf:pdf},
issn = {20411723},
journal = {Nature Communications},
number = {May},
pages = {1--8},
title = {{Plate tectonics drive tropical reef biodiversity dynamics}},
volume = {7},
year = {2016}
}
@article{Terui2018a,
abstract = {Intraspecific population diversity (specifically, spatial asynchrony of population dynamics) is an essential component of metapopulation stability and persistence in nature. In 2D systems, theory predicts that metapopulation stability should increase with ecosystem size (or habitat network size): Larger ecosystems will harbor more diverse subpopulations with more stable aggregate dynamics. However, current theories developed in simplified landscapes may be inadequate to predict emergent properties of branching ecosystems, an overlooked but widespread habitat geometry. Here, we combine theory and analyses of a unique long-term dataset to show that a scale-invariant characteristic of fractal river networks, branching complexity (measured as branching probability), stabilizes watershed metapopulations. In riverine systems, each branch (i.e., tributary) exhibits distinctive ecological dynamics, and confluences serve as "merging" points of those branches. Hence, increased levels of branching complexity should confer a greater likelihood of integrating asynchronous dynamics over the landscape. We theoretically revealed that the stabilizing effect of branching complexity is a consequence of purely probabilistic processes in natural conditions, where within-branch synchrony exceeds among-branch synchrony. Contrary to current theories developed in 2D systems, metapopulation size (a variable closely related to ecosystem size) had vague effects on metapopulation stability. These theoretical predictions were supported by 18-y observations of fish populations across 31 watersheds: Our cross-watershed comparisons revealed consistent stabilizing effects of branching complexity on metapopulations of very different riverine fishes. A strong association between branching complexity and metapopulation stability is likely to be a pervasive feature of branching networks that strongly affects species persistence during rapid environmental changes.},
author = {<NAME> <NAME> <NAME> <NAME> <NAME> <NAME>},
doi = {10.1073/pnas.1800060115},
file = {:Users/mtalluto/work/Mendeley/Terui et al.{\_}2018.pdf:pdf},
issn = {1091-6490},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
keywords = {dendritic ecological network,dispersal,portfolio effect,spatially structured population,stream},
month = {jun},
number = {26},
pages = {E5963--E5969},
pmid = {29895695},
publisher = {National Academy of Sciences},
title = {{Metapopulation stability in branching river networks.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/29895695 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC6042068},
volume = {115},
year = {2018}
}
@article{Graham:2006ii,
author = {<NAME> and Wilson, <NAME> and Jennings, Simon and Polunin, <NAME> and Bijoux, <NAME> and Robinson, Jan},
file = {:Users/mtalluto/work/Mendeley//Teske et al.{\_}2015.pdf:pdf},
journal = {Proceedings of the National Academy of Sciences},
month = {may},
number = {22},
pages = {8425--8429},
title = {{Dynamic fragility of oceanic coral reef ecosystems.}},
volume = {103},
year = {2006}
}
@article{Descombes2015,
abstract = {Coral bleaching events threaten coral reef habitats globally and cause severe declines of local biodiversity and productivity. Related to high sea surface temperatures (SST), bleaching events are expected to increase as a consequence of future global warming. However, response to climate change is still uncertain as future low-latitude climatic conditions have no present-day analogue. Sea surface temperatures during the Eocene epoch were warmer than forecasted changes for the coming century, and distributions of corals during the Eocene may help to inform models forecasting the future of coral reefs. We coupled contemporary and Eocene coral occurrences with information on their respective climatic conditions to model the thermal niche of coral reefs and its potential response to projected climate change. We found that under the RCP8.5 climate change scenario, the global suitability for coral reefs may increase up to 16{\%} by 2100, mostly due to improved suitability of higher latitudes. In contrast, in its current range, coral reef suitability may decrease up to 46{\%} by 2100. Reduction in thermal suitability will be most severe in biodiversity hotspots, especially in the Indo-Australian Archipelago. Our results suggest that many contemporary hotspots for coral reefs, including those that have been refugia in the past, spatially mismatch with future suitable areas for coral reefs posing challenges to conservation actions under climate change.},
author = {Descombes, <NAME>, <NAME>. and Leprieur, <NAME>, <NAME>, Christian and Olsen, <NAME>. and Swingedouw, Didier and Kulbicki, Michel and Mouillot, David and Pellissier, Lo{\"{i}}c},
doi = {10.1111/gcb.12868},
file = {:Users/mtalluto/work/Mendeley/Descombes et al.{\_}2015.pdf:pdf},
issn = {13652486},
journal = {Global Change Biology},
keywords = {Fish,Fossil,Sea surface temperature,Specialists,Species distribution model,Species richness},
number = {7},
pages = {2479--2487},
title = {{Forecasted coral reef decline in marine biodiversity hotspots under climate change}},
volume = {21},
year = {2015}
}
@article{Teske2015,
abstract = {The spinal canal stenosis is a common disease in elderly. The thecal sac narrowing is considered as the anatomical cause for the disease. There is evidence that the anatomical proportions of the lumbar spinal canal are influenced by postural changes. The liquor volume shift during these postural changes is a valuable parameter to estimate the dynamic qualities of this disease. OBJECTIVE: The aim of this human cadaver study was the determination of intrathecal fluid volume changes during the lumbar flexion and the extension. A special measuring device was designed and built for the study to investigate this issue under controlled conditions. METHODS: The measuring apparatus fixed the lumbar spine firmly and allowed only flexion and extension. The dural sac was closed water tight. The in vitro changes of the intrathecal volumes during the motion cycle were determined according to the principle of communicating vessels. Thirteen human cadaver spines from the Institute of Anatomy were examined in a test setting with a continuous adjustment of motion. The diagnosis of the lumbar spinal stenosis was confirmed by a positive computer tomography prior testing. The volume changes during flexion and extension cycles were measured stepwise in a 2 degree distance between 18° flexion and 18° extension. Three complete series of measurements were performed for each cadaver. RESULTS: Two specimens were excluded because of fluid leaks from further investigation. The flexion of the lumbar spine resulted in an intrathecal volume increase. The maximum volume effects were seen in the early flexion positions of 2° and 4°. The spine reclination resulted in a volume reduction. The maximum extension effect was seen between 14° and 16°. CONCLUSION: According to our results, remarkable volume effects were seen in the early movements of the lumbar spine especially for the flexion. The results support the concept of the spinal stenosis as a dynamic disease and allow a better understanding of the pathophysiology of this nosological entity. Under clinical aspects our data support the value of a body upright position under avoiding of extended spinal inclination and reclination.},
author = {<NAME>, <NAME>, <NAME>, <NAME> Wiese, <NAME> Lahner, Matthias},
doi = {10.3233/THC-151011},
file = {:Users/mtalluto/work/Mendeley//Teske et al.{\_}2015.pdf:pdf},
issn = {09287329},
journal = {Technology and Health Care},
keywords = {Lumbar spinal canal stenosis,dural sac volume determination,lumbar flexion and extension},
number = {5},
pages = {645--652},
title = {{Intrathecal volume changes in lumbar spinal canal stenosis following extension and flexion: An experimental cadaver study}},
volume = {23},
year = {2015}
}
@article{Huang2015,
abstract = {One-third of the world's reef-building corals are facing heightened extinction risk from climate change and other anthropogenic impacts. Previous studies have shown that such threats are not distributed randomly across the coral tree of life, and future extinctions have the potential to disproportionately reduce the phylogenetic diversity of this group on a global scale. However, the impact of such losses on a regional scale remains poorly known. In this study, we use phylogenetic metrics in conjunction with geographical distributions of living reef coral species to model how extinctions are likely to affect evolutionary diversity across different ecoregions. Based on two measures—phylogenetic diversity and phylogenetic species variability—we highlight regions with the largest losses of evolutionary diversity and hence of potential conservation interest. Notably, the projected loss of evolutionary diversity is relatively low in the most species-rich areas such as the Coral Triangle, while many regions with fewer species stand to lose much larger shares of their diversity. We also suggest that for complex ecosystems like coral reefs it is important to consider changes in phylogenetic species variability; areas with disproportionate declines in this measure should be of concern even if phylogenetic diversity is not as impacted. These findings underscore the importance of integrating evolutionary history into conservation planning for safeguarding the future diversity of coral reefs.},
