Extinction Research Articles

Spatial diversity and distribution of fern and lycophyte species in karst and non-karst landscapes towards conservation needs

Karst formations are distinguished by their high levels of species diversity and endemism, including ferns and lycophytes. However, the existing data on plant community composition in karst formations remains deficient. Addressing these knowledge gaps is imperative, given the current accelerated rates of species loss, to enhance efforts to conserve biodiversity in these habitats. This study documents and explains patterns of fern and lycophyte species diversity within karst landscapes (KL) and non-karst landscapes (NKL) in the Philippines. Our comprehensive analysis involved aggregating 19,529 occurrence points encompassing 1,024 fern and lycophyte species sourced from field expeditions, voucher records from local herbaria, and online databases. Indices for species richness, weighted endemism, and corrected weighted endemism were then computed across KL and NKL areas to describe spatial diversity and identify fern and lycophyte hotspot areas. Gap analyses were also performed to determine if established protected areas (PAs) were sufficient to cover the identified fern and lycophyte diversity hotspots. Principal Component Analysis (PCA) was conducted to determine potential ecological drivers of distribution between KL and NKL areas. The findings reveal that most fern and lycophyte species were recorded to occur in NKL areas, with 995 (97.16%) species identified, while 676 (66.02%) species were documented to occur in KLs, including 29 (2.83%) exclusive to karsts. Identified hotspots for NKL are within mountain ecosystems, which are already under existing legal protection. In contrast, KLs have five areas identified as congruent hotspots but considered gap areas due to their exclusion from current PA boundaries. Existing PAs thus provide less protection to karst habitats and their associated floras. PCA did not reveal any significant environmental predictors, suggesting separation of KL and NKL species distributions, possibly due to lack of high-resolution environment data available for karsts. To facilitate the conservation of fern and lycophyte species in karsts, we propose installing and expanding existing PA boundaries, along with conducting more focused surveys in karst regions to better understand their ecological dynamics.

Using phylogenetic data for island biogeography analyses: The DAISIEprep package.

Using phylogenetic data for island biogeography analyses: The DAISIEprep package.

Coevolution increases robustness to extinctions in mutualistic but not exploitative communities.

Coextinctions may exacerbate the current biodiversity crisis. Yet, we do not understand all the factors that shape the robustness of communities to the loss of species. Here we analyze how coevolution influences the robustness to secondary extinctions of mutualistic and exploitative communities. We find that coevolution increases robustness in mutualism but reduces it under exploitative interactions. These differences are due to coevolution altering the density of interactions in communities. Coevolution leads to densely connected mutualistic communities and sparsely connected exploitative communities. We find the magnitude of these effects depends on the strength of coevolution and the size of the community. The largest changes to the density of interactions and robustness of communities occur when coevolutionary selection is strong. Moreover, the changes to network robustness are greater for small mutualistic communities and large exploitative communities. Our results broaden our understanding of the suite of mechanisms affecting the resilience of ecological communities. These insights may inform efforts to reduce the risk of species loss in the face of global change.

Exceedance probability model for predicting the frequency of summer hot day patterns and temperature variability in Florida.

Exceedance probability model for predicting the frequency of summer hot day patterns and temperature variability in Florida.

Exploring the dynamics of Lotka-Volterra systems: Efficiency, extinction order, and predictive machine learning.

For years, a main focus of ecological research has been to better understand the complex dynamical interactions between species that comprise food webs. Using the connectance properties of a widely explored synthetic food web called the cascade model, we explore the behavior of dynamics on Lotka-Volterra ecological systems. We show how trophic efficiency, a staple assumption in mathematical ecology, affects species extinction. With clustering analysis, we show how straightforward inequalities of the summed values of birth, death, self-regulation, and interaction strengths provide insight into which food webs are more enduring or stable. Through these simplified summed values, we develop a random forest model and a neural network model, both of which are able to predict the number of extinctions that would occur without the need to simulate the dynamics. To conclude, we highlight the death rate as the variable that plays the dominant role in determining the order in which species go extinct.

The first detailed morphological treatment of a Cretaceous psocid and the character evolution of Trogiomorpha (Insecta: Psocodea).

The first detailed morphological treatment of a Cretaceous psocid and the character evolution of Trogiomorpha (Insecta: Psocodea).

