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146 results for “species loss”
Input data for the analysis of changes in functional structures of Japanese tree species by species loss simulation
<p>The dataset was used in Kusumoto, Shiono & Kubota (2020). It includes functional structure indices (community means, functional richness, and Rao's quadratic entropy) for 514 Japanese timber and non-timber tree species at 10-km grid cell level. The community means were based on specific leaf area and leaf nitrogen content, respectively. Functional richness and Rao's Q were based on wood density and tree height. There functional metrics were calculated for the observed species assemblages and simulated assemblages at 10-km grid cell level. The simulated assemblages were computed by removing species in each grid cell at 5 levels of species loss (10%, 20%, 30%, 40% and 50%) with two scenarios: random loss and ordered loss depending on species successional niche score (i.e. later successinal species are preferentially lost). See "README" sheet for detailed explanations of the contents.</p> <p>Kusumoto, Shiono & Kubota (2020) Ethnobotany-informed trait ecology: measuring vulnerability of timber provisioning services across forest biomes in Japan. Biodiversity and Conservation. DOI: 10.1007/s10531-020-01974-y</p>
Drought survival is positively associated with high turgor loss points in temperate perennial grassland species
<p>1. Turgor loss point (π<sub>tlp</sub>) has been suggested to be a key trait for drought resistance in woody species. In herbaceous grassland species the role of π<sub>tlp</sub> for species drought survival has not yet been tested, although grasslands are projected to experience more frequent and intense droughts with climate change.</p> <p>2. To gain insights into the role of π<sub>tlp</sub> for drought resistance of temperate perennial grassland species, we assessed π<sub>tlp</sub> of 41 species common in Germany (20 forbs, 21 grasses). We directly related them to the species' comparative whole-plant drought survival and midday leaf water potentials under drought (Ψ<sub>MD</sub>) assessed in a common garden drought experiment, and to species moisture association.</p> <p>3. Species drought survival increased with increasing π<sub>tlp</sub> across all species as well as within forbs or grasses separately. Ψ<sub>MD</sub> was positively related to π<sub>tlp</sub> and drought survival. Our results imply that high π<sub>tlp</sub> promotes drought survival of common perennial European temperate mesic grassland species by enabling them to maintain high leaf water potentials under drought, i.e., a desiccation avoidance strategy. However, π<sub>tlp</sub> was not related to species moisture association.</p> <p>4. The positive relationship between π<sub>tlp</sub> and drought survival in herbaceous grassland species was opposite to the negative relationship previously established in woody plants, implying that mechanisms of drought resistance differ between woody and herbaceous species. Our results highlight the necessity of directly testing the relationship of functional traits to whole-plant drought survival in different plant life forms, before using trait assessments for predicting plant responses to drought.</p>
Incorporating plant phenological responses into species distribution models (SDMs) reduces estimates of future species loss and turnover
<p>Anthropogenetic climate change has caused distribution shifts of many species, and species distribution models (SDMs) are central for documenting this relationship. However, most SDMs rarely consider the evolution of climate-sensitive functional traits, such as phenology, which strongly affect species fitness. Using >120,000 herbarium specimens representing 360 plant species across the eastern United States, we developed a novel "phenology-informed" SDM that integrates dynamic phenological responses to changing climates. Compared to standard SDMs, our phenology-informed SDMs forecast lower species habitat loss and less species turnover under climate change. These results suggest that phenotypic plasticity or local adaptation in phenology may help species adjust their ecological niches and persist in their habitats under rapid environmental change. Our findings reveal how phenology variation mediates species distributions and affects regional biodiversity patterns. Our newly developed model also circumvents the need for mechanistic models, facilitating the deployment of trait-based SDMs across unprecedented spatial and taxonomic scales.</p>
Bryosphere loss impairs litter decomposition consistently across moss species, litter types, and micro-arthropod abundance
<p>The bryosphere (i.e., ground mosses and their associated biota) is a key driver of nutrient and carbon dynamics in many terrestrial ecosystems, in part because it regulates litter decomposition. However, we have a poor understanding of how litter decomposition responds to changes in the bryosphere, including changes in bryosphere cover, moss species, and bryosphere-associated biota. Specifically, the contribution of micro-arthropods to litter decomposition in the bryosphere is unclear. Here, we used a 16-month litterbag field experiment in two boreal forests to investigate bryosphere effects on litter decomposition rates among two moss species (<i>Pleurozium schreberi</i> and <i>Hylocomium splendens</i>), and two litter types (higher-quality <i>Betula pendula</i> litter and lower-quality <i>P. schreberi</i> litter). Additionally, we counted all micro-arthropods in the litterbags and identified them to functional groups. We found that bryosphere removal reduced litter decomposition rates by 28% and micro-arthropod abundance by 29%, and led to a colder micro-climate. Litter decomposition rates and micro-arthropod abundance were uncorrelated overall, but were positively correlated in <i>B. pendula</i> litterbags. Bryosphere effects on litter decomposition rates were consistent across moss species, litter types, and micro-arthropod abundances and community compositions. These findings suggest that micro-arthropods play a minor role in litter decomposition in the boreal forest floor, suggesting that other factors (e.g., micro-climate, nutrient availability) likely drive the positive effect of the bryosphere on decomposition rates. Our results point to a substantial and consistent impairment of litter decomposition in response to loss of moss cover, which could have important implications for nutrient and carbon cycling in moss-dominated ecosystems.</p>
