Multinational evaluation of genetic diversity indicators for the Kunming‐Montreal Global Biodiversity Framework

Ecology Letters, Journal Year: 2024, Volume and Issue: 27(7)

Published: July 1, 2024

Abstract Under the recently adopted Kunming‐Montreal Global Biodiversity Framework, 196 Parties committed to reporting status of genetic diversity for all species. To facilitate reporting, three indicators were developed, two which focus on processes contributing conservation: maintaining genetically distinct populations and ensuring are large enough maintain diversity. The major advantage these is that they can be estimated with or without DNA‐based data. However, demonstrating their feasibility requires addressing methodological challenges using data gathered from diverse sources, across taxonomic groups, countries varying socio‐economic biodiversity levels. Here, we assess 919 taxa, representing 5271 nine countries, including megadiverse developing economies. Eighty‐three percent taxa assessed had available calculate at least one indicator. Our results show although majority species most populations, 58% have too small Moreover, indicator values suggest IUCN Red List other initiatives fail status, highlighting critical importance indicators.

Language: Английский

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Redlisting genetics: towards inclusion of genetic data in IUCN Red List assessments

Conservation Genetics, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 10, 2025

Abstract Genetic diversity is critical for adaptation in response to changing environments and provides a valuable metric predicting species’ extinction risk. The International Union Conservation of Nature (IUCN) broader scientific community have acknowledged that genetic component biodiversity conservation. However, there remain gaps the incorporation or application data risk assessments. Here, we describe how metrics can inform species Specifically, focus on information gained from metrics, temporal reporting changes complement existing IUCN Red List Threatened Species criteria. We conclude by advocating standardized sequence calculated facilitate use threat assessments List-assessed species. This perspective highlights need for, step towards, integration into expect our recommendations will ongoing work Survival Commission’s Genetics Specialist Group protect globally.

Language: Английский

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Large-scale genome sequencing of giant pandas improves the understanding of population structure and future conservation initiatives

Proceedings of the National Academy of Sciences, Journal Year: 2024, Volume and Issue: 121(36)

Published: Aug. 26, 2024

The extinction risk of the giant panda has been demoted from “endangered” to “vulnerable” on International Union for Conservation Nature Red List, but its habitat is more fragmented than ever before, resulting in 33 isolated populations according fourth national survey released by Chinese government. Further comprehensive investigations genetic background and in-depth assessments conservation status wild are still necessary urgently needed. Here, we sequenced genomes 612 pandas with an average depth ~26× generated a high-resolution map genomic variation 20 million variants covering individuals six mountain ranges captive representatives China. We identified distinct clusters within Minshan population performing fine-grained structure. estimation inbreeding load associated historical dynamics suggested that future efforts should pay special attention Qinling Liangshan populations. Releasing similar recipient appears be advantageous rescue strategy recovering populations, as this approach introduces fewer deleterious mutations into mating differentiated lineages. These findings emphasize superiority large-scale genomics provide precise guidelines panda.

Language: Английский

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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

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Detection of antimicrobial resistance via state-of-the-art technologies versus conventional methods

Frontiers in Microbiology, Journal Year: 2025, Volume and Issue: 16

Published: Feb. 25, 2025

Antimicrobial resistance (AMR) is recognized as one of the foremost global health challenges, complicating treatment infectious diseases and contributing to increased morbidity mortality rates. Traditionally, microbiological culture susceptibility testing methods, such disk diffusion minimum inhibitory concentration (MIC) assays, have been employed identify AMR bacteria. However, these conventional techniques are often labor intensive time consuming lack requisite sensitivity for early detection resistance. Recent advancements in molecular genomic technologies-such next-generation sequencing (NGS), matrix-assisted laser desorption ionization-time flight mass spectrometry (MALDI-TOF MS), lateral flow immunoassays (LFIAs), PCR-based diagnostic CRISPR-based diagnostics-have revolutionized diagnosis AMR. These innovative approaches provide sensitivity, reduced turnaround times, ability genetic mechanisms. This review seeks examine advantages disadvantages both emerging technologies traditional methods detecting AMR, emphasizing potential benefits limitations inherent each. By understanding strengths technologies, stakeholders, including researchers, healthcare professionals, regulatory agencies, authorities, financial managers, patients, can make informed decisions aimed at preventing emergence dissemination antibiotic-resistant strains, thereby ultimately increasing patient safety.

