An overview of current population genomics methods for the analysis of whole‐genome resequencing data in eukaryotes

Bourgeois, Yann; Warren, Ben

doi:10.1111/mec.15989

Cited by 46 publications

(43 citation statements)

References 299 publications

(210 reference statements)

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“…However, the number of SNPs obtained and the ability to detect genes underlying local adaptation from the abovementioned methods may be influenced due to the differences in library preparation, SNP densities, and the bioinformatics parameters applied to SNP filtering ( Hoban et al, 2016 ; Lowry et al, 2017 ; McKinney et al, 2017 ). As more and more forest tree genomes have been published (e.g., Table 1 in Ingvarsson et al, 2016 ) and sequencing costs fall, whole-genome resequencing is thriving and becoming an option for landscape genomics studies ( Lin et al, 2018 ; Zhu et al, 2020 ), which can provide unprecedented marker density and determine other genetic variation such as structural variants and mutations in regulatory elements, increasing power for the detection of local adaptation and providing novel insights into the role of selection, recombination, and gene flow in promoting or impairing local adaptation to new habitats compared with reduced-representation methods ( Fuentes-Pardo and Ruzzante, 2017 ; Bourgeois and Warren, 2021 ). In addition, the degrees of linkage disequilibrium (LD) in the studied species will also influence the power of detecting adaptive SNPs.…”

Section: Challenges and Future Directionsmentioning

confidence: 99%

Landscape Genomics in Tree Conservation Under a Changing Environment

Feng

2022

Front. Plant Sci.

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Understanding the genetic basis of how species respond to changing environments is essential to the conservation of species. However, the molecular mechanisms of adaptation remain largely unknown for long-lived tree species which always have large population sizes, long generation time, and extensive gene flow. Recent advances in landscape genomics can reveal the signals of adaptive selection linking genetic variations and landscape characteristics and therefore have created novel insights into tree conservation strategies. In this review article, we first summarized the methods of landscape genomics used in tree conservation and elucidated the advantages and disadvantages of these methods. We then highlighted the newly developed method “Risk of Non-adaptedness,” which can predict the genetic offset or genomic vulnerability of species via allele frequency change under multiple scenarios of climate change. Finally, we provided prospects concerning how our introduced approaches of landscape genomics can assist policymaking and improve the existing conservation strategies for tree species under the ongoing global changes.

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Section: Challenges and Future Directionsmentioning

confidence: 99%

Landscape Genomics in Tree Conservation Under a Changing Environment

Feng

2022

Front. Plant Sci.

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“…These genomic measures can be used to accurately estimate distinct genetic areas and assess inbreeding in populations, they have been used to design breeding schemes to select against deleterious alleles or to increase heterozygosity, and they have the potential to increase the long-term survival of breeds and wild populations in view of climate change (for an overview see . For evaluating overall adaptive potential whole genome, or at least genome-wide screenings, may remain the preferred option (Flanagan et al 2018;Bourgeois and Warren 2021).…”

Section: How Can Genomic Information Help?mentioning

confidence: 99%

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

et al. 2021

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

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“…Additional articles that compare WGS to the in‐vogue methods of reduced representation libraries (RRL), genotyping by sequencing (GBS) and restriction site associated DNA sequencing (RADseq) provide convincing evidence for the superiority of WGS in many regards (Duntsch et al, 2021; Lou et al, 2021; Szarmach et al, 2021), while others use WGS to address previously insurmountable challenges (Vekemans et al, 2021; Yoder & Tiley, 2021). Many of the manuscripts in this special issue provide methodological resources that will undoubtedly serve our community for years to come, including bioinformatics pipelines (Lou et al, 2021; Ribeiro et al, 2021) and a compendium of tools for WGS data analysis (Bourgeois & Warren, 2021). A second theme within the special issue is that of empirical studies using WGS to infer demographic dynamics across evolutionary timescales.…”

Section: Highlights Of 2021mentioning

confidence: 99%