The contribution of historical processes to contemporary extinction risk in placental mammals

Science, Journal Year: 2023, Volume and Issue: 380(6643)

Published: April 27, 2023

Species persistence can be influenced by the amount, type, and distribution of diversity across genome, suggesting a potential relationship between historical demography resilience. In this study, we surveyed genetic variation single genomes 240 mammals that compose Zoonomia alignment to evaluate how effective population size (

Language: Английский

---

The impact of habitat loss and population fragmentation on genomic erosion

Conservation Genetics, Journal Year: 2023, Volume and Issue: 25(1), P. 49 - 57

Published: Aug. 8, 2023

Abstract Habitat loss and population fragmentation pose severe threats to biodiversity the survival of many species. Population isolation decline in effective size lead increased genetic drift inbreeding. In turn, this reduces neutral diversity, it also affects load deleterious mutations. Here, we analyse effect such genomic erosion by designing a spatially explicit, individual based model SLiM, simulating effects recorded habitat Mauritius over past ~ 250 years. We show that diversity (genome-wide heterozygosity) was barely noticeable during first 100 years loss. Changes took even more time register, they only became apparent circa 200 after start decline. Although considerable number mutations were lost drift, others frequency. The masked thus converted into realised load, which compromised fitness viability much native had been lost. Importantly, continued metapopulation stabilised at low numbers. Our study shows historic can sustained threat populations future generations, without further UN’s Decade on Ecosystem Restoration needs transformative change save species from extinction, requires urgent restoration natural habitats.

Language: Английский

---

Real‐time genomics for One Health

Molecular Systems Biology, Journal Year: 2023, Volume and Issue: 19(8)

Published: June 16, 2023

The ongoing degradation of natural systems and other environmental changes has put our society at a crossroad with respect to future relationship planet. While the concept One Health describes how human health is inextricably linked health, many these complex interdependencies are still not well-understood. Here, we describe advent real-time genomic analyses can benefit it enable timely, in-depth ecosystem assessments. We introduce nanopore sequencing as only disruptive technology that currently allows for already being used worldwide improve accessibility versatility sequencing. showcase studies on zoonotic disease, food security, microbiome, emerging pathogens, their antimicrobial resistances, itself - from resource creation wildlife conservation monitoring biodiversity, invasive species, trafficking. stress why equitable access genomics in context will be paramount discuss related practical, legal, ethical limitations.

Language: Английский

---

High genetic load without purging in caribou, a diverse species at risk

Current Biology, Journal Year: 2024, Volume and Issue: 34(6), P. 1234 - 1246.e7

Published: Feb. 27, 2024

High intra-specific genetic diversity is associated with adaptive potential, which key for resilience to global change. However, high variation may also support deleterious alleles through load, thereby increasing the risk of inbreeding depression if population sizes decrease. Purging has been demonstrated in some threatened species. less known about costs declines and species large even though this encompasses many globally that are expected undergo declines. Caribou a ecological cultural significance North America wide distribution supporting extensive phenotypic but populations undergoing significant resulting their at-risk status Canada. We assessed variation, divergence, inbreeding, load across different demographic histories using an annotated chromosome-scale reference genome 66 whole-genome sequences. found nine phylogenomic lineages continent diversification genes, among lineages. highly divergent levels individuals, including loss by drift not increased purging inbred had more homozygous alleles. comparable frequencies between regardless nucleotide diversity. Thus, further need be mitigated conservation efforts. Our results highlight "double-edged sword" representative other atrisk affected anthropogenic activities.

Language: Английский

---

Genomic Diversity as a Key Conservation Criterion: Proof‐of‐Concept From Mammalian Whole‐Genome Resequencing Data

Evolutionary Applications, Journal Year: 2024, Volume and Issue: 17(9)

Published: Sept. 1, 2024

ABSTRACT Many international, national, state, and local organizations prioritize the ranking of threatened endangered species to help direct conservation efforts. For example, International Union for Conservation Nature (IUCN) assesses Green Status publishes influential Red List species. Unfortunately, such yardsticks do not explicitly consider genetic or genomic diversity (GD), even though GD is positively associated with contemporary evolutionary fitness, individual viability, future potential. To test whether populations genome sequences could improve assessments, we estimated metrics from 82 publicly available mammalian datasets examined their statistical association attributes related conservation. We also considered intrinsic biological factors, including trophic level body mass, that impact quantified relative influences. Our results identify key population are both reflective predictive IUCN categories. Specifically, our analyses revealed Watterson's theta (the mutation rate) autozygosity (a product inbreeding) current categorization, likely because demographic declines lead “listing” decisions reduce levels standing variation. argue by virtue this relationship, like leverage emerging sequence data categorize threat rankings (especially in otherwise data‐deficient species) and/or enhance assessments establish a baseline monitoring. Thus, paper (1) outlines theoretical empirical justification new GD‐based assessment criterion, (2) provides bioinformatic pipeline estimating data, (3) suggests an analytical framework can be used measure while providing quantitative context consideration authorities.