The Impact of Microbiota on Neurological Disorders: Mechanisms and Therapeutic Implications

Interactions in the gut-brain crosstalk have led to the development of an entirely new concept: the "microbiota-gut-brain axis". Microbiota has gained considerable attention in relation to disorders of a more neurological nature, such as neurodevelopmental and neuropsychiatric illnesses like autism spectrum disorder, anxiety, and mood disorders. This review aims to summarize the recent trends and insights into the role and consequences of gut microbiota in brain health and pediatric neurological disorders. Dysbiosis may be associated with an increased risk of neurological diseases that lead to different disruptions and conditions, including mental health issues. During microbiota dysbiosis, neuropsychological stress hormones that usually affect oxytocin and GABA neurons are significantly reduced. Current studies report that anxiety, major depression, and cognitive dysfunction are closely associated with dysbiosis. In the last few years, a handful of clinical studies have emerged, illustrating the potential for a bidirectional relationship of gut-brain interactions in humans. Perhaps some of the most crucial clinical investigations demonstrating overlapping relationships with the human gut-brain axis come from human trials focusing on modulating the microbiota significantly and noting significant cognitive correlates. A new field is emerging such as gene-editing technology that could represent a potential tool to improve gut microbial characteristics. This approach could be particularly relevant for neurodevelopmental and neurodegenerative disorders and brain-gut axis diseases linked with loss of microbial species and/or high pathobiont load.

Animal Genetic Resources and Biodiversity in the North-Eastern State of Assam, India: An Overview

Assam is a rich repository of diverse livestock and poultry genetic resources, which form a vital component of global biodiversity. The region's indigenous livestock and poultry breeds are highly valued for their milk, meat, eggs, and adaptability. The unique genes and adaptive traits of these breeds hold immense potential for enhancing agricultural resilience, productivity, and sustainability in the face of future challenges. However, many native breeds are experiencing rapid genetic decline and dilution due to intensive production systems and the unregulated introduction of exotic germplasm. The conservation of animal biodiversity has become increasingly crucial in recent years as the rate of species extinction continues to accelerate. Numerous organizations have been instrumental in promoting development and conservation initiatives to protect livestock biodiversity. Assam is renowned for its rich diversity of indigenous livestock breeds. Among cattle, the region is home to the Lakhimi breed, while the unique Luit and Manah buffaloes add to its distinctiveness. In smaller hoofed animals, the Assam Hill goat is a notable native breed. The state also takes pride in its indigenous pig breeds, such as the Doom pig. Furthermore, Assam boasts hardy native poultry breeds like the Daothigir and Miri chickens, as well as the Pati duck, all well-adapted to local conditions. Additionally, the Manipuri horse, known for its cultural and historical significance, highlights the rich genetic diversity of Northeast, India. These valuable genetic resources highlight Assam’s significant role in conserving biodiversity and promoting sustainable livestock farming.

Respiratory challenges and oedema development in zebra finch embryos under reduced pore area.

Global warming is one of the primary drivers of habitat loss and population decline in numerous species, including birds, amphibians and marine life. Avian embryos exhibit ectothermic phenotypes during most of their incubation period and are also vulnerable to rising temperatures when parents cannot cool the nests. This vulnerability stems from their unique respiratory mechanisms, which utilize eggshell pores to exchange respiratory gases. The number of pores is fixed at oviposition, and embryos may experience hypoxia during later developmental stages, especially when exposed to elevated ambient/incubation temperatures. Our preliminary study on zebra finch (Taeniopygia guttata castanotis) embryos, where we covered 30% of the shell surface with beeswax and incubated at high (38.9°C) temperature, revealed that half of the individuals that failed to hatch had developed oedema in the hind neck region. This study shows that such physical anomalies occur during incubation prior to death. We found that embryos with oedema had a higher head-to-body ratio, independent of their relative brain mass. Furthermore, oedema formation was correlated with darker-coloured hearts, suggesting reduced blood oxygenation in these embryos. These results highlight the physiological challenges embryos face under suboptimal incubation conditions.This article is part of the theme issue 'The biology of the avian respiratory system'.

Amphibian skin bacteria contain a wide repertoire of genes linked to their antifungal capacities

