scholarly journals Phylogenetic and Spatial Distribution of Evolutionary Isolation and Threat in Turtles and Crocodilians (Non-Avian Archosauromorphs)

2019 ◽  
Author(s):  
Timothy J. Colston ◽  
Pallavi Kulkarni ◽  
Walter Jetz ◽  
R. Alexander Pyron
Keyword(s):  
Extinction Risk ◽  
Morphological Evidence ◽  
Mass Extinctions ◽  
Turtle Species ◽  
Terrestrial Vertebrates ◽  
Terrestrial Vertebrate ◽  
Threat Status ◽  
Extant Species ◽  
Anthropogenic Habitat ◽  
Evolutionary Distinctiveness

AbstractThe origin of turtles and crocodiles and their easily recognized body forms dates to the Triassic. Despite their long-term success, extant species diversity is low, and endangerment is extremely high compared to other terrestrial vertebrate groups, with ~ 65% of ~25 crocodilian and ~360 turtle species now threatened by exploitation and habitat loss. Here, we combine available molecular and morphological evidence with machine learning algorithms to present a phylogenetically-informed, comprehensive assessment of diversification, threat status, and evolutionary distinctiveness of all extant species. In contrast to other terrestrial vertebrates and their own diversity in the fossil record, extant turtles and crocodilians have not experienced any mass extinctions or shifts in diversification rate, or any significant jumps in rates of body-size evolution over time. We predict threat for 114 as-yet unassessed or data-deficient species and identify a concentration of threatened crocodile and turtle species in South and Southeast Asia, western Africa, and the eastern Amazon. We find that unlike other terrestrial vertebrate groups, extinction risk increases with evolutionary distinctiveness: a disproportionate amount of phylogenetic diversity is concentrated in evolutionarily isolated, at-risk taxa, particularly those with small geographic ranges. Our findings highlight the important role of geographic determinants of extinction risk, particularly those resulting from anthropogenic habitat-disturbance, which affect species across body sizes and ecologies.

scholarly journals Spatiophylogenetic modelling of extinction risk reveals evolutionary distinctiveness and brief flowering period as risk factors in a diverse hotspot plant genus

2018 ◽  
Author(s):  
Russell Dinnage ◽  
Alex Skeels ◽  
Marcel Cardillo
Keyword(s):  
Spatial Data ◽  
Extinction Risk ◽  
Individual Species ◽  
Flowering Period ◽  
Spatial Effects ◽  
Relative Contribution ◽  
Threat Status ◽  
Latent Extinction ◽  
Evolutionary Distinctiveness ◽  
Combine Information

AbstractComparative models used to predict species threat status often combine variables measured at the species level with spatial variables, causing multiple statistical challenges, including phylogenetic and spatial non-independence. We present a novel bayesian approach for modelling threat status that simultaneously deals with both forms of non-independence and estimates their relative contribution, and we apply the approach to modelling threat status in the Australian plant genus Hakea. We find that after phylogenetic and spatial effects are accounted for, species with greater evolutionary distinctiveness and a shorter annual flowering period are more likely to be threatened. The model allows us to combine information on evolutionary history, species biology, and spatial data, to calculate latent extinction risk (potential for non-threatened species to become threatened), and estimate the most important drivers of risk for individual species. This could be of value for proactive conservation decision-making that targets species of concern before they become threatened.

scholarly journals Expected time-invariant effects of biological traits on mammal species duration

2015 ◽  
Vol 112 (42) ◽  
pp. 13015-13020 ◽  
Author(s):  
Peter D. Smits
Keyword(s):  
Anthropogenic Impacts ◽  
Extinction Risk ◽  
Ecological Factors ◽  
Biological Traits ◽  
Mass Extinctions ◽  
Mammal Species ◽  
Expected Time ◽  
Species Vulnerability ◽  
Extant Species ◽  
Time Invariant

Determining which biological traits influence differences in extinction risk is vital for understanding the differential diversification of life and for making predictions about species’ vulnerability to anthropogenic impacts. Here I present a hierarchical Bayesian survival model of North American Cenozoic mammal species durations in relation to species-level ecological factors, time of origination, and phylogenetic relationships. I find support for the survival of the unspecialized as a time-invariant generalization of trait-based extinction risk. Furthermore, I find that phylogenetic and temporal effects are both substantial factors associated with differences in species durations. Finally, I find that the estimated effects of these factors are partially incongruous with how these factors are correlated with extinction risk of the extant species. These findings parallel previous observations that background extinction is a poor predictor of mass extinction events and suggest that attention should be focused on mass extinctions to gain insight into modern species loss.