author = {<NAME> and <NAME>},
doi = {10.1098/rstb.2014.0010},
file = {:Users/mtalluto/work/Mendeley/Huang, Roy{\_}2015.pdf:pdf},
issn = {14712970},
journal = {Philosophical Transactions of the Royal Society B: Biological Sciences},
keywords = {Coral reef,Ecoregions,Extinction risk,Phylogenetic diversity,Scleractinia,Tree shape},
number = {1662},
pages = {1--11},
title = {{The future of evolutionary diversity in reef corals}},
volume = {370},
year = {2015}
}
@article{Halpern2008,
abstract = {Functional diversity in biological communities is critical for providing the full suite of ecosystem functions and services, yet the relationship between functional diversity and species richness - how diversity is usually measured - remains largely unknown. Here we evaluate empirically how different measures of functional diversity change with increasing species richness across 36 Atlantic reef fish communities that vary greatly in species richness. We show that (1) the definition used for functional groups strongly influences the perceived relationship: (2) when using more comprehensive definitions of functional groups the relationship is asymptotic and highly unsaturated; and (3) increasing species richness primarily leads to the addition of species to a few key functional groups rather than the addition of novel functional groups. Consequently, non-random assembly of fish assemblages leaves many possible functional groups empty, and high species redundancy within functional groups is limited to relatively few groups. Consequences of future extirpation or extinction of species for the loss of ecosystem functions will be variable, in part depending on the proportion of species lost within a functional group, but potentially profound due to the large number of functional groups represented by only a single species and the targeted nature of most species extraction and extirpations. {\textcopyright} Inter-Research 2008.},
author = {Halpern, <NAME>. and Floeter, <NAME>.},
doi = {10.3354/meps07553},
file = {:Users/mtalluto/work/Mendeley/Halpern, Floeter{\_}2008.pdf:pdf},
issn = {01718630},
journal = {Marine Ecology Progress Series},
keywords = {Biodiversity,Community assembly,Ecological filtering,Ecosystem services,Species loss},
pages = {147--156},
title = {{Functional diversity responses to changing species richness in reef fish communities}},
volume = {364},
year = {2008}
}
@article{Cinner2018,
abstract = {Coral reefs provide ecosystem goods and services for millions of people in the tropics, but reef conditions are declining worldwide. Effective solutions to the crisis facing coral reefs depend in part on understanding the context under which different types of conservation benefits can be maximized. Our global analysis of nearly 1,800 tropical reefs reveals how the intensity of human impacts in the surrounding seascape, measured as a function of human population size and accessibility to reefs (“gravity”), diminishes the effectiveness of marine reserves at sustaining reef fish biomass and the presence of top predators, even where compliance with reserve rules is high. Critically, fish biomass in high-compliance marine reserves located where human impacts were intensive tended to be less than a quarter that of reserves where human impacts were low. Similarly, the probability of encountering top predators on reefs with high human impacts was close to zero, even in high-compliance marine reserves. However, we find that the relative difference between openly fished sites and reserves (what we refer to as conservation gains) are highest for fish biomass (excluding predators) where human impacts are moderate and for top predators where human impacts are low. Our results illustrate critical ecological trade-offs in meeting key conservation objectives: reserves placed where there are moderate-to-high human impacts can provide substantial conservation gains for fish biomass, yet they are unlikely to support key ecosystem functions like higher-order predation, which is more prevalent in reserve locations with low human impacts.},
author = {Cinner, <NAME>. and Maire, Eva and Huchery, Cindy and {<NAME>}, M. and Graham, <NAME>. and Mora, Camilo and McClanahan, <NAME>. and Barnes, <NAME>. and Kittinger, <NAME>. and Hicks, <NAME>. and D'Agata, Stephanie and Hoey, <NAME>. and Gurney, <NAME>. and Feary, <NAME>. and Williams, <NAME>. and Kulbicki, <NAME>, <NAME>, <NAME> <NAME>. and Stuart-Smith, <NAME>. and Sandin, <NAME>. and Green, Alison and Hardt, <NAME>. and Beger, Maria and Friedlander, <NAME>. and Wilson, <NAME>. and Brokovich, Eran and Brooks, <NAME>. and Cruz-Motta, <NAME>. and Booth, <NAME>. and Chabanet, Pascale and Gough, Charlotte and Tupper, Mark and Ferse, <NAME>. and {<NAME>}, U. and Pardede, Shinta and Mouillot, David},
doi = {10.1073/pnas.1708001115},
file = {:Users/mtalluto/work/Mendeley/Cinner et al.{\_}2018.pdf:pdf},
isbn = {1708001115},
issn = {10916490},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
keywords = {Coral reefs,Fisheries,Marine reserves,Social-ecological,Socioeconomic},
number = {27},
pages = {E6116--E6125},
title = {{Gravity of human impacts mediates coral reef conservation gains}},
volume = {115},
year = {2018}
}
@article{Cowman2017,
abstract = {ABSTRACT The largest marine biodiversity hotspot straddles the Indian and Pacific Oceans, driven by taxa associated with tropical coral reefs. Centred on the Indo-Australian Archipelago (IAA), this biodiversity hotspot forms the ‘bullseye' of a steep gradient in species richness from this centre to the periphery of the vast Indo-Pacific region. Complex patterns of endemism, wide-ranging species and assemblage differences have obscured our understanding of the genesis of this biodiversity pattern and its maintenance across two-thirds of the world's oceans. But time-calibrated molecular phylogenies coupled with ancestral biogeographic estimates have provided a valuable framework in which to examine the origins of coral reef fish biodiversity across the tropics. Herein, we examine phylogenetic and biogeographic data for coral reef fishes to highlight temporal patterns of marine endemism and tropical provinciality. The ages and distribution of endemic lineages have often been used to identify areas of species creation and demise in the marine tropics and discriminate among multiple hypotheses regarding the origins of biodiversity in the IAA. Despite a general under-sampling of endemic fishes in phylogenetic studies, the majority of locations today contain a mixture of potential paleo- and neo-endemic fishes, pointing to multiple historical processes involved in the origin and maintenance of the IAA biodiversity hotspot. Increased precision and sampling of geographic ranges for reef fishes has permitted the division of discrete realms, regions and provinces across the tropics. Yet, such metrics are only beginning to integrate phylogenetic relatedness and ancestral biogeography. Here, we integrate phylogenetic diversity with ancestral biogeographic estimation of lineages to show how assemblage structure and tropical provinciality has changed through time.},
author = {<NAME> and Parravicini, Valeriano and Kulbicki, Michel and Floeter, <NAME>},
doi = {10.1111/brv.12323},
file = {:Users/mtalluto/work/Mendeley/Cowman et al.{\_}2017.pdf:pdf},
journal = {Biological Reviews},
keywords = {assemblage similarity,biodiversity,biogeography,coral reef fishes,endemism,hotspot,provinciality},
number = {4},
pages = {2112--2130},
title = {{The biogeography of tropical reef fishes: endemism and provinciality through time}},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/brv.12323},
volume = {92},
year = {2017}
}
@article{Wernberg2013,
abstract = {Extreme climatic events, such as heat waves, are predicted to increase in frequency and magnitude as a consequence of global warming but their ecological effects are poorly understood, particularly in marine ecosystems. In early 2011, the marine ecosystems along the west coast of Australia - a global hotspot of biodiversity and endemism - experienced the highest-magnitude warming event on record. Sea temperatures soared to unprecedented levels and warming anomalies of 2-4C persisted for more than ten weeks along {\textgreater}2,000 km of coastline. We show that biodiversity patterns of temperate seaweeds, sessile invertebrates and demersal fish were significantly different after the warming event, which led to a reduction in the abundance of habitat-forming seaweeds and a subsequent shift in community structure towards a depauperate state and a tropicalization of fish communities. We conclude that extreme climatic events are key drivers of biodiversity patterns and that the frequency and intensity of such episodes have major implications for predictive models of species distribution and ecosystem structure, which are largely based on gradual warming trends. {\textcopyright} 2013 Macmillan Publishers Limited. All rights reserved.},
author = {<NAME> Smale, <NAME>. and Tuya, Fernando and Thomsen, <NAME>. and Langlois, <NAME>. and {De Bettignies}, Thibaut and Bennett, Scott and Rousseaux, <NAME>.},
doi = {10.1038/nclimate1627},
