Extinction Research Articles

Narrating Loss in James Bradley’s "Clade" (2015); or, Introducing Arrested Narrative in Climate Fiction

In James Bradley’s futuristic novel of climate crises, Clade (2015), characters constructed to evoke empathy and readerly attachment, characters we expect to be further developed narratologically, are prone to sudden, unexpected and unexplained disappearances. The development of cared-for characters is thus ‘arrested’ at the level of narration. For readers, this is disarming and disconcerting. However, we find purpose in such acts of narratorial breakage in cli-fi like Clade. In contemporary stories of climate crises, which project environmental destruction, the loss of habitats and species, and severe disruption to human and nonhuman lives, the arrestation of a character’s development parallels a sense of environmental loss evoked at the level of storied content. Put another way, the sudden disappearance of character-story at the level of form imitates the sudden erasure of species, ecosystems and lived experience in the storyworld of Clade. We call such narratological innovation arrested narrative. In this essay we define and describe the appearance and function of arrested narrative in Clade, in some depth, as well as its emergence in two other novels of climate crises, Megan Hunter’s The End We Start From (2017) and Diane Cook’s The New Wilderness (2020). While investigations into narrative form in stories of the Anthropocene are not new, ecocritical literary scholarship remains largely focussed on story-level content. This examination of the way arrests in narrative discourse parallel environmental ruptures at the level of content, in selected cli-fi, is aimed at contributing to the emerging field of “econarratology” (James), concerned with the study of the workings of both form and content in ecocritical narratives.

The Economic Value of Biodiversity Preservation

AbstractWe study the decision to preserve diverse species when the value of biodiversity is uncertain, or even affected by ambiguity. Optimal decisions are derived both from the perspective of the producer/investor and the policy regulator (ecosystem planner). We find that while calculated risk creates a scope for biodiversity preservation, the presence of ambiguity aversion reduces it, thus accelerating the extinction of species with lower value. Our results suggest that effective conservation strategies would involve a reduction of ambiguity aversion by creating a stable and transparent policy environment. Furthermore, they may involve a two tier strategy, with one tier addressing output targets and the other conservation targets.

Assessment of the impact of chemical pollution on endangered migratory fish in two major rivers of France, including spawning grounds

Water pollution is a one of the most contributors to aquatic biodiversity decline. Consequently, ecological risk assessment methods have been developed to investigate the effects of existing stresses on the environment, including the toxic effects of chemicals. One of the existing approaches to quantify toxic risks is called “Potentially Affected Fraction of species” (PAF), which estimates the potential loss of species within a group of species studied. In this study, the PAF method was applied to the Garonne catchment (southwest France) due to the limited information available on the involvement of water pollution in the decline of diadromous fish populations. This approach was used to quantify the potential toxic risk associated with chemical contamination of water for fish species. The objectives were to quantify this risk (1) in the Garonne and Dordogne rivers and (2) in the spawning grounds of two endangered anadromous fish species: the allis shad and the European sturgeon during the development period of their early life stages. Environmental pollution data was provided for 21 sites within the Garonne catchment between 2007 and 2022, and toxicity data was obtained specifically from freshwater toxicity tests on fish species. Then, for each site and each year, the potential toxic risk for a single substance (ssPAF) and for a mixture of substances (msPAF) was calculated and classified as high (>5 %), moderate (>1 % and < 5 %) or low (<1 %). Potential toxic risks were mostly moderate and mainly associated with: metals > other industrial pollutants and hygiene and care products > agrochemicals. In summary, this study highlights the probable involvement of water contamination on the decline, fate and restoration of diadromous fish populations in the Garonne catchment, focusing notably on the toxic effects on early life stages, a previously understudied topic.

