Sixth Extinction Research Articles

New insights into the origin of the Galápagos tortoises with a tip-dated analysis of Testudinidae

ABSTRACT The giant tortoises of the Galápagos Archipelago influenced Darwin’s early thinking on transmutation and now constitute a famous example of island-based speciation and evolutionary dynamics. Questions regarding their evolutionary origin still exist and include whether their giant size evolved before or after the lineage arrived in the Galápagos from the South American continent. Here we present new evidence supporting the ‘before’ hypothesis based on previously reported fossil specimens from the Late Pleistocene of Ecuador. Despite the isolated and fragmentary nature of these tortoise fossils, phylogenetically informative features are preserved. A tip-dated phylogenetic analysis recovers the Ecuador form as the sister taxon to the Galápagos lineage, thus supporting the existence of a closely related, giant tortoise population at approximately the same time and place that the Humboldt Current is thought to have carried the ancestral Galápagos tortoise to the archipelago. The phylogeny also raises the possibility that the same evolution of continental gigantism also facilitated the dispersal of South American tortoises into the Caribbean Basin where they diversified before succumbing to Holocene extinction.

How is the coming generation to go on living? Bonhoeffer's preservation orders for the ‘sixth extinction’

AbstractThis essay adapts Dietrich Bonhoeffer's ‘orders of preservation’ to address the sharp rise in species extinctions due to human causes. I argue that Bonhoeffer's creative use of preservation orders to build an international alliance provides the scope required to meet the present biodiversity crisis while pre-empting Karl Barth's criticism of static regionalism and avoiding problematic elements in Carl Schmitt's concept of the ‘restraining force’. Drawing on Bonhoeffer's 1932 address, ‘On the Theological Foundation of the Work of the World Alliance’, I present three convictions to guide the task of preservation today, which include the formation of alliances between ecclesial and scientific communities in order to properly specify God's commandment.

Freedom and Heteronomy in the Anthropocene

AbstractThe concept of the Anthropocene reflects a particular meaning of the “human” as it exists in society, and a specific understanding of freedom, which only became possible at the close of the twentieth century. Whereas Enlightenment thinkers such as Kant, Rousseau, and Adam Smith attempted to grasp the potential for humanity to be changed through society in a self-conscious process of attaining freedom, the “Age of Man” today appears entirely disconnected from human agency. Indeed, the Anthropocene is associated not with the flourishing of life but with the sixth mass extinction. Drawing insight from classical and contemporary critical theory, this paper seeks to explicate the emancipatory potential within the concept of the Anthropocene, and the ways in which this potential is blocked by material circumstances that masquerade as “freedom.”

Dead Shells Bring to Life Baselines for Conservation: Case Studies from The Bahamas, Southern California, and Wisconsin, USA

We are living in a time of rapid biodiversity loss. Numerous studies have shown that modern extinction rates are higher than pre-human background rates. However, these studies of biodiversity decline almost exclusively focus on large vertebrates. The scientific community lacks the sufficient long-term records necessary to track biodiversity loss for many invertebrate taxa. However, aquatic, benthic, and skeletonized invertebrates have the advantage of leaving a long-term record that can readily be sampled in conjunction with living communities because the mineralized skeletons accumulate in the very same sediments in which the animals that produced them once lived. These not-quite-fossil “death assemblages” contain an underutilized record for long-term monitoring. Here, we leverage three case studies of calcareous micro- and macro-faunal remains from three aquatic environments spanning two gradients: freshwater to fully marine and polluted to pristine and remediated. We compared the death assemblages to living assemblages in these case studies using Spearman’s rho and the Jaccard–Chao agreement to determine the degree of fidelity. Death assemblages of lacustrine, calcareous microcrustaceans (Ostracoda), collected from lakes in The Bahamas and Wisconsin, USA, faithfully record human impacts, both for degradation and remediation, as determined by a mismatch in the live–dead comparisons. Likewise, the live–dead comparisons of calcareous marine macrofauna (Bivalvia) from the southern California shelf also indicate human impact, including pollution and remediation. These case studies demonstrate how death assemblages can be used to gauge the changes in community assembly and population structures at local and regional scales, even in the absence of a systemic monitoring program. Conservation, restoration, and biomonitoring efforts would benefit from the inclusion of live–dead comparisons of taxa with easily fossilized, identifiable parts. Live–dead studies, such as those presented in these case studies, can be used as tools for recognizing targets and establishing baselines for conservation, tracking community responses to remediation efforts, and identifying local species extinctions.