file = {:Users/mtalluto/work/Mendeley/Wernberg et al.{\_}2013.pdf:pdf},
issn = {1758678X},
journal = {Nature Climate Change},
number = {1},
pages = {78--82},
publisher = {Nature Publishing Group},
title = {{An extreme climatic event alters marine ecosystem structure in a global biodiversity hotspot}},
url = {http://dx.doi.org/10.1038/nclimate1627},
volume = {3},
year = {2013}
}
@article{Lough2018,
abstract = {Tropical corals live close to their upper thermal limit making them vulnerable to unusually warm summer sea temperatures. The resulting thermal stress can lead to breakdown of the coral-algal symbiosis, essential for the functioning of reefs, and cause coral bleaching. Mass coral bleaching is a modern phenomenon associated with increases in reef temperatures due to recent global warming. Widespread bleaching has typically occurred during El Ni{\~{n}}o events. We examine the historical level of stress for 100 coral reef locations with robust bleaching histories. The level of thermal stress (based on a degree heating month index, DHMI) at these locations during the 2015-2016 El Ni{\~{n}}o was unprecedented over the period 1871-2017 and exceeded that of the strong 1997-1998 El Ni{\~{n}}o. The DHMI was also 5 times the level of thermal stress associated with the 'pre-industrial', 1877-1878, El Ni{\~{n}}o. Coral reefs have, therefore, already shown their vulnerability to the modest (∼0.92 °C) global warming that has occurred to date. Estimates of future levels of thermal stress suggest that even the optimistic 1.5 °C Paris Agreement target is insufficient to prevent more frequent mass bleaching events for the world's reefs. Effectively, reefs of the future will not be the same as those of the past.},
author = {<NAME>. and <NAME>. and <NAME>.},
doi = {10.1038/s41598-018-24530-9},
file = {:Users/mtalluto/work/Mendeley/Lough, Anderson, Hughes{\_}2018.pdf:pdf},
isbn = {4159801824530},
issn = {20452322},
journal = {Scientific Reports},
number = {1},
pages = {1--8},
publisher = {Springer US},
title = {{Increasing thermal stress for tropical coral reefs: 1871-2017}},
url = {http://dx.doi.org/10.1038/s41598-018-24530-9},
volume = {8},
year = {2018}
}
@article{Stuart-Smith2018,
abstract = {Global warming is markedly changing diverse coral reef ecosystems through an increasing frequency and magnitude of mass bleaching events1–3. How local impacts scale up across affected regions depends on numerous factors, including patchiness in coral mortality, metabolic effects of extreme temperatures on populations of reef-dwelling species4 and interactions between taxa. Here we use data from before and after the 2016 mass bleaching event to evaluate ecological changes in corals, algae, fishes and mobile invertebrates at 186 sites along the full latitudinal span of the Great Barrier Reef and western Coral Sea. One year after the bleaching event, reductions in live coral cover of up to 51{\%} were observed on surveyed reefs that experienced extreme temperatures; however, regional patterns of coral mortality were patchy. Consistent declines in coral-feeding fishes were evident at the most heavily affected reefs, whereas few other short-term responses of reef fishes and invertebrates could be attributed directly to changes in coral cover. Nevertheless, substantial region-wide ecological changes occurred that were mostly independent of coral loss, and instead appeared to be linked directly to sea temperatures. Community-wide trophic restructuring was evident, with weakening of strong pre-existing latitudinal gradients in the diversity of fishes, invertebrates and their functional groups. In particular, fishes that scrape algae from reef surfaces, which are considered to be important for recovery after bleaching2, declined on northern reefs, whereas other herbivorous groups increased on southern reefs. The full impact of the 2016 bleaching event may not be realized until dead corals erode during the next decade5,6. However, our short-term observations suggest that the recovery processes, and the ultimate scale of impact, are affected by functional changes in communities, which in turn depend on the thermal affinities of local reef-associated fauna. Such changes will vary geographically, and may be particularly acute at locations where many fishes and invertebrates are close to their thermal distribution limits7.},
author = {Stuart-Smith, <NAME> Brown, <NAME> Ceccarelli, <NAME> <NAME>.},
doi = {10.1038/s41586-018-0359-9},
file = {:Users/mtalluto/work/Mendeley/Stuart-Smith et al.{\_}2018.pdf:pdf},
issn = {14764687},
journal = {Nature},
number = {7716},
pages = {92--96},
publisher = {Springer US},
title = {{Ecosystem restructuring along the Great Barrier Reef following mass coral bleaching}},
url = {http://dx.doi.org/10.1038/s41586-018-0359-9},
volume = {560},
year = {2018}
}
@article{Graham2015,
abstract = {Climate-induced coral bleaching is among the greatest current threats to coral reefs, causing widespread loss of live coral cover. Conditions under which reefs bounce back from bleaching events or shift from coral to algal dominance are unknown, making it difficult to predict and plan for differing reef responses under climate change. Here we document and predict long-term reef responses to a major climate-induced coral bleaching event that caused unprecedented region-wide mortality of Indo-Pacific corals. Following loss of {\textgreater}90{\%} live coral cover, 12 of 21 reefs recovered towards pre-disturbance live coral states, while nine reefs underwent regime shifts to fleshy macroalgae. Functional diversity of associated reef fish communities shifted substantially following bleaching, returning towards pre-disturbance structure on recovering reefs, while becoming progressively altered on regime shifting reefs. We identified threshold values for a range of factors that accurately predicted ecosystem response to the bleaching event. Recovery was favoured when reefs were structurally complex and in deeper water, when density of juvenile corals and herbivorous fishes was relatively high and when nutrient loads were low. Whether reefs were inside no-take marine reserves had no bearing on ecosystem trajectory. Although conditions governing regime shift or recovery dynamics were diverse, pre-disturbance quantification of simple factors such as structural complexity and water depth accurately predicted ecosystem trajectories. These findings foreshadow the likely divergent but predictable outcomes for reef ecosystems in response to climate change, thus guiding improved management and adaptation.},
author = {Graham, <NAME>. and <NAME> MacNeil, <NAME> Mouillot, <NAME> <NAME>.},
doi = {10.1038/nature14140},
file = {:Users/mtalluto/work/Mendeley/Graham et al.{\_}2015.pdf:pdf},
issn = {14764687},
journal = {Nature},
number = {7537},
pages = {94--97},
publisher = {Nature Publishing Group},
title = {{Predicting climate-driven regime shifts versus rebound potential in coral reefs}},
url = {http://dx.doi.org/10.1038/nature14140},
volume = {518},
year = {2015}
}
@article{Duffy2016,
abstract = {Fishes are the most diverse group of vertebrates, play key functional roles in aquatic ecosystems, and provide protein for a billion people, especially in the developing world. Those functions are compromised by mounting pressures on marine biodiversity and ecosystems. Because of its economic and food value, fish biomass production provides an unusually direct link from biodiversity to critical ecosystem services. We used the Reef Life Survey's global database of 4,556 standardized fish surveys to test the importance of biodiversity to fish production relative to 25 environmental drivers. Temperature, biodiversity, and human influence together explained 47{\%} of the global variation in reef fish biomass among sites. Fish species richness and functional diversity were among the strongest predictors of fish biomass, particularly for the largebodied species and carnivores preferred by fishers, and these biodiversity effects were robust to potentially confounding influences of sample abundance, scale, and environmental correlations. Warmer temperatures increased biomass directly, presumably by raising metabolism, and indirectly by increasing diversity, whereas temperature variability reduced biomass. Importantly, diversity and climate interact, with biomass of diverse communities less affected by rising and variable temperatures than species-poor communities. Biodiversity thus buffers global fish biomass from climate change, and conservation of marine biodiversity can stabilize fish production in a changing ocean.},
author = {<NAME> and Lefcheck, <NAME>. and Stuart-Smith, <NAME>. and Navarrete, <NAME>. and Edgar, <NAME>.},
doi = {10.1073/pnas.1524465113},
file = {:Users/mtalluto/work/Mendeley/Duffy et al.{\_}2016.pdf:pdf},
issn = {10916490},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
keywords = {Fisheries,Functional diversity,Global change,Macroecology,Structural equation model},
number = {22},
pages = {6230--6235},
title = {{Biodiversity enhances reef fish biomass and resistance to climate change}},
volume = {113},
year = {2016}
}
@article{Material2007,