Language: Английский

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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

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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

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Can genetic rescue help save Arabia's last big cat?

Evolutionary Applications, Journal Year: 2024, Volume and Issue: 17(5)

Published: May 1, 2024

Abstract Genetic diversity underpins evolutionary potential that is essential for the long‐term viability of wildlife populations. Captive populations harbor genetic potentially lost in wild, which could be valuable release programs and rescue. The Critically Endangered Arabian leopard ( Panthera pardus nimr ) has disappeared from most its former range across Peninsula, with fewer than 120 individuals left an additional 64 leopards captivity. We (i) examine wild captive to identify global patterns structure; (ii) estimate size remaining population Dhofar mountains Oman using spatially explicit capture–recapture models on DNA camera trap data, (iii) explore impact rescue three complementary computer modeling approaches. estimated a 51 (95% CI 32–79) found 8 out 25 microsatellite alleles present eight loci were undetected wild. This includes two only founders known have been wild‐sourced Yemen, suggests this represents important source then assessed benefits reintroducing novel into as well risks elevating load through captive‐bred individuals. Simulations indicate can improve by reducing realized load. model also partly purged population, making it However, greater loss exacerbate genomic erosion during program, these should carefully evaluated. An next step recovery empirically validate conclusions, implement monitor genomics‐informed management plan, optimize strategy tool recover Arabia's last big cat.

Language: Английский

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AI-informed conservation genomics

Heredity, Journal Year: 2023, Volume and Issue: 132(1), P. 1 - 4

Published: Dec. 27, 2023

Genomic data and Artificial Intelligence (AI) models will start to play an increasingly important role in conservation biology.In a recent study, Wilder et al. (2023) analysed genomic from 240 mammal species predict their extinction risk categories the Red List of International Union for Conservation Nature (IUCN).The study processed with machine learning model, thereby demonstrating value these biodiversity.Wilder ( 2023) thus show how reference genomes-and thus, more broadly -could be used initial, cost-effective assessments, accelerating progress made List.

Language: Английский

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Climate, population size, and dispersal influences mutational load across the landscape inVitis arizonica

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Aug. 23, 2024

ABSTRACT The interplay between genetics and the environment determines a population’s ability to survive. Plants, being immobile, are particularly vulnerable environmental shifts must adapt their local or face extinction. While considerable efforts have been devoted identifying adaptive genetic variation model its relationship with climate, role of deleterious has largely overlooked. To address this gap, we studied landscape genomics Vitis arizonica , grape species endemic American Southwest crop wild relative domesticated grapevine. We estimated mutational load, component in 162 individuals sampled across present range built temporal distribution models (SDMs) project historical, present, future distributions V. infer species’ dynamics. Mutational load was highest for at an inferred leading edge expansion. Using random forest regression (RF) models, examined climatic variation. RF which transformed by weighting method account correlated predictors, identified variables, historical dispersion distances, heterozygosity as high-ranking features. Our findings show that can be predicted identifies features contribute load. These results provide foundation integrating into broader understand adaptation maladaptation climate change. SIGNIFICANCE STATEMENT accumulation (i.e., load) genome reduce organismal fitness hinder conditions. mechanisms contributing well-studied, interaction is less understood. Here explored variation, range, native Southwest. associations machine learning predict under scenarios. suggest will expand slightly increase population level end century. This work enhances our understanding factors influencing

Language: Английский

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