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2,441 results for “extinct”
Recolonization of secondary forests by a locally extinct Caribbean anole through the lens of range expansion theory
<p>Disturbance and recovery dynamics are characteristic features of many ecosystems. Disturbance dynamics are widely studied in ecology and conservation biology. Still, we know less about the ecological processes that drive ecosystem recovery. The ecological processes that mediate ecosystem recovery stand at the intersection of many theoretical frameworks. Range expansion theory is one of these complementary frameworks that can provide unique insights into the population-level processes that mediate ecosystem recovery, particularly fauna recolonization. Although the biodiversity patterns that follow fauna recolonization of recovering forests have been well described in the literature, the ecological processes at the population level that drive these patterns remain conspicuously unknown. In this study, we tested three fundamental predictions of range expansion theory during the recolonization of recovering forests in Puerto Rico by a shade specialist anole, <em>Anolis</em> <em>gundlachi</em>. Range expansion theory predicts that individuals at the early stages of recolonization (i.e., younger forests) would have a high prevalence of dispersive traits, experience less density dependence, and suffer less parasitism. To test these predictions, we conducted a chronosequence study applying space-for-time substitution where we compared phenotypic traits (i.e., body size, body condition, and relative limb size), population density, population growth rates, and <em>Plasmodium</em> parasitism rates among lizard populations living in young (< 30 years), mid (40–60 years), and old-growth forests (> 75 years). Lizard populations in younger forests had lower densities, higher population growth rates, and lower rates of <em>Plasmodium</em> parasitism compared with old-growth forests. Still, while we found that individuals had larger body sizes, and longer forelimbs in young forests in one site, this result was not consistent among sites. This suggests a potential trade-off between the traits that provide a dispersal advantage during the initial stages of recolonization and those that are advantageous to establish in novel environmental conditions. Overall, our study emphasizes the suitability of range expansion theory to describe fauna recolonization but also highlights that the ecological processes that drive recolonization are time-dependent, complex, and nuanced.</p>
Biotic and abiotic factors and the phylogenetic structure of extinction in the evolution of Tethysuchia
<p>Crocodylomorpha is a large and diverse clade with a long evolutionary history now restricted to modern crocodylians. Tethysuchia is a less-inclusive clade of semi-amphibious taxa that crossed two biological crises: the second Oceanic Anoxic Event (OAE 2) and the Cretaceous/Paleogene (K/Pg) Crisis. Numerous studies have sought to find the driving factors explaining crocodylomorph evolution producing contradictory conclusions. Studies of included groups may be useful. Here, we study factors driving tethysuchian evolution using phylogenetically informed statistical analyses. First, we tested the phylogenetic structure of tethysuchian extinction at the OAE 2 and K/Pg crises. We then used phylogenetic comparative methods to test the influence of intrinsic (body size, snout proportion) and extrinsic (temperature, paleolatitude) factors on the evolution of tethysuchian diversity at the OAE 2 and the K/Pg crises. Finally, we tested whether temperature influenced the evolution of body size. We conclude that (1) extinction was not random in regards to phylogeny for Tethysuchia at the OAE 2 and K/Pg crises; (2) while an important tethysuchian turnover follows OAE 2, the K/Pg crisis was followed by an explosion in diversity of tethysuchians, probably linked to the colonization of emptied ecological niches; (3) tethysuchians lived in warmer environments after the OAE 2 crisis, possibly because of both global warming and latitude distribution shifts; (4) there is a significant change of snout proportion after the OAE 2 and the K/Pg crises, likely caused by niche partitioning; and (5) there is a positive correlation between body size and temperature, possibly because of a longer growth season</p>
La Silla (ESO) Atmospheric Extinctions
Open the record for dataset details and reuse information.