Biodiversity loss impacts top-down regulation of insect herbivores across ecosystem boundaries

Biodiversity loss, as driven by anthropogenic global change, imperils biosphere intactness and integrity. Ecosystem services such as top-down regulation (or biological control; BC) are susceptible to loss of extinction-prone taxa at upper trophic levels and secondary ‘support’ species e.g., herbivores. Here, drawing upon curated open-access interaction data, we structurally analyze trophic networks centered on the fall armyworm Spodoptera frugiperda (Lepidoptera: Noctuidae) and assess their robustness to species loss. Tri-partite networks link 80 BC organisms (invertebrate or microbial), 512 lepidopteran hosts and 1194 plants (including 147 cultivated crops) in the Neotropics. These comprise threatened herbaceous or woody plants and conservation flagships such as saturniid moths. Treating all interaction partners functionally equivalent, random herbivore loss exerts a respective 26 % or 108 % higher impact on top-down regulation in crop and non-crop settings than that of BC organisms (at 50 % loss). Equally, random loss of BC organisms affects herbivore regulation to a greater extent (13.8 % at 50 % loss) than herbivore loss mediates their preservation (11.4 %). Yet, under moderate biodiversity loss, (non-pest) herbivores prove highly susceptible to loss of BC organisms. Our topological approach spotlights how agriculturally-subsidized BC agents benefit vegetation restoration, while non-pest herbivores uphold biological control in on- and off-farm settings alike. Our work underlines how the on-farm usage of endemic biological control organisms can advance conservation, restoration, and agricultural sustainability imperatives. We discuss how integrative approaches and close interdisciplinary cooperation can spawn desirable outcomes for science, policy and practice.

Species diversity and extinction risk of vertebrate pollinators in India

Animal pollinators underpin the functioning and persistence of ecosystems globally. However, the vital role of pollination is being progressively eroded by the worldwide decline of pollinator species caused by human-induced environmental degradation, resulting in rising costs to biodiversity, agriculture, and economy. Most studies quantifying pollinator diversity and declines have focused on insects, whereas vertebrate pollinators remain comparatively neglected. Here, we present the first comprehensive study quantifying the macroecological patterns of species richness and extinction risk of bird and mammal pollinators in India, a region of extremely high biodiversity and increasing anthropogenic pressure. Our results reveal that hotspots of mammal pollinator diversity are restricted to the south of the Western Ghats, whereas bird pollinator diversity hotspots are scattered throughout the country. Analyses of hotspots of threatened species (based on the IUCN Red List) show that only mammal pollinators are currently classified as threatened in India, whereas multiple hotspots of population declines were observed for birds, and primarily in the Southwest for mammal pollinators. Our analyses failed to identify a role for species traits as drivers of these patterns, whereas most pollinators appear to be threatened by agriculture, logging and hunting for food, and medicinal purposes. Pollinator endangerment has widescale ecological and economic implications such as reduced food production, plant extinction, loss of functional and genetic diversity, and economic damage. We suggest protection of vertebrate pollinators should be emphasised in active conservation agendas in India.

Medicinal Chemistry Gone Wild.

Earth is currently experiencing a mass extinction event. The flora and fauna of our planet are experiencing mass die-offs from a multitude of factors, with wildlife disease emerging as one parameter where medicinal chemists are equipped to intervene. While contemporary medicinal chemistry focuses on human health, many traditional pharmaceutical companies have historic roots in human health, animal health, and plant health. This trifecta of health sciences perfectly maps to the current field of One Health, which recognizes that optimal health outcomes can only be achieved through the health of humans, plants, animals, and their shared environments. This Perspective imagines a world where state-of-the-art medicinal chemistry tactics are used to prevent the extinction of endangered species and points to preliminary work in the emerging area of conservation medicine.

The Hasli Formation of the Irchel Plateau – A key record for older Early Pleistocene interglacial sediments in northern Switzerland

