Biology subjects

Halpern, B.

Publications and source records attributed to Halpern, B..

6 recordsLinked to original sources

bioRxiv2024

Unveiling the evolutionary history of European vipers and their venoms from a multi-omic approach

Snake genomes attract significant attention from multiple disciplines, including medicine, drug bioprospection, and evolutionary biology, due to the unique features found in snakes, especially, the evolution of venom. However, genomic research within the family Viperidae has mostly focused to date on the subfamily Crotalinae, while overlooking Viperinae, the Old World vipers. Among Viperinae, European vipers (Vipera) have been the subject of extensive research because of their venoms, phylogeographic, and ecological diversification. Nevertheless, venom research in this group has been conducted using mostly proteomes alone, while phylogeography and systematics in the genus have relied on biased information from mitochondrial phylogenies. Here, we generated chromosome-level genome assemblies for three Vipera species and whole-genome sequencing data for 94 samples representing 15 Vipera taxa. This comprehensive dataset has enabled us to disentangle the phylogenomic relationships of this genus, affected by mito-nuclear discordance and pervaded by ancestral introgression. Population-level analyses in the Iberian Peninsula, where the three oldest lineages within Vipera meet, revealed signals of recent adaptive introgression between ecologically dissimilar species, whereas chromosomal rearrangements isolate species occupying similar niches. Finally, using transcriptomic and proteomic data, we characterized the Vipera toxin-encoding genes, in which opposing selective forces were unveiled as common drivers of the evolution of venom as an integrated phenotype.

genomics↗

bioRxiv2022

Hotspots for snake fungal disease across Europe are maintained by host and pathogen identity

1. Infectious diseases are influenced by interactions between host and pathogen, and are rarely homogenous across the landscape. Areas with elevated pathogen prevalence maintain a high force of infection, can facilitate pathogen spread to new regions, and may indicate areas with impacts on host populations. However, isolating the ecological processes that result in increases in infection prevalence and intensity remains a challenge. 2. Here we elucidate the contribution of pathogen clade and host species in disease hotspots of Ophidiomyces ophidiicola, the pathogen that causes snake fungal disease, in 21 species of snakes infected with multiple pathogen strains across 10 countries in Europe. 3. We found isolated areas of disease hotspots in a landscape where infections were otherwise low. O. ophidiicola clade had important effects on transmission, and areas with multiple pathogen clades had higher host infection prevalence. Snake species identity further influenced infection, with most positive detections coming from the Natrix genus. Most species present in the community only experienced increased levels of infection when multiple strains were present. However, one species, N. tessellata, appeared highly susceptible, having increased infection prevalence regardless of pathogen strain, indicating that this species may be important in pathogen maintenance. 4. Our results suggest that both host and pathogen identity are essential components contributing to increased pathogen prevalence. More broadly, our findings indicate that coevolutionary relationships between hosts and pathogens may be key mechanisms explaining variation in landscape patterns of disease.

ecology↗

bioRxiv2022

No branch left behind: tracking terrestrial biodiversity from a phylogenetic completeness perspective

Biodiversity, as we see it today, ultimately is the outcome of millions of years of evolution; however, biodiversity in its multiple dimensions is changing rapidly due to increasing human domination of Earth. Here, we present the "phylogenetic completeness" (PC) a concept and methodology that intends to safeguard Earths evolutionary heritage by maintaining all branches of the tree of life. We performed a global evaluation of the PC approach using data from five major terrestrial clades and compared the results to an approach in which species are conserved or lost randomly. We demonstrate that under PC, for a given number of species extinctions, it is possible to maximize the protection of evolutionary innovations in every clade. The PC approach is flexible and can be used to conduct a phylogenetic audit of biodiversity under different conservation scenarios. The PC approach complements existing conservation efforts and is linked to the post-2020 Convention of Biodiversity targets.

ecology↗

bioRxiv2021

Prioritizing Management for Cumulative Impacts

Determining where environmental management is best applied, either through regulating single sectors of human activities or across sectors, is complicated by interactions between human impacts and the environment. In this article, we show how an explicit representation of human-environment interactions can help, via "impact networks" including activities (e.g. shipping), stressors (e.g. ship strikes), species (e.g. humpback whales) or ecosystem services (e.g. marine recreation). Impact networks can enable the identification of "leverage nodes", which, if present, can direct managers to the activities and stressors crucial for reducing risk to important ecosystem components. Exploring an impact network for a coastal ecosystem in British Columbia, Canada, we seek to identify these leverage nodes using a new approach employing Bayesian Belief Networks of risks to ecosystems. In so doing, we address three key questions: (1) Do leverage nodes exist? (2) Do management plans for species correctly identify leverage nodes? (3) Does the management of leverage nodes for certain species realize benefits for other species and ecosystem services? We show that there are several leverage nodes across all species investigated, and show that preconceptions about the regulation of risk to species can misidentify leverage nodes, potentially leading to ineffective management. Notably, we show that managing fisheries does not reduce overall risk to herring whereas managing diverse cumulative impacts including nutrient runoff, oil spills, and marine debris can reduce risk to herring, additional species, and related ecosystem services. Thus, by targeting leverage nodes, managers can efficiently mitigate risks for whole communities, ecosystems, and ecosystem services.

ecology↗

bioRxiv2021

The global rarity of intact coastal regions

Management of the land-sea interface is considered essential for global conservation and sustainability objectives, as coastal regions maintain natural processes that support biodiversity and the livelihood of billions of people. However, assessments of coastal regions have focused on either strictly the terrestrial or marine realm, and as a consequence, we still have a poor understanding of the overall state of Earths coastal regions. Here, by integrating the terrestrial human footprint and marine cumulative human impact maps, we provide a global assessment of the anthropogenic pressures affecting coastal areas. Just 15.5% of coastal areas globally can be considered having low anthropogenic pressure, mostly found in Canada, Russia, and Greenland. Conversely, 47.9% of coastal regions are heavily impacted by humanity with most countries (84.1%) having >50% of their coastal regions degraded. Nearly half (43.3%) of protected areas across coastal regions are exposed to high human pressures. In order to meet global sustainability objectives, we identify those nations that must undertake greater actions to preserve and restore coastal regions so as to ensure global sustainable development objectives can be met.

ecology↗

bioRxiv2019

Mapping Cumulative Impacts to Coastal Ecosystem Services in British Columbia

Ecosystem services are impacted through restricting service supply, through limiting people from accessing services, and by affecting the quality of services. We map cumulative impacts to 8 different ecosystem services in coastal British Columbia using InVEST models, spatial data, and expert elicitation to quantify risk to each service from anthropogenic activities. We find that impact to service access and quality as well as impact to service supply results in greater severity of impact and a greater diversity of causal processes of impact than only considering impact to service supply. This suggests that limiting access to services and impacts to service quality may be important and understanding these kinds of impacts may complement our knowledge of impacts to biophysical systems that produce services. Some ecosystem services are at greater risk from climate stressors while others face greater risk from local activities. Prominent causal pathways of impact include limiting access and affecting quality. Mapping cumulative impacts to ecosystem services can yield rich insights, including highlighting areas of high impact and understanding causes of impact, and should be an essential management tool to help maintain the flow of services we benefit from.

ecology↗