Publications
155 results found
Stiller J, Feng S, Chowdhury A-A, et al., 2024, Complexity of avian evolution revealed by family-level genomes., Nature
Despite tremendous efforts in the past decades, relationships among main avian lineages remain heavily debated without a clear resolution. Discrepancies have been attributed to diversity of species sampled, phylogenetic method, and the choice of genomic regions 1-3. Here, we address these issues by analyzing genomes of 363 bird species 4 (218 taxonomic families, 92% of total). Using intergenic regions and coalescent methods, we present a well-supported tree but also a remarkable degree of discordance. The tree confirms that Neoaves experienced rapid radiation at or near the Cretaceous-Paleogene (K-Pg) boundary. Sufficient loci rather than extensive taxon sampling were more effective in resolving difficult nodes. Remaining recalcitrant nodes involve species that challenge modeling due to extreme GC content, variable substitution rates, incomplete lineage sorting, or complex evolutionary events such as ancient hybridization. Assessment of the impacts of different genomic partitions showed high heterogeneity across the genome. We discovered sharp increases in effective population size, substitution rates, and relative brain size following the K-Pg extinction event, supporting the hypothesis that emerging ecological opportunities catalyzed the diversification of modern birds. The resulting phylogenetic estimate offers novel insights into the rapid radiation of modern birds and provides a taxon-rich backbone tree for future comparative studies.
Neyret M, Le Provost G, Boesing AL, et al., 2024, A slow-fast trait continuum at the whole community level in relation to land-use intensification., Nat Commun, Vol: 15
Organismal functional strategies form a continuum from slow- to fast-growing organisms, in response to common drivers such as resource availability and disturbance. However, whether there is synchronisation of these strategies at the entire community level is unclear. Here, we combine trait data for >2800 above- and belowground taxa from 14 trophic guilds spanning a disturbance and resource availability gradient in German grasslands. The results indicate that most guilds consistently respond to these drivers through both direct and trophically mediated effects, resulting in a 'slow-fast' axis at the level of the entire community. Using 15 indicators of carbon and nutrient fluxes, biomass production and decomposition, we also show that fast trait communities are associated with faster rates of ecosystem functioning. These findings demonstrate that 'slow' and 'fast' strategies can be manifested at the level of whole communities, opening new avenues of ecosystem-level functional classification.
Drury JP, Clavel J, Tobias JA, et al., 2024, Limited ecological opportunity influences the tempo of morphological evolution in birds, Current Biology, Vol: 34, Pages: 661-669.E4, ISSN: 0960-9822
According to classic models of lineage diversification and adaptive radiation, phenotypic evolution should accelerate in the context of ecological opportunity and slow down when niches become saturated.1,2 However, only weak support for these ideas has been found in nature, perhaps because most analyses make the biologically unrealistic assumption that clade members contribute equally to reducing ecological opportunity, even when they occur in different continents or specialize on different habitats and diets. To view this problem through a different lens, we adapted a new phylogenetic modeling approach that accounts for the fact that competition for ecological opportunity only occurs between species that coexist and share similar habitats and diets. Applying this method to trait data for nearly all extant species of landbirds,3 we find a widespread signature of decelerating trait evolution in lineages adapted to similar habitats or diets. The strength of this pattern was consistent across latitudes when comparing tropical and temperate assemblages. Our results provide little support for the idea that increased diversity and tighter packing of niches accentuates evolutionary slowdowns in the tropics and instead suggest that limited ecological opportunity can be an important factor determining the rate of morphological diversification at a global scale.