In the Alpine region of Central Europe, terrestrial Early Pleistocene deposits with preserved faunal and botanical remains are rare. The predominantly gravelly Höhere Deckenschotter (HDS) deposits of northern Switzerland and adjoining south-western Germany are considered the oldest Quaternary sediments in the northern Alpine Foreland, linked with the first extensive Quaternary Alpine glaciations.This multidisciplinary study investigates the Hasli Formation (HF), a unique silty unit with well-preserved biological remains within an HDS sequence at the Irchel Plateau north of Zürich, providing new climatic and environmental data for these exceptional deposits, as well as crucial information about their age. Systematic mapping of the HF, in addition to the underlying and covering gravel units, has been coupled with sedimentary logging and biostratigraphic analysis at several sites. The HF is present over an area c.4 by up to 1.4 km, and where studied is 1.6–6.2 m thick. The sediments and biological material are indicative of overbank deposits accumulating within the damp floodplain of a large meandering river.The recovered small mammal remains are from eight arvicolid species or genera, including Mimomys pliocaenicus, M. reidi/tigliensis and Clethrionomys cf. kretzoii, which became extinct c.1.8 Ma, and Pliomys episcopalis/simplicior, which first appeared c.2 Ma ago. The over 75k identified molluscs, include c.72k coming from 89 terrestrial species and over 3k from 28 aquatic taxa. The molluscan faunas from all locations where the HF has been studied share important biostratigraphic marker species, and indicate analogous climatic and environmental conditions. The marker species include several that became extinct during the Early Pleistocene, of which Clausilia stranzendorfensis and Cochlostoma salomoni, present throughout the HF, are the most important as they disappeared c.1.8 Ma. Many marker species have modern or palaeo-distributions that lie far to the west, south and east of the Swiss Plateau, showing that the climate was much warmer than today, typical for the Tiglian warm stage. The alluvial floodplain was covered by rather dense, mature woodland.Amino acid (AA) analysis shows that molluscan remains from the HF are among the oldest of the Quaternary shell material studied from across the Swiss Plateau. Palaeomagnetic data shows a change from reversed to normal polarity within the upper part of the HF. When combined, the small mammal and molluscan remains, palaeomagnetic measurements, AA geochronology and sedimentary data, suggest an age of 2.1–1.8 Ma for the HF. Recently produced cosmogenic dates bracket the age of the HDS gravels beneath the HF to depositional periods between 2.6 and 0.9 Ma, with the youngest ages being in disagreement with our findings. The abundance and diversity of the molluscs from the Irchel Plateau, with several rare extinct species, together with a notable small mammal assemblage, make this a key palaeontological site and an important reference point for European Quaternary biostratigraphy.

Discrimination of ivory from extant and extinct elephant species using Raman spectroscopy: A potential non-destructive technique for combating illegal wildlife trade.

The use of elephant ivory as a commodity is a factor in declining elephant populations. Despite recent worldwide elephant ivory trade bans, mammoth ivory trade remains unregulated. This complicates law enforcement efforts, as distinguishing between ivory from extant and extinct species requires costly, destructive and time consuming methods. Elephant and mammoth ivory mainly consists of dentine, a mineralized connective tissue that contains an organic collagenous component and an inorganic component of calcium phosphate minerals, similar in structure to hydroxyapatite crystals. Raman spectroscopy is a non-invasive laser-based technique that has previously been used for the study of bone and mineral chemistry. Ivory and bone have similar biochemical properties, making Raman spectroscopy a promising method for species identification based on ivory. This study aimed to test the hypothesis that it is possible to identify differences in the chemistry of mammoth and elephant ivory using Raman spectroscopy. Mammoth and elephant tusks were obtained from the Natural History Museum in London, UK. Included in this study were eight samples of ivory from Mammuthus primigenius, two samples of carved ivory bangles from Africa (Loxodonta species), and one cross section of a tusk from Elephas maximus. The ivory was scanned using an inVia Raman micro spectrometer equipped with a x50 objective lens and a 785nm laser. Spectra were acquired using line maps and individual spectral points were acquired randomly or at points of interest on all samples. The data was then analysed using principal component analysis (PCA) with use of an in-house MATLAB script. Univariate analysis of peak intensity ratios of phosphate to amide I and III peaks, and carbonate to phosphate peaks showed statistical differences (p<0.0001) in the average peak intensity ratios between Mammuthus primigenius, Loxodonta spp. and Elephas maximus. Full width at half maximum hight (FWHM)analysis of the phosphate peak demonstrated higher crystal maturity of Mammuthus primigenius compared to living elephant species. The results of the study have established that spectra acquired by Raman spectroscopy can be separated into distinct classes through PCA. In conclusion, this study has shown that well-preserved mammoth and elephant ivory has the potential to be characterized using Raman spectroscopy, providing a promising method for species identification. The results of this study will be valuable in developing quick and non-destructive methods for the identification of ivory, which will have direct applications in archaeology and the regulation of international trade.