Language: Английский

---

Genetic load and viability of a future restored northern white rhino population

Evolutionary Applications, Journal Year: 2024, Volume and Issue: 17(4)

Published: April 1, 2024

Abstract As biodiversity loss outpaces recovery, conservationists are increasingly turning to novel tools for preventing extinction, including cloning and in vitro gametogenesis of biobanked cells. However, restoration populations can be hindered by low genetic diversity deleterious load. The persistence the northern white rhino ( Ceratotherium simum cottoni ) now depends on cryopreserved cells 12 individuals. These banked genomes have higher than southern rhinos C. s. ), a sister subspecies that successfully recovered from severe bottleneck, but potential impact load is unknown. We estimated how demographic history has shaped genome‐wide nine 13 rhinos. bottleneck left with more fixed homozygous alleles longer runs homozygosity, whereas retained masked heterozygosity. To gauge fitness population restored cells, we simulated recovery using as benchmark viable population. Unlike traditional restoration, cell‐derived founders reintroduced subsequent generations boost lost relieve inbreeding. In simulations repeated reintroduction into population, cost remained lower borne Without reintroductions, rapid growth (>20–30% per generation) would needed maintain comparable fitness. Our results suggest inbreeding depression not necessarily barrier demonstrate relieves some constraints conventional limited founder pool. Established conservation methods protect healthy will remain paramount, emerging technologies hold promise bolster these combat extinction crisis.

Language: Английский

---

Time-lagged genomic erosion and future environmental risks in a bird on the brink of extinction

Proceedings of the Royal Society B Biological Sciences, Journal Year: 2025, Volume and Issue: 292(2043)

Published: March 1, 2025

Global biodiversity is rapidly declining due to habitat degradation and genomic erosion, highlighting the urgent need monitor endangered species their genetic health. Temporal genomics ecological modelling offer finer resolution than single-time-point measurements, providing a comprehensive view of species’ recent future trajectories. We investigated erosion environmental suitability in critically regent honeyeater ( Anthochaera phrygia ) by sequencing whole genomes historical modern specimens building multi-temporal distribution models (SDMs) across last century. The has declined from hundreds thousands individuals fewer 300 over past 100 years. SDMs correctly predicted known patterns local extinction southeast Australia. Our demographic reconstructions revealed gradual population decline 2000 2500 years ago, sharply accelerating 500 climate variability loss. Despite this substantial collapse, lost only 9% its diversity, with no evidence inbreeding or connectivity Also, it exhibits higher diversity many other threatened bird species. Forward-in-time simulations indicate that time lag between loss conceals risk ongoing into degrading suitability. work underscores for targeted conservation efforts continuous monitoring prevent extinction.

Language: Английский

---

Temporal Loss of Genome‐Wide and Immunogenetic Diversity in a Near‐Extinct Parrot

Molecular Ecology, Journal Year: 2025, Volume and Issue: unknown

Published: March 25, 2025

Loss of genetic diversity threatens a species' adaptive potential and long-term resilience. Predicted to be extinct by 2038, the orange-bellied parrot (Neophema chrysogaster) is critically endangered migratory bird threatened numerous viral, bacterial fungal diseases. The species has undergone multiple population crashes, reaching low three wild-born females 13 males in 2016, now represented only single wild individuals captive breeding program. Here we used our high-quality long-read reference genome, contemporary (N = 19) historical 16) resequenced genomes from as early 1829, track genomic erosion immunogenetic decline this species. 62% was lost between (mean autosomal heterozygosity 0.00149 ± 0.000699 SD) (0.00057 0.000026) parrots. A greater number length runs homozygosity samples were also observed. temporal reduction alleles at Toll-like receptor genes found (historical average 5.78 2.73; 3.89 2.10), potentially exacerbating disease susceptibility population. Of particular concern new threat avian influenza strain (HPAI) Australia. We discuss conservation implications findings propose that hybridisation synthetic biology may required address catastrophic loss occurred order prevent extinction.

Language: Английский

---

When birds of a feather flock together: Severe genomic erosion and the implications for genetic rescue in an endangered island passerine

Evolutionary Applications, Journal Year: 2024, Volume and Issue: 17(7)

Published: June 28, 2024

Abstract The Seychelles magpie‐robin's (SMR) five island populations exhibit some of the lowest recorded levels genetic diversity among endangered birds, and high inbreeding. These collapsed during 20th century, species was listed as Critically Endangered in IUCN Red List 1994. An assisted translocation‐for‐recovery program initiated 1990s increased number mature individuals, resulting its downlisting to 2005. Here, we explore temporal genomic erosion SMR based on a dataset 201 re‐sequenced whole genomes that span past ~150 years. Our sample set includes individuals predate bottleneck by up 100 years, well from contemporary established recovery program. Despite SMR's recent demographic recovery, our data reveal marked increase both load realized extant when compared historical samples. Conservation management may have reduced intensity selection increasing juvenile survival relaxing intraspecific competition between accumulation loss‐of‐function mutations (i.e. severely deleterious variants) rapidly recovering population. In addition, found 3‐fold decrease While low modern limit species' adaptability future environmental changes, conservation efforts (including assessments) also need assess threats posed their load. computer simulations highlight value translocations for rescue show how this could halt threatened such SMR.

Language: Английский

---

Range-wide and temporal genomic analyses reveal the consequences of near-extinction in Swedish moose

Communications Biology, Journal Year: 2023, Volume and Issue: 6(1)

Published: Oct. 17, 2023

Ungulate species have experienced severe declines over the past centuries through overharvesting and habitat loss. Even if many game recovered thanks to strict hunting regulation, genome-wide impacts of are still unclear. Here, we examine temporal geographical differences in diversity moose (Alces alces) its whole range Sweden by sequencing 87 modern historical genomes. We found limited impact 1900s near-extinction event but local variation inbreeding load populations, as well suggestion a risk future reduction genetic gene flow. Furthermore, candidate genes for adaptation, rapid allele frequency shifts involving coding since 1980s, possibly due selective harvesting. Our results highlight that genomic changes potentially impacting fitness can occur short time scales underline need track both deleterious selectively advantageous variation.

Language: Английский

---