Emerging diseases caused by fungi are a serious threat to wildlife biodiversity. The widespread fungal pathogen Batrachochytrium dendrobatidis (Bd) has caused dramatic amphibian population declines and species extinctions worldwide. While many amphibians have been negatively affected by Bd, some populations/species have persisted despite its presence. One factor contributing to amphibian protection against this fungus is the host-associated skin microbiome. In this study, we aimed to identify gene clusters associated with the antifungal activity of amphibian skin bacteria. Specifically, we explored skin bacteria isolated from species that have persisted in the wild despite the presence of Bd: the frogs Agalychnis callidryas, Craugastor fitzingeri, Dendropsophus ebraccatus, and the axolotl Ambystoma altamirani. Bacterial isolates were tested in vitro for their capacity to inhibit the growth of two fungal pathogens: Bd and the phytopathogen Botrytis cinerea (Bc). Genome mining of these bacterial isolates revealed a diverse repertoire of Biosynthetic Gene Clusters (BGCs) and chitin-degrading gene families (ChDGFs) whose composition and abundance differed among bacterial families. We found specific BGCs and ChDGFs that were associated with the capacity of bacteria to inhibit the growth of either Bd or Bc, suggesting that distinct fungi could be inhibited by different molecular mechanisms. By using similarity networks and machine learning, we identified BGCs encoding known antifungal compounds such as viscosin, fengycin, zwittermicin, as well as siderophores and a novel family of beta-lactones. Finally, we propose that the diversity of BGCs found in amphibian skin bacteria comprise a substantial genetic reservoir that could collectively explain the antifungal properties of the amphibian skin microbiome.

Youth arts pedagogy for climate justice: radical relationality and interspecies poiesis in a yet-to-be-known world

ABSTRACT In this climate-changed reality, where young people regularly experience devastating floods, extreme temperatures, and species extinctions, the Anthropocene child is called to act as the earth's and humanity's protector. This article seeks to understand how children and youth are reimagining hierarchical relationships between child-adult and human-nature binaries in climate-responsive projects and programs. We provide a contextual framing of youth activism and frustrations in realizing climate justice; describe four case studies from Australia, New Zealand, and the United States focused on radical relationality with stream, forest, fish, and birds; and analyze how these cases connect with the concepts of inventive agency, radical relationality and interspecies poiesis. We find that inventive agency not only disrupts harmful dichotomies but also invites open dialogue, develops action competencies, and builds on Indigenous principles of reciprocity and relationality. The fluidity of the process and in many ways the literal embodiment of river, forest, birds, and fish, enable interspecies poiesis, or the emergence of something new. While many framings of climate justice center on equity and action, the cases presented here convey how a distinctive interspecies poiesis serves to reconfigure emotions and reconstruct possibilities as relational visions for a yet-to-be-known world.

Dinosaurs as skeletons or lifelike replicas - effects on interest in extinct animals

Dinosaurs as skeletons or lifelike replicas - effects on interest in extinct animals

The Presence and Portrayal of Climate Change and Other Environmental Problems in Popular Films: A Quantitative Content Analysis

ABSTRACT How have popular films responded to – or avoided – the climate and nature crises? To begin to answer this question systematically, quantitative content analysis was applied to 250 of the most-rated fictional films on IMDb that were released between 2013 and 2022. We found that climate change existed in 12.8% of these films, while a global environmental problem (climate change, freshwater pollution, marine pollution, air pollution, deforestation, species extinction and biodiversity decline, or toxic waste) existed in 26%; the presence of climate change, as well as common climate impacts, increased substantially over time; when climate change and other environmental problems were present, they were generally mentioned in just one or two scenes, and their gravity and/or urgency was not emphasized. As the first systematic, large-scale analysis of the presence and portrayal of climate change and other environmental problems in fictional narratives in the academic literature, this article illustrates a potentially productive area of future research, which is discussed.

Is Brazil’s biodiversity offset policy effective in conserving the Cerrado?

Summary Brazilian landowners are obligated to conserve a minimum percentage of native vegetation within their properties (termed a ‘legal reserve’), but non-compliance can be compensated elsewhere through a biodiversity offset. Recent changes in rules for legal reserve compensation (LRC) have increased the allowed spatial scale and softened the ecological criteria required to select properties for compensation, potentially leading to considerable biodiversity losses. In this paper, we analyse whether these rules promote the conservation of tree species on private lands through LRC in the Cerrado biome, the most biodiverse savannah in the world. We modelled the potential distribution of 126 Cerrado tree species and simulated several potential biodiversity offsets to calculate expected species losses under former and current LRC rules. Our results show that biodiversity offsets established under current and former LRC rules can lead to up to 100% tree species losses. In contrast, setting a minimum similarity threshold between watersheds can reduce median tree species loss in biodiversity offsets to as low as 3% and prevents LRC with no common species between sites. Therefore, the current rule is expected to strongly impact biodiversity in the Cerrado. Similarity in species composition between watersheds must be considered in order to implement LRC offsets that effectively conserve Cerrado biodiversity on private lands.