Climate and anthropogenic activities threaten two langur species irrespective of their range size

AbstractAimIf species fail to track the pace of climate change, areas of suitable habitat and population size are likely to decline, threatening species survivorship. Here, we incorporated multiple measures of environmental change and species‐specific habitat requirements to assess the responses of two closely related primate species to future changes in climate and habitat conversion. Specifically, we tested whether the comparatively wider‐ranging and Endangered François' langur (Trachypithecus francoisi) is better suited to withstand future anthropogenic habitat conversion and climate change than is the more narrowly ranging and critically endangered white‐headed langurs (T. leucocephalus).LocationChina.MethodsWe used species distribution models (SDMs) models and population viability analyses, and calculated dispersal velocity and biotic velocity, to predict the impact of climate and anthropogenic activity on the distribution and survivorship of two closely related primate species.ResultsWe found that: (1) by the year 2050, the area of suitable habitat for both primate species is expected to decline by 45% to 47%; (2) the population size of François' langurs is expected to increase to 4000 individuals (129%) and the population size of white‐headed langurs is expected to increase to 1400 individuals (133%); (3) biotic velocity, defined as the minimum migration rate required by a species to track its preferred climatic conditions, was 2.84 and 1.48 km/year for François' langurs and white‐headed langurs, respectively; and (4) dispersal velocity, defined as the distance a species has spread over a given period, was 0.82 km/year for both langur species.Main ConclusionsWe demonstrate that despite expected population growth, by the year 2050, habitat contraction and insufficient opportunities for dispersal will likely prevent both primate species from tracking and adjusting to changing climate conditions. Moreover, the more widely ranging species, T. francoisi, was not found to have a survival advantage over the more narrowly ranging species (T. leucocephalus) under future conditions of climate change and continued anthropogenic habitat conversion, resulting in a high risk of extinction for both langur species. The modelling approach used here is robust and can be successfully applied to other threatened animal taxa.

Inverted loading strategy regulates the Mn–OV–Ce sites for efficient fenton-like catalysis

Regulating interfacial active sites to improve peroxymonosulfate (PMS) activation efficiency is a hot topic in the heterogeneous catalysis field. In this study, we develop an inverted loading strategy to engineer asymmetric Mn–OV–Ce sites for PMS activation. Mn3O4@CeO2 prepared by loading CeO2 nanoparticles onto Mn3O4 nanorods exhibits the highest catalytic activity and stability, which is due to the formation of more oxygen vacancies (OV) at the Mn–OV–Ce sites, and the surface CeO2 layer effectively inhibits corrosion by preventing the loss of manganese ion active species into the solution. In situ characterizations and density functional theory (DFT) studies have revealed effective bimetallic redox cycles at asymmetric Mn–OV–Ce active sites, which promote surface charge transfer, enhance the adsorption reaction activity of active species toward pollutants, and favor PMS activation to generate (•OH, SO4•−, O2•− and 1O2) active species. This study provides a brand-new perspective for engineering the interfacial behavior of PMS activation.

The pseudosuchian record in paleohistology: A small review.