Demography and environment modulate the effects of genetic diversity on extinction risk in a butterfly metapopulation
<p>Linking genetic diversity to extinction is a common goal in genomic studies. Recently, a debate has arisen regarding the importance of genetic variation in conservation as some studies have failed to find associations between genome-wide genetic diversity and extinction risk. However, only rarely are genetic diversity and fitness measured together in the wild, and typically variation in demographic history or environment are ignored. It is therefore difficult to infer whether a lack of an association is real or obscured by confounding factors. To address these shortcomings, we analysed genetic data from 7,501 individuals with extinction data from 279 meadows and mortality of 1,742 larval nests in a butterfly metapopulation. We found strong negative associations between genetic diversity and extinction when heterozygosity was included alone in models. However, this association was no longer present when ecological covariates were included. Interactions between heterozygosity and demographic variables revealed that associations are context-dependent or only detectable when confounding factors are controlled. For example, extinction declined with increasing heterozygosity in large but not currently small populations, although negative associations between heterozygosity, extinction, and mortality were detected in populations with a recent history of decline. We conclude that low genetic diversity is an important predictor of extinction, predicting >25% increase in extinction beyond ecological factors in certain contexts. This highlights that inferences about the importance of genetic diversity should not rely on genomic data alone but requires investments in obtaining demographic and environmental data from natural populations to jointly assess their impact on population extinction risk.</p>
A nuclear genome assembly of an extinct flightless bird, the little bush moa
<p>We present a draft genome of the little bush moa (<em>Anomalopteryx didiformis</em>) - one of approximately nine species of extinct flightless birds from Aotearoa, New Zealand - using ancient DNA recovered from a fossil bone from the South Island. We recover a complete mitochondrial genome at 249.9X depth of coverage and almost 900 Mb of a male moa nuclear genome at ~4-5X coverage, with sequence contiguity sufficient to identify more than 85% of avian universal single-copy orthologs. We describe a diverse landscape of transposable elements and satellite repeats; estimate a long-term effective population size of ~240,000; identify a diverse suite of olfactory receptor genes and an opsin repertoire with sensitivity in the UV range; show that the wingless moa phenotype is likely not attributable to gene loss or pseudogenization; and identify potential function-altering coding sequence variants in moa that could be synthesized for future functional assays. This genomic resource should support further studies of avian evolution and morphological divergence.</p>
DArTseq genetic dataset associated with the article "Hybrids as mirrors of the past: genomic footprints reveal spatio-temporal dynamics and extinction risk of alpine extremophytes in the mountains of Central Asia"
<p>Description: This file stores genetic information on the single nucleotide polymorphism markers (SNPs) in the examined alkali grasses (Poaceae: Puccinellia). The dataset was generetad by Genome-Wide Restriction Fragment Analysis via the DArTseq platform (Diversity Arrays Technology Pty Ltd, Canberra, Australia), which combines complexity reduction methods, fragment size selection, and high-throughput sequencing, optimised for a target organism. The file contains raw data.<br> <br>Usage notes: We used R (version 4.2.2, 2022-10-31; https://www.R-project.org/) and RStudio (version 2022.07.2+576 "Spotted Wakerobin" Release (e7373ef832b49b2a9b88162cfe7eac5f22c40b34, 2022-09-06; http://www.rstudio.com/) on Windows 8.1 to handle this file. We used the dartR R-package (version 2.7.2) with necessary dependencies to import, proccess and analyse this data file as an object of a class genlight (dartR) in the R environment. You may also handle the file as an object of a class genlight using the adegenet and ade4 R-packages. To learn more about installation procedure and how to use of the R-packages visit: https://cran.r-project.org/web/packages/available_packages_by_name.html.<br> </p>
Supplement to Mechanistic phylodynamic models do not provide conclusive evidence that non-avian dinosaurs were in decline before their final extinction