NetworkExtinction: An R package to simulate extinction propagation and rewiring potential in ecological networks

Abstract Earth's biosphere is undergoing drastic reorganization due to the sixth mass extinction brought on by the Anthropocene. Impacts of local and regional extirpation of species have been demonstrated to propagate through the complex interaction networks they are part of, leading to secondary extinctions and exacerbating biodiversity loss. Contemporary ecological theory has developed several measures to analyse the structure and robustness of ecological networks under biodiversity loss. However, a toolbox for directly simulating and quantifying extinction cascades and creating novel interactions (i.e. rewiring) remains absent. Here, we present NetworkExtinction—a novel R package which we have developed to explore the propagation of species extinction sequences through ecological networks and quantify the effects of rewiring potential in response to primary species extinctions. With NetworkExtinction, we integrate ecological theory and computational simulations to develop functionality with which users may analyse and visualize the structure and robustness of ecological networks. The core functions introduced with NetworkExtinction focus on simulations of sequential primary extinctions and associated secondary extinctions, allowing user‐specified secondary extinction thresholds and realization of rewiring potential. With the package NetworkExtinction, users can estimate the robustness of ecological networks after performing species extinction routines based on several algorithms. Moreover, users can compare the number of simulated secondary extinctions against a null model of random extinctions. In‐built visualizations enable graphing topological indices calculated by the deletion sequence functions after each simulation step. Finally, the user can estimate the network's degree distribution by fitting different common distributions. Here, we illustrate the use of the package and its outputs by analysing a Chilean coastal marine food web. NetworkExtinction is a compact and easy‐to‐use R package with which users can quantify changes in ecological network structure in response to different patterns of species loss, thresholds and rewiring potential. Therefore, this package is particularly useful for evaluating ecosystem responses to anthropogenic and environmental perturbations that produce nonrandom and sometimes targeted, species extinctions.

Conservation implications of a new fossil species of hopping-mouse, Notomys magnus sp. nov. (Rodentia: Muridae), from the Broken River Region, northeastern Queensland

