How genomics can help biodiversity conservation

Trends in Genetics, Journal Year: 2023, Volume and Issue: 39(7), P. 545 - 559

Published: Feb. 16, 2023

The availability of public genomic resources can greatly assist biodiversity assessment, conservation, and restoration efforts by providing evidence for scientifically informed management decisions. Here we survey the main approaches applications in conservation genomics, considering practical factors, such as cost, time, prerequisite skills, current shortcomings applications. Most perform best combination with reference genomes from target species or closely related species. We review case studies to illustrate how facilitate research across tree life. conclude that time is ripe view fundamental integrate their use a practice genomics.

Language: Английский

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Conservation genetics as a management tool: The five best-supported paradigms to assist the management of threatened species

Proceedings of the National Academy of Sciences, Journal Year: 2021, Volume and Issue: 119(1)

Published: Dec. 20, 2021

About 50 y ago, Crow and Kimura [ An Introduction to Population Genetics Theory (1970)] Ohta Genet. Res. 22, 201–204 (1973)] laid the foundations of conservation genetics by predicting relationship between population size genetic marker diversity. This work sparked an enormous research effort investigating importance dynamics, in particular small size, for mean performance, viability, evolutionary potential. In light a recent perspective [J. C. Teixeira, D. Huber, Proc. Natl. Acad. Sci. U.S.A. 118, 10 (2021)] that challenges some fundamental assumptions genetics, it is timely summarize what field has achieved, robust patterns have emerged, worthwhile future directions. We consider theory methodological breakthroughs helped management, we outline applied genetics.

Language: Английский

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Global genetic diversity status and trends: towards a suite of Essential Biodiversity Variables (EBVs) for genetic composition

Biological reviews/Biological reviews of the Cambridge Philosophical Society, Journal Year: 2022, Volume and Issue: 97(4), P. 1511 - 1538

Published: April 12, 2022

Biodiversity underlies ecosystem resilience, function, sustainable economies, and human well-being. Understanding how biodiversity sustains ecosystems under anthropogenic stressors global environmental change will require new ways of deriving applying data. A major challenge is that data knowledge are scattered, biased, collected with numerous methods, stored in inconsistent ways. The Group on Earth Observations Observation Network (GEO BON) has developed the Essential Variables (EBVs) as fundamental metrics to help aggregate, harmonize, interpret observation from diverse sources. Mapping analyzing EBVs can evaluate aspects distributed geographically they over time. also intended serve inputs validation forecast status trends biodiversity, support policy decision making. Here, we assess feasibility implementing Genetic Composition (Genetic EBVs), which within-species genetic variation. We review bring together areas field genetics each contributes regional monitoring respect theory, sampling logistics, metadata, archiving, aggregation, modeling, technological advances. propose four EBVs: (i) Diversity; (ii) Differentiation; (iii) Inbreeding; (iv) Effective Population Size (Ne ). rank according their relevance, sensitivity change, generalizability, scalability, availability. outline workflow for generating underlying EBVs, advances needs archiving composition metadata. discuss be operationalized by visualizing space time across species forecasting beyond current observations using various modeling approaches. Our then explores challenges standardization, costs operationalizing well future directions opportunities maximize uptake globally research policy. collection, annotation, availability made past decade, practical standardized framework large-scale reporting. Rapid DNA sequencing technology present opportunities, but regionally globally. With these advances, starting integrated into conservation policy, foundation all species' long-term persistence face change. conclude a summary concrete steps researchers makers advancing operationalization EBVs. technical analytical foundations developed, practitioners should anticipate increasing application efforts emerge scale up

Language: Английский

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dartR v2: An accessible genetic analysis platform for conservation, ecology and agriculture

Methods in Ecology and Evolution, Journal Year: 2022, Volume and Issue: 13(10), P. 2150 - 2158

Published: June 11, 2022

Abstract Innumerable approaches to analyse genetic data are now available guide conservation, ecological and agricultural projects. However, streamlined accessible tools needed bring these within the reach of a broader user base. dartR was released in 2018 lessen intrinsic complexity analysing single nucleotide polymorphisms (SNPs) dominant markers (presence/absence amplified sequence tags) by providing user‐friendly quality control marker selection functions. users have grown steadily since its release provided valuable feedback on their interaction with package allowing us enhance capabilities. Here, we present Version 2 . In this version, substantially increased number functions from 45 144. addition improved functionality, focused enhancing experience extending plot customisation, function standardisation, increasing support speed. provides for various stages data, manipulation reporting. many importing, exporting linking other packages, provide an easy‐to‐navigate conduit between generation analysis options already via packages. We also implemented simulation whose results can be analysed seamlessly several As more methods mature inform envision that platforms will play crucial role translating science into practice.

Language: Английский

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Conservation and the Genomics of Populations

Oxford University Press eBooks, Journal Year: 2022, Volume and Issue: unknown

Published: Feb. 10, 2022

Abstract Loss of biodiversity is among the greatest problems facing world today. Conservation and Genomics Populations gives a comprehensive overview essential background, concepts, tools needed to understand how genetic information can be used conserve species threatened with extinction, manage ecological or commercial importance. New molecular techniques, statistical methods, computer programs, principles, methods are becoming increasingly useful in conservation biological diversity. Using balance data theory, coupled basic applied research examples, this book examines phenotypic variation natural populations, principles mechanisms evolutionary change, interpretation from these conservation. The includes examples plants, animals, microbes wild captive populations. This third edition has been thoroughly revised include advances genomics contains new chapters on population genomics, monitoring, genetics practice, as well sections climate emerging diseases, metagenomics, more. More than one-third references were published after previous edition. Each 24 Appendix end Guest Box written by an expert who provides example presented chapter their own work. for advanced undergraduate graduate students genetics, resource management, biology, professional biologists policy-makers working wildlife habitat management agencies. Much will also interest nonprofessionals curious about role

