A beginner's guide to low‐coverage whole genome sequencing for population genomics

Molecular Ecology, Journal Year: 2021, Volume and Issue: 30(23), P. 5966 - 5993

Published: July 12, 2021

Abstract Low‐coverage whole genome sequencing (lcWGS) has emerged as a powerful and cost‐effective approach for population genomic studies in both model nonmodel species. However, with read depths too low to confidently call individual genotypes, lcWGS requires specialized analysis tools that explicitly account genotype uncertainty. A growing number of such have become available, but it can be difficult get an overview what types analyses performed reliably data, how the distribution effort between samples analysed per‐sample affects inference accuracy. In this introductory guide lcWGS, we first illustrate cost is now comparable RAD‐seq Pool‐seq many systems. We then provide software packages uncertainty different inference. Next, use simulated empirical data assess accuracy allele frequency, genetic diversity, linkage disequilibrium estimation, detection structure, selection scans under strategies. Our results show spreading given amount across more lower depth per sample consistently improves most inference, few notable exceptions. Finally, potential using imputation bolster from species, discuss current limitations future perspectives lcWGS‐based genomics research. With overview, hope make approachable stimulate its broader adoption.

Language: Английский

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Extensive hybridization reveals multiple coloration genes underlying a complex plumage phenotype

Proceedings of the Royal Society B Biological Sciences, Journal Year: 2021, Volume and Issue: 288(1943), P. 20201805 - 20201805

Published: Jan. 20, 2021

Coloration is an important target of both natural and sexual selection. Discovering the genetic basis colour differences can help us to understand how this visually striking phenotype evolves. Hybridizing taxa with clear shallow genomic divergences are unusually tractable for associating coloration phenotypes their causal genotypes. Here, we leverage extensive admixture between two common North American woodpeckers—yellow-shafted red-shafted flickers—to identify bases six distinct plumage patches involving melanin carotenoid pigments. Comparisons flickers across approximately 7.25 million genome-wide SNPs show that these forms differ at only a small proportion genome (mean F ST = 0.008). Within few highly differentiated regions, 368 significantly associated four patches. These linked multiple genes known be involved in pigmentation. For example, gene ( CYP2J19 ) cause yellow red transitions other birds strongly versus wing tail feathers flickers. Additionally, our analyses suggest novel links coloration. Our finding patch-specific control adds growing body literature suggesting diversity animals could created through selection acting on combinations genes.

Language: Английский

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Historical DNA as a tool to address key questions in avian biology and evolution: A review of methods, challenges, applications, and future directions

Molecular Ecology Resources, Journal Year: 2019, Volume and Issue: 19(5), P. 1115 - 1130

Published: July 23, 2019

Abstract Museum specimens play a crucial role in addressing key questions systematics, evolution, ecology, and conservation. With the advent of high‐throughput sequencing technologies, that have long been foundation important biological discoveries can inform new perspectives as sources genomic data. Despite many possibilities associated with analyzing DNA from historical specimens, several challenges persist. Using avian systems model, we review extraction protocols, capture methods are helping researchers overcome some these difficulties. We highlight empirical examples which used technologies to address fundamental related conservation evolution. Increasing accessibility will provide tools tap into wealth information contained within our valuable natural history collections.

Language: Английский

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The genomic revolution and species delimitation in birds (and other organisms): Why phenotypes should not be overlooked

Ornithology, Journal Year: 2021, Volume and Issue: 138(2)

Published: March 1, 2021

Abstract Given the availability of genomic data to identify separately evolving groups organisms, many researchers establish species limits based on assessments extent gene flow among populations and often use analytical approaches in which is explicitly disallowed. Strictly considering lack of—or limited—gene as main or only criterion delimit involves two complications practice. First, used analyze genome-wide cannot by themselves distinguish from within-species population structure, particularly allopatric organisms. Second, recognizing those lineages one can using such fails embrace role other evolutionary forces (i.e. various forms selection) defining lineages. Using examples birds, we call for importance additional delimitation explain why commonly taxonomic studies may be insufficient properly uncover limits. By processes that structure genotypic phenotypic variation during speciation, argue rigorous analyses remain crucial genomics era because phenotypes uniquely inform us about selection maintaining cohesion Evolutionary theory describing roles flow, genetic drift natural sexual origin maintenance calls an integration with phenomics avian delimitation.