Revising the late Cambrian time scale and the duration of the SPICE event using a novel Bayesian age modeling approach

We present a refined global Furongian (late Cambrian) time scale derived through the application of Bayesian age modeling, using an integrative assemblage of conditioning likelihoods (age constraints) including U-Pb zircon maximum depositional ages in the Steptoean positive isotopic carbon excursion (SPICE) reference section in Smithfield Canyon (Utah, USA) and nearby McPherson Canyon (Idaho, USA); Re-Os geochronology from the SPICE-bearing interval of the Andrarum-3 core (Scania, Sweden); and new high-precision chemical abrasion−isotope dilution−thermal ionization mass spectrometry U-Pb zircon tuff ages from Avalonian Wales. We embed these radioisotopic ages within a novel probabilistic treatment of biozones to establish temporal constraints on rock accumulation rates in the Great Basin (USA), the duration of the SPICE event, and Laurentian trilobite biozones correlated to the global Cambrian time scale. Results reveal a beginning of 494.5 (+0.7/−0.6) Ma and an end of 487.3 ± 0.08 Ma for the Furongian Epoch, representing a reduction of the traditional late Cambrian by ∼30% and an extension of the Ordovician by nearly half a million years. Furthermore, the SPICE is confined to a duration of 2.6 (+0.9/−0.8) m.y. Our new approach to integrating faunal succession into Bayesian age modeling can help to constrain rock accumulation rates and possible hiatuses in sections with limited radioisotopic ages. Additionally, it offers a robust calibration tool for further refining the numerical calibration of the geologic time scale, for testing hypotheses about the rates of trilobite evolution and extinction, for evaluating causes of the SPICE, and for constraining paleoclimatic conditions including atmospheric O2 levels.

Non-native species drive the global loss of freshwater fish beta-diversity

Freshwater ecosystems are facing mounting challenges. The widespread introduction of non-native species, for example, has resulted in the loss of native species and the substantial reconfiguration of diversity patterns across regions. Documenting such impacts remains critical for informing national-level biosecurity policies. Here, we explore changes in biogeographic patterns in freshwater fish diversity in response to the spread of non-native species, teasing apart the geographic (watersheds) and taxonomic (species) drivers of patterns at the global scale. We leveraged global databases of fish species occurrence to estimate the unique contributions of local watersheds and species (native and non-native origin) to beta-diversity for biogeographic domains. Beta-diversity metrics of watersheds and species at a domain scale can be interpreted as their importance for the uniqueness in freshwater fish composition. We report significant changes in freshwater fish beta-diversity in response to non-native species, with the largest impacts in the Ethiopian, Nearctic and Palearctic domains, even though non-natives decreased the contribution of watersheds to beta-diversity in all domains, particularly in watersheds with known impacts. Watersheds identified as most important for promoting beta-diversity were not evenly distributed across domains, were influenced by geographical isolation and their unique compositions were composed of many endemic and threatened species. Highest values of species contributions to enhancing beta-diversity were mainly observed for native and threatened species, although mean values of species contributions were higher for non-threatened species. Species from the most important watersheds had wide ecological tolerances, were, in general, natives, endemics and/or with IUCN threat status. Our findings underscore the widespread consequences of non-native species for shaping biogeographic patterns of freshwater fishes in the Anthropocene.

Around the World in 26 Million Years: Diversification and Biogeography of Pantropical Grass‐Yellow Eurema Butterflies (Pieridae: Coliadinae)

ABSTRACTAimGrass‐yellow butterflies (Eurema) are a group of pantropical Pieridae distributed throughout Asia, Australasia, Africa and the New World. However, little is known about their diversification, including the biogeographic mechanism(s) explaining their circumglobal distribution. We present the first densely sampled, time‐calibrated phylogeny and biogeographic reconstruction of grass‐yellows to confirm the monophyly of the genera, re‐evaluate their taxonomy and infer the biogeographic events contributing to their worldwide distribution.LocationGlobal tropics and subtropics.TaxonThe butterfly tribe Euremini (Pieridae: Coliadinae).MethodsWe analysed up to 391 genetic loci from 126 samples of 66 ingroup species. Divergence dating was accomplished in a Bayesian phylogenetic framework using secondary calibration points, and maximum likelihood models of various biogeographic models were fitted to the data using the R package BioGeoBEARS. We used the best fitting model to estimate relative dispersal events with biogeographical stochastic mapping. Finally, we estimated branch‐specific speciation and extinction rates to assess the diversification history of the group.ResultsDifferent phylogenomic analyses converged on similar topologies with robust support. Grass‐yellows emerged ca. 26 Mya in the New World, and a single extant lineage dispersed to Asia in the early Miocene, where they diversified and dispersed to Africa and Australasia. The fastest rates of diversification occurred in the Old World tropics during the late Miocene. Many of the grass‐yellow genera were either paraphyletic or polyphyletic as traditionally circumscribed. To maintain nomenclatural stability, we place all grass‐yellows in Eurema sensu lato and recognise two subgenera: Eurema (Abaeis) and Eurema (Eurema).Main ConclusionsGrass‐yellow butterflies originated in the Americas and attained their global distributional patterns via dispersal. The Indo‐Australian and Caribbean archipelagoes seem to have accelerated the diversification of the group, and movement in and out of these island regions was frequent. Although the traditional view of founder‐event speciation envisions migrants from large landmasses (‘mainland’) colonising smaller landmasses (‘islands’), we find that island to mainland dispersal and differentiation were equally or more common.

