Biology subjects

Chapman, C. A.

Publications and source records attributed to Chapman, C. A..

9 recordsLinked to original sources

bioRxiv2026

A data-driven redefinition of global biodiversity hotspots

The 36 global biodiversity hotspots harbor a disproportionate share of the worlds endemic species, making their conservation critical for planetary health. Traditionally hotspots were defined as ecoregions with [≥]1,500 endemic vascular plant species and >70% natural habitat loss; this relied heavily on expert judgment, with subjective assessments of endemism and habitat loss applied. Challenges in defining endemism, quantifying habitat loss, and the global unevenness in available vascular plant data have hindered hotspot identification over the past decades. Here, we built a global dataset of 150,487 rare vascular plants, identified from 88.1% of the worlds known vascular species, and recognize hotspots based on their richness using three complementary conservation targets and algorithms. We then quantified natural habitat loss and habitat fragmentation using high-resolution remote sensing data and assessed the diversity and distribution of terrestrial vertebrates within these newly identified hotspots. Our data-driven method recovered all the 36 established global biodiversity hotspots, revised 17, and identified 11 new hotspots spanning diverse ecosystems across six continents. These 47 hotspots cover 26.63% of global land area, yet contain 83.8% of rare vascular plants, 92.4% of mammals, 96.1% of birds, 87.8% of reptiles, and 95.0% of amphibians. Collectively, they encompass >89% of terrestrial vertebrates classified as IUCN threatened species. Only 10 hotspots have undergone [≥]70% habitat loss, and the lack of a consistent relationship with habitat fragmentation suggests that this criterion is not globally applicable. Effectively protecting [~]27% of Earths land could theoretically safeguard >89.8% of threatened terrestrial species and >67% of threatened terrestrial species hotspot area, assuming effective protection of the identified biodiversity hotspots. Targeted conservation efforts within these global biodiversity hotspots can meet the established biodiversity targets of the Kunming-Montreal Global Biodiversity Framework as well as post-2030 biodiversity targets. Most importantly, our framework enables conservation scientists to iteratively identify and update global biodiversity hotspots in step with growing global biodiversity data.

ecology↗

bioRxiv2026

Beyond dual hubs: Task and aging shape taxonomic and thematic semantic relationships in the human brain

Semantic knowledge about concepts and their relationships is central to human cognition. Taxonomic relationships link concepts belonging to the same category (e.g. dog and bear), while thematic relationships connect concepts co-occurring in the same events (e.g. dog and leash). The dual-hub theory proposes that taxonomic relations preferentially engage the anterior temporal lobe (ATL), whereas thematic relations preferentially involve the temporo-parietal cortex (TPC). However, it remains unclear whether taxonomic and thematic representations depend on the concurrent task and how they change with aging. The present fMRI study addressed these gaps by jointly investigating the effects of semantic relationship, task, and age on semantic processing. 41 young and 34 older adults performed taxonomic and thematic judgments on picture pairs that were taxonomically related, thematically related, or unrelated. Our results do not support the dual-hub theory: Both TPC and ATL preferentially responded to thematic over taxonomic relationships. Moreover, their activity was task-dependent. Semantic control regions flexibly responded to task-relevant semantic relations, while inhibiting task-irrelevant relations. Finally, aging was associated with a decline in domain-general and domain-specific semantic control, more bilateral ATL engagement, as well as behavioral and neural shifts from taxonomic towards thematic processing. Increased thematic activity was associated with higher accuracy but slower responses. These findings support accounts of age-related neural dedifferentiation and semanticization: Older adults require increased cognitive resources to maintain accuracy at a high level, but this comes at the cost of efficiency.

neuroscience↗

bioRxiv2025

Chronic benzodiazepine treatment triggers gephyrin scaffold destabilization and GABAAR subsynaptic reorganization