Language: Английский

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Revisiting a classic hybrid zone: Movement of the northern flicker hybrid zone in contemporary times

Evolution, Journal Year: 2022, Volume and Issue: 76(5), P. 1082 - 1090

Published: March 23, 2022

Natural hybrid zones have provided important insights into the evolutionary process, and their geographic dynamics over time can help to disentangle underlying biological processes that maintain them. Here, we leverage replicated sampling of an identical transect across zone between yellow‐shafted red‐shafted flickers in Great Plains assess its stability ∼60 years (1955–1957 2016–2018). We identify a ∼73‐km westward shift center toward range flicker, but find no associated changes width our period. In fact, remains remarkably narrow, suggesting some kind selective pressure maintains zone. By comparing previous work same region, it appears likely movement has occurred since early 1980s. This recent may be related climate or land management practices allowed Plains.

Language: Английский

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Dynamic Outlier Slicing Allows Broader Exploration of Adaptive Divergence: A Comparison of Individual Genome and Pool‐Seq Data Linked to Humic Adaptation in Perch

Molecular Ecology, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 23, 2025

ABSTRACT How genetic variation contributes to adaptation at different environments is a central focus in evolutionary biology. However, most free‐living species still lack comprehensive understanding of the primary molecular mechanisms adaptation. Here, we characterised targets selection associated with drastically aquatic environments—humic and clear water—in common freshwater fish, Eurasian perch ( Perca fluviatilis ). By using whole‐genome sequencing (WGS) on large population dataset n = 42 populations) analysing 873,788 SNPs, our aim was uncover novel confirm known footprints selection. We compared individual pooled WGS, developed approach, termed dynamic outlier slicing, assess how choice outlier‐calling stringency influences functional Gene Ontology (GO) enrichment. integrating genome‐environment association (GEA) analysis allele frequency‐based approaches, estimated composite signals (CSS) identified 2679 SNPs distributed across 324 genomic regions, involving 468 genes. Dynamic slicing robust enrichment five annotation categories (upstream, downstream, synonymous, 5′UTR 3′UTR) highlighting crucial role regulatory elements adaptive evolution. Furthermore, GO analyses revealed strong functions gated channel activity, transmembrane transporter activity ion emphasising importance osmoregulation balance maintenance. Our findings demonstrate that despite substantial random drift divergence, WGS high number pools enabled identification both humic water environments, providing evidence widespread anticipate method will enable more thorough exploration divergence diverse range species.

Language: Английский

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Comparing divergence landscapes from reduced‐representation and whole genome resequencing in the yellow‐rumped warbler (Setophaga coronata) species complex

Molecular Ecology, Journal Year: 2021, Volume and Issue: 30(23), P. 5994 - 6005

Published: May 2, 2021

Researchers seeking to generate genomic data for non-model organisms are faced with a number of trade-offs when deciding which method use. The selection reduced representation approaches versus whole genome resequencing will ultimately affect the marker density, sequencing depth, and individuals that can multiplexed. These factors researchers' ability accurately characterize certain features, such as landscapes divergence-how FST varies across genomes. To provide insight into effect on estimation divergence landscapes, we applied an identical bioinformatic pipeline three generations (GBS, ddRAD, WGS) produced same system, yellow-rumped warbler species complex. We compare generated using each myrtle (Setophaga coronata coronata) Audubon's (S. c. auduboni), warblers deeply divergent mtDNA resulting from mitochondrial introgression. found most high-FST peaks were not detected in ddRAD set, while both GBS WGS able identify presence large peaks, was superior at finer scale. Comparing haplotypes, only allowed us small (10-20 kb) regions elevated differentiation, one contained nuclear-encoded gene NDUFAF3. calculated cost per base pair it comparable between WGS, but significantly higher ddRAD. comparisons highlight advantages over methods characterizing divergence.