The Australian hopping-mouse Notomys includes 10 species, eight of which are considered extinct, vulnerable, near-threatened or endangered. Here we report a new fossil species from the Broken River Region, northeastern Queensland. Notomys magnus sp. nov. is represented by craniodental material from late Quaternary cave deposits. It was a relatively large-bodied species of Notomys with a mass estimated to be ca 83 g. Notomys magnus sp. nov. is immediately distinguishable from the spinifex hopping-mouse (Notomys alexis), the northern hopping-mouse (Notomys aquilo), the fawn hopping-mouse (Notomys cervinus), the dusky hopping-mouse (Notomys fuscus), Mitchell’s hopping-mouse (Notomys mitchellii) and the big-eared hopping-mouse (Notomys macrotis) by its larger size (especially its longer upper molar crown length). Notomys magnus sp. nov. differs from the large-bodied Darling Downs hopping-mouse (Notomys mordax), long-tailed hopping-mouse (Notomys longicaudatus), short-tailed hopping-mouse (Notomys amplus) and broad-cheeked hopping-mouse (Notomys robustus) by possessing a unique first upper molar (M1) morphology including relatively well-developed buccal cusps, cusp T1 prominently isolated from T4, a relatively narrow posterior loph and an incipient anterior accessory cusp. Fossils of N. magnus sp. nov. are found in association with remains of several arid-adapted taxa, including the plains mouse (Pseudomys australis), the northern pig-footed bandicoot (Chaeropus yirratji), and N. longicaudatus, possibly indicating that N. magnus sp. nov. was also arid-adapted. Dating of fossil deposits containing N. magnus sp. nov. demonstrates that it was extant in the mid-Holocene (ca 8.5 ka) so it may have been still extant at the time of European colonization but suffered extinction soon after, mirroring the fate of similarly arid-adapted contemporaneous taxa (Chaeropus yirratji and N. longicaudatus). Historical extinctions in Notomys are biased towards larger species (N. amplus, N. longicaudatus and N. robustus), and the discovery of N. magnus sp. nov. adds further to that list. Given the already high number of extinct and endangered species within Notomys, the discovery of another member that suffered geologically recent extinction has conservation implications for modern critical weight range mammals (including other species of rodents) that are particularly susceptible to extinction. Most historical extinctions of critical weight range mammals were in southern and central Australia, but the discovery of N. magnus sp. nov. suggests that species in the tropical north also were detrimentally affected.Vikram Vakil [vikram.vakil@uqconnect.edu.au], School of Earth and Environmental Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia;Jonathan Cramb [jonathan.cramb@qm.qld.gov.au], Queensland Museum, Brisbane, Australia;Gilbert J. Price [g.price1@uq.edu.au], School of Earth and Environmental Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia;Gregory E. Webb [g.webb@uq.edu.au], School of Earth and Environmental Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia;Julien Louys [j.louys@griffith.edu.au], Australian Research Centre for Human Evolution, Griffith University, Brisbane, Queensland 4101, Australia.

The World's Most Imperiled Raptors Present Substantial Conservation Challenges

ABSTRACT Potential extinction of raptor species is especially important given their outsized roles in ecosystems and human cultures. We examined Red List data for raptor species listed as critically endangered by the International Union for the Conservation of Nature. Our goal was to highlight the plight of these critically endangered raptor species while identifying the reasons for their imperiled status, the most important countries for their conservation, and the actions needed for their persistence. We categorized the 17 critically endangered raptor species into two groups—Accipitrid vultures and species with small populations. Accipitrid vultures had relatively large populations and ranges, and were listed under Criterion A due to precipitous population declines. The threat listed for the most Accipitrid vultures was “pollution,” reflecting poisoning as the principal cause of declines. Conversely, the small population species were listed under Criteria C and D and were most threatened by “agriculture and aquaculture.” Countries in Africa and south Asia were hotspots of critically endangered raptors. The conservation action listed for the most species was “education and awareness” followed by “land protection” and “law and policy.” The most-listed monitoring category was “population trends.” The Multi-species Action Plan to Conserve African-Eurasian Vultures should be implemented to prevent extinction of Accipitrid vultures. Conversely, species with small populations are generally isolated and must be managed individually. Conservation of the world's most imperiled raptor species is an important facet of assuaging the sixth mass extinction.

The ELIXIR Biodiversity Community: Understanding short- and long-term changes in biodiversity

Biodiversity loss is now recognised as one of the major challenges for humankind to address over the next few decades. Unless major actions are taken, the sixth mass extinction will lead to catastrophic effects on the Earth’s biosphere and human health and well-being. ELIXIR can help address the technical challenges of biodiversity science, through leveraging its suite of services and expertise to enable data management and analysis activities that enhance our understanding of life on Earth and facilitate biodiversity preservation and restoration. This white paper, prepared by the ELIXIR Biodiversity Community, summarises the current status and responses, and presents a set of plans, both technical and community-oriented, that should both enhance how ELIXIR Services are applied in the biodiversity field and how ELIXIR builds connections across the many other infrastructures active in this area. We discuss the areas of highest priority, how they can be implemented in cooperation with the ELIXIR Platforms, and their connections to existing ELIXIR Communities and international consortia. The article provides a preliminary blueprint for a Biodiversity Community in ELIXIR and is an appeal to identify and involve new stakeholders.

More losers than winners: investigating Anthropocene defaunation through the diversity of population trends.