scholarly journals Wege: A New Metric for Ranking Locations for Biodiversity Conservation

2020 ◽  
Author(s):  
Harith Farooq ◽  
Josue Anderson ◽  
Francesco Belluardo ◽  
Cristovao Nanvonamuquitxo ◽  
Dominic Bennett ◽  
...  
Keyword(s):  
Extinction Risk ◽  
Real Life ◽  
Decision Making Process ◽  
International Union ◽  
Know How ◽  
Conservation Policies ◽  
Threat Status ◽  
Continuous Scale ◽  
Evolutionary Distinctiveness ◽  
Effective Conservation

ABSTRACTAimIn order to implement effective conservation policies, it is crucial to know how biodiversity is distributed and one of the most widely used systems is the Key Biodiversity Areas (hereafter KBA) criteria, developed by the International Union for Conservation of Nature (IUCN). Here we develop a tool to rank Key Biodiversity Areas in a continuous scale to allow the ranking between KBAs and test this tool on a simulated dataset of 10 000 scenarios of species compositions of reptiles and mammals in eight locations in Mozambique.LocationMozambique, AfricaMethodsWe compare the KBA criteria with four priorisation metrics (weighted endemism, extinction risk, evolutionary distinctiveness and EDGE score) to rank the biodiversity importance of eight sites with a randomly generated species composition of reptiles and mammals in Mozambique.ResultsWe find that none of these metrics is able to provide a suitable ranking of the sites surveyed that would ultimately allow prioritization. We therefore develop and validate the “WEGE index” (Weighted Endemism including Global Endangerment index), which is an adaptation of the EDGE score (Evolutionarily Distinct and Globally Endangered) and allows the ranking of sites according to the KBA criteria but on a continuous scale.Main conclusionsFor our study system, the WEGE index scores areas that trigger KBA status higher and is able to rank their importance in terms of biodiversity by using the range and threat status of species present at the site. Prioritization may be crucial for policy making and real-life conservation, allowing the choice between otherwise equally qualified sites according to the KBA categories. WEGE is intended to support a transparent decision-making process in conservation.

scholarly journals Spatiophylogenetic modelling of extinction risk reveals evolutionary distinctiveness and brief flowering period as threats in a hotspot plant genus

2020 ◽  
Vol 287 (1926) ◽  
pp. 20192817
Author(s):  
Russell Dinnage ◽  
Alexander Skeels ◽  
Marcel Cardillo
Keyword(s):  
Spatial Data ◽  
Extinction Risk ◽  
Individual Species ◽  
Flowering Period ◽  
Spatial Effects ◽  
Diagnostic Features ◽  
Relative Contribution ◽  
Threat Status ◽  
Latent Extinction ◽  
Evolutionary Distinctiveness

Comparative models used to predict species threat status can help identify the diagnostic features of species at risk. Such models often combine variables measured at the species level with spatial variables, causing multiple statistical challenges, including phylogenetic and spatial non-independence. We present a novel Bayesian approach for modelling threat status that simultaneously deals with both forms of non-independence and estimates their relative contribution, and we apply the approach to modelling threat status in the Australian plant genus Hakea. We find that after phylogenetic and spatial effects are accounted for, species with greater evolutionary distinctiveness and a shorter annual flowering period are more likely to be threatened. The model allows us to combine information on evolutionary history, species biology and spatial data, calculate latent extinction risk (potential for non-threatened species to become threatened), estimate the most important drivers of risk for individual species and map spatial patterns in the effects of different predictors on extinction risk. This could be of value for proactive conservation decision-making based on the early identification of species and regions of potential conservation concern.

scholarly journals Forensic application of DNA barcoding for identification of illegally traded African pangolin scales

Genome ◽  
2017 ◽  
Vol 60 (3) ◽  
pp. 272-284 ◽  
Author(s):  
Monica Mwale ◽  
Desire L. Dalton ◽  
Raymond Jansen ◽  
Marli De Bruyn ◽  
Darren Pietersen ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Extinction Risk ◽  
Central Africa ◽  
Wildlife Trade ◽  
African Species ◽  
Extant Species ◽  
Anthropogenic Habitat ◽  
Manis Javanica ◽  
D Loop ◽  
Specific Species