Archosauria originated around the Earth's largest biotic crisis that severely affected all ecosystems globally, the Permotriassic Mass extinction event, and comprises two crown-group lineages: the bird-lineage and the crocodylian lineage. The bird lineage includes the iconic pterosaurs, as well as dinosaurs and birds, whereas the crocodylian lineage includes clades such as aetosaurs, poposaurs, "rauisuchians," as well as Crocodylomorpha; the latter being represented today only by less than 30 extant species of Crocodylia. Despite playing important roles during Mesozoic and Cenozoic ecosystems, both on land and in water, Pseudosuchia received far less attention compared to the bird-lineage, which is also reflected in number and scope of histological studies so far. Lately, the field has seen a shift of focus toward pseudosuchians, however, and the symposium on "Paleohistological Inferences of Paleobiological Traits in Pseudosuchia" held during the International Congress of Vertebrate Morphology 2023 in Cairns, Queensland, Australia, is the latest proof of that. To put these novel aspects of paleohistological and paleobiological research into context, an overview of the non-extant pseudosuchian taxa whose postcranial bones were studied so far is provided here (c. 80 species out of a total of more than 700 extinct species described) and recent trends in pseudosuchian osteohistology are highlighted. In addition, histological studies on cranial and dental material and other potential hard tissues, such as eggshells and otoliths, are briefly reviewed as well.

A New Extinct Species of Malagodon (Cyprinodontiformes: Pantanodontidae) from Southeastern Coastal Madagascar, with a Discussion of its Phylogenetic Relationships and a Redescription of the Genus

A New Extinct Species of Malagodon (Cyprinodontiformes: Pantanodontidae) from Southeastern Coastal Madagascar, with a Discussion of its Phylogenetic Relationships and a Redescription of the Genus

Loss of amphibian species alters periphyton communities in montane ponds

AbstractAmphibian larvae can affect the structure and functioning of freshwater ecosystems, but their effects have been little explored although amphibian biodiversity is rapidly declining. Given that larvae of different amphibian species belong to different trophic levels, their effects on freshwater communities and processes can be expected to differ, with herbivores likely having direct effects on algae and predators having indirect effects through trophic cascades. We explored this question through a mesocosm experiment conducted in montane ponds, using an anuran and a urodele species affected by emergent diseases. We used different scenarios of reduction and loss of one or both species, and compared them to a control scenario representing a typical amphibian community in the study area composed of four species, with total larval density held constant. Loss of the anuran resulted in lower chlorophyll concentration and algal density, likely due to replacement by more efficient grazers. Loss of the urodele produced similar trends but weaker, possibly due to an increase of invertebrate grazing activity in the absence of this predator. Our study shows how the loss of amphibian species can alter the structure of montane ponds, but also how the mechanisms involved and the intensity of effects differ for different species.

Testing extinction events and temporal shifts in diversification and fossilization rates through the skyline Fossilized Birth-Death (FBD) model: The example of some mid-Permian synapsid extinctions.

In the last decade, the Fossilized Birth-Death (FBD) process has yielded interesting clues about the evolution of biodiversity through time. To facilitate such studies, we extend our method to compute the probability density of phylogenetic trees of extant and extinct taxa in which the only temporal information is provided by the fossil ages (i.e. without the divergence times) in order to deal with the piecewise constant FBD process, known as the "skyline FBD", which allows rates to change between pre-defined time intervals, as well as modelling extinction events at the bounds of these intervals. We develop approaches based on this method to assess hypotheses about the diversification process and to answer questions such as "Does a mass extinction occur at this time?" or "Is there a change in the fossilization rate between two given periods?". Our software can also yield Bayesian and maximum-likelihood estimates of the parameters of the skyline FBD model under various constraints. These approaches are applied to a simulated dataset in order to test their ability to answer the questions above. Finally, we study an updated dataset of Permo-Carboniferous synapsids to get additional insights into the dynamics of biodiversity change in three clades (Ophiacodontidae, Edaphosauridae and Sphenacodontidae) in the Pennsylvanian (Late Carboniferous) and Cisuralian (Early Permian), and to assess support for end-Sakmarian (or Artinskian) and end-Cisuralian mass extinction events discussed in previous studies.