The global-scale decline of animal biodiversity ('defaunation') represents one of the most alarming consequences of human impacts on the planet. The quantification of this extinction crisis has traditionally relied on the use of IUCN Red List conservation categories assigned to each assessed species. This approach reveals that a quarter of the world's animal species are currently threatened with extinction, and ~1% have been declared extinct. However, extinctions are preceded by progressive population declines through time that leave demographic 'footprints' that can alert us about the trajectories of species towards extinction. Therefore, an exclusive focus on IUCN conservation categories, without consideration of dynamic population trends, may underestimate the true extent of the processes of ongoing extinctions across nature. In fact, emerging evidence (e.g. the Living Planet Report), reveals a widespread tendency for sustained demographic declines (an average 69% decline in population abundances) of species globally. Yet, animal species are not only declining. Many species worldwide exhibit stable populations, while others are even thriving. Here, using population trend data for >71,000 animal species spanning all five groups of vertebrates (mammals, birds, reptiles, amphibians and fishes) and insects, we provide a comprehensive global-scale assessment of the diversity of population trends across species undergoing not only declines, but also population stability and increases. We show a widespread global erosion of species, with 48% undergoing declines, while 49% and 3% of species currently remain stable or are increasing, respectively. Geographically, we reveal an intriguing pattern similar to that of threatened species, whereby declines tend to concentrate around tropical regions, whereas stability and increases show a tendency to expand towards temperate climates. Importantly, we find that for species currently classed by the IUCN Red List as 'non-threatened', 33% are declining. Critically, in contrast with previous mass extinction events, our assessment shows that the Anthropocene extinction crisis is undergoing a rapid biodiversity imbalance, with levels of declines (a symptom of extinction) greatly exceeding levels of increases (a symptom of ecological expansion and potentially of evolution) for all groups. Our study contributes a further signal indicating that global biodiversity is entering a mass extinction, with ecosystem heterogeneity and functioning, biodiversity persistence, and human well-being under increasing threat.

Complex Organisms Must Deal with Complex Threats: How Does Amphibian Conservation Deal with Biphasic Life Cycles?

The unprecedented rate of global amphibian decline is attributed to The Anthropocene, with human actions triggering the Sixth Mass Extinction Event. Amphibians have suffered some of the most extreme declines, and their lack of response to conservation actions may reflect challenges faced by taxa that exhibit biphasic life histories. There is an urgent need to ensure that conservation measures are cost-effective and yield positive outcomes. Many conservation actions have failed to meet their intended goals of bolstering populations to ensure the persistence of species into the future. We suggest that past conservation efforts have not considered how different threats influence multiple life stages of amphibians, potentially leading to suboptimal outcomes for their conservation. Our review highlights the multitude of threats amphibians face at each life stage and the conservation actions used to mitigate these threats. We also draw attention to the paucity of studies that have employed multiple actions across more than one life stage. Conservation programs for biphasic amphibians, and the research that guides them, lack a multi-pronged approach to deal with multiple threats across the lifecycle. Conservation management programs must recognise the changing threat landscape for biphasic amphibians to reduce their notoriety as the most threatened vertebrate taxa globally.

A global analysis of avian island diversity-area relationships in the Anthropocene.

Research on island species-area relationships (ISAR) has expanded to incorporate functional (IFDAR) and phylogenetic (IPDAR) diversity. However, relative to the ISAR, we know little about IFDARs and IPDARs, and lack synthetic global analyses of variation in form of these three categories of island diversity-area relationship (IDAR). Here, we undertake the first comparative evaluation of IDARs at the global scale using 51 avian archipelagic data sets representing true and habitat islands. Using null models, we explore how richness-corrected functional and phylogenetic diversity scale with island area. We also provide the largest global assessment of the impacts of species introductions and extinctions on the IDAR. Results show that increasing richness with area is the primary driver of the (non-richness corrected) IPDAR and IFDAR for many data sets. However, for several archipelagos, richness-corrected functional and phylogenetic diversity changes linearly with island area, suggesting that the dominant community assembly processes shift along the island area gradient. We also find that archipelagos with the steepest ISARs exhibit the biggest differences in slope between IDARs, indicating increased functional and phylogenetic redundancy on larger islands in these archipelagos. In several cases introduced species seem to have 're-calibrated' the IDARs such that they resemble the historic period prior to recent extinctions.