<p>This repository contains the supplementary files for:</p> <p>Allen BJ, Volkova Oliveria MV, Stadler T, Vaughan TG, Warnock RCM. 2024. Mechanistic phylodynamic models do not provide conclusive evidence that non-avian dinosaurs were in decline before their final extinction. Cambridge Prisms: Extinction.</p> <p><strong>Description of files</strong></p> <p>This repository contains the cleaned tree files, tables of age constraints, XML files for running the analyses in BEAST2, and R code to process the datasets.</p> <p>Benson1clean.tree, Benson2clean.tree, Lloyd1clean.tree, Lloyd2clean.tree - the cleaned tree files containing the phylogenies inputted into BEAST2, with tip names matched to age data from the Paleobiology Database</p> <p>Tree modifications log.xlsx - a description of the modifications made to each input phylogeny compared to their state in the data supplement of their original papers</p> <p>dinosaur_ages.csv - the raw dinosaur age data downloaded from the Paleobiology Database</p> <p>tip_constraints.csv - the dinosaur age data converted into a format to input into BEAST2, to provide age constraints for tips</p> <p>change_times.txt - a text file describing the change times for the piecewise constant trajectories in the two phylodynamic analyses</p> <p>BDSKY.xml, PiecewiseCoalescent.xml - XML files describing the BEAST2 configuration for each of the two phylodynamic models</p> <p>BDSKY_logs.zip, BDSKY_trees.zip, Coalescent_logs.zip, Coalescent_trees.zip - compressed folders containing the output log files and inferred phylogenies for each of the 16 analysed phylogenies</p> <p>Supplementary_tables.zip - Tables containing summary statistics for each of the parameters inferred in each of the models</p> <p><strong>Description of R code</strong></p> <p>The R code is subdivided into the following files:</p> <p>Wrangle_trees.R - code for checking, cleaning, and splitting the phylogenies used in the analyses</p> <p>PBDB_tip_constraints.R - code for converting the raw age data from the Paleobiology Database into a format ready for input into BEAST2 as tip constraints</p> <p>BDSKY_post_processing.R, Coalescent_post_processing.R - code for cleaning and plotting data from the BEAST2 log files, for each of the two phylodynamic models</p>
Defensins identified through molecular de-extinction
<p>Dataset used in the Article</p> <p>The programs used were Augustus, HMMER and Gromacs.</p> <p>The files are:</p> <p>-Augustusresults (results obtained from augutus)</p> <p>-BirdsTree (the data to create the bird tree)</p> <p>-Commands (the commands used for augustus and hmmer)</p> <p>-Hmmer.Finding (the findings from hmmer)</p> <p>-Hmmer Results (results from the searches)</p> <p>-HmmProfiles (the profiles used to serch in augustus)</p>
Global extinction probabilities of terrestrial, freshwater, and marine species groups
<p>This is the updated dataset presented in the manuscript titled "Global extinction probabilities of terrestrial, freshwater, and marine species groups".</p> <p>The dataset gives the code (R code), as well as the resulting raster files for the suggested Global extinction probabilities for different taxonomic groups, for use in Life Cycle Impact Assessment (LCIA). We supply the results on 5arc minute resolution, aggregated for relevant spatial scales (e.g. terrestrial ecoregions or watersheds), as well as at country scale.</p> <p>For application in LCIA, we recommend applying GEPs to CFs with corresponding species groups and spatial scales. If the species group of the CFs do not match any of the provided GEPs, see (1); if the spatial scale of the CFs do not match any of the provided GEPs, see (2).</p> <ol> <li>If the species groups of the CFs do not match any of the provided sets of GEPs, we recommend recalculating GEPs for corresponding species groups and spatial scales based on the provided R scripts (e.g., see the R script for the freshwater heterotroph GEPs). Alternatively, GEPs can be aggregated to species group combinations by calculating species number-weighted GEP averages of the existing GEPs (see Table 4 in the article for species numbers per species group). In case of the latter approach, we recommend calculate GEP averages for all regions across the world (and not just those included in the analysis) and normalise the region-level average GEPs by the sum of the region-level average GEPs for consistency with the GEP concept.</li> <li>In addition to species group aggregation, GEPs can be aggregated to different spatial scales by calculating the sum of the cell-level GEPs contained per region (e.g., see R scripts).</li> </ol> <p> </p> <p>Updates: corrected mistakes in cnidarians. Removedcpiuntry GEPs for marine species groups.</p>