Hatfield JH, Banks-Leite C, Barlow J, et al., 2024, Constraints on avian seed dispersal reduce potential for resilience in degraded tropical forests, Functional Ecology, Vol: 38, Pages: 315-326, ISSN: 0269-8463
Seed dispersal is fundamental to tropical forest resilience. Forest loss or degradation typically leads to defaunation, altering seed transfer dynamics and impairing the ability of forested habitats to regenerate or recover from perturbation. However, the extent of defaunation, and its likely impacts on the seed dispersers needed to restore highly degraded or clear-felled areas, remains poorly understood in tropical forest landscapes. To quantify defaunation of seed-dispersing birds, we used field survey data from 499 transects in three forested regions of Brazil, first comparing the observed assemblages with those predicted by geographic range maps, and then assessing habitat associations of frugivores across land cover gradients. We found that current bird assemblages have lower functional diversity (FD) than predicted by species range maps in Amazonia (4%–6%), with a greater reduction in FD (28%) for the Atlantic Forest, which has been more heavily deforested for a longer period. Direct measures of seed dispersal are difficult to obtain, so we focused on potential seed transfer inferred from shared species occurrence. Of 83 predominantly frugivorous bird species recorded in relatively intact forests, we show that 10% were absent from degraded forest, and 57% absent from the surrounding matrix of agricultural land covers, including many large-gaped species. Of 112 frugivorous species using degraded forest, 47% were absent from matrix habitats. Overall, frugivores occurring in both intact forest and matrix habitats were outnumbered by (mostly small-gaped) frugivores occurring in both degraded forest and matrix habitats (23 additional species; 64% higher diversity). These findings suggest that birds have the potential to disperse seeds from intact and degraded forest to adjacent cleared lands, but that direct seed transfer from intact forests is limited, particularly for large-seeded trees. Degraded forests may play a vital role in supporting natural regenerat
Mayfield MM, Lau JA, Tobias JA, et al., 2023, What Can Evolutionary History Tell Us about the Functioning of Ecological Communities? The ASN Presidential Debate, AMERICAN NATURALIST, ISSN: 0003-0147
Stewart K, Carmona CP, Clements C, et al., 2023, Functional diversity metrics can perform well with highly incomplete data sets, Methods in Ecology and Evolution, Vol: 14, Pages: 2856-2872
Characterising changes in functional diversity at large spatial scales provides insight into the impact of human activity on ecosystem structure and function. However, the approach is often based on trait data sets that are incomplete and unrepresentative, with uncertain impacts on functional diversity estimates. To address this knowledge gap, we simulated random and biased removal of data from three empirical trait data sets: an avian data set (9579 species), a plant data set (2185 species) and a crocodilian data set (25 species). For these data sets, we assessed whether functional diversity metrics were robust to data incompleteness with and without using imputation to fill data gaps. We compared two metrics each calculated with two methods: functional richness (calculated with convex hulls and trait probabilities densities) and functional divergence (calculated with distance-based Rao and trait probability densities). Without imputation, estimates of functional diversity (richness and divergence) for birds and plants were robust when 20%–70% of species had missing data for four out of 11 and two out of six continuous traits, respectively, depending on the severity of bias and method used. However, when missing traits were imputed, functional diversity metrics consistently remained representative of the true value when 70% of bird species were missing data for four out of 11 traits and when 50% of plant species were missing data for two out of six traits. Trait probability densities and distance-based Rao were particularly robust to missingness and bias when combined with imputation. Convex hull-based estimations of functional richness were less reliable. When applied to a smaller data set (crocodilians, 25 species), all functional diversity metrics were much more sensitive to missing data. Expanding global morphometric data sets to represent more taxa and traits, and to quantify intraspecific variation, remains a priority. In the meantime, our results show
Devenish AJM, Schmitter P, Jellason NP, et al., 2023, One hundred priority questions for the development of sustainable food systems in Sub-Saharan Africa, Land, Vol: 12, ISSN: 2073-445X
Sub-Saharan Africa is facing an expected doubling of human population and tripling of food demand over the next quarter century, posing a range of severe environmental, political, and socio-economic challenges. In some cases, key Sustainable Development Goals (SDGs) are in direct conflict, raising difficult policy and funding decisions, particularly in relation to trade-offs between food production, social inequality, and ecosystem health. In this study, we used a horizon-scanning approach to identify 100 practical or research-focused questions that, if answered, would have the greatest positive impact on addressing these trade-offs and ensuring future productivity and resilience of food-production systems across sub-Saharan Africa. Through direct canvassing of opinions, we obtained 1339 questions from 331 experts based in 55 countries. We then used online voting and participatory workshops to produce a final list of 100 questions divided into 12 thematic sections spanning topics from gender inequality to technological adoption and climate change. Using data on the background of respondents, we show that perspectives and priorities can vary, but they are largely consistent across different professional and geographical contexts. We hope these questions provide a template for establishing new research directions and prioritising funding decisions in sub-Saharan Africa.