Language: Английский

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Bat responses to climate change: a systematic review

Biological reviews/Biological reviews of the Cambridge Philosophical Society, Journal Year: 2022, Volume and Issue: 98(1), P. 19 - 33

Published: Aug. 21, 2022

Understanding how species respond to climate change is key informing vulnerability assessments and designing effective conservation strategies, yet research efforts on wildlife responses fail deliver a representative overview due inherent biases. Bats are species-rich, globally distributed group of organisms that thought be particularly sensitive the effects because their high surface-to-volume ratios low reproductive rates. We systematically reviewed literature bat provide an current state knowledge, identify gaps biases highlight future needs. found studies geographically biased towards Europe, North America Australia, temperate Mediterranean biomes, thus missing substantial proportion diversity thermal responses. Less than half published concrete evidence for change. For over third studied species, response only based predictive distribution models. Consequently, most frequently reported involve range shifts (57% species) changes in patterns (26%). showed variety responses, including both positive (e.g. expansion population increase) negative (range contraction decrease), although extreme events were always or neutral. Spatial varied outcome across families, with almost all taxonomic groups featuring expansions contractions, while demographic strongly outcomes, among Pteropodidae Molossidae. The commonly used correlative modelling approaches can applied many but do not mechanistic insight into behavioural, physiological, phenological genetic There was paucity experimental (26%), small 396 covered examined using long-term and/or (11%), even though they more informative about emphasise need empirical unravel multifaceted nature bats' standardised study designs will enable synthesis meta-analysis literature. Finally, we stress importance overcoming geographic disparities through strengthening capacity Global South comprehensive view terrestrial biodiversity

Language: Английский

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Purging and accumulation of genetic load in conservation

Trends in Ecology & Evolution, Journal Year: 2023, Volume and Issue: 38(10), P. 961 - 969

Published: June 19, 2023

Our ability to assess the threat posed by genetic load small and declining populations has been greatly improved advances in genome sequencing computational approaches. Yet, considerable confusion remains around definitions of its dynamics, how they impact individual fitness population viability. We illustrate both selective purging drift affect distribution deleterious mutations during size decline recovery. show this impacts composition load, affects extinction risk recovery potential populations. propose a framework examine dynamics advocate for introduction estimates management endangered

Language: Английский

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Neutral and adaptive genetic diversity in plants: An overview

Frontiers in Ecology and Evolution, Journal Year: 2023, Volume and Issue: 11

Published: Feb. 16, 2023

Genetic diversity is a prerequisite for evolutionary change in all kinds of organisms. It generally acknowledged that populations lacking genetic variation are unable to evolve response new environmental conditions (e.g., climate change) and thus may face an increased risk extinction. Although the importance incorporating into design conservation measures now well understood, less attention has been paid distinction between neutral (NGV) adaptive (AGV) variation. In this review, we first focus on utility NGV by examining ways quantify it, reviewing applications infer ecological processes, exploring its designing plant species. Against background, then summarize identify estimate AGV discuss potential use conservation. After comparing considering their pros cons context, conclude there urgent need better understanding role adaptation. To date, however, only few studies non-model species aimed at deciphering genomic basis complex trait Therefore, researchers practitioners should keep utilizing develop relevant strategies rare endangered until more estimates available.

Language: Английский

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Applications of environmental DNA (eDNA) to detect subterranean and aquatic invasive species: A critical review on the challenges and limitations of eDNA metabarcoding

Environmental Advances, Journal Year: 2023, Volume and Issue: 12, P. 100370 - 100370

Published: April 19, 2023

The world is struggling to solve a devastating biodiversity loss that not only affects the extinction of treasured species and irreplaceable genetic variation, but also jeopardizes food production, health, safety people. All initiatives aimed conserve rely heavily on monitoring both populations get accurate spatial patterns overall population assessments. Conventional techniques, such as visual surveys counting individuals, are problematic due challenges in identifying cryptic or immature life stages. Environmental DNA (eDNA) relatively new technology has potential be faster, non-invasive, cost-effective tool for biodiversity, conservation, management practices. eDNA been extracted from materials ancient present, its applications range identification individual study entire ecosystems. In past few years, there substantial increase usage research pertaining ecological preservation conservation. However, several technological problems still need solved. To reduce number false positives and/or negatives produced by current technologies, it necessary improve optimize calibration validation at every stage procedure. There significant greater information about physical constraints use, well synthesis, state, expected lifespan, modes movement. Due widespread use research, essential assess extent breadth these studies. this article, we critically reviewed primary subterranean aquatic invasive species. Through review, readers can better understand limitations metabarcoding.

Language: Английский

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Local genetic adaptation to habitat in wild chimpanzees

Science, Journal Year: 2025, Volume and Issue: 387(6730)

Published: Jan. 9, 2025

How populations adapt to their environment is a fundamental question in biology. Yet, we know surprisingly little about this process, especially for endangered species, such as nonhuman great apes. Chimpanzees, our closest living relatives, are particularly notable because they inhabit diverse habitats, from rainforest woodland-savannah. Whether genetic adaptation facilitates habitat diversity remains unknown, despite it having wide implications evolutionary biology and conservation. By using newly sequenced exomes 828 wild chimpanzees (388 postfiltering), found evidence of fine-scale habitat, with signatures positive selection forest the same genes underlying malaria humans. This work demonstrates power noninvasive samples reveal adaptations highlights importance adaptive chimpanzees.

Language: Английский

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