Bushmeat yields, species extinction rates and ecosystem-level impacts of bushmeat harvesting as predicted by the Madingley General Ecosystem Model
<p>The datasets contain data generated using the Madingley General Ecosystem Model for experiments decribed in the paper: "T. Barychka, G.M.Mace and D.W.Purves (2021) The Madingley General Ecosystem Model predicts bushmeat yields, species extinction rates and ecosystem-level impacts of bushmeat harvesting. Oikos."</p> <p>The Madingley General Ecosystem Model was used to generate predictions of bushmeat yields, extinction rates and broader ecosystem impacts for a range of harvesting intensities of duiker-sized endothermic herbivores. Duiker antelope (such as <i>Cephalophus callipygus</i> and <i>Cephalophus dorsalis</i>) are the most heavily hunted species in sub-Saharan Africa, contributing 34%-95% of all bushmeat in the Congo Basin. In the Madingley, the harvested group was described as "Heterotroph – Herbivore – Terrestrial – Mobile – Iteroparous– Endotherm", with adult bodymasses of 13-21 kg and juvenile bodymasses of >100 g. Harvesting period was set at 30 years (<em>n </em>=30).</p> <p>In the first experiment, we used the Madingley model to predict bushmeat yields ("Harvested Biomasses") and extinction rates ("Density") from harvesting duiker-sized herbivores using proportional harvesting strategy, with harvest rates ranging from 0 to 0.90. These were compared to the estimates of bushmeat yields and survival probabilities for two duiker antelope species (<i>Cephalophus callipygus</i> and <i>Cephalophus dorsalis) </i>from conventional single-species Beverton-Holt model. </p> <p>In the second experiment, we used the Madingley model to generate data on the state ("State") of the harvested ecosystem. The datasets contain estimates of biomasses, abundances, adult and juvenile bodymasses, etc. of the harvested duiker-sized herbivores as well as unharvested herbivores, omnivores and carnivores present in the simulated ecosystem. In the paper we focused on abundances; however, other estimates e.g., adult bodymasses can be used to conduct further studies on the effects of harvesting in tropical ecosystems.</p> <p>Main results of the experiments are that: 1) the Madingley model gave estimates for optimal harvesting rate, and extinction rate, that were qualitatively and quantitatively similar to the estimates from conventional single-species Beverton-Holt model; 2) the Madingley model predicted a background local extinction probability for the target species of at least 10%; 3) at medium and high levels of harvesting of duiker-sized herbivores, the Madingley model predicted statistically significant, but moderate, reductions in the densities of the targeted functional group; increases in small-bodied herbivores; decreases in large-bodied carnivores; and minimal ecosystem-level impacts overall.</p>
Data from: Machine learning identifies ecological selectivity patterns across the end-Permian mass extinction
<p>The end-Permian mass extinction occurred alongside a large swathe of environmental changes that are often invoked as extinction mechanisms, even when a direct link is lacking. One way to elucidate the cause(s) of a mass extinction is to investigate extinction selectivity as it can reveal critical information on organismic traits as key determinants of extinction and survival. Here we show that machine learning algorithms, specifically gradient boosted decision trees, can be used to identify determinants of extinction as well as predict extinction risk. To understand which factors led to the end-Permian mass extinction during an extreme global warming event, we quantified the ecological selectivity of marine extinctions in the well-studied South China region. We find that extinction selectivity varies between different groups of organisms and that a synergy of multiple environmental stressors best explains the overall end-Permian extinction selectivity pattern. Extinction risk was greater for genera that had a low species richness, had narrow bathymetric ranges limited to deep-water habitats, had a stationary mode of life, possessed a siliceous skeleton or, less critically, had calcitic skeletons. These selective losses directly link the extinction to the environmental effects of rapid injections of carbon dioxide into the ocean-atmosphere system, specifically the combined effects of expanded oxygen minimum zones, rapid warming, and potentially ocean acidification.</p>
Codes for simulation and data for: The relationship between local and regional extinction rates depends on species distribution patterns