Hunt ESE, Felice RN, Tobias JA, et al., 2023, Ecological and life-history drivers of avian skull evolution, EVOLUTION, Vol: 77, Pages: 1720-1729, ISSN: 0014-3820
Tobias JA, 2023, First record of Campina Thrush Turdus arthuri for Bolivia, Bulletin of the British Ornithologists' Club, Vol: 143, Pages: 260-264, ISSN: 0007-1595
An adult thrush trapped in a mist-net near Guayaramerin, dpto. Beni, Bolivia, in April 2005, was initially identified as Black-billed Thrush Turdus ignobilis although several subtle plumage features appeared to differ from the expected race T. i. debilis. These features match those of Campina Thrush T. arthuri, a cryptic species subsequently split from Black-billed Thrush based on molecular evidence, and now known to occur widely in shrubby thickets and stunted campina forest across much of Amazonia. This record extends the known distribution of T. arthuri south-west from the nearest known localities in Amazonas and Rondônia, Brazil. T. arthuri is presumably resident in north-west dpto. Beni in suitable habitat, and potentially occurs elsewhere in Bolivia from Pando to eastern Santa Cruz in similar campina-like habitats associated with weathered outcrops of the Brazilian Shield.
Matthews TJ, Wayman JP, Whittaker RJ, et al., 2023, A global analysis of avian island diversity-area relationships in the Anthropocene, ECOLOGY LETTERS, Vol: 26, Pages: 965-982, ISSN: 1461-023X
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- Citations: 2
Germain RR, Feng S, Chen G, et al., 2023, Species-specific traits mediate avian demographic responses under past climate change, NATURE ECOLOGY & EVOLUTION, Vol: 7, Pages: 862-872, ISSN: 2397-334X
Weeks TL, Betts MG, Pfeifer M, et al., 2023, Climate-driven variation in dispersal ability predicts responses to forest fragmentation in birds, Nature Ecology and Evolution, Vol: 7, Pages: 1079-1091, ISSN: 2397-334X
Species sensitivity to forest fragmentation varies latitudinally, peaking in the tropics. A prominent explanation for this pattern is that historical landscape disturbance at higher latitudes has removed fragmentation-sensitive species or promoted the evolution of more resilient survivors. However, it is unclear whether this so-called extinction filter is the dominant driver of geographic variation in fragmentation sensitivity, particularly because climatic factors may also cause latitudinal gradients in dispersal ability, a key trait mediating sensitivity to habitat fragmentation. Here we combine field survey data with a morphological proxy for avian dispersal ability (hand-wing index) to assess responses to forest fragmentation in 1,034 bird species worldwide. We find that fragmentation sensitivity is strongly predicted by dispersal limitation and that other factors—latitude, body mass and historical disturbance events—have relatively limited explanatory power after accounting for species differences in dispersal. We also show that variation in dispersal ability is only weakly predicted by historical disturbance and more strongly associated with intra-annual temperature fluctuations (seasonality). Our results suggest that climatic factors play a dominant role in driving global variation in the impacts of forest fragmentation, emphasizing the need for more nuanced environmental policies that take into account local context and associated species traits.
Santini L, Tobias JA, Callaghan C, et al., 2023, Global patterns and predictors of avian population density, GLOBAL ECOLOGY AND BIOGEOGRAPHY, ISSN: 1466-822X
Hong P, Li Z, Yang Q, et al., 2023, Functional traits and environment jointly determine the spatial scaling of population stability in North American birds, ECOLOGY, Vol: 104, ISSN: 0012-9658
Germain RR, Feng S, Buffan L, et al., 2023, Changes in the functional diversity of modern bird species over the last million years., Proc Natl Acad Sci U S A, Vol: 120, Pages: e2201945119-e2201945119
Despite evidence of declining biosphere integrity, we currently lack understanding of how the functional diversity associated with changes in abundance among ecological communities has varied over time and before widespread human disturbances. We combine morphological, ecological, and life-history trait data for >260 extant bird species with genomic-based estimates of changing effective population size (Ne) to quantify demographic-based shifts in avian functional diversity over the past million years and under pre-anthropogenic climate warming. We show that functional diversity was relatively stable over this period, but underwent significant changes in some key areas of trait space due to changing species abundances. Our results suggest that patterns of population decline over the Pleistocene have been concentrated in particular regions of trait space associated with extreme reproductive strategies and low dispersal ability, consistent with an overall erosion of functional diversity. Further, species most sensitive to climate warming occupied a relatively narrow region of functional space, indicating that the largest potential population increases and decreases under climate change will occur among species with relatively similar trait sets. Overall, our results identify fluctuations in functional space of extant species over evolutionary timescales and represent the demographic-based vulnerability of different regions of functional space among these taxa. The integration of paleodemographic dynamics with functional trait data enhances our ability to quantify losses of biosphere integrity before anthropogenic disturbances and attribute contemporary biodiversity loss to different drivers over time.