The escalating growth in illegal wildlife trade and anthropogenic habitat changes threaten the survival of pangolin species worldwide. All eight extant species have experienced drastic population size reductions globally with a high extinction risk in Asia. Consequently, forensic services have become critical for law enforcement, with a need for standardised and validated genetic methods for reliable identifications. The seizure of three tonnes of pangolin scales, believed to have originated from Africa, by Hong Kong Customs Authorities provided an opportunity for the application of DNA barcoding in identifying scales. Three mitochondrial DNA gene regions (COI, Cyt b, and D-loop) were amplified for a subsample of the confiscated material and compared with taxonomically verified references. All four African species were recovered as monophyletic with high interspecific uncorrected p-distance estimates (0.048–0.188) among genes. However, only three of four African species (Phataginus tricuspis, Phataginus tetradactyla, and Smutsia gigantea, originating from West and Central Africa) and one of four Asian species (Manis javanica from Southeast Asia) were identified among scales. Although the assignment of unknown scales to specific species was reliable, additional genetic tools and representative reference material are required to determine geographic origins of confiscated pangolin specimens.

scholarly journals Historical climate change and megafaunal extinctions linked to genetic diversity declines in shorebirds

2021 ◽  
Author(s):  
Hui Zhen Tan ◽  
Justin J.F.J. Jansen ◽  
Gary A. Allport ◽  
Kritika M Garg ◽  
Balaji Chattopadhyay ◽  
...  
Keyword(s):  
Climate Change ◽  
Genetic Diversity ◽  
Late Quaternary ◽  
Extinction Risk ◽  
Breeding Habitat ◽  
Human Populations ◽  
Mass Extinctions ◽  
Effective Population ◽  
Extant Species ◽  
The Impact

The impact of accelerated climate change on extinction risk is not well-characterised despite its increasing relevance. Comparative genomics of extinct versus extant species might be useful in elucidating broad trends in faunal endangerment. We investigated fluctuations in genetic diversity and extinction timing in our genomic dataset of nine species of particularly vulnerable migratory shorebirds (Numenius), including two species widely thought to be extinct. Most species faced generally sharp declines in effective population sizes, a proxy for genetic diversity, soon after the Last Glacial Maximum. During this time, a warming climate supported forest expansions at the expense of open habitats, exacerbated by human-induced mass extinctions of megafauna only a few thousand years prior, resulting in unprecedented reductions in shorebird breeding habitat. Species breeding in temperate regions, where they widely overlap with human populations, have been most strongly affected. Late Quaternary events can exert long-lasting effects on some species' susceptibility to extinction. Genomic inquiry is crucial in informing conservation actions in the fight against ongoing biodiversity loss.

scholarly journals Initial terrestrial vertebrate diversity assessment in upland Cavite, Philippines

2019 ◽  
Vol 12 (2) ◽  
Keyword(s):  
Diversity Index ◽  
Conservation Status ◽  
Wildlife Habitat ◽  
Direct Result ◽  
Forest Fragments ◽  
Terrestrial Vertebrates ◽  
Terrestrial Vertebrate ◽  
Wiener Diversity Index ◽  
Diversity Assessment ◽  
Animal Diversity

Cavite’s remaining upland forest fragments are either remnant from commercial logging activities ca. 25-45 years ago or as a direct result of land conversions for agriculture or human settlements. These forest fragments are very significant because they represent areas where pockets of wildlife habitat still remain. The terrestrial vertebrates are often used to assess animal diversity because they are ideal biological indicators of environmental change and anthropogenic disturbances. The study aimed to determine terrestrial vertebrate diversity, conservation status, and identify major anthropogenic threats in these fragments. Terrestrial vertebrates were surveyed using a combination of strip-transect sampling, time-constrained searches, visual encounter survey (VES), and acoustic encounter survey (AES; for amphibians only), point counts, live trapping and mist netting from October 2014 to March 2016. Species richness and biodiversity estimation were computed using Shannon-Wiener Diversity Index, linear regression, detection and probability modeling using PAST, and confidence limits for nestedness (0.05α) using EpiTools. A total of 175 terrestrial vertebrates were documented and among the vertebrate groups, the birds had the highest observed diversity. Twenty-nine (19 birds, 3 mammals, 3 lizards, and 4 anurans) species are listed as threatened. Habitat loss and degradation due to the conversion of habitats to agricultural and/or residential areas remained to be the most prevalent threat in the remaining forested areas in upland Cavite. Baseline data generated shall be used in the different government biodiversity monitoring activities as the basis for impacts and mitigation and initial planning for the management and conservation of these remaining forest patches.