abstract = {Atmospheric carbon dioxide concentration is expected to exceed 500 parts per million and global temperatures to rise by at least 2C by 2050 to 2100, values that significantly exceed those of at least the past 420,000 years during which most extant marine organisms evolved. Under conditions expected in the 21st century, global warming and ocean acidification will compromise carbonate accretion, with corals becoming increasingly rare on reef systems. The result will be less diverse reef communities and carbonate reef structures that fail to be maintained. Climate change also exacerbates local stresses from declining water quality and overexploitation of key species, driving reefs increasingly toward the tipping point for functional collapse. This review presents future scenarios for coral reefs that predict increasingly serious consequences for reef-associated fisheries, tourism, coastal protection, and people. As the International Year of the Reef 2008 begins, scaled-up management intervention and decisive action on global emissions are required if the loss of coral-dominated ecosystems is to be avoided.},
author = {Material, Supporting Online and York, New and Nw, Avenue},
doi = {10.1126/science.1152509},
file = {:Users/mtalluto/work/Mendeley/Hoegh-Guldberg et al.{\_}2007.pdf:pdf},
journal = {Science},
number = {December 2007},
pages = {1737--1743},
title = {{Change and Ocean Acidification}},
volume = {1737},
year = {2007}
}
@article{Hughes2017b,
abstract = {During 2015-2016, record temperatures triggered a pan-tropical episode of coral bleaching, the third global-scale event since mass bleaching was first documented in the 1980s. Here we examine how and why the severity of recurrent major bleaching events has varied at multiple scales, using aerial and underwater surveys of Australian reefs combined with satellite-derived sea surface temperatures. The distinctive geographic footprints of recurrent bleaching on the Great Barrier Reef in 1998, 2002 and 2016 were determined by the spatial pattern of sea temperatures in each year. Water quality and fishing pressure had minimal effect on the unprecedented bleaching in 2016, suggesting that local protection of reefs affords little or no resistance to extreme heat. Similarly, past exposure to bleaching in 1998 and 2002 did not lessen the severity of bleaching in 2016. Consequently, immediate global action to curb future warming is essential to secure a future for coral reefs.},
author = {Hughes, <NAME>. and Kerry, <NAME>. and {\'{A}}lvarez-Noriega, Mariana and {\'{A}}lvarez-Romero, <NAME>. and Anderson, <NAME>. and Baird, <NAME>. and Babcock, <NAME>. and Beger, Maria and Bellwood, <NAME>. and Berkelmans, Ray and Bridge, <NAME>. and Butler, <NAME>. and Byrne, Maria and Cantin, <NAME>. and Comeau, Steeve and Connolly, <NAME>. and Cumming, <NAME>. and Dalton, <NAME>. and Diaz-Pulido, Guillermo and Eakin, <NAME> Figueira, <NAME>. and Gilmour, <NAME>. and Harrison, <NAME>. and Heron, <NAME>. and Hoey, <NAME>. and Hobbs, <NAME>. and Hoogenboom, <NAME>. and Kennedy, <NAME>. and Kuo, <NAME> and Lough, <NAME>. and Lowe, <NAME>. and <NAME> and McCulloch, <NAME>. and Malcolm, <NAME>. and McWilliam, <NAME>. and Pandolfi, <NAME>. and Pears, <NAME>. and Pratchett, <NAME>. and Schoepf, Verena and Simpson, Tristan and Skirving, <NAME>. and Sommer, Brigitte and Torda, Gergely and Wachenfeld, <NAME>. and Willis, <NAME>. and Wilson, <NAME>.},
doi = {10.1038/nature21707},
file = {:Users/mtalluto/work/Mendeley/Hughes et al.{\_}2017(2).pdf:pdf},
issn = {14764687},
journal = {Nature},
number = {7645},
pages = {373--377},
pmid = {28300113},
title = {{Global warming and recurrent mass bleaching of corals}},
volume = {543},
year = {2017}
}
@article{Hughes2017a,
abstract = {Coral reefs support immense biodiversity and provide important ecosystem services to many millions of people. Yet reefs are degrading rapidly in response to numerous anthropogenic drivers. In the coming centuries, reefs will run the gauntlet of climate change, and rising temperatures will transform them into new configurations, unlike anything observed previously by humans. Returning reefs to past configurations is no longer an option. Instead, the global challenge is to steer reefs through the Anthropocene era in a way that maintains their biological functions. Successful navigation of this transition will require radical changes in the science, management and governance of coral reefs.},
author = {<NAME>. and Barnes, <NAME>. and Bellwood, <NAME>. and Cinner, <NAME>. and Cumming, <NAME>. and Jackson, <NAME>. and Kleypas, Joanie and {Van <NAME>}, <NAME>. and Lough, <NAME>. and Morrison, <NAME>. and Palumbi, <NAME>. and {Van Nes}, <NAME>. and Scheffer, Marten},
doi = {10.1038/nature22901},
file = {:Users/mtalluto/work/Mendeley/Hughes et al.{\_}2017.pdf:pdf},
issn = {14764687},
journal = {Nature},
number = {7656},
pages = {82--90},
pmid = {28569801},
title = {{Coral reefs in the Anthropocene}},
volume = {546},
year = {2017}
}
@article{HoeghGuldberg:2007fo,
author = {Hoegh-Guldberg, <NAME>, <NAME> Hooten, <NAME>, <NAME>, <NAME>, <NAME>, <NAME> and Sale, <NAME> and Edwards, <NAME> and Caldeira, K and Knowlton, N and Eakin, <NAME> and Iglesias-Prieto, R and Muthiga, N and Bradbury, <NAME> and Dubi, A and Hatziolos, <NAME>},
file = {:Users/mtalluto/work/Mendeley/Hoegh-Guldberg et al.{\_}2007.pdf:pdf},
journal = {Science},
month = {dec},
number = {5857},
pages = {1737--1742},
title = {{Coral reefs under rapid climate change and ocean acidification.}},
volume = {318},
year = {2007}
}
@article{Cheung2009,
abstract = {Climate change can impact the pattern of marine biodiversity through changes in species' distributions. However, global studies on climate change impacts on ocean biodiversity have not been performed so far. Our paper aims to investigate the global patterns of such impacts by projecting the distributional ranges of a sample of 1066 exploited marine fish and invertebrates for 2050 using a newly developed dynamic bioclimate envelope model. Our projections show that climate change may lead to numerous local extinction in the sub-polar regions, the tropics and semi-enclosed seas. Simultaneously, species invasion is projected to be most intense in the Arctic and the Southern Ocean. Together, they result in dramatic species turnovers of over 60{\%} of the present biodiversity, implying ecological disturbances that potentially disrupt ecosystem services. Our projections can be viewed as a set of hypothesis for future analytical and empirical studies. {\textcopyright} 2009 Blackwell Publishing Ltd.},
author = {Cheung, <NAME>. and Lam, <NAME>. and Sarmiento, <NAME> Kearney, <NAME> Watson, <NAME>, Daniel},
doi = {10.1111/j.1467-2979.2008.00315.x},
file = {:Users/mtalluto/work/Mendeley/Cheung et al.{\_}2009.pdf:pdf},
issn = {14672960},
journal = {Fish and Fisheries},
keywords = {Bioclimate envelope,Climate change impact,Global marine biodiversity,Niche-based model,Species turnover},
number = {3},
pages = {235--251},
title = {{Projecting global marine biodiversity impacts under climate change scenarios}},
volume = {10},
year = {2009}
}
@article{Lane2015,
abstract = {We analyzed the potential physical and economic impacts of climate change on freshwater fisheries and coral reefs in the United States, examining a reference case and two policy scenarios that limit global greenhouse gas (GHG) emissions. We modeled shifts in suitable habitat for three freshwater fish guilds and changes in coral reef cover for three regions. We estimated resulting economic impacts from projected changes in recreational fishing and changes in recreational use of coral reefs. In general, coldwater fisheries are projected to be replaced by less desirable fisheries over the 21st century, but these impacts are reduced under the GHG mitigation scenarios. Similarly, coral cover is projected to decline over the 21st century primarily due to multiple bleaching events, but the GHG mitigation scenarios delay these declines in Hawaii (but not in South Florida or Puerto Rico). Using a benefit-transfer approach, we estimated that global policies limiting GHG emissions would provide economic benefits in the range of {\$}10–28 billion over the 21st century through maintaining higher values for recreational services for all freshwater fisheries and coral reefs, compared to the reference scenario. These economic values are a subset of the total economic and societal benefits associated with avoiding projected future declines in freshwater fisheries and coral reef cover due to unmitigated climate change.},
author = {Lane, <NAME> Jones, <NAME> Mills, <NAME> Wobus, <NAME>, <NAME>. and Buddemeier, <NAME>. and English, Eric and Martinich, Jeremy and Shouse, Kate and Hosterman, Heather},
doi = {10.1007/s10584-014-1107-2},
file = {:Users/mtalluto/work/Mendeley/Lane et al.{\_}2015.pdf:pdf},
issn = {15731480},
journal = {Climatic Change},
number = {1},
pages = {143--157},
title = {{Climate change impacts on freshwater fish, coral reefs, and related ecosystem services in the United States}},
volume = {131},
year = {2015}
}
@article{Munday2008,
