How genomics can help biodiversity conservation

Trends in Genetics, Год журнала: 2023, Номер 39(7), С. 545 - 559

Опубликована: Фев. 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.

Язык: Английский

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Deleterious Variation in Natural Populations and Implications for Conservation Genetics

Annual Review of Animal Biosciences, Год журнала: 2022, Номер 11(1), С. 93 - 114

Опубликована: Ноя. 4, 2022

Deleterious mutations decrease reproductive fitness and are ubiquitous in genomes. Given that many organisms face ongoing threats of extinction, there is interest elucidating the impact deleterious variation on extinction risk optimizing management strategies accounting for such mutations. Quantifying understanding effects population history complex endeavors because we do not know strength selection acting each mutation. Further, effect demographic depends against mutation degree dominance. Here clarify how can be quantified studied natural populations. We then discuss different factors, as small size, nonequilibrium size changes, inbreeding, gene flow, affect variation. Lastly, provide guidance studying nonmodel populations conservation concern.

Язык: Английский

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

Conservation Genetics, Год журнала: 2025, Номер unknown

Опубликована: Янв. 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.

Язык: Английский

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Translating genomic advances into biodiversity conservation

Nature Reviews Genetics, Год журнала: 2023, Номер 25(5), С. 362 - 373

Опубликована: Ноя. 27, 2023

Язык: Английский

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Balancing read length and sequencing depth: Optimizing Nanopore long‐read sequencing for monocots with an emphasis on the Liliales

Applications in Plant Sciences, Год журнала: 2023, Номер 11(3)

Опубликована: Май 1, 2023

We present approaches used to generate long-read Nanopore sequencing reads for the Liliales and demonstrate how modifications standard protocols directly impact read length total output. The goal is help those interested in generating data determine which steps may be necessary optimizing output results.

Язык: Английский

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Tigerfish designs oligonucleotide-based in situ hybridization probes targeting intervals of highly repetitive DNA at the scale of genomes

Nature Communications, Год журнала: 2024, Номер 15(1)

Опубликована: Фев. 3, 2024

Abstract Fluorescent in situ hybridization (FISH) is a powerful method for the targeted visualization of nucleic acids their native contexts. Recent technological advances have leveraged computationally designed oligonucleotide (oligo) probes to interrogate > 100 distinct targets same sample, pushing boundaries FISH-based assays. However, even most highly multiplexed experiments, repetitive DNA regions are typically not included as targets, computational design specific against such presents significant technical challenges. Consequently, many open questions remain about organization and function sequences. Here, we introduce Tigerfish, software tool genome-scale oligo intervals. We showcase Tigerfish by designing panel 24 interval-specific repeat each human chromosomes imaging this on metaphase spreads interphase nuclei. extends toolkit oligo-based FISH DNA.

Язык: Английский

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Population Genomics for Insect Conservation

Annual Review of Animal Biosciences, Год журнала: 2022, Номер 11(1), С. 115 - 140

Опубликована: Ноя. 14, 2022

Insects constitute vital components of ecosystems. There is alarming evidence for global declines in insect species diversity, abundance, and biomass caused by anthropogenic drivers such as habitat degradation or loss, agricultural practices, climate change, environmental pollution. This raises important concerns about human food security ecosystem functionality calls more research to assess population trends identify threatened the causes inform conservation strategies. Analysis genetic diversity a powerful tool address these goals, but so far animal genetics has focused strongly on endangered vertebrates, devoting less attention invertebrates, insects, that most biodiversity. Insects' shorter generation times larger sizes likely necessitate different analytical methods management The availability high-quality reference genome assemblies enables genomics several key issues. These include precise inference past demographic fluctuations recent declines, measurement load levels, delineation evolutionarily significant units cryptic species, analysis adaptation stressors. identification populations are particularly vulnerable future threats, considering their potential adapt evolve. We review application outlook averting declines.

Язык: Английский

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Coral Reef Population Genomics in an Age of Global Change

Annual Review of Genetics, Год журнала: 2023, Номер 57(1), С. 87 - 115

Опубликована: Июнь 29, 2023

Coral reefs are both exceptionally biodiverse and threatened by climate change other human activities. Here, we review population genomic processes in coral reef taxa their importance for understanding responses to global change. Many on characterized weak genetic drift, extensive gene flow, strong selection from complex biotic abiotic environments, which together present a fascinating test of microevolutionary theory. Selection, hybridization have played will continue play an important role the adaptation or extinction face rapid environmental change, but research remains limited compared urgent needs. Critical areas future investigation include evolutionary potential mechanisms local adaptation, developing historical baselines, building greater capacity countries where most diversity is concentrated.

Язык: Английский

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Using Computational Simulations to Model Deleterious Variation and Genetic Load in Natural Populations

The American Naturalist, Год журнала: 2023, Номер 202(6), С. 737 - 752

Опубликована: Июль 17, 2023

AbstractDeleterious genetic variation is abundant in wild populations, and understanding the ecological conservation implications of such an area active research. Genomic methods are increasingly used to quantify impacts deleterious natural populations; however, these approaches remain limited by inability accurately predict selective dominance effects mutations. Computational simulations offer a complementary tool that can help overcome limitations, although have yet be widely employed. In this perspective article, we aim encourage genomics researchers adopt greater use computational aid deepening our populations. We first provide overview components simulation variation, describing key parameters involved models. Next, discuss several for validating Finally, compare validate recently proposed mutation models, demonstrating models based on estimates selection from experimental systems biased toward highly describe new model supported multiple orthogonal lines evidence example scripts implementing (https://github.com/ckyriazis/simulations_review).

Язык: Английский

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The Ruminant Telomere-to-Telomere (RT2T) Consortium

Nature Genetics, Год журнала: 2024, Номер 56(8), С. 1566 - 1573

Опубликована: Авг. 1, 2024

Язык: Английский

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