Deforestation alters species interactions

AbstractInterspecific interactions are a major determinant of stability in ecological communities and are known to vary with biotic and abiotic conditions. Deforestation is the primary driver of the ongoing sixth mass extinction, yet its effect on species interactions remains largely unexplored. We investigate how deforestation affects species interactions using a complex systems model and a co‐occurrence dataset of 363 bird species, observed across 134 sites, from 5 regions across the Brazilian Atlantic Forest totalling 27,226 interactions. Both theoretical and empirical results show that interspecific interactions vary non‐monotonically with forest cover and are more positive than average in areas with higher forest cover, and to a lesser extent in highly deforested areas. Observed differences in interactions reflect both species turnover and changes in pairwise interactions. Our results point to changes in stability across the gradient of deforestation that may lead to varying community resilience to environmental perturbations.Key Interdisciplinary Aspects Species interactions are expected to vary due to the biological, chemical and physical changes caused by deforestation on their local environment. We use a mathematical complex systems approach, as well as ecological data, to show that species interactions are more positive in highly forested areas. We propose that the alteration of species interactions caused by deforestation will affect the stability of communities and their resilience to future perturbations (e.g. climate change).

An integrative approach to assess non‐native iguana presence on Saba and Montserrat: Are we losing all native Iguana populations in the Lesser Antilles?

AbstractInvasive alien species are among the main drivers of the ongoing sixth mass extinction wave, especially affecting island populations. Although the Caribbean is well‐known for its high species richness and endemism, also for reptiles, equally important is the regional contribution of non‐native species to island biodiversity. The Lesser Antilles encompass high genetic diversity in Iguana, though most native populations either have gone extinct or are declining following competitive hybridization with invasive non‐native green iguanas. Here, we assessed non‐native presence in two poorly‐studied native melanistic Iguana iguana populations using available genetic tools and explored utilizing size‐dependent body measurements to discriminate between native and non‐native iguanas. Genetic samples from Saba and Montserrat were genotyped across 17 microsatellite loci with STRUCTURE, and multivariate analyses indicating non‐native iguana presence only on Saba. This was corroborated by mtDNA and nDNA sequences, highlighting a non‐native origin in Central America and the ABC islands. We identified preliminary evidence suggestive of hybridization. Morphological variation among size‐dependent characteristics showed that non‐native iguanas have significantly larger subtympanic plates than native iguanas. Non‐native individuals also differed in scalation and coloration patterns. Overall, our findings demonstrate the need for continuous monitoring of non‐native iguanas within remaining native Iguana populations in the Lesser Antilles, as those not directly threatened by non‐native green iguanas are restricted to only 8.7% of the historic range. Although genetic data allow for the identification of non‐native or hybrid iguana presence, this field‐to‐lab workflow is time‐consuming. Rapid in‐situ identification of non‐native individuals is crucial for conservation management. In addition to patterns of scalation and coloration, we have highlighted the utility of size‐dependent variables for rapid diagnosis. We urge regional partners to build morphometric databases for native Iguana populations allowing the quick detection of future incursions of non‐native green iguanas and the rapid implementation of effective countermeasures during the early phase of invasion.

Genomes of two Extinct-in-the-Wild reptiles from Christmas Island reveal distinct evolutionary histories and conservation insights.