abstract = {Climate change will impact coral-reef fishes through effects on individual performance, trophic linkages, recruitment dynamics, population connectivity and other ecosystem processes. The most immediate impacts will be a loss of diversity and changes to fish community composition as a result of coral bleaching. Coral-dependent fishes suffer the most rapid population declines as coral is lost; however, many other species will exhibit long-term declines due to loss of settlement habitat and erosion of habitat structural complexity. Increased ocean temperature will affect the physiological performance and behaviour of coral reef fishes, especially during their early life history. Small temperature increases might favour larval development, but this could be counteracted by negative effects on adult reproduction. Already variable recruitment will become even more unpredictable. This will make optimal harvest strategies for coral reef fisheries more difficult to determine and populations more susceptible to overfishing. A substantial number of species could exhibit range shifts, with implications for extinction risk of small-range species near the margins of reef development. There are critical gaps in our knowledge of how climate change will affect tropical marine fishes. Predictions are often based on temperate examples, which may be inappropriate for tropical species. Improved projections of how ocean currents and primary productivity will change are needed to better predict how reef fish population dynamics and connectivity patterns will change. Finally, the potential for adaptation to climate change needs more attention. Many coral reef fishes have geographical ranges spanning a wide temperature gradient and some have short generation times. These characteristics are conducive to acclimation or local adaptation to climate change and provide hope that the more resilient species will persist if immediate action is taken to stabilize Earth's climate. {\textcopyright} 2008 The Authors.},
author = {<NAME> <NAME>. and <NAME>. and <NAME>.},
doi = {10.1111/j.1467-2979.2008.00281.x},
file = {:Users/mtalluto/work/Mendeley/Munday et al.{\_}2008.pdf:pdf},
issn = {14672960},
journal = {Fish and Fisheries},
keywords = {Climate change adaptation,Community structure,Global warming,Habitat loss,Population dynamics,Range shifts},
number = {3},
pages = {261--285},
title = {{Climate change and the future for coral reef fishes}},
volume = {9},
year = {2008}
}
@article{Gonzalez2020,
author = {<NAME>, <NAME>, <NAME>, <NAME>, <NAME>. and <NAME>},
doi = {10.1111/ele.13456},
file = {:Users/mtalluto/work/Mendeley/Gonzalez et al.{\_}2020.pdf:pdf},
issn = {14610248},
journal = {Ecology Letters},
keywords = {Beta diversity,biological diversity,ecosystem functioning,ecosystems,environmental heterogeneity,scale,turnover},
title = {{Scaling-up biodiversity-ecosystem functioning research}},
year = {2020}
}
@article{Hunt2009,
author = {Hunt, <NAME>. and Bonsall, <NAME>.},
doi = {10.1111/j.1365-2656.2009.01532.x},
file = {:Users/mtalluto/work/Mendeley/Hunt, Bonsall{\_}2009.pdf:pdf},
issn = {00218790},
journal = {Journal of Animal Ecology},
keywords = {Allee effects,Density dependence,Metacommunity,Population dynamics,Time series},
number = {4},
pages = {866--879},
title = {{The effects of colonization, extinction and competition on co-existence in metacommunities}},
volume = {78},
year = {2009}
}
@article{Levins1969,
author = {<NAME>},
doi = {10.1093/besa/15.3.237},
file = {:Users/mtalluto/work/Mendeley/Levins{\_}1969.pdf:pdf},
journal = {Bulletin of the Entomological Society of America},
number = {3},
pages = {237--240},
title = {{Some Demographic and Genetic Consequences of Environmental Heterogeneity for Biological Control}},
url = {http://besa.oxfordjournals.org/cgi/doi/10.1093/besa/15.3.237},
volume = {15},
year = {1969}
}
@article{Holt2005,
author = {<NAME>. and Keitt, <NAME>. and Lewis, <NAME>. and Maurer, <NAME>. and Taper, <NAME>.},
doi = {10.1111/j.0030-1299.2005.13147.x},
file = {:Users/mtalluto/work/Mendeley/Holt et al.{\_}2005.pdf:pdf},
issn = {00301299},
journal = {Oikos},
number = {1},
pages = {18--27},
title = {{Theoretical models of species' borders: Single species approaches}},
volume = {108},
year = {2005}
}
@article{Holt2000,
author = {<NAME>. and Keitt, <NAME>.},
doi = {10.1046/j.1461-0248.2000.00116.x},
file = {:Users/mtalluto/work/Mendeley/Holt, Keitt{\_}2000.pdf:pdf},
issn = {1461023X},
journal = {Ecology Letters},
keywords = {Ecological constraints on evolutionary dynamics,Gradients,Metapopulation dynamics,Species borders},
number = {1},
pages = {41--47},
title = {{Alternative causes for range limits: A metapopulation perspective}},
volume = {3},
year = {2000}
}
@article{Talluto2017,
author = {<NAME> <NAME> <NAME> <NAME>},
doi = {10.1038/s41559-017-0182},
file = {:Users/mtalluto/work/Mendeley/Talluto et al.{\_}2017.pdf:pdf},
issn = {2397-334X},
journal = {Nature Ecology {\&} Evolution},
number = {7},
title = {{Extinction debt and colonization credit delay range shifts of eastern North American trees}},
volume = {1},
year = {2017}
}
@article{Anderson2011,
abstract = {A recent increase in studies of $\beta$ diversity has yielded a confusing array of concepts, measures and methods. Here, we provide a roadmap of the most widely used and ecologically relevant approaches for analysis through a series of mission statements. We distinguish two types of $\beta$ diversity: directional turnover along a gradient vs. non-directional variation. Different measures emphasize different properties of ecological data. Such properties include the degree of emphasis on presence/absence vs. relative abundance information and the inclusion vs. exclusion of joint absences. Judicious use of multiple measures in concert can uncover the underlying nature of patterns in $\beta$ diversity for a given dataset. A case study of Indonesian coral assemblages shows the utility of a multi-faceted approach. We advocate careful consideration of relevant questions, matched by appropriate analyses. The rigorous application of null models will also help to reveal potential processes driving observed patterns in $\beta$ diversity. {\textcopyright} 2010 Blackwell Publishing Ltd/CNRS.},
author = {<NAME>. and <NAME>. and Chase, <NAME>. and <NAME>, <NAME>. and Freestone, <NAME>. and Sanders, <NAME>. and Cornell, <NAME>. and <NAME>. and Davies, <NAME>. and Harrison, <NAME>. and Kraft, <NAME>. and <NAME>. and Swenson, <NAME>.},
doi = {10.1111/j.1461-0248.2010.01552.x},
file = {:Users/mtalluto/work/Mendeley/Anderson et al.{\_}2011.pdf:pdf},
issn = {1461023X},
journal = {Ecology Letters},
keywords = {Biodiversity,Community ecology,Environmental gradients,Heterogeneity,Multivariate analysis,Species composition,Turnover,Variance partitioning,Variation},
number = {1},
pages = {19--28},
pmid = {21070562},
title = {{Navigating the multiple meanings of $\beta$ diversity: A roadmap for the practicing ecologist}},
volume = {14},
year = {2011}
}
@article{Mazel2017b,
abstract = {Aim: We aimed to assess the relative influence of the historical and contemporary processes determining global patterns of current $\beta$-diversity. Specifically, we quantified the relative effects of contemporary climate and historical plate tectonics on $\beta$-diversity at different phylogenetic scales. Location: Global. Time Period: Contemporaneous. Major taxa studied: Mammals and birds. Methods: We analysed the current $\beta$-diversity patterns of birds and mammal assemblages at sequential depths in the phylogeny, that is, from the tips to deeper branches. This was done by slicing bird and mammal phylogenetic trees into 66 time slices of 1 Ma (from 0 to 65 Ma) and recording the branches within each slice. Using global distribution data, we defined the branches' geographical distribution as the union of the corresponding downstream species distributions. For each time slice, we (a) computed pairwise $\beta$-diversity across all the grid cells for the whole world and (b) estimated the correlation between this $\beta$-diversity matrix and contemporary climatic and geographical distances, and past geological distances, a proxy for plate tectonics. Results: Contemporary climate best explained the $\beta$-diversity of shallow branches (i.e., species). For mammals, the geographical isolation of landmasses generated by plate tectonics best explained the $\beta$-diversity of deeper branches, whereas the effect of past isolation was weaker for birds. Main conclusions: Our study shows that the relative influence of contemporary climate and plate tectonics on the $\beta$-diversity of bird and mammal assemblages varies along the phylogenetic time-scale. Our phylogenetic time-scale approach is general and flexible enough to be applied to a broad spectrum of study systems and spatial scales.},
author = {Mazel, <NAME>{\"{u}}est, <NAME> <NAME> Renaud, <NAME>, <NAME>, S{\'{e}}<NAME>},
doi = {10.1111/geb.12632},
file = {:Users/mtalluto/work/Mendeley/Mazel et al.{\_}2017.pdf:pdf},
issn = {14668238},
journal = {Global Ecology and Biogeography},
keywords = {biogeographical regions,biogeography,continental drift,geological time-scale,macroecology,taxonomic scale},
number = {10},
pages = {1211--1221},
title = {{Global patterns of $\beta$-diversity along the phylogenetic time-scale: The role of climate and plate tectonics}},
volume = {26},
year = {2017}
}
@article{Mouillot2016,
abstract = {Although coral reefs support the largest concentrations of marine biodiversity worldwide, the extent to which the global system of marine-protected areas (MPAs) represents individual species and the breadth of evolutionary history across the Tree of Life has never been quantified. Here we show that only 5.7{\%} of scleractinian coral species and 21.7{\%} of labrid fish species reach the minimum protection target of 10{\%} of their geographic ranges within MPAs. We also estimate that the current global MPA system secures only 1.7{\%} of the Tree of Life for corals, and 17.6{\%} for fishes. Regionally, the Atlantic and Eastern Pacific show the greatest deficit of protection for corals while for fishes this deficit is located primarily in the Western Indian Ocean and in the Central Pacific. Our results call for a global coordinated expansion of current conservation efforts to fully secure the Tree of Life on coral reefs.},