Successions of terrestrial invertebrate communities during the Tsey Glacier retreat, Central Caucasus

In the Caucasus, the total area taken up by glaciers is known to have reduced by 23% over the last 20 years. This natural experiment allows for additive and replacement models of autogenic succession of biocoenoses within paraglacial landscapes to be tested. A certain risk of the extinction of cryophilic species also exists. However, montane paraglacial successions of invertebrate assemblages have hitherto been studied neither in the Caucasus nor in Russia as a whole. Structural changes of taxocoenoses were traced in a spatial and temporal sequence of ten properly dated paraglacial sites in the Tsey Gorge, North Ossetia − Alania (1–170-years old) among the testate amoebae, earthworms, molluscs, myriapods, mites, spiders, harvestmen, pseudoscorpions, collembolans, and beetles. As the glacier retreats, in place of bare paraglacial wastelands, grassland communities are formed that, after 10–14 years, are replaced by shrub vegetation and, on 30–35-year old surfaces, by forest communities. Most of the invertebrate groups, once “appearing” along a postglacial transect, were recorded from most older plots as well. Yet, their taxocoenoses underwent considerable transformations through increasing (or an increase turning into some decline in beetles) the species diversity and a strong, often complete change in the taxonomic composition and dominance structure. The most considerable transformations were observed at all major vegetation changes. The “appearance” of some groups in the transect was determined not only by dispersion capacities but mainly by the environmental conditions of particular habitats. When comparing the composition of the pioneer postglacial species complex of the study region with that in the mountains of Europe’s south and north, its high-degree regional specificity was noted, sometimes shown at the family level (in spiders). Spatial β-diversity of all larger taxa studied was mainly attributed to turnover (due to “the replacement model” of succession). The general level of change diminished towards the later succession stages. Endemic arthropod species were revealed both in pioneer grassland and developed forest communities.

Charting the Course of Pinniped Evolution: insights from molecular phylogeny and fossil record integration.

Pinnipeds (seals, sea lions, walruses, and their fossil relatives) are one of the most successful mammalian clades to live in the oceans. Despite a well-resolved molecular phylogeny and a global fossil record, a complete understanding of their macroevolutionary dynamics remains hampered by a lack of formal analyses that combine these two rich sources of information. We used a meta-analytic approach to infer the most densely sampled pinniped phylogeny to-date (36 recent and 93 fossil taxa) and used phylogenetic paleobiological methods to study their diversification dynamics and biogeographic history. Pinnipeds mostly diversified at constant rates. Walruses however experienced rapid turnover in which extinction rates ultimately exceeded speciation rates from 12-6 Ma, possibly due to changing sea-levels and/or competition with otariids (eared seals). Historical biogeographic analyses including fossil data allowed us to confidently identify the North Pacific and the North Atlantic (plus or minus Paratethys) as the ancestral ranges of Otarioidea (eared seals + walrus) and crown phocids (earless seals), respectively. Yet, despite the novel addition of stem pan-pinniped taxa, the region of origin for Pan-Pinnipedia remained ambiguous. These results suggest further avenues of study in pinnipeds and provide a framework for investigating other groups with substantial extinct and extant diversity.

Forensic genetics associated with hair analysis as a tool for jaguar (Panthera onca) identification

Animal smuggling and illegal wildlife trade comprise one of the most common crimes being committed on an international level. This action can affect biodiversity and most certainly increases the risk of extinction of several endangered species. Wildlife taxonomic identification is becoming routine to forensic experts. The aim of this study was to identify a possible jaguar sample (Panthera onca Linnaeus, 1958) from legal evidence using hair morphology and mitochondrial DNA (mtDNA) to help in an official animal identification. Scanning and optical microscope images of hair samples were used to compare diagnostic characteristics of felines to reference studies. A preserved region, (cytochrome oxidase subunit 1 (COI)), from mtDNA was sequenced and compared to a DNA database (GenBank) to perform genetic identification. Forensic genetic and hair analysis techniques combined positively identified the sample as jaguar. These methods can help practitioners and forensics experts to identify evidence collected in wildlife crimes suspected to involve jaguars.

Diversity-dependent speciation and extinction in hominins.