Habitat loss shapes the structure and species roles in mutualistic seed dispersal networks
<p>This dataset has the variables used in the paper "Habitat loss shapes the structure and species roles in tropical seed dispersal networks" as well as the script to perform the analysis.</p>
Data from: Species tree estimation and the impact of gene loss following whole-genome duplication
<p>Whole-genome duplication (WGD) has been demonstrated to occur broadly and repeatedly in the evolutionary history of eukaryotes, and is recognized as a prominent evolutionary force, especially in plants. Immediately following WGD, most genes are present in two copies as paralogs. Due to this redundancy, one copy of a paralog pair commonly undergoes pseudogenization and is eventually lost. When speciation occurs shortly after WGD, however, differential loss of paralogs may lead to spurious phylogenetic inference resulting from the inclusion of pseudoorthologs – paralogous genes mistakenly identify as orthologs because they are present in single copes within each sampled species. The influence and impact of including pseudoorthologs versus true orthologs as result of gene extinction (or incomplete laboratory sampling) in a phylogenetic context is only recently starting to gain empirical attention. Moreover, few of these studies have yet to investigate this phenomenon in an explicit coalescent framework. Here, using mathematical models, numerous simulated data sets, and two newly assembled empirical data sets, we assess the effect of pseudoorthologs on species tree estimation under varying levels of incomplete lineage sorting (ILS) and different patterns of gene loss following WGD. When gene loss occurs in the terminal branches of the species tree, the alignment-based (BPP) and gene-tree-based (ASTRAL, MP-EST, and STAR) coalescent methods are adversely affected as the level of ILS increases. This can be greatly improved by sampling a sufficiently large number of genes. Under the same circumstances, however, concatenation methods consistently estimate incorrect species trees as the number of sampled genes increases. Furthermore, pseudoorthologs can mislead species tree inference if gene loss occurs in the internal branches of the species tree, where both coalescent and concatenation methods are prone to produce inconsistent results. However, pseudoorthologs are problematic when filtering only for single-copy genes in phylogenomic data sets. Pruning orthologs or even randomly selecting a copy from multi-copy genes can avoid most of those pseudoorthologs. These results underscore the importance of understanding the influence of pseudoorthologs in the phylogenomics era.</p>
Data from: Why are plant communities stable? Disentangling the role of dominance, asynchrony and averaging effect following realistic species loss scenario
<p>A growing number of studies have demonstrated that biodiversity is a strong and positive predictor of ecosystem temporal stability by simultaneously affecting multiple underlying mechanisms of stability <em>i.e.</em> dominance, asynchrony, and averaging effects. However, to date, no study has disentangled the relative role of these key mechanisms of stability in biodiversity experiments. We created a species richness gradient by mimicking a loss of rare species and assessed the role of species richness on community stability and, more importantly, quantified the relative role of three stabilizing mechanisms <em>i.e.</em> dominance (stabilization due to stable dominants compared to the rest of the species in the community), asynchrony (stabilization due to temporal asynchrony between species), and averaging effects (pure effect of diversity) on community stability across a species richness gradient. We found that extreme species loss negatively impacted community stability, but just three species were enough to stabilize biomass production to a level similar to highly diverse communities. However, the similar stability of communities resulted from differing contributions from each stability mechanism, depending on the community diversity. Since less abundant species were more temporally variable, species loss stabilized the populations of the remaining species. The loss of rare and subordinate species reduced the dominance and averaging effects, but increased the asynchrony effect. Hence, the asynchrony effect played a major role in the stability of species poor communities, while the averaging effect drove most of the stability of species rich communities. Overall, dominance played only a minor role, accounting for 5-15% of the stabilization, while asynchrony and averaging effects were dominating forces contributing to ~ 85-95% of the total stabilization.</p> <p><em>Synthesis</em>. This study highlights the importance of biodiversity and roles of dominant and rare species for long-term community stability and, for the first time, disentangles relative roles of dominance effect, asynchrony, and averaging effect on community stability in a real-world biodiversity experiment.</p>
