Comparative study of population genomic approaches for mapping colony-level traits

Inbar, Shani; Cohen, Pnina; Yahav, Tal; Privman, Eyal

doi:10.1371/journal.pcbi.1007653

Cited by 15 publications

(23 citation statements)

References 42 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…For instance, for heuristic approaches such as PoolSNP, an exhaustive simulation-based inference for choosing the SNP calling parameters that maximizes the performance of the calling process for specific genomic data can be performed (Kapun et al, 2020). The conclusions drawn from this study could be relevant not only for large-scale population genomics studies but also in cases where the Pool-seq strategy is the only option such as in metagenomic studies and studies with polyploids, among others (Clevenger et al, 2015;Inbar et al, 2020;Pespeni et al, 2013;Shockey et al, 2019).…”

Section: Discussionmentioning

confidence: 96%

Benchmarking the performance of Pool‐seq SNP callers using simulated and real sequencing data

Guirao-Rico

González

2021

Molecular Ecology Resources

View full text Add to dashboard Cite

Population genomics is a fast‐developing discipline with promising applications in a growing number of life sciences fields. Advances in sequencing technologies and bioinformatics tools allow population genomics to exploit genome‐wide information to identify the molecular variants underlying traits of interest and the evolutionary forces that modulate these variants through space and time. However, the cost of genomic analyses of multiple populations is still too high to address them through individual genome sequencing. Pooling individuals for sequencing can be a more effective strategy in Single Nucleotide Polymorphism (SNP) detection and allele frequency estimation because of a higher total coverage. However, compared to individual sequencing, SNP calling from pools has the additional difficulty of distinguishing rare variants from sequencing errors, which is often avoided by establishing a minimum threshold allele frequency for the analysis. Finding an optimal balance between minimizing information loss and reducing sequencing costs is essential to ensure the success of population genomics studies. Here, we have benchmarked the performance of SNP callers for Pool‐seq data, based on different approaches, under different conditions, and using computer simulations and real data. We found that SNP callers performance varied for allele frequencies up to 0.35. We also found that SNP callers based on Bayesian (SNAPE‐pooled) or maximum likelihood (MAPGD) approaches outperform the two heuristic callers tested (VarScan and PoolSNP), in terms of the balance between sensitivity and FDR both in simulated and sequencing data. Our results will help inform the selection of the most appropriate SNP caller not only for large‐scale population studies but also in cases where the Pool‐seq strategy is the only option, such as in metagenomic or polyploid studies.

show abstract

Section: Discussionmentioning

confidence: 96%

Benchmarking the performance of Pool‐seq SNP callers using simulated and real sequencing data

Guirao-Rico

González

2021

Molecular Ecology Resources

View full text Add to dashboard Cite

show abstract

“…More broadly, polygenic traits are difficult to characterize under ideal situations, and so the approach presented here is particularly promising for discrete traits, rare alleles and moderate-to-large effect loci (e.g. [ 17 , 18 , 25 ]). As we continue to identify and validate candidate QTLs, it is conceivable that a gene panel could be developed in white-tailed deer and assist in breeding and management programs or assess the effects of artificial selection by trophy hunting; however, until a reasonable amount of phenotypic variation can be attributed to specific QTL, a gene targeted approach for management and breeding of white-tailed deer will remain a challenge.…”

Section: Discussionmentioning

confidence: 99%

“…Coalescent simulations by Hivert et al [ 24 ] showed high accuracy of F ST estimates from pool-seq, at times more precise than individual genomes. Similarly, Inbar et al [ 25 ] showed that pooled approaches produced near identical allele frequency distributions to that of whole and reduced genome sequencing, with simulations reliably detecting moderate to large effect QTL. While Bastide et al [ 26 ] showed that low frequency alleles and small effect sizes, particularly for complex traits, were difficult to detect, this is also the case for non-pooled studies (e.g.…”

Section: Introductionmentioning

confidence: 97%

Genomic architecture of phenotypic extremes in a wild cervid

Côté

Richard

et al. 2022

BMC Genomics

View full text Add to dashboard Cite

Identifying the genes underlying fitness-related traits such as body size and male ornamentation can provide tools for conservation and management and are often subject to various selective pressures. Here we performed high-depth whole genome re-sequencing of pools of individuals representing the phenotypic extremes for antler and body size in white-tailed deer (Odocoileus virginianus). Samples were selected from a tissue repository containing phenotypic data for 4,466 male white-tailed deer from Anticosti Island, Quebec, with four pools representing the extreme phenotypes for antler and body size after controlling for age. Our results revealed a largely homogenous population but detected highly divergent windows between pools for both traits, with the mean allele frequency difference of 14% for and 13% for antler and body SNPs in outlier windows, respectively. Genes in outlier antler windows were enriched for pathways associated with cell death and protein metabolism and some of the most differentiated windows included genes associated with oncogenic pathways and reproduction, processes consistent with antler evolution and growth. Genes associated with body size were more nuanced, suggestive of a highly complex trait. Overall, this study revealed the complex genomic make-up of both antler morphology and body size in free-ranging white-tailed deer and identified target loci for additional analyses.

show abstract

“…DNA of males collected from a monogynous colony at Lake Henshaw (H-population) in 2019 was used to construct reduced representation genomic libraries following Inbar et al (Inbar et al, 2020), using a modified double-digest (EcoR1 and Mse1) Restriction-site Associated DNA sequencing (ddRADseq) protocol (Parchman et al, 2012; Peterson et al, 2012). Briefly, genomic DNA was digested at 37°C for 8hrs and ligated with uniquely barcoded adaptors.…”

Section: Methodsmentioning

confidence: 99%

Evolutionary genomics of socially polymorphic populations ofPogonomyrmex californicus

Errbii

Lajmi

et al. 2021

Preprint

Self Cite

View full text Add to dashboard Cite

The societies of social insects are highly variable, including variation in the number of reproductives in a colony. In the California harvester ant, Pogonomyrmex californicus (Buckley 1867), colonies are commonly founded by a single queen (haplometrosis, primary monogyny). However, in some populations in California (USA), two or more queens cooperate in colony founding (pleometrosis) and continue to share a nest over several years (primary polygyny). Here, we use population genomics and linkage mapping to study the evolutionary dynamics and genetic architecture of this social niche polymorphism. Our analyses show that both populations underwent consecutive bottlenecks over the last 100,000 generations, particularly decreasing population size in the P-population and that the two populations diverged until 1,000 generations ago, after which gene flow increased again and we found signs of recent genetic admixture between the two populations. We further uncover an 8 Mb non-recombining region segregating with the observed social niche polymorphism, showing characteristics of a supergene comparable to the ones underlying social niche polymorphism in other ant species. In addition, 57 genes in five genomic regions outside the supergene show signatures of a selective sweep in the P-population, some of which are differentially expressed between haplo- and pleometrotic queens during colony founding. Our findings expose the social niche polymorphism in P. californicus as a polygenic trait involving a supergene.

show abstract

Comparative study of population genomic approaches for mapping colony-level traits

Cited by 15 publications

References 42 publications

Benchmarking the performance of Pool‐seq SNP callers using simulated and real sequencing data

Benchmarking the performance of Pool‐seq SNP callers using simulated and real sequencing data

Genomic architecture of phenotypic extremes in a wild cervid

Evolutionary genomics of socially polymorphic populations ofPogonomyrmex californicus

Contact Info

Product

Resources

About