author = {<NAME> <NAME>. and <NAME>. and <NAME>. and <NAME>. and <NAME>.},
doi = {10.1038/ncomms10359},
file = {:Users/mtalluto/work/Mendeley/Mouillot et al.{\_}2016.pdf:pdf},
issn = {20411723},
journal = {Nature Communications},
number = {May 2015},
pages = {1--8},
pmid = {26756609},
publisher = {Nature Publishing Group},
title = {{Global marine protected areas do not secure the evolutionary history of tropical corals and fishes}},
url = {http://dx.doi.org/10.1038/ncomms10359},
volume = {7},
year = {2016}
}
@article{Harborne2017,
abstract = {Coral reefs provide critical services to coastal communities, and these services rely on ecosystem functions threatened by stressors. By summarizing the threats to the functioning of reefs from fishing, climate change, and decreasing water quality, we highlight that these stressors have multiple, conflicting effects on functionally similar groups of species and their interactions, and that the overall effects are often uncertain because of a lack of data or variability among taxa. The direct effects of stressors on links among functional groups, such as predator-prey interactions, are particularly uncertain. Using qualitative modeling, we demonstrate that this uncertainty of stressor impacts on functional groups (whether they are positive, negative, or neutral) can have significant effects on models of ecosystem stability, and reducing uncertainty is vital for understanding changes to reef functioning. This review also provides guidance for future models of reef functioning, which should include interacti...},
author = {Harborne, <NAME>. and <NAME> Bozec, <NAME> <NAME>.},
doi = {10.1146/annurev-marine-010816-060551},
file = {:Users/mtalluto/work/Mendeley/Harborne et al.{\_}2017.pdf:pdf},
issn = {1941-1405},
journal = {Annual Review of Marine Science},
keywords = {climate change,ecological uncertainty,ecosystem functioning,ecosystem service,fishing,quality,water},
number = {1},
pages = {445--468},
title = {{Multiple Stressors and the Functioning of Coral Reefs}},
volume = {9},
year = {2017}
}
@article{DAgata2014,
abstract = {Summary Beyond the loss of species richness [1-3], human activities may also deplete the breadth of evolutionary history (phylogenetic diversity) and the diversity of roles (functional diversity) carried out by species within communities, two overlooked components of biodiversity. Both are, however, essential to sustain ecosystem functioning and the associated provision of ecosystem services, particularly under fluctuating environmental conditions [1-7]. We quantified the effect of human activities on the taxonomic, phylogenetic, and functional diversity of fish communities in coral reefs, while teasing apart the influence of biogeography and habitat along a gradient of human pressure across the Pacific Ocean. We detected nonlinear relationships with significant breaking points in the impact of human population density on phylogenetic and functional diversity of parrotfishes, at 25 and 15 inhabitants/km2, respectively, while parrotfish species richness decreased linearly along the same population gradient. Over the whole range, species richness decreased by 11.7{\%}, while phylogenetic and functional diversity dropped by 35.8{\%} and 46.6{\%}, respectively. Our results call for caution when using species richness as a benchmark for measuring the status of ecosystems since it appears to be less responsive to variation in human population densities than its phylogenetic and functional counterparts, potentially imperiling the functioning of coral reef ecosystems. {\textcopyright} 2014 Elsevier Ltd.},
author = {D'Agata, St{\'{e}}phanie and Mouillot, David and Kulbicki, Michel and Andr{\'{e}}fou{\"{e}}t, Serge and Bellwood, <NAME>. and Cinner, <NAME>. and Cowman, <NAME>. and Kronen, Mecki and Pinca, Silvia and Vigliola, Laurent},
doi = {10.1016/j.cub.2014.01.049},
file = {:Users/mtalluto/work/Mendeley/D'Agata et al.{\_}2014.pdf:pdf},
issn = {09609822},
journal = {Current Biology},
number = {5},
pages = {555--560},
title = {{Human-mediated loss of phylogenetic and functional diversity in coral reef fishes}},
volume = {24},
year = {2014}
}
@article{Leprieur2016,
abstract = {Identifying the main determinants of tropical marine biodiversity is essential for devising appropriate conservation measures mitigating the ongoing degradation of coral reef habitats. Based on a gridded distribution database and phylogenetic information, we compared the phylogenetic structure of assemblages for three tropical reef fish families (Labridae: wrasses, Pomacentridae: damselfishes and Chaetodontidae: butterflyfishes) using the net relatedness (NRI) and nearest taxon (NTI) indices. We then related these indices to contemporary and historical environmental conditions of coral reefs using spatial regression analyses. Higher levels of phylogenetic clustering were found for fish assemblages in the Indo-Australian Archipelago (IAA), and more particularly when considering the NTI index. The phylogenetic structure of the Pomacentridae, and to a lower extent of the Chaeotodontidae and Labridae, was primarily associated with the location of refugia during the Quaternary period. Phylogenetic clustering in the IAA may partly result from vicariance events associated with coral reef fragmentation during the glacial periods of the Quaternary. Variation in the patterns among fish families further suggest that dispersal abilities may have interacted with past habitat availability in shaping the phylogenetic structure of tropical reef fish assemblages.},
author = {<NAME> <NAME>, <NAME>, <NAME> Kulbicki, <NAME>, <NAME>, <NAME>. and Mouillot, <NAME>, Lo{\"{i}}c},
doi = {10.1111/ecog.01638},
file = {:Users/mtalluto/work/Mendeley/Leprieur et al.{\_}2016.pdf:pdf},
issn = {16000587},
journal = {Ecography},
number = {9},
pages = {825--835},
title = {{Historical and contemporary determinants of global phylogenetic structure in tropical reef fish faunas}},
volume = {39},
year = {2016}
}
@article{Tittensor2010,
abstract = {Global patterns of species richness and their structuring forces have fascinated biologists since Darwin and provide critical context for contemporary studies in ecology, evolution and conservation. Anthropogenic impacts and the need for systematic conservation planning have further motivated the analysis of diversity patterns and processes at regional to global scales. Whereas land diversity patterns and their predictors are known for numerous taxa, our understanding of global marine diversity has been more limited, with recent findings revealing some striking contrasts to widely held terrestrial paradigms. Here we examine global patterns and predictors of species richness across 13 major species groups ranging from zooplankton to marine mammals. Two major patterns emerged: coastal species showed maximum diversity in the Western Pacific, whereas oceanic groups consistently peaked across broad mid-latitudinal bands in all oceans. Spatial regression analyses revealed sea surface temperature as the only environmental predictor highly related to diversity across all 13 taxa. Habitat availability and historical factors were also important for coastal species, whereas other predictors had less significance. Areas of high species richness were disproportionately concentrated in regions with medium or higher human impacts. Our findings indicate a fundamental role of temperature or kinetic energy in structuring cross-taxon marine biodiversity, and indicate that changes in ocean temperature, in conjunction with other human impacts, may ultimately rearrange the global distribution of life in the ocean. {\textcopyright} 2010 Macmillan Publishers Limited. All rights reserved.},
author = {Tittensor, <NAME>. and <NAME>, <NAME>, <NAME>. and <NAME>, <NAME> and Worm, Boris},
doi = {10.1038/nature09329},
file = {:Users/mtalluto/work/Mendeley/Tittensor et al.{\_}2010.pdf:pdf},
issn = {00280836},
journal = {Nature},
number = {7310},
pages = {1098--1101},
publisher = {Nature Publishing Group},
title = {{Global patterns and predictors of marine biodiversity across taxa}},
url = {http://dx.doi.org/10.1038/nature09329},
volume = {466},
year = {2010}
}
@article{Datry2018,
abstract = {Perennial rivers and streams make a disproportionate contribution to global carbon (C) cycling. However, the contribution of intermittent rivers and ephemeral streams (IRES), which sometimes cease to flow and can dry completely, is largely ignored although they represent over half the global river network. Substantial amounts of terrestrial plant litter (TPL) accumulate in dry riverbeds and, upon rewetting, this material can undergo rapid microbial processing. We present the results of a global research collaboration that collected and analysed TPL from 212 dry riverbeds across major environmental gradients and climate zones. We assessed litter decomposability by quantifying the litter carbon-to-nitrogen ratio and oxygen (O2) consumption in standardized assays and estimated the potential short-term CO2 emissions during rewetting events. Aridity, cover of riparian vegetation, channel width and dry-phase duration explained most variability in the quantity and decomposability of plant litter in IRES. Our estimates indicate that a single pulse of CO2 emission upon litter rewetting contributes up to 10{\%} of the daily CO2 emission from perennial rivers and stream, particularly in temperate climates. This indicates that the contributions of IRES should be included in global C-cycling assessments.},