Processed species-level data for "Global Biodiversity Loss from Outsourced Deforestation"
<p>This repository holds processed species-level data for the following paper:</p> <blockquote> <p>Wiebe, R.A.* and Wilcove, D.S. <em>2025</em>. Global Biodiversity Loss from Outsourced Deforestation.</p> </blockquote> <p>*<a href="mailto:rwiebe@princeton.edu">rwiebe@princeton.edu</a>, Guyot Hall, Princeton University, Princeton, NJ</p> <p>In this analysis, we quantified the range loss to forest-dwelling vertebrates that is attributable to demand for agricultural and forestry products by developed countries in 2001-2015.</p> <p>We used several datasets in this analysis. Data on forest cover and forest loss were sourced from <em>Hansen et al.</em> and publicly available to download online: <a href="https://earthenginepartners.appspot.com/science-2013-global-forest/download_v1.7.html" rel="nofollow">https://earthenginepartners.appspot.com/science-2013-global-forest/download_v1.7.html</a>. Data on range maps for species were sourced from the IUCN and downloaded from the IUCN’s API (<a href="https://www.iucnredlist.org/resources/spatial-data-download" rel="nofollow">https://www.iucnredlist.org/resources/spatial-data-download</a>) and its partner BirdLife International’s API (<a href="http://datazone.birdlife.org/species/requestdis" rel="nofollow">http://datazone.birdlife.org/species/requestdis</a>). These datasets are made available for academic research on request, and an API key is necessary for their downloads. We sourced data on land use attribution from Nguyen Tien Hoang and Keiichiro Kanemoto, from their 2021 publication “Mapping the deforestation footprint of nations reveals growing threat to tropical forests.” These data are not publicly available, but the authors kindly provided the data on request.</p> <p>Code necessary to replicate the analysis can be found in a public repository at: https://github.com/AlexWiebe/Outsourced-Biodiversity-Loss.</p>
Resources do not limit compensatory response of a tallgrass prairie plant community to the loss of a dominant species
<p>The effect of species loss on ecosystem productivity is determined by both the functional contribution of the species lost, and the response of the remaining species in the community. According to the mass-ratio hypothesis, the loss of a dominant plant species, which has a larger proportionate contribution to productivity, is expected to exert an overwhelming effect on this important ecosystem function. However, via competitive release, loss of a dominant species can provide the opportunity for other plant species to establish, thrive and become abundant in the community, potentially compensating for the function lost. Furthermore, if resource limitation is removed, then compensatory response of function to the loss of a dominant species should be greater and more rapid than if resources are more limiting.</p> <p>To evaluate how resources may limit compensation of aboveground productivity to the loss of a dominant plant species, we experimentally removed the C<sub>4</sub> perennial tallgrass, <em>Andropogon gerardii</em>, from intact plant communities. We added water for four years, as well as nitrogen in the fourth year, to test the effect of resource limitation on the compensatory response.</p> <p>Overall, aboveground biomass production increased in the remaining community with both water and nitrogen addition. However, this increase in biomass production was not sufficient to fully compensate for the loss of A. gerardii, indicating water and nitrogen were not limiting short-term compensation in this community.</p> <p>Following the removal of the dominant species, there was a reordering of species abundances in the community, rather than changes in species richness. The C<sub>4</sub> grass <em>Bouteloua curtipendula</em> was the most responsive species, increasing by 57.9% in abundance with water addition and 91.0% with both water and nitrogen addition. Despite this dramatic increase in abundance, its short stature and lower per capita biomass production prevented this species from compensating for the loss of <em>A. gerardii</em>.</p> <p>Our results suggest that short-term compensation after the loss of a dominant plant species can be hastened by increased resource availability, but ultimately full compensation appears to be limited by the presence and abundance of species in the remaining community that possess traits that allow them compensate for the species lost.</p>
Community biomass is driven by dominants and their characteristics –the insight from a field biodiversity experiment with realistic species loss scenario
<p>1. Revealing the role of biodiversity in ecosystem functioning (BEF) has been a major focus of ecological research over recent decades. In general, results from artificially assembled communities point to the important role of biodiversity showing that the loss of species has a negative effect on various ecosystem functions (mostly assessed by aboveground peak biomass). However, the evidence from manipulations of natural communities is scarce and results are often contradictory between these two approaches. In particular, the importance of species dominance for ecosystem functioning remains poorly understood.</p> <p>2. We created a gradient of plant species richness in a meadow community following a realistic species loss scenario (removal of less abundant species) to test the effect of diversity on community biomass and assess the importance of subordinate species compared to dominants in a five-year experiment.