scholarly journals Adding fossil occupancy trajectories to the assessment of modern extinction risk

2016 ◽  
Vol 12 (10) ◽  
pp. 20150813 ◽  
Author(s):  
Wolfgang Kiessling ◽  
Ádám T. Kocsis
Keyword(s):  
Fossil Record ◽  
Extinction Risk ◽  
Strong Predictor ◽  
Marine Species ◽  
Species Traits ◽  
Latent Extinction ◽  
Extant Species ◽  
Temporal Trajectory

Besides helping to identify species traits that are commonly linked to extinction risk, the fossil record may also be directly relevant for assessing the extinction risk of extant species. Standing geographical distribution or occupancy is a strong predictor of both recent and past extinction risk, but the role of changes in occupancy is less widely assessed. Here we demonstrate, based on the Cenozoic fossil record of marine species, that both occupancy and its temporal trajectory are significant determinants of risk. Based on extinct species we develop a model on the additive and interacting effects of occupancy and its temporal changes on extinction risk. We use this model to predict extinction risk of extant species. The predictions suggest a moderate risk for marine species on average. However, some species seem to be on a long-term decline and potentially at a latent extinction risk, which is not considered in current risk assessments.

Within- and among-genus components of size evolution during mass extinction, recovery, and background intervals: a case study of Late Permian through Late Triassic foraminifera

Paleobiology ◽  
2012 ◽  
Vol 38 (4) ◽  
pp. 627-643 ◽  
Author(s):  
Brianna L. Rego ◽  
Steve C. Wang ◽  
Demir Altiner ◽  
Jonathan L. Payne
Keyword(s):  
Mass Extinction ◽  
Extinction Risk ◽  
Maximum Size ◽  
Size Reduction ◽  
Late Triassic ◽  
Mass Extinctions ◽  
Late Permian ◽  
Biotic Recovery ◽  
Size Evolution ◽  
Selective Extinction

One of the best-recognized patterns in the evolution of organismal size is the tendency for mean and maximum size within a clade to decrease following a major extinction event and to increase during the subsequent recovery interval. Because larger organisms are typically thought to be at higher extinction risk than their smaller relatives, it has commonly been assumed that size reduction mostly reflects the selective extinction of larger species. However, to our knowledge the relative importance of within- and among-lineage processes in driving overall trends in body size has never been compared quantitatively. In this study, we use a global, specimen-level database of foraminifera to study size evolution from the Late Permian through Late Triassic. We explicitly decompose size evolution into within- and among-genus components. We find that size reduction following the end-Permian mass extinction was driven more by size reduction within surviving species and genera than by the selective extinction of larger taxa. Similarly, we find that increase in mean size across taxa during Early Triassic biotic recovery was a product primarily of size increase within survivors and the extinction of unusually small taxa, rather than the origination of new, larger taxa. During background intervals we find no strong or consistent tendency for extinction, origination, or within-lineage change to move the overall size distribution toward larger or smaller sizes. Thus, size stasis during background intervals appears to result from small and inconsistent effects of within- and among-lineage processes rather than from large but offsetting effects of within- and among-taxon components. These observations are compatible with existing data for other taxa and extinction events, implying that mass extinctions do not influence size evolution by simply selecting against larger organisms. Instead, they appear to create conditions favorable to smaller organisms.

scholarly journals Brain size is correlated with endangerment status in mammals

2016 ◽  
Vol 283 (1825) ◽  
pp. 20152772 ◽  
Author(s):  
Eric S. Abelson
Keyword(s):  
Brain Size ◽  
Extinction Risk ◽  
Small Body ◽  
Cost Benefit ◽  
Metabolic Cost ◽  
Trade Offs ◽  
Extant Species ◽  
Body Sizes ◽  
The Cost ◽  
The Relationship

Increases in relative encephalization (RE), brain size after controlling for body size, comes at a great metabolic cost and is correlated with a host of cognitive traits, from the ability to count objects to higher rates of innovation. Despite many studies examining the implications and trade-offs accompanying increased RE, the relationship between mammalian extinction risk and RE is unknown. I examine whether mammals with larger levels of RE are more or less likely to be at risk of endangerment than less-encephalized species. I find that extant species with large levels of encephalization are at greater risk of endangerment, with this effect being strongest in species with small body sizes. These results suggest that RE could be a valuable asset in estimating extinction vulnerability. Additionally, these findings suggest that the cost–benefit trade-off of RE is different in large-bodied species when compared with small-bodied species.

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