Population genomics for wildlife conservation and management

Molecular Ecology, Journal Year: 2020, Volume and Issue: 30(1), P. 62 - 82

Published: Nov. 4, 2020

Biodiversity is under threat worldwide. Over the past decade, field of population genomics has developed across nonmodel organisms, and results this research have begun to be applied in conservation management wildlife species. Genomics tools can provide precise estimates basic features populations, such as effective size, inbreeding, demographic history structure, that are critical for efforts. Moreover, studies identify particular genetic loci variants responsible inbreeding depression or adaptation changing environments, allowing efforts estimate capacity populations evolve adapt response environmental change manage adaptive variation. While connections from been slow develop, these increasingly strengthening. Here we review primary areas which approaches management, highlight examples how they used, recommendations building on progress made field.

Language: Английский

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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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SambaR: An R package for fast, easy and reproducible population‐genetic analyses of biallelic SNP data sets

Molecular Ecology Resources, Journal Year: 2021, Volume and Issue: 21(4), P. 1369 - 1379

Published: Jan. 27, 2021

Abstract SNP data sets can be used to infer a wealth of information about natural populations, including their structure, genetic diversity, and the presence loci under selection. However, analysis time‐consuming challenging process, not in least because at present many different software packages are needed execute depict wide variety mainstream population‐genetic analyses. Here, we SambaR, an integrative user‐friendly R package which automates simplifies quality control analyses biallelic sets. SambaR allows users perform generate ready publish graphs with minimum number commands (less than 10). These wrapper call functions existing (including adegenet, ape, LEA, poppr, pcadapt StAMPP) as well new tools uniquely implemented SambaR. We tested on online available found that process over 100,000 SNPs hundreds individuals within hours, given sufficient computing power. Newly developed facilitate optimization filter settings, objective interpretation ordination analyses, enhance comparability diversity estimates from reduced representation library sets, panels structure‐like plots Bayesian population assignment probabilities. facilitates rapid by removing three major time sinks: file handling, learning, plotting. In addition, provides convenient platform for storage management, several utilities, guidance setting appropriate filters. The source script, manual example set distributed through GitHub: https://github.com/mennodejong1986/SambaR .

Language: Английский

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New developments in the field of genomic technologies and their relevance to conservation management

Conservation Genetics, Journal Year: 2021, Volume and Issue: 23(2), P. 217 - 242

Published: Nov. 11, 2021

Abstract Recent technological advances in the field of genomics offer conservation managers and practitioners new tools to explore for applications. Many these are well developed used by other life science fields, while others still development. Considering possibilities, choosing right tool(s) from toolbox is crucial can pose a challenging task. With this mind, we strive inspire, inform illuminate on how efforts benefit current genomic biotechnological revolution. inspirational case studies show technologies help resolve some main challenges, also informing implementable different are. We here focus specifically small population management, highlight potential genetic rescue, discuss opportunities gene editing with adaptation changing environments. In addition, delineate applications drives controlling invasive species. that offers added efforts, but comes limitations use novel emerging techniques.

Language: Английский

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The application gap: Genomics for biodiversity and ecosystem service management

Biological Conservation, Journal Year: 2023, Volume and Issue: 278, P. 109883 - 109883

Published: Jan. 4, 2023

The conservation of biodiversity from the genetic to community levels is fundamental for continual provision ecosystem services (ES), benefits that ecosystems provide people. Genetic and genomic diversity enhance resilience populations communities underpin functions services. We show genomics applications are mostly limited flagship species their ES management underachieved. propose a framework on how can guide sustainable bridge this genomics-ES 'application gap'. review knowledge in single (relatedness, potentially adaptive variants) or interacting (host-microorganism coevolution, hybridization) effective actions. These include population supplementation, assisted migration hybridization promote climate-adapted variants potential, control invasives, delimitation areas, provenancing strategies restoration, managing microbial function solving trade-offs. Genomics-informed actions improved outcomes supported through synergies between scientists managers at local, regional international levels, development standardized workflows, training incorporation local information. Such facilitate implementation policies such as UN 2030 goals EU Biodiversity strategy 2030, support inclusion ambitious new CBD post-2020 Global Framework hybrids.