Language: Английский

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Shallow genetic divergence and distinct phenotypic differences between two Andean hummingbirds: Speciation with gene flow?

Ornithology, Journal Year: 2019, Volume and Issue: 136(4)

Published: Aug. 30, 2019

Abstract Ecological speciation can proceed despite genetic interchange when selection counteracts the homogenizing effects of migration. We tested predictions this divergence-with-gene-flow model in Coeligena helianthea and C. bonapartei, 2 parapatric Andean hummingbirds with marked plumage divergence. sequenced putatively neutral markers (mitochondrial DNA [mtDNA] nuclear ultraconserved elements [UCEs]) to examine structure gene flow, a candidate (MC1R) assess its role underlying divergence coloration. also prediction Gloger’s rule that darker forms occur more humid environments, examined morphological variation adaptive mechanisms potentially promoting Genetic differentiation between species was low both ND2 UCEs. Coalescent estimates migration were consistent but we cannot reject incomplete lineage sorting reflecting recent as an explanation for patterns variation. MC1R unrelated phenotypic differences. Species did not differ macroclimatic niches distinct morphology. Although adaptation conditions cause divergence, may have occurred face flow driven by other ecological pressures or sexual selection. Marked no is remarkable Neotropical birds, makes bonapartei appropriate system which search basis differences employing genomics.

Language: Английский

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Population genomics of two congeneric Palaearctic shorebirds reveals differential impacts of Quaternary climate oscillations across habitats types

Scientific Reports, Journal Year: 2019, Volume and Issue: 9(1)

Published: Dec. 3, 2019

Abstract Intracontinental biotic divisions across the vast Palaearctic region are not well-characterized. Past research has revealed patterns ranging from a lack of population structure to deep divergences along varied lines separation. Here we compared biogeographic two shorebirds with different habitat preferences, Whimbrel ( Numenius phaeopus ) and Eurasian curlew N. arquata ). Using genome-wide markers populations Palaearctic, applied multitude genomic phylogenomic approaches elucidate structure. Most importantly, tested for isolation by distance visualized barriers corridors gene flow. We found shallow in subpolar bog tundra-breeding whimbrels, consistent other species breeding at similarly high latitude, indicating connectivity tundra belt, both presently during southward shifts periods global cooling. In contrast, temperate grassland-breeding emerged three distinct clades corresponding glacial refugia. Barriers flow coincided areas topographic relief central whimbrels further east curlews. Our findings highlight interplay historic ecological factors influencing present-day biota.

Language: Английский

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Population divergence and gene flow in two East Asian shorebirds on the verge of speciation

Scientific Reports, Journal Year: 2019, Volume and Issue: 9(1)

Published: June 12, 2019

Genetic isolation of populations over evolutionary time leads to the formation independent species. We examined a pair shorebirds - Kentish Plover Charadrius alexandrinus and enigmatic White-faced C. dealbatus which display strong plumage differentiation, yet show minimal genetic divergence based on previous mitochondrial microsatellite work. Two scenarios may lead this situation: (1) they represent clinal or poorly diverged with limited genomic differentiation despite substantial variation, (2) are diverging taxa at cusp speciation, ongoing gene flow obliterating signals in traditional markers. compared genotypes 98 plovers (59 Plovers, 35 Plovers 4 hybrids) sampled eastern Asia Europe using ddRADSeq harvest 8000 genome-wide SNPs. In contrast studies, our analyses revealed two well defined clusters, hybridization narrow contact zone. also uncovered significant differences bill length further sex-specific size, signal mate choice between Plovers. Our results support hypothesis that shorebird duo is verge speciation.

Language: Английский

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