author = {<NAME> <NAME>. and {<NAME>}, D. and <NAME> <NAME>. and Cl{\'{e}}ment, <NAME>. and <NAME>. and Mole{\'{o}}<NAME>. and <NAME> G{\"{u}}<NAME>. and Albarin{\~{o}}, R. and <NAME> <NAME> <NAME>. and <NAME>. and <NAME>. and <NAME>. and <NAME>. and <NAME>. and Bo{\"{e}}<NAME>. and <NAME>. and <NAME>. and Bonada, N. and Bond, <NAME>. and {Brintrup Barri{\'{a}}}, K. C. and <NAME>. and Burrows, <NAME>. and Cancellario, T. and Canhoto, C. and <NAME>. and Cauvy-Frauni{\'{e}}, S. and <NAME>. and Danger, M. and {De Freitas Terra}, Bianca and {De Girolamo}, A. M. and {De La Barra}, Evans and {Del Campo}, R. and Diaz-Villanueva, <NAME>. and <NAME> <NAME>. and <NAME>. and Febria, C. and Four, B. and <NAME>. and <NAME>. and G{\'{o}}mez, <NAME>{\'{o}}<NAME>. and Grac{\c{a}}, M. A.S. and <NAME>{\'{<NAME>. and Mili{\v{s}}<NAME>. and <NAME>. and Pe{\v{s}}i{\'{c}}, V. and Pol{\'{a}}{\v{s}}<NAME>. and <NAME> Rodr{\'{i}}<NAME>{\'{a}}<NAME>. and Savi{\'{c}}, A. and <NAME>. and <NAME>. and {Vander Vorste}, Ross and <NAME>. and <NAME>.},
doi = {10.1038/s41561-018-0134-4},
file = {:Users/mtalluto/work/Mendeley/Datry et al.{\_}2018.pdf:pdf},
issn = {17520908},
journal = {Nature Geoscience},
number = {7},
pages = {497--503},
publisher = {Springer US},
title = {{A global analysis of terrestrial plant litter dynamics in non-perennial waterways}},
url = {http://dx.doi.org/10.1038/s41561-018-0134-4},
volume = {11},
year = {2018}
}
@article{Boulton1991,
abstract = {Eucalypt leaf packs were placed at two sites in an intermittent stream during summer to examine the hypothesis that terrestrially-exposed leaf litter accumulates a richer microbial flora than submerged leaves - a phenomenon observed in Canadian temporary vernal pools. This did not occur; during the experiment, microbial biomass (as ATP) rose steadily on submerged leaves but remained low on terrestrially-exposed leaves. Densities of most functional feeding groups on the submerged leaves increased with time. Scrapers appeared to be more important than shredders in eucalypt leaf breakdown at both sites. {\textcopyright} 1991 Kluwer Academic Publishers.},
author = {<NAME>.},
doi = {10.1007/BF00037368},
file = {:Users/mtalluto/work/Mendeley/Boulton{\_}1991.pdf:pdf},
issn = {00188158},
journal = {Hydrobiologia},
keywords = {Australia,Leaf decomposition,functional feeding groups,intermittent stream,microbial conditioning},
number = {2},
pages = {123--136},
title = {{Eucalypt leaf decomposition in an intermittent stream in south-eastern Australia}},
volume = {211},
year = {1991}
}
@incollection{Boulton2017,
address = {London, UK},
author = {Boulton, <NAME> <NAME> Jaeger, <NAME>. and <NAME>},
booktitle = {Intermittent rivers and ephemeral streams: Ecology and management},
chapter = {2.3},
editor = {<NAME>},
pages = {79--108},
publisher = {Elsevier},
title = {{Hydrological connectivity in intermittent rivers and ephemeral streams}},
year = {2017}
}
@article{Koehler2015,
abstract = {Large carbon dioxide amounts are released to the atmosphere during organic matter decomposition. Yet the large-scale and long-term regulation of this critical process in global carbon cycling by litter chemistry and climate remains poorly understood. We used reactivity continuum (RC) modeling to analyze the decadal data set of the "Long-term Intersite Decomposition Experiment," in which fine litter and wood decomposition was studied in eight biome types (224 time series). In 32 and 46{\%} of all sites the litter content of the acid-unhydrolyzable residue (AUR, formerly referred to as lignin) and the AUR/nitrogen ratio, respectively, retarded initial decomposition rates. This initial rate-retarding effect generally disappeared within the first year of decomposition, and rate-stimulating effects of nutrients and a rate-retarding effect of the carbon/nitrogen ratio became more prevalent. For needles and leaves/grasses, the influence of climate on decomposition decreased over time. For fine roots, the climatic influence was initially smaller but increased toward later-stage decomposition. The climate decomposition index was the strongest climatic predictor of decomposition. The similar variability in initial decomposition rates across litter categories as across biome types suggested that future changes in decomposition may be dominated by warming-induced changes in plant community composition. In general, the RC model parameters successfully predicted independent decomposition data for the different litter-biome combinations (196 time series). We argue that parameterization of large-scale decomposition models with RC model parameters, as opposed to the currently common discrete multiexponential models, could significantly improve their mechanistic foundation and predictive accuracy across climate zones and litter categories. Key Points The LIDET decomposition data are simulated using reactivity continuum modeling Apparent temperature sensitivity varied across litter categories and time Changes in plant community composition will strongly affect decomposition},
author = {<NAME> Tranvik, <NAME>.},
doi = {10.1002/2015JG002908},
file = {:Users/mtalluto/work/Mendeley/Koehler, Tranvik{\_}2015.pdf:pdf},
issn = {21698961},
journal = {Journal of Geophysical Research G: Biogeosciences},
keywords = {LIDET,climate,decomposition,exponential model,litter chemistry,reactivity continuum model},
number = {7},
pages = {1196--1214},
title = {{Reactivity continuum modeling of leaf, root, and wood decomposition across biomes}},
volume = {120},
year = {2015}
}
@article{Dieter2011,
abstract = {Autumnal input of leaf litter is a pivotal energy source in most headwater streams. In temporary streams, however, water stress may lead to a seasonal shift in leaf abscission. Leaves accumulate at the surface of the dry streambed or in residual pools and are subject to physicochemical preconditioning before decomposition starts after flow recovery. In this study, we experimentally tested the effect of photodegradation on sunlit streambeds and anaerobic fermentation in anoxic pools on leaf decomposition during the subsequent flowing phase. To mimic field preconditioning, we exposed Populus tremula leaves to UV-VIS irradiation and wet-anoxic conditions in the laboratory. Subsequently, we quantified leaf mass loss of preconditioned leaves and the associated decomposer community in five low-order temporary streams using coarse and fine mesh litter bags. On average, mass loss after approximately 45 days was 4 and 7{\%} lower when leaves were preconditioned by irradiation and anoxic conditions, respectively. We found a lower chemical quality and lower ergosterol content (a proxy for living fungal biomass) in leaves from the anoxic preconditioning, but no effects on macroinvertebrate assemblages were detected for any preconditioning treatment. Overall, results from this study suggest a reduced processing efficiency of organic matter in temporary streams due to preconditioning during intermittence of flow leading to reduced substrate quality and repressed decomposer activity. These preconditioning effects may become more relevant in the future given the expected worldwide increase in the geographical extent of intermittent flow as a consequence of global change. {\textcopyright} 2011 Springer Basel AG.},
author = {<NAME> <NAME> Garc{\'{<NAME> S{\'{a}}<NAME> G{\'{o}}<NAME> Mora-G{\'{<NAME>.},
doi = {10.1007/s00027-011-0231-6},
file = {:Users/mtalluto/work/Mendeley/Dieter et al.{\_}2011.pdf:pdf},
issn = {10151621},
journal = {Aquatic Sciences},
keywords = {Anoxic pond,Drought,Mediterranean,Organic carbon dynamics,Temporary stream,UV radiation},
number = {4},
pages = {599--609},
title = {{Preconditioning effects of intermittent stream flow on leaf litter decomposition}},
volume = {73},
year = {2011}
}
@article{Abril2016,
abstract = {In temporary Mediterranean streams, flow fragmentation during summer droughts originates an ephemeral mosaic of terrestrial and aquatic habitat types. The heterogeneity of habitat types implies a particular ecosystem functioning in temporary streams that is still poorly understood. We assessed the initial phases of leaf litter decomposition in selected habitat types: running waters, isolated pools and moist and dry streambed sediments. We used coarse-mesh litter bags containing Populus nigra leaves to examine decomposition rates, microbial biomass, macroinvertebrate abundance and dissolved organic carbon (DOC) release rates in each habitat type over an 11-day period in late summer. We detected faster decomposition rates in aquatic (running waters and isolated pools) than in terrestrial habitats (moist and dry streambed sediments). Under aquatic conditions, decomposition was characterized by intense leaching and early microbial colonization, which swiftly started to decompose litter. Microbial colonization in isolated pools was primarily dominated by bacteria, whereas in running waters fungal biomass predominated. Under terrestrial conditions, leaves were most often affected by abiotic processes that resulted in small mass losses. We found a substantial decrease in DOC release rates in both aquatic habitats within the first days of the study, whereas DOC release rates remained relatively stable in the moist and dry sediments. This suggests that leaves play different roles as a DOC source during and after flow fragmentation. Overall, our results revealed that leaf decomposition is heterogeneous during flow fragmentation, which has implications related to DOC utilization that should be considered in future regional carbon budgets.},