</p> <p>3. Contrasting with the results of BEF experiments with artificial assembly, we did not find any relationship between plant species diversity and aboveground biomass across the timeframe of the experiment. We provide evidence that dominant species' identity and traits are the main drivers of community biomass, because dominant species were able to maintain biomass production after substantial species loss. Further, dominants prevented community biomass from declining and biomass was indirectly influenced not by species richness but through differences in functional diversity. Our results support the mass ratio hypothesis, showing a much bigger effect of dominant species on community biomass production and hints at the rather minor importance of the complementarity effect between species. We emphasize that BEF research should more focus on the role of dominant species in maintaining various ecosystem functions.</p> <p>4. Synthesis. Species diversity is a poor predictor of community aboveground biomass production and dominant species can effectively compensate the total production after substantial loss of other species in a grassland community.</p>
Habitat loss shapes the structure and species roles in tropical plant-frugivore networks
<p>Habitat loss is a global threat to biodiversity with pervasive effects on species and populations. These impacts may generate cascading effects on ecological processes propagating across ecological networks. Thus, understanding how habitat loss affects ecological networks is fundamental for conservation. We used a database of 25 plant-frugivore networks distributed across the whole Brazilian Atlantic Forest to understand how landscape-scale habitat loss shapes network structure, robustness, species role and traits related to seed dispersal. We compared whether these network properties have linear or non-linear relationships and used centrality metrics and indirect effects to evaluate if habitat loss change the role of species in plant-frugivore networks. We found linear and non-linear relationships with negative effects of habitat loss on the network structure. As a consequence of shifts in species richness and number of links, the number of interactions and the proportion of possible interactions observed (connectance) were negatively associated with habitat loss. In contrast, nestedness increased with habitat loss. Network robustness, mean bill width and mean seed size were not significantly related to habitat loss. In addition to changes in interaction patterns at network level, habitat loss also favors changes in interaction among species, shifting the species playing central roles in network organization or contributing to indirect effects in the networks. In forested landscapes, obligate frugivores are the main central species in the network, and the ones potentially contributing to indirect effects, while in deforested landscapes these roles are fulfilled by occasional frugivores. Thus, our results emphasize the widespread effect of habitat loss on plant-frugivore systems, adding evidence that its pervasive effects on biodiversity also proliferate on mutualistic interactions with negative consequences for seed dispersal that potentially go beyond the direct pairs of interacting species. </p>
Nutrient addition drives declines in grassland species richness primarily via enhanced species loss
<p><span>Declines in grassland diversity in response to nutrient addition are a general consequence of global change. This decline in species richness may be driven by multiple underlying processes operating at different timescales. Nutrient addition can reduce diversity by enhancing the rate of local extinction via competitive exclusion, or by reducing the rate of colonization by constraining the pool of species able to colonize under new conditions. Partitioning net change into extinction and colonization rates will better delineate the long-term effect of global change in grasslands. </span></p> <p><span>We synthesized changes in richness in response to experimental fertilization with nitrogen, phosphorus, and potassium with micronutrients across 30 grasslands. We quantified changes in local richness, colonization, and extinction over 8-10 years of nutrient addition, and compared these rates against control conditions to isolate the effect of nutrient addition from background dynamics. </span></p> <p><span>Total richness at steady state in the control plots was the sum of equal, relatively high rates of local colonization and extinction. On aggregate, 30-35% of initial species were lost and the same proportion of new species was gained at least once over a decade. Absolute turnover increased with site-level richness but was proportionately greater at lower-richness sites relative to starting richness. Loss of total richness with nutrient addition, especially N in combination with P or K, was driven by enhanced rates of extinction with a smaller contribution from reduced colonization. Enhanced extinction and reduced colonization were disproportionately among native species, perennials, and forbs. Reduced colonization plateaued after the first few (< 5) years after nutrient addition, while enhanced extinction continued throughout the first decade. </span></p> <p><span><strong>Synthesis</strong>:</span><span> Our results indicate a high rate of colonizations and extinctions underlying the richness of ambient communities, and that nutrient enhancement drives overall declines in diversity primarily by the exclusion of previously established species. Moreover, enhanced extinction continues over long time scales, suggesting continuous, long-term community responses and a need for long-term study to fully realize the extinction impact of increased nutrients on grassland composition. </span></p>