Benzodiazepines (BZDs) are important clinical drugs with anxiolytic, anticonvulsant, and sedative effects mediated by potentiation of inhibitory GABA type A receptors (GABAARs). Tolerance limits the clinical utility of BZDs, yet the mechanisms underlying tolerance after chronic exposure have not been thoroughly investigated. Here, we assessed the impact of chronic (7-day) treatment with the BZD diazepam (DZP) on the dynamic plasticity and subsynaptic organization of the gephyrin scaffold and {gamma}2 subunit-containing GABAARs in primary neurons. After functional confirmation of diminished BZD sensitivity, we provide the first super-resolution analysis of inhibitory nanoscale plasticity induced by chronic BZD exposure: gephyrin subsynaptic domains were smaller and the inhibitory postsynaptic area was overall diminished by DZP treatment, resulting in a condensation of synaptic {gamma}2-GABAARs into smaller subsynaptic areas. Using a novel fluorescence-based in situ proximity ligation assay and biochemical fractionation analysis, the mechanism for gephyrin downregulation was revealed to be dependent on phosphorylation and protease cleavage. Accordingly, DZP treatment impaired gephyrin synaptic stability, demonstrated by live-imaging photobleaching experiments. Despite the loss of BZD sensitivity and stable synaptic gephyrin, 7-day DZP treatment did not reduce the surface or total protein levels of BZD-sensitive {gamma}2-GABAARs, as shown in prior short-term BZD treatment studies. Instead, chronic DZP treatment induced an accumulation of {gamma}2-GABAARs in the extrasynaptic membrane. Surprisingly, {gamma}2-GABAAR interactions with gephyrin were also enriched extrasynaptically. An identified rise in extrasynaptically-localized gephyrin cleavage fragments may function to confine receptors away from the synapse, as supported by a decrease in extrasynaptic {gamma}2-GABAAR mobility. Altogether, we find that chronic BZD treatment triggers several subtle converging plasticity events at inhibitory synapses which effectively restrict the synaptic renewal of BZD-sensitive GABAARs via mechanisms distinct from those observed with short-term treatment.

neuroscience↗

bioRxiv2025

Elephants inhabiting two forested sites in western Uganda exhibit contrasting patterns of species identity, density, and history of hybridization

Elephant populations across much of Africa face severe rates of decline due to poaching and habitat loss. The recent decision by the International Union for the Conservation of Nature (IUCN) to separately list African forest (Loxodonta cyclotis) and savanna (L. africana) elephants on the IUCN Red List both highlights the different threats of extinction faced by these two species and emphasizes the need for genetic data to classify taxonomically undefined populations across the continent. This includes western Uganda - a region that harbors the largest known modern hybrid zone between the two species. We combined a new high-throughput amplicon sequencing (HTAS) approach with fecal DNA-based Capture Mark Recapture (CMR) analysis to infer the population sizes and species compositions of elephants living in two forests. We demonstrate that Kibale National Park hosts a relatively large elephant population (573 individuals, 95% CI: 410 to 916; 0.72 elephants/km2) composed primarily of hybrids (81.5%) and savanna elephants (17.7%), while Bwindi Impenetrable National Park hosts a smaller population (96 individuals, 95% CI: 64 to 145; 0.29 elephants/km2) composed of forest elephants (86.8%) and hybrids (13.2%). We then sequenced maternally inherited (mtDNA) and paternally inherited (AMELY) genetic markers and found that the two parks populations exhibit different patterns of sex-linked genetic variation. The contrasting patterns of species identity and genetic variation between these parks demonstrate different histories of hybridization and highlight the importance of site-specific monitoring where elephants are taxonomically undefined.

ecology↗

bioRxiv2025

Genomes reveal age and demographic consequence of ultrafast adaptive radiation

New species typically evolve over several million years1. However, rates of speciation and ecological diversification vary by orders of magnitude across the tree of life1-3, with the fastest shown by some adaptive radiations. Eight hundred endemic species of cichlid fishes emerged and formed entire food webs in Lake Victoria and nearby lakes in East Africa. According to Victorias paleolimnological history4, five hundred may have arisen within the past 16,700 years, but molecular phylogenies estimated a much older origin5-8. We reconstruct the age and demography of all Lake Victoria region radiations from whole genomes. We show that indeed, in Lake Victoria all trophic guilds diverged <16,700 years ago, corresponding to between 537 and nearly 30000 speciation events per species per million years, the fastest speciation rate in metazoans1,2. Cichlid radiations in lakes Edward, Albert and Kivu too began <20,000 years ago, an order of magnitude faster than previously thought. Evolutionary transitions between trophic levels led to divergence in effective population sizes as predicted by the trophic pyramid of numbers concept9 and replicated across three parallel food web radiations. Our results demonstrate that classical theory of trophic interactions in ecologically assembled food webs applies equally to food webs that assembled through rapid adaptive radiation.

evolutionary biology↗

bioRxiv2021

The role of the angular gyrus in semantic cognition - A synthesis of five functional neuroimaging studies