Language: Английский

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Overcoming the limitations of wildlife disease monitoring

Research Directions One Health, Journal Year: 2024, Volume and Issue: 2

Published: Jan. 1, 2024

Abstract Integrated wildlife monitoring (IWM) combines infection dynamics and the ecology of populations, including aspects defining host community network. Developing implementing IWM is a worldwide priority that faces major constraints biases should be considered addressed when these systems. We identify eleven main limitations in establishment IWM, which could summarized into funding lack harmonization information exchange. The solutions proposed to overcome comprise: (i) selecting indicator species through network analysis, (ii) identifying key pathogens investigate monitor, potentially nonspecific health markers, (iii) improve standardize harmonized methodologies can applied as well communication among stakeholders across within countries, (iv) integration new noninvasive technologies (e.g., camera trapping (CT) environmental nucleic acid detection) tools are under ongoing research artificial intelligence speed-up CT analyses, microfluidic polymerase chain reaction sample volume constraints, or filter paper samples facilitate transport). Achieving optimizing must allows drivers epidemics predicting trends changes disease population before pathogen crosses interspecific barriers.

Language: Английский

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Development and validation of a minimal SNP genotyping panel for the differentiation of Cannabis sativa cultivars

BMC Genomics, Journal Year: 2025, Volume and Issue: 26(1)

Published: Jan. 28, 2025

Due to its previously illicit nature, Cannabis sativa had not fully reaped the benefits of recent innovations in genomics and plant sciences. However, Canada's legalization C. products derived from flower 2018 triggered significant new demand for robust genotyping tools assist breeders meeting consumer demands. Early molecular marker-based research on focused screening sex chemotype, more has sought use markers target traits agronomic interest, study populations differentiate between cultivars. In this study, we have conducted whole genome sequencing 32 cultivars, mined data SNPs, developed a reduced SNP panel discriminate sequenced then validated 20-SNP using DNA cultivars tested assays commercially available dried flower. The assay conversion rate was higher extracted fresh material than samples. called genotypes were internally consistent, highlighting discrepancies detected observed assays. primary contributions work are clearly document process used develop minimal panels, feasibility such panels outline improvements goals future iterations PCR-based, enable efficient development identify screen Our key recommendations increase sampling density account intra-cultivar variability; leverage read length paired-end short-read technology; conduct in-depth pre- post-processing reads, mapping, variant calling data; integrate trait-associated loci multi-purpose panels; iterative approaches vitro validation ensure that only most discriminant performant SNPs retained.

Language: Английский

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Genomic basis for drought resistance in European beech forests threatened by climate change

eLife, Journal Year: 2021, Volume and Issue: 10

Published: June 16, 2021

In the course of global climate change, Central Europe is experiencing more frequent and prolonged periods drought. The drought years 2018 2019 affected European beeches ( Fagus sylvatica L.) differently: even in same stand, drought-damaged trees neighboured healthy trees, suggesting that genotype rather than environment was responsible for this conspicuous pattern. We used natural experiment to study genomic basis resistance with Pool-GWAS. Contrasting extreme phenotypes identified 106 significantly associated single-nucleotide polymorphisms (SNPs) throughout genome. Most annotated genes SNPs (>70%) were previously implicated reaction plants. Non-synonymous substitutions led either a functional amino acid exchange or premature termination. An SNP assay 70 loci allowed predicting phenotype 98.6% validation sample 92 trees. Drought beech moderately polygenic trait should respond well selection, selective management, breeding.

Language: Английский

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Single trait versus principal component based association analysis for flowering related traits in pigeonpea

Scientific Reports, Journal Year: 2022, Volume and Issue: 12(1)

Published: June 21, 2022

Pigeonpea, a tropical photosensitive crop, harbors significant diversity for days to flowering, but little is known about the genes that govern these differences. Our goal in current study was use genome wide association strategy discover loci regulate flowering pigeonpea. A single trait as well principal component based conducted on diverse collection of 142 pigeonpea lines first and fifty percent over 3 years, besides plant height number seeds per pod. The analysis used seven mapping models (GLM, MLM, MLMM, CMLM, EMLM, FarmCPU SUPER) further comparison revealed more robust controlling both false positives negatives it incorporates multiple markers covariates eliminate confounding between testing marker kinship. Cumulatively, set 22 SNPs were found be associated with either (DOF), (DFF) or both, which 15 unique based, 4 PC GWAS while shared by both. Because PC1 represents DOF, DFF (PH), four can inferred pleiotropic. window ± 2 kb aligned available transcriptome data generated transition from vegetative reproductive phase Annotation regions presence might involved floral induction like Cytochrome p450 Tata box binding protein, Auxin response factors, Pin genes, F U domain chromatin remodelling complex RNA methyltransferase. In summary, appears auxin responsive could regulating DOF majority contained are signaling pathways their vicinity. Overall, our findings indicates statistically terms identifying better choice compared other aforementioned dealing positive negative associations thus traits inheritance.

Language: Английский

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Genomic insights into the conservation of wild and domestic animal diversity: A review

Gene, Journal Year: 2023, Volume and Issue: 886, P. 147719 - 147719

Published: Aug. 18, 2023

Language: Английский

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