<p>The rapid loss of biodiversity poses a great threat to ecosystem functions and services. Credible estimation of species extinction rates is essential for understanding the magnitude of biodiversity loss and for informing conservation, but this has been a challenge because estimated extinctions are unverifiable due to the lack of data. In this study, we investigated the relationship between local and regional extinctions and assessed the effects of range size, spatial segregation, and patchiness of species distribution on this local-regional extinction relationship. We found that regional extinction rates had a convex relationship with local extinction rates, that is, the regional extinction rate was most likely to be lower than the average local rate. The regional rates deviated from local rates as the sampling area decreased. The difference between local and regional extinction rates (local-regional extinction difference) became larger if a higher number of species had larger range sizes and patchiness. We also detected that there were interactive effects among these factors. Species segregation had a weak positive relationship with the local-regional extinction difference if more species had relatively large range sizes. As the sampling areas increased, the range size showed smaller positive effects on local-regional differences, but patchiness showed larger positive effects. The local-regional extinction relationship of this study provides insights into the spatial scaling of biodiversity loss and offers some important cues for estimating regional extinctions from local data in future studies.</p>
The hidden legacy of megafaunal extinction: loss of functional diversity and resilience over the late Quaternary at Hall's Cave
<p>This dataset contains trait data and R code used in the analysis for the paper "Hedberg, C.P., Lyons S.K., & Smith F.A. (2021). THe Hidden Legacy of megafaunal extinction: loss of functional diversity and resilience over the Late Quaternary at Hall's Cave. Global Ecology and Biogeography. https://doi.org/10.1111/geb.13428"</p> <p>We collected data for eight functional traits (mass, diet, arboreality, cursoriality, soil disturbance, group size, activity period, migration habit) that collectively describe a species' ecological role and influence on ecosystem processes. With these data, we investigated changes in functional diversity and redundancy of a local mammal community over time at Hall's Cave, a site in Central Texas with a continuous record from 21,000 years ago to the present. Additionally, we included several common introduced and domestic species to the modern community to test whether they restore some lost ecological function. </p> <p>We found that declines in functional diversity were greater than expected given the decrease in species richness, implying lost taxa contributed higher than average distinct ecological function. Functional distances between remaining species increased through time leading to lowered functional redundancy in younger communities. However, recently introduced taxa increased functional diversity to levels similar to the Holocene and partially restored functional space occupied by Late Pleistocene fauna. Our local-scale analysis demonstrates how prolonged biodiversity erosion not only leads to functionally depauperate communities, but critically lowers ecological resilience to future disturbance.</p>
Supporting Information for: Microbial blooms triggered pyrite framboid enrichment and oxygen depletion in carbonate platforms immediately after the latest Permian extinction
<p>Supporting Information for:</p> <p><strong>Microbial blooms triggered pyrite framboid enrichment and oxygen depletion in carbonate platforms immediately after the latest Permian extinction</strong></p> <p>The supporting information includes: (1) conodont biostratigraphic and carbon isotopic chemostratigraphic correlations of the uppermost Permian to lowest Triassic successions from nine studied sections across South China and (2) pyrite framboid size distributions and redox variations throughout the Permian-Triassic boundary successions of the nine studied sections.</p> <p> </p>
Figure 33 in Extinct or extant? A new species of Termitodius Wasmann, 1894, (Coleoptera: Scarabaeidae: Aphodiinae: Rhyparini) with a short review of the genus
Figure 33. Distribution of Termitodius species.
Figure 26. Large copal piece with about 100 T in Extinct or extant? A new species of Termitodius Wasmann, 1894, (Coleoptera: Scarabaeidae: Aphodiinae: Rhyparini) with a short review of the genus
Figure 26. Large copal piece with about 100 T. woodruffi paratypes (FSCA).