Semantic knowledge is central to human cognition. The angular gyrus (AG) is widely considered a key brain region for semantic cognition. However, the role of the AG in semantic processing is controversial. Key controversies concern response polarity (activation vs. deactivation) and its relation to task difficulty, lateralization (left vs. right AG), and functional-anatomical subdivision (PGa vs. PGp subregions). Here, we combined the fMRI data of five studies on semantic processing (n = 172) and analyzed the response profiles from the same anatomical regions-of-interest for left and right PGa and PGp. We found that the AG was consistently deactivated during non-semantic conditions, whereas response polarity during semantic conditions was inconsistent. However, the AG consistently showed relative response differences between semantic and non-semantic conditions, and between different semantic conditions. A combined analysis across all studies revealed that AG responses could be best explained by separable effects of task difficulty and semantic processing demand. Task difficulty effects were stronger in PGa than PGp, regardless of hemisphere. Semantic effects were stronger in left than right AG, regardless of subregion. These results suggest that the AG is engaged in both domain-general task-difficulty-related processes and domain-specific semantic processes. In semantic processing, we propose that left AG acts as a "multimodal convergence zone" that binds different semantic features associated with the same concept, enabling efficient access to task-relevant features.

neuroscience↗

bioRxiv2019

Genomic and transcriptomic evidence for descent from Plasmodium and loss of blood schizogony in Hepatocystis parasites from naturally infected red colobus monkeys

Hepatocystis is a genus of single-celled parasites infecting monkeys, bats and squirrels. Although thought to descend from malaria parasites (Plasmodium spp.), Hepatocystis spp. are thought not to undergo replication in the blood - the part of the Plasmodium life cycle which causes the symptoms of malaria. Furthermore, Hepatocystis is transmitted by midges, not mosquitoes. Comparative genomics of Hepatocystis and Plasmodium species therefore presents an opportunity to better understand some of the most important aspects of malaria parasite biology. We were able to generate a draft genome for Hepatocystis using DNA sequencing reads from the blood of a naturally infected red colobus monkey. We provide robust phylogenetic support for Hepatocystis as a sister group to Plasmodium parasites infecting rodents. We show transcriptomic support for a lack of replication in the blood and genomic support for a complete loss of a family of genes involved in red blood cell invasion. Our analyses highlight the rapid evolution of genes involved in parasite vector stages, revealing genes that may be critical for interactions between malaria parasites and mosquitoes.

genomics↗

bioRxiv2018

Divergent mesolimbic dopamine circuits support alcohol-seeking triggered by discrete cues and contexts

Discrete and contextual cues that predict alcohol trigger alcohol-seeking. However, the extent to which context influences alcohol-seeking triggered by discrete cues, and the neural mechanisms underlying these responses, are not well known. We show that, relative to a neutral context, a context associated with alcohol persistently elevated alcohol-seeking triggered by a discrete cue, and supported higher levels of priming-induced reinstatement. Alcohol-seeking triggered by a discrete cue in a neutral context was reduced by designer receptor-mediated inhibition of ventral tegmental area (VTA) dopamine neurons in TH::Cre rats. Inhibiting terminals of VTA dopamine neurons in the nucleus accumbens (NAc) core reduced alcohol-seeking triggered by a discrete cue, irrespective of context, whereas inhibiting VTA dopamine terminals in the NAc shell selectively reduced the elevation of alcohol-seeking triggered by a discrete cue in an alcohol context. This dissociation highlights unique roles for divergent mesolimbic dopamine circuits in alcohol-seeking driven by discrete and contextual environmental cues.

neuroscience↗

bioRxiv2018

Genome-wide patterns of gene expression in a wild primate indicate species-specific mechanisms associated with tolerance to natural simian immunodeficiency virus infection

Over 40 species of nonhuman primates host simian immunodeficiency viruses (SIVs). In natural hosts, infection is generally assumed to be nonpathogenic due to a long coevolutionary history between host and virus, although pathogenicity is difficult to study in wild nonhuman primates. We used whole-blood RNA-seq and SIV prevalence from 29 wild Ugandan red colobus (Piliocolobus tephrosceles) to assess the effects of SIV infection on host gene expression in wild, naturally SIV-infected primates. We found no evidence for chronic immune activation in infected individuals, suggesting that SIV is not immunocompromising in this species, in contrast to HIV in humans. Notably, an immunosuppressive gene, CD101, was upregulated in infected individuals. This gene has not been previously described in the context of nonpathogenic SIV infection. This expands the known variation associated with SIV infection in natural hosts, and may suggest a novel mechanism for tolerance of SIV infection in the Ugandan red colobus.

genomics↗