The systematic status and evolutionary significance of the robust tuco-tuco Ctenomys latidens from the Pleistocene of central Argentina

ABSTRACT We conduct a systematic review of the extinct robust species of Ctenomys from the Early-Middle Pleistocene of central Argentina to assess the systematic status of †Ctenomys latidens. Based on qualitative comparisons and geometric morphometric evidence, †Ctenomys latidens is identified as a well-supported species, clearly distinguishable from †Ctenomys magnus and †Ctenomys kraglievichi. We propose †Ctenomys intermedius Rusconi, 1931a, and †Ctenomys dasseni Rusconi, 1931a as junior synonyms of †C. latidens. Accordingly, †Ctenomys latidens is recorded in the late Ensenadan age (late Early to early Middle Pleistocene) of Buenos Aires Province in central Argentina. Additionally, we suggest upgrading †Ctenomys intermedius tandilensis Rusconi, 1931a, and †Ctenomys latidens orthognathus Rusconi, 1931a to full species status. Finally, we demonstrate that the name †Plateomys scindens cannot be applied to the Early Pliocene Octodontidae currently recognised as †Pseudoplataeomys formosus, as that taxon is a potential junior synonym of †Ctenomys latidens.

Compounded extraction: An examination of early agro-extractivism in the US Heartland

The concept of agro-extractivism was developed by scholars of Latin America to characterize socio-ecological processes of dispossession and the commodification of human and nonhuman nature by colonial and capitalist actors. Here, I use it to understand the process of white settlement in the US Heartland in the nineteenth century. With the state of Iowa as the case study, I analyze how the creation of the state's infrastructure, from railroads to education, was based on land expropriation through a variety of land grants in what I define as compounded extraction: a massive redistribution of wealth that used the land itself to bootstrap extractivist development activities. I use a variety of primary and secondary sources, from historical documents to census data, to illustrate how the land grants helped finance the changes in the landscape that accompanied the settlement process. I show that the structure of the land grants and their effects on agriculture put the state in the middle of global financialization processes, which were reinforced via feedback loops and boom-bust cycles, and predicated on export markets and tech fixes that create treadmill accelerationist effects to this day. I present evidence that these rapid and massive land use changes had multiple negative environmental effects, many of which were clear to scientists at the time, from soil erosion to species extinction. The infrastructure created via the land grants is still at the core of many environmental and socio-economic issues the state faces today, having become one of the planet's landscapes most modified by humans. I conclude that agro-extractivism in general and as manifested via compounded extraction is a compelling organizing concept in considering the past and present of settler agriculture in the Heartland and in other settings because it illuminates the complexity of dispossession and financialization processes.

The genomic consequences and persistence of sociality in spiders.

In cooperatively breeding social animals, a few individuals account for all reproduction. In some taxa, sociality is accompanied by a transition from outcrossing to inbreeding. In concert, these traits reduce effective population size, potentially rendering transitions to sociality 'evolutionarily dead-ends'. We addressed this hypothesis in a comparative genomic study in spiders, where sociality has evolved independently at least 23 times, but social branches are recent and short. We present genomic evidence for the evolutionary dead-end hypothesis in a spider genus with three independent transitions to sociality. We assembled and annotated high-quality, chromosome-level reference genomes from three pairs of closely related social and subsocial Stegodyphus species. We timed the divergence between the social and subsocial species pairs to be from 1.3 to 1.8 million years. Social evolution in spiders involves a shift from outcrossing to inbreeding and from equal to female-biased sex ratio, causing severe reductions in effective population size and decreased efficacy of selection. We show that transitions to sociality only had full effect on purifying selection at 119, 260 and 279 kya respectively, and follow similar convergent trajectories of progressive loss of diversity and shifts to an increasingly female-biased sex ratio. This almost deterministic genomic response to sociality may explain why social spider species do not persist. What causes species extinction is not clear, but could be either selfish meiotic drive eliminating the production of males, or an inability to retain genome integrity in the face of extremely reduced efficacy of selection.