The search for drivers of hominin speciation and extinction has tended to focus on the impact of climate change. Far less attention has been paid to the role of interspecific competition. However, research across vertebrates more broadly has shown that both processes are often correlated with species diversity, suggesting an important role for interspecific competition. Here we ask whether hominin speciation and extinction conform to the expected patterns of negative and positive diversity dependence, respectively. We estimate speciation and extinction rates from fossil occurrence data with preservation variability priors in a validated Bayesian framework and test whether these rates are correlated with species diversity. We supplement these analyses with calculations of speciation rate across a phylogeny, again testing whether these are correlated with diversity. Our results are consistent with clade-wide diversity limits that governed speciation in hominins overall but that were not quite reached by the Australopithecus and Paranthropus subclade before its extinction. Extinction was not correlated with species diversity within the Australopithecus and Paranthropus subclade or within hominins overall; this is concordant with climate playing a greater part in hominin extinction than speciation. By contrast, Homo is characterized by positively diversity-dependent speciation and negatively diversity-dependent extinction-both exceedingly rare patterns across all forms of life. The genus Homo expands the set of reported associations between diversity and macroevolution in vertebrates, underscoring that the relationship between diversity and macroevolution is complex. These results indicate an important, previously underappreciated and comparatively unusual role of biotic interactions in Homo macroevolution, and speciation in particular. The unusual and unexpected patterns of diversity dependence in Homo speciation and extinction may be a consequence of repeated Homo range expansions driven by interspecific competition and made possible by recurrent innovations in ecological strategies. Exploring how hominin macroevolution fits into the general vertebrate macroevolutionary landscape has the potential to offer new perspectives on longstanding questions in vertebrate evolution and shed new light on evolutionary processes within our own lineage.

Two Major Extinction Events in the Evolutionary History of Turtles: One Caused by an Asteroid, the Other by Hominins.

AbstractWe live in a time of accelerated biological extinctions that has the potential to mirror past mass extinction events. However, the rarity of mass extinctions and the restructuring of diversity they cause complicate direct comparisons between the current extinction crisis and earlier events. Among animals, turtles (Testudinata) are one of few groups that have both a rich fossil record and sufficiently stable ecological and functional roles to enable meaningful comparisons between the end-Cretaceous mass extinction (∼66 Ma) and the ongoing wave of extinctions. Here we analyze the fossil record of the entire turtle clade and identify two peaks in extinction rates over their evolutionary history. The first coincides with the Cretaceous-Paleogene transition, reflecting patterns previously reported for other taxa. The second major extinction event started in the Pliocene and continues until now. This peak is detectable only for terrestrial turtles and started much earlier in Africa and Eurasia than elsewhere. On the basis of the timing, geography, and functional group of this extinction event, we postulate a link to co-occurring hominins rather than climate change as the cause. These results lend further support to the view that negative biodiversity impacts were already incurred by our ancestors and related lineages and demonstrate the severity of this continued impact through human activities.

Inferring the evolutionary history of the Sino-Himalayan biodiversity hotspot using a Bayesian birth-death skyline model

Abstract The current status of the Sino-Himalayan region as a biodiversity hotspot, particularly for flora, has often been linked to the uplift of the Sino-Tibetan Plateau and Himalayan and Hengduan Mountains. However, the relationship between the topological development of the region and the onset of diversification is yet to be confirmed. Here, we apply Bayesian phylodynamic methods to a large phylogeny of angiosperm species from the Sino-Himalayas, to infer changes in their evolutionary rates through time. We find strong evidence for high diversification rates in the Paleocene, late Miocene and Pliocene, and for negative diversification rates in the Quaternary, driven by an increase in extinction rates. Our analyses suggest that changes in global palaeotemperatures are unlikely to be a driving force for these rate shifts. Instead, the collision of the Indian continent with Eurasia and coeval topographic change in the Sino-Himalayas, the Miocene Grassland Expansion, and the impact of Pleistocene glaciations on this altitudinally-variable region may have driven these rates. We also demonstrate the strong influence of change time choice on the shape of inferred piecewise-constant trajectories in Bayesian phylodynamics, and advocate for the use of prior information when making this decision. Supplementary material at https://doi.org/10.6084/m9.figshare.c.7179254