Schleuning M, Garcia D, Tobias JA, 2023, Animal functional traits: Towards a trait-based ecology for whole ecosystems, Functional Ecology, Vol: 37, Pages: 4-12, ISSN: 0269-8463
Ali JR, Blonder BW, Pigot AL, et al., 2023, Bird extinctions threaten to cause disproportionate reductions of functional diversity and uniqueness, FUNCTIONAL ECOLOGY, Vol: 37, Pages: 162-175, ISSN: 0269-8463
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- Citations: 3
Buehne HST, Tobias JAA, Durant SMM, et al., 2022, Indirect interactions between climate and cropland distribution shape fire size in West African grasslands, Landscape Ecology, Vol: 38, Pages: 1-16, ISSN: 0921-2973
ContextClimate and land use changes often interact, yet our ability to predict their combined effects on biodiversity is currently limited. In particular, the combined effects of climate and land use on key ecosystem dynamics, such as disturbance regimes, that shape biodiversity across large spatial scales, are poorly understood.ObjectivesWe assess how indirect climate–land use interactions influence disturbance regimes by examining the mechanistic pathways by which climate and proximity to cropland interact to shape fire size in a West African grassland ecosystem, the W-Arly-Pendjari transboundary protected area complex.MethodsWe use remotely sensed indicators of burned area, rainfall, cropland distribution, and vegetation dynamics to test two spatially explicit hypotheses about the interaction between climate and land use effects on fire dynamics.ResultsWe demonstrate that in areas where wet season grass production (which is driven by rainfall) is higher, fires are larger, but that this relationship depends on the distance to cropland. Close to cropland, environmental drivers of fire size (wet season grass production, and progressive loss of fire fuel during the fire season) have little effect on fire size, as fuel breaks induced by cropland limit fire size.
Matthews TJ, Wayman JP, Cardoso P, et al., 2022, Threatened and extinct island endemic birds of the world: Distribution, threats and functional diversity, JOURNAL OF BIOGEOGRAPHY, Vol: 49, Pages: 1920-1940, ISSN: 0305-0270
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- Citations: 9
Triantis KA, Rigal F, Whittaker RJ, et al., 2022, Deterministic assembly and anthropogenic extinctions drive convergence of island bird communities, GLOBAL ECOLOGY AND BIOGEOGRAPHY, Vol: 31, Pages: 1741-1755, ISSN: 1466-822X
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- Citations: 4
Rurangwa ML, Niyigaba P, Tobias JA, et al., 2022, Functional and phylogenetic diversity of an agricultural matrix avifauna: The role of habitat heterogeneity in Afrotropical farmland, Ecology and Evolution, Vol: 12, ISSN: 2045-7758
Varied strategies to alleviate the loss of farmland biodiversity have been tested, yet there is still insufficient evidence supporting their effectiveness, especially when considering phylogenetic and functional diversity alongside traditional taxonomic diversity metrics. This conservation challenge is accentuated in the Afrotropics by the rapid agricultural expansion and intensification for the production of cash crops and by a comparative lack of research. In this study, we assessed how farming practices influence avian phylogenetic and functional diversity. We conducted point-count surveys to assess avian diversity in monocultures of tea and mixed crop farming systems surrounding the Nyungwe rainforest in south-west Rwanda, allowing us to investigate the drivers of avian diversity at farm level. Species composition was found to be moderately different between farm types, with mixed crop farms supporting higher phylogenetic diversity than tea plantations. There were no significant seasonal differences in species composition, functional or phylogenetic diversity. Overall, functional diversity did not differ between farm types, but the dispersion of trophic-related traits was significantly higher in mixed crop farms. Both functional and phylogenetic diversity were influenced by floristic diversity, vegetation height, tree number, and elevation to varying degrees. Our results also (i) highlight the role of farmland heterogeneity (e.g., crop species composition, height, and tree cover extent) in encouraging avian functional and phylogenetic diversity in the Afrotropics and (ii) indicate that the generally negative biodiversity impacts of monoculture agriculture can be partially alleviated by extensive agroforestry with an emphasis on indigenous tree species.