author = {<NAME> and Mu{\~{n}}<NAME> Men{\'{e}}<NAME>},
doi = {10.1016/j.scitotenv.2016.02.082},
file = {:Users/mtalluto/work/Mendeley/Abril, Mu{\~{n}}oz, Men{\'{e}}ndez{\_}2016.pdf:pdf},
issn = {18791026},
journal = {Science of the Total Environment},
keywords = {Black poplar,DOC release,Drought,Flow fragmentation,Habitat heterogeneity,Microbial biomass},
pages = {330--339},
publisher = {Elsevier B.V.},
title = {{Heterogeneity in leaf litter decomposition in a temporary Mediterranean stream during flow fragmentation}},
url = {http://dx.doi.org/10.1016/j.scitotenv.2016.02.082},
volume = {553},
year = {2016}
}
@article{DelCampo2016,
abstract = {In stream ecosystems, coarse organic matter from the riparian vegetation, a key food resource, is often retained in the floodplains before reaching the channel. During floodplain exposure, organic matter can be affected by abiotic and biotic processes ("preconditioning"), which alter its quality and affect its subsequent decomposition in streams. We analyzed the effect of floodplain preconditioning on wood quality (lignin, C, N, P, K, among others), and its subsequent aquatic breakdown, paying special attention to microbial activity. We simulated preconditioned standard wooden sticks on one arid stream floodplain for 3 and 4. months, and then monitored their breakdown in three different streams, together with control (non-preconditioned) sticks. Preconditioning reduced lignin mass and C:N and lignin:N ratios, caused the leaching of soluble nutrients such as P and K, as well as N immobilization by microbes. These changes enhanced the breakdown of wood in the first week of immersion, but had no effect on breakdown rates after 4. months of incubation in the streams, although N immobilization was diminished. Our results suggest that terrestrial preconditioning could alter the role of wood as a long-lasting nutrients and energy source for freshwater ecosystem.},
author = {<NAME>, Rub{\'{<NAME>{\'{<NAME>},
doi = {10.1016/j.scitotenv.2015.11.050},
file = {:Users/mtalluto/work/Mendeley/del Campo, G{\'{o}}mez{\_}2016.pdf:pdf},
issn = {18791026},
journal = {Science of the Total Environment},
keywords = {Abiotic factors,C processing,Floods,Microbial activity,Terrestrial decomposition,Wood},
number = {April 2018},
pages = {652--661},
publisher = {Elsevier B.V.},
title = {{Exposure of wood in floodplains affects its chemical quality and its subsequent breakdown in streams}},
url = {http://dx.doi.org/10.1016/j.scitotenv.2015.11.050},
volume = {543},
year = {2016}
}
@book{Datry2017Ires,
address = {London, UK},
editor = {<NAME> and <NAME>. and <NAME>},
file = {:Users/mtalluto/work/Mendeley/Unknown{\_}2017.pdf:pdf},
isbn = {9789896540821},
publisher = {Elsevier},
title = {{Intermittent rivers and ephemeral streams ecology and management}},
year = {2017}
}
@article{Larned2010,
abstract = {Temporary rivers and streams are among the most common and most hydrologically dynamic freshwater ecosystems. The number of temporary rivers and the severity of flow intermittence may be increasing in regions affected by climatic drying trends or water abstraction. Despite their abundance, temporary rivers have been historically neglected by ecologists. A recent increase in temporary-river research needs to be supported by new models that generate hypotheses and stimulate further research. In this article, we present three conceptual models that address spatial and temporal patterns in temporary-river biodiversity and biogeochemistry. Temporary rivers are characterised by the repeated onset and cessation of flow, and by complex hydrological dynamics in the longitudinal dimension. Longitudinal dynamics, such as advancing and retreating wetted fronts, hydrological connections and disconnections, and gradients in flow permanence, influence biotic communities and nutrient and organic matter processing. The first conceptual model concerns connectivity between habitat patches. Variable connectivity suggests that the metacommunity and metapopulation concepts are applicable in temporary rivers. We predict that aggregations of local communities in the isolated water bodies of temporary rivers function as metacommunities. These metacommunities may become longitudinally nested due to interspecific differences in dispersal and mortality. The metapopulation concept applies to some temporary river species, but not all. In stable metapopulations, rates of local extinction are balanced by recolonisation. However, extinction and recolonisation in many temporary-river species are decoupled by frequent disturbances, and populations of these species are usually expanding or contracting. The second conceptual model predicts that large-scale biodiversity varies as a function of aquatic and terrestrial patch dynamics and water-level fluctuations. Habitat mosaics in temporary rivers change in composition and configuration in response to inundation and drying, and these changes elicit a range of biotic responses. In the model, aquatic biodiversity initially increases directly with water level due to increasing abundance of aquatic patches. When most of the channel is inundated and most aquatic patches are connected, further increases in aquatic habitat and connectivity cause aquatic biodiversity to decline due to community homogenisation and reduced habitat diversity. The predicted responses of terrestrial biodiversity to changes in water level are the inverse of aquatic biodiversity responses. The third conceptual model represents temporary rivers as longitudinal, punctuated biogeochemical reactors. Advancing fronts carry water, solutes and particulate organic matter downstream; subsequent flow recessions and drying result in deposition of transported material in reserves such as pools and bar tops. Material processing is rapid during inundated periods and slower during dry periods. The efficiency of material processing is predicted to increase with the number of cycles of transport, deposition and processing that occur down the length of a temporary river. We end with a call for conservation and resource management that addresses the unique properties of temporary rivers. Primary objectives for effective temporary river management are preservation or restoration of aquatic-terrestrial habitat mosaics, preservation or restoration of natural flow intermittence, and identification of flow requirements for highly valued species and processes. {\textcopyright} 2009 Blackwell Publishing Ltd.},
author = {Larned, <NAME>. and <NAME> Arscott, <NAME> Tockner, Klement},
doi = {10.1111/j.1365-2427.2009.02322.x},
file = {:Users/mtalluto/work/Mendeley/Larned et al.{\_}2010.pdf:pdf},
issn = {00465070},
journal = {Freshwater Biology},
keywords = {Aquatic-terrestrial habitat mosaics,Connectivity,Flow intermittence,Meta-systems,Temporary rivers},
number = {4},
pages = {717--738},
title = {{Emerging concepts in temporary-river ecology}},
volume = {55},
year = {2010}
}
@book{Soetaert2009,
abstract = {Mathematical modelling is an essential tool in present-day ecological research. Yet for many ecologists it is still problematic to apply modelling in their research. In our experience, the major problem is at the conceptual level: proper understanding of what a model is, how ecological relations can be translated consistently into mathematical equations, how models are solved, steady states calculated and interpreted. Many textbooks jump over these conceptual hurdles to dive into detailed formulations or the mathematics of solution. This book attempts to fill that gap. It introduces essential concepts for mathematical modelling, explains the mathematics behind the methods, and helps readers to implement models and obtain hands-on experience. Throughout the book, emphasis is laid on how to translate ecological questions into interpretable models in a practical way.The book aims to be an introductory textbook at the undergraduate-graduate level, but will also be useful to seduce experienced ecologists into the world of modelling. The range of ecological models treated is wide, from Lotka-Volterra type of principle-seeking models to environmental or ecosystem models, and including matrix models, lattice models and sequential decision models. All chapters contain a concise introduction into the theory, worked-out examples and exercises. All examples are implemented in the open-source package R, thus taking away problems of software availability for use of the book. All code used in the book is available on a dedicated website.},
author = {<NAME> Herman, <NAME>},
booktitle = {A Practical Guide to Ecological Modelling},
publisher = {Springer},
title = {{A Practical Guide to Ecological Modelling}},
year = {2009}
}