Going, going, gone: evidence for loss of an endemic species pair of threespine sticklebacks (Gasterosteus aculeatus) with implications for protection under species-at-risk legislation
<p>Genomic extinction occurs when the unique combination of genetic traits that characterize distinct phenotypes is eliminated by introgressive hybridization even if population size is greater than zero. Benthic and limnetic threespine sticklebacks (<em>Gasterosteus aculeatus</em>) constitute reproductively isolated undescribed biological species that have evolved independently in several lakes in southwestern British Columbia, Canada (known as "species pairs" in each lake). Here we investigated whether the two species that comprise the pair from Enos Lake, southeastern Vancouver Island, remain as two distinct gene pools. Multi-season samples (>1200 fish) obtained over two years from throughout the lake and assayed for variation in morphological traits characteristic of the two species (i.e., body depth, dorsal spine count, gill raker counts) and at 12 microsatellite DNA loci consistently indicated the existence of only a single group of sticklebacks. There was no consistent evidence of two groups in any morphological trait, and mean gill raker counts were consistently intermediate (20–21) to those of known benthics (~18) and limnetics (~24) which together comprised strikingly bimodal distributions in historical samples. Genetic analyses employing model-based clustering also consistently indicated the presence of only a single genetic group of sticklebacks. Compared to historical samples and to benthics and limnetics from other lakes, no Enos Lake fish could be identified confidently as a pure benthic or limnetic. Our results provide the strongest evidence yet that the Enos Lake sticklebacks now consist of a single morphological and genetic population of sticklebacks, that the unique combination of genetic and morphological traits that characterized benthic and limnetic sticklebacks no longer exist, and that their current status under Canada's <em>Species-at Risk Act</em> as Endangered should be re-evaluated.</p>
Isolation drives species gains and losses of insect metacommunities over time in a mountaintop forest archipelago
<p><strong>Aim: </strong>We evaluated the effects of forest island size, isolation, and area in the landscape driving temporal changes of insect biodiversity in a mountaintop forest archipelago. We tested the following hypotheses: (i) changes in insect species composition is higher and dominated by species gains through time in smaller but less isolated forest islands; (ii) larger amounts of forest in the landscape result in higher gains of more vagile species over time, regardless of their size and isolation; (iii) heterogenization processes will prevail in less vagile groups, while homogenization processes will dominate in highly vagile groups due to differences in dispersal capability.</p> <p><strong>Location:</strong> Espinhaço Range Biosphere Reserve, Brazil.</p> <p><strong>Taxon:</strong> Insects.</p> <p><strong>Methods:</strong> We used ants, dung beetles, bees, wasps, and butterflies as study models to represent a gradient of low-to-high dispersal capability. We evaluated the colonization- and extirpation-resultant components of temporal β-diversity using area- and isolation-related variables as predictors.</p> <p><strong>Results:</strong> We found distinct colonization- and extirpation-resultant homogenization and heterogenization processes acting according to each insect group, likely due to different dispersal capabilities. Ants were dominated by species losses, with widespread and rare species being lost. Butterflies gained species, represented mainly by widespread species, leading to an increased colonization-resultant homogenization. Distance to neighboring forest islands was the underlying predictor affecting the temporal β-diversity of insect groups and on species gains and losses but differed according to the survey period. Effects of the forest amount in the landscape increased the temporal β-diversity of bees and butterflies but decreased that of ants, dung beetles, and wasps.</p> <p><strong>Main Conclusions:</strong> We recommend conserving the forest amount in the landscape and keeping forest connectivity among forest islands since the temporal dynamics of local colonization and extirpation can depend on the organisms' dispersal capability. Fragmentation and habitat loss-related hypotheses will benefit from incorporating colonization-extirpation processes into their predictions.</p>
DupLoss-2: Improved phylogenomic species tree inference under gene duplication and loss
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Experimental warming drives local grassland plant species loss
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Nutrient addition drives declines in grassland species richness primarily via enhanced species loss
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Incorporating plant phenological responses into species distribution models (SDMs) reduces estimates of future species loss and turnover
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Data from: Observational and experimental evidence that rapid mass loss is consistent with the flight efficiency hypothesis and not caused by reproductive effort in three passerine species
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Data and code from: Loss of resource-conservative species affects plant phylogenetic and functional structure under long-term snow addition
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