Weeks BC, O'Brien BK, Chu JJ, et al., 2022, Morphological adaptations linked to flight efficiency and aerial lifestyle determine natal dispersal distance in birds, Functional Ecology, Vol: 36, Pages: 1681-1689, ISSN: 0269-8463
Natal dispersal—the movement from birthplace to breeding location—is often considered the most significant dispersal event in an animal's lifetime. Natal dispersal distances may be shaped by a variety of intrinsic and extrinsic factors, and remain poorly quantified in most groups, highlighting the need for indices that capture variation in dispersal among species.In birds, it is hypothesized that dispersal distance can be predicted by flight efficiency, which can be estimated using wing morphology. However, the use of morphological indices to predict dispersal remains contentious and the mechanistic links between flight efficiency and natal dispersal are unclear.Here, we use phylogenetic comparative models to test whether hand-wing index (HWI, a morphological proxy for wing aspect ratio) predicts natal dispersal distance across a global sample of 114 bird species. In addition, we assess whether HWI is correlated with flight usage in foraging and daily routines.We find that HWI is a strong predictor of both natal dispersal distance and a more aerial lifestyle.Our results support the use of HWI as a valid proxy for relative natal dispersal distance, and also suggest that evolutionary adaptation to aerial lifestyles is a major factor connecting flight efficiency with patterns of natal dispersal.
Iglesias-Carrasco M, Tobias JA, Duchene DA, 2022, Bird lineages colonizing urban habitats have diversified at high rates across deep time, Global Ecology and Biogeography, Vol: 31, Pages: 1784-1793, ISSN: 1466-822X
AimUrbanization exposes species to novel ecological conditions. Some species thrive in urban areas, whereas many others are excluded from these human-made environments. Previous analyses suggest that the ability to cope with rapid environmental change is associated with long-term patterns of diversification, but whether the suite of traits associated with the ability to colonize urban environments is linked to this process remains poorly understood.LocationWorld.Time periodCurrent.Major taxa studiedPasserine birds.MethodsWe applied macroevolutionary models to a large dataset of passerine birds to compare the evolutionary history of urban-tolerant species with that of urban-avoidant species. Specifically, we examined models of state-dependent speciation and extinction to assess the macroevolution of urban tolerance as a binary trait, in addition to models of quantitative trait-dependent diversification based on relative urban abundance. We also ran simulation-based model assessments to explore potential sources of bias.ResultsWe provide evidence that historically, species with traits promoting urban colonization have undergone faster diversification than urban-avoidant species, indicating that urbanization favours clades with a historical tendency towards rapid speciation or reduced extinction. In addition, we find that past transitions towards states that currently impede urban colonization by passerines have been more frequent than in the opposite direction. Furthermore, we find a portion of urban-avoidant passerines to be recent and to undergo fast diversification. All highly supported models give this result consistently.Main conclusionsUrbanization is mainly associated with the loss of lineages that are inherently more vulnerable to extinction over deep time, whereas cities tend to be colonized by less vulnerable lineages, for which urbanization might be neutral or positive in terms of longer-term diversification. Urban avoidance is associated with high rates of
Freeman BG, Weeks T, Schluter D, et al., 2022, The latitudinal gradient in rates of evolution for bird beaks, a species interaction trait, Ecology Letters, Vol: 25, Pages: 635-646, ISSN: 1461-023X
Where is evolution fastest? The biotic interactions hypothesis proposes that greater species richness creates more ecological opportunity, driving faster evolution at low latitudes, whereas the ‘empty niches’ hypothesis proposes that ecological opportunity is greater where diversity is low, spurring faster evolution at high latitudes. We tested these contrasting predictions by analysing rates of beak evolution for a global dataset of 1141 avian sister species. Rates of beak size evolution are similar across latitudes, with some evidence that beak shape evolves faster in the temperate zone, consistent with the empty niches hypothesis. The empty niches hypothesis is further supported by a meta-analysis showing that rates of trait evolution and recent speciation are generally faster in the temperate zone, whereas rates of molecular evolution are slightly faster in the tropics. Our results suggest that drivers of evolutionary diversification are either similar across latitudes or more potent in the temperate zone, thus calling into question multiple hypotheses that invoke faster tropical evolution to explain the latitudinal diversity gradient.