Data from: The megaherbivore gap after the non-avian dinosaur extinctions modified trait evolution and diversification of tropical palms
<p><span>The Cretaceous–Paleogene (K-Pg) extinction of the non-avian dinosaurs (66 Ma) led to a 25 million year gap of megaherbivores (>1000 kg) before the evolution of megaherbivorous mammals in the Late Eocene (40 Ma). The botanical consequences of this 'Paleocene megaherbivore gap' (PMHG) remain poorly explored. We hypothesize that the absence of megaherbivores should result in changes in the diversification and trait evolution of associated plant lineages. We used phylogenetic time- and trait-dependent diversification models with palms (Arecaceae) and show that the PMHG was characterized by speciation slowdowns, decreased evolution of armature, and increased evolution of megafaunal (</span>≥<span>4cm) fruits. This suggests that the absence of browsing by megaherbivores during the PMHG may have led to a loss of defence traits, but absence of megaherbivorous seed dispersers did not lead to a loss of megafaunal fruits. Instead, increases in PMHG fruit sizes may be explained by Late Paleocene rising temperatures, rainforest expansion, and the subsequent radiation of seed dispersing birds and mammals. We show that the profound impact of the PMHG on plant diversification can be detected even with the overwriting of adaptations by the subsequent Late Eocene opening-up of megaherbivore-associated ecological opportunities. Our study provides a quantitative, comparative framework to assess </span>diversification and adaptation during one of the most enigmatic periods in angiosperm history.</p>
The last representatives of the Superfamily Wellerelloidea (Brachiopoda, Rhynchonellida) in the westernmost Tethys (Iberian paleomargins) prior to their demise in the Early Toarcian Mass Extinction Event
<p><span>The last clade-level extinction episode affecting the Phylum Brachiopoda has been long-established in the Early Toarcian Mass Extinction Event (ETMEE) around the Pliensbachian-Toarcian transition, when several rhynchonellide groups became extinct and others underwent a notable renewal in the western Tethys. Among them, Wellerelloidea is a long-range superfamily severely affected by this environmental crisis, embodying the subfamily Cirpinae as the last wellerelloids worldwide, prior to their global extinction in the Pb-To transition. The profuse record of Lower Jurassic cirpines in the peri-Iberian paleomargins provides an opportunity to clarify the taxonomy of wellerelloid species in the pre-extinction interval. A new species (<em>Cirpa lucentina</em>) is erected and the revision of the Cirpinae taxa around the ETMEE is carried out. Morphometric analysis and the study of internal structures of the shells support the splitting between the genera <em>Cirpa</em> and <em>Salgirella</em>, adding new supplementary diagnostic criteria. The biogeographic distribution of this clade in the western Tethys and its evolutionary history in the Early Jurassic reveal </span><span>a <em>pervasive</em> colonization pattern of both epicontinental and epioceanic habitats. T</span><span>he Mediterranean origin of the last representatives of this group is ascertained, but while diversification of <em>Salgirella</em> took place in epioceanic habitats, speciation of <em>Cirpa</em> is unrelated to biochorema boundaries, even colonizing epicontinental seas until their extinction prior to the hyperwarming event that occurred in the basal Serpentinum Zone. A rhynchonellide morphogroup epitomized by cirpines was resilient to this event in the epicontinental seas. This morphogroup is also recorded after the extinction interval by means of the genus <em>Pseudogibbirhynchia</em>, thus postulating potential pre- and post-extinction phyletic relationships.</span></p>
Fig. 1 in A New Species Of The Extinct Ant Genus Electromyrmex (Hymenoptera, Formicidae)
Fig. 1. Electromyrmex wheeleri sp. n., holotype male, body in lateral view (photo by E. Martynova).
Fig. 3 in A New Species Of The Extinct Ant Genus Electromyrmex (Hymenoptera, Formicidae)
Fig. 3. Electromyrmex wheeleri sp. n., paratype male, body in lateral view.
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