Genomics can play important roles in biodiversity conservation, especially for Extinct-in-the-Wild species where genetic factors greatly influence risk of total extinction and probability of successful reintroductions. The Christmas Island blue-tailed skink (Cryptoblepharus egeriae) and Lister's gecko (Lepidodactylus listeri) are two endemic reptile species that went extinct in the wild shortly after the introduction of a predatory snake. After a decade of management, captive populations have expanded from 66 skinks and 43 geckos to several thousand individuals; however, little is known about patterns of genetic variation in these species. Here, we use PacBio HiFi long-read and Hi-C sequencing to generate highly contiguous reference genomes for both reptiles, including the XY chromosome pair in the skink. We then analyse patterns of genetic diversity to infer ancient demography and more recent histories of inbreeding. We observe high genome-wide heterozygosity in the skink (0.007 heterozygous sites per base-pair) and gecko (0.005), consistent with large historical population sizes. However, nearly 10% of the blue-tailed skink reference genome falls within long (>1Mb) runs of homozygosity (ROH), resulting in homozygosity at all major histocompatibility complex (MHC) loci. In contrast, we detect a single ROH in Lister's gecko. We infer from the ROH lengths that related skinks may have established the captive populations. Despite a shared recent extinction in the wild, our results suggest important differences in these species' histories and implications for management. We show how reference genomes can contribute evolutionary and conservation insights, and we provide resources for future population-level and comparative genomic studies in reptiles.

“Dead as a Dodo”

Among the species that went extinct in the last 500 plus years under colonial regimes, the ill-fated dodo became an early icon of the Anthropocene Extinction. While much has been written on the biotechnological apparatuses that expedited the extinction of the dodo, it was the complicity of Western European imperialism and early modern aesthetic regimes that were responsible for the ecocide of the Anthropocene (read Eurocene) Extinction.

Homo Sapiens

Inspired by Elizabeth Kolbert’s The Sixth Extinction: An Unnatural History, the short play Homo Sapiens humorously explores whether Homo sapiens caused their own demise or managed to evolve into a new, more enlightened species.

Extinction in Public

AbstractThis essay argues that the concept of extinction, polysemous if not overdetermined, is becoming an emergent keyword of contemporary public life as it faces the climate crisis. To make this argument the essay critically considers the ways in which extinction is currently being made public—within and by the environmental humanities but also in the wider public sphere of political and cultural contestation. The essay begins by problematizing the concept of extinction itself, positing that it makes sense to think of the Sixth Extinction as the first historical extinction event—that is, as a social articulation of an organic process in which the causes and impacts are at once natural and social. Then the essay discusses the different extinction imaginaries that have operated across modernity, before finally turning to the writings of the Extinction Studies Working Group, whose conception of extinction as a process rather than event, and whose arguments that mass extinction presents an ethical call to responsibility, have become a template for how extinction is thought about within the field of the environmental humanities. The essay ends by posing some companionly criticisms of the extinction studies project.

Retraction: An Eocene army ant

Retraction: An Eocene army ant

How predictable are mass extinction events?

Many modern extinction drivers are shared with past mass extinction events, such as rapid climate warming, habitat loss, pollution and invasive species. This commonality presents a key question: can the extinction risk of species during past mass extinction events inform our predictions for a modern biodiversity crisis? To investigate if it is possible to establish which species were more likely to go extinct during mass extinctions, we applied a functional trait-based model of extinction risk using a machine learning algorithm to datasets of marine fossils for the end-Permian, end-Triassic and end-Cretaceous mass extinctions. Extinction selectivity was inferred across each individual mass extinction event, before testing whether the selectivity patterns obtained could be used to 'predict' the extinction selectivity exhibited during the other mass extinctions. Our analyses show that, despite some similarities in extinction selectivity patterns between ancient crises, the selectivity of mass extinction events is inconsistent, which leads to a poor predictive performance. This lack of predictability is attributed to evolution in marine ecosystems, particularly during the Mesozoic Marine Revolution, associated with shifts in community structure alongside coincident Earth system changes. Our results suggest that past extinctions are unlikely to be informative for predicting extinction risk during a projected mass extinction.

Pheromones for amphibian conservation – considering new approaches in conservation breeding programmes

Pheromones for amphibian conservation – considering new approaches in conservation breeding programmes