Tobias JA, Sheard C, Pigot AL, et al., 2022, AVONET: morphological, ecological and geographical data for all birds, Ecology Letters, Vol: 25, Pages: 581-597, ISSN: 1461-023X
Functional traits offer a rich quantitative framework for developing and testing theories in evolutionary biology, ecology and ecosystem science. However, the potential of functional traits to drive theoretical advances and refine models of global change can only be fully realised when species-level information is complete. Here we present the AVONET dataset containing comprehensive functional trait data for all birds, including six ecological variables, 11 continuous morphological traits, and information on range size and location. Raw morphological measurements are presented from 90,020 individuals of 11,009 extant bird species sampled from 181 countries. These data are also summarised as species averages in three taxonomic formats, allowing integration with a global phylogeny, geographical range maps, IUCN Red List data and the eBird citizen science database. The AVONET dataset provides the most detailed picture of continuous trait variation for any major radiation of organisms, offering a global template for testing hypotheses and exploring the evolutionary origins, structure and functioning of biodiversity.
Hordley LA, Powney GD, Brereton T, et al., 2022, Developing a national indicator of functional connectivity, Ecological Indicators, Vol: 136, ISSN: 1470-160X
Habitat loss is a significant driver of biodiversity loss, causing fragmentation into small, isolated patches of suitable land cover. This reduces the permeability of landscapes to the movement of individuals and reduces the likelihood of metapopulation persistence. Quantifying functional connectivity, the ability of a focal species to move between resource patches, is therefore essential for conservation management. There is substantial evidence supporting a technique based on ‘population synchrony’- the degree of correlation in time-series of annual population growth rates between different long-term monitoring sites, to provide a measure of functional connectivity. However, synchronised population dynamics are not only driven by the movement of individuals between sites, but also shared environmental conditions which must be accounted for. Here, we use species survey data from over four decades to investigate average levels and temporal trends in population synchrony for 58 British bird and butterfly species. We first show that population synchrony is significantly associated with synchrony in some seasonal climatic variables. Once we accounted for spatiotemporal climatic patterns, we found that synchrony in butterflies declined over time by 71% between 1985 and 2000 but increased by 64% in recent years. Synchrony in birds showed some decline between 1999 and 2005, after which there appears to being recovery, however most species (74%) show no significant overall change in synchrony. Our proposed indicator provides a ‘species-eye-view’ of functional connectivity using widely available abundance data. Developing such indicators of functional connectivity, which can be updated annually, is crucial to improve the effectiveness of land management strategies for conservation under increasing environmental change.
Tobias JA, 2022, A bird in the hand: global-scale morphological trait datasets open new frontiers of ecology, evolution and ecosystem science, Ecology Letters, Vol: 25, Pages: 573-580, ISSN: 1461-023X
Stewart PS, Voskamp A, Santini L, et al., 2022, Global impacts of climate change on avian functional diversity, ECOLOGY LETTERS, Vol: 25, Pages: 673-685, ISSN: 1461-023X
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- Citations: 18
Sol D, Garcia-Porta J, Gonzalez-Lagos C, et al., 2022, A test of Darwin's naturalization conundrum in birds reveals enhanced invasion success in the presence of close relatives, ECOLOGY LETTERS, Vol: 25, Pages: 661-672, ISSN: 1461-023X
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- Citations: 5
Weeks BC, Naeem S, Lasky JR, et al., 2022, Diversity and extinction risk are inversely related at a global scale, ECOLOGY LETTERS, Vol: 25, Pages: 697-707, ISSN: 1461-023X
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- Citations: 10
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