Genomic architecture and introgression shape a butterfly radiation

Science, Journal Year: 2019, Volume and Issue: 366(6465), P. 594 - 599

Published: Oct. 31, 2019

We used 20 de novo genome assemblies to probe the speciation history and architecture of gene flow in rapidly radiating Heliconius butterflies. Our tests distinguish incomplete lineage sorting from introgression indicate that has obscured several ancient phylogenetic relationships this group over large swathes genome. Introgressed loci are underrepresented low-recombination gene-rich regions, consistent with purging foreign alleles more tightly linked incompatibility loci. Here, we identify a hitherto unknown inversion traps color pattern switch locus. infer was transferred between lineages by is convergent similar rearrangement another part genus. These multiple sequences enable improved understanding importance selective processes adaptive radiation.

Language: Английский

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Lep-MAP3: robust linkage mapping even for low-coverage whole genome sequencing data

Bioinformatics, Journal Year: 2017, Volume and Issue: 33(23), P. 3726 - 3732

Published: Aug. 1, 2017

Accurate and dense linkage maps are useful in family-based association studies, quantitative trait locus mapping, analysis of genome synteny other genomic data analyses. Moreover, mapping is one the best ways to detect errors de novo assemblies, as well orient place assembly contigs within chromosomes. A small cross tens individuals will many where distant parts erroneously joined together. With more markers, even local can be detected oriented. However, tools that currently available for constructing not suited large, possible low-coverage, whole sequencing datasets.Here we present a software Lep-MAP3, capable high-throughput datasets. Such allows cost-efficient genotyping millions single nucleotide polymorphisms (SNPs) thousands individual samples, enabling, among analyses, comprehensive validation refinement assemblies. The algorithms Lep-MAP3 analyse low-coverage datasets reduce filtering curation on any data. This yields markers final with less manual work problematic We demonstrate obtains very good performance already 5x coverage outperforms fastest simulated accuracy often speed. also construct 7-12x whole-genome Red postman butterfly (Heliconius erato) almost 3 million markers.Lep-MAP3 source code under GNU general public license from http://sourceforge.net/projects/[email protected] at Bioinformatics online.

Language: Английский

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Recombination rate variation shapes barriers to introgression across butterfly genomes

PLoS Biology, Journal Year: 2019, Volume and Issue: 17(2), P. e2006288 - e2006288

Published: Feb. 7, 2019

Hybridisation and introgression can dramatically alter the relationships among groups of species, leading to phylogenetic discordance across genome between populations. Introgression also erode species differences over time, but selection against at certain loci acts maintain postmating barriers. Theory predicts that barriers made up many throughout should lead a broad correlation recombination rate, which determines extent on deleterious foreign alleles will affect neutral physically linked loci. Here, we describe variation in genealogical three Heliconius butterflies: H. melpomene (mel), cydno (cyd), timareta (tim), using whole genomes 92 individuals, ask whether this be explained by heterogeneous introgression. We find vary predictably chromosomal scale. By quantifying rate admixture proportions, then show rates are predicted rate. This implies highly polygenic, with acting introgressed most genome. In addition, long chromosomes, have lower rates, produce stronger average than short chromosomes. Finally, consistent difference two pairs either side Andes, suggests architecture Our findings illustrate how combined effects hybridisation, recombination, natural selection, multitudes periods, sculpt species.

Language: Английский

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Genome sequence of Gossypium herbaceum and genome updates of Gossypium arboreum and Gossypium hirsutum provide insights into cotton A-genome evolution

Nature Genetics, Journal Year: 2020, Volume and Issue: 52(5), P. 516 - 524

Published: April 13, 2020

Abstract Upon assembling the first Gossypium herbaceum (A 1 ) genome and substantially improving existing arboreum 2 hirsutum ((AD) genomes, we showed that all A-genomes may have originated from a common ancestor, referred to here as A 0 , which was more phylogenetically related than . Further, allotetraploid formation shown preceded speciation of Both evolved independently, with no ancestor–progeny relationship. Gaussian probability density function analysis indicates several long-terminal-repeat bursts occurred 5.7 million years ago less 0.61 contributed compellingly A-genome size expansion, evolution. Abundant species-specific structural variations in genic regions changed expression many important genes, led fiber cell improvement (AD) Our findings resolve controversial concepts surrounding origins provide valuable genomic resources for cotton genetic improvement.

Language: Английский

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Exploring Evolutionary Relationships Across the Genome Using Topology Weighting

Genetics, Journal Year: 2017, Volume and Issue: 206(1), P. 429 - 438

Published: March 25, 2017

Abstract We introduce the concept of topology weighting, a method for quantifying relationships between taxa that are not necessarily monophyletic, and visualizing how these change across genome. A given set can be related in limited number ways, but if each taxon is represented by multiple sequences, possible topologies becomes very large. Topology weighting reduces this complexity contribution to full tree. describe our iterative sampling subtrees (Twisst), test it on both simulated real genomic data. Overall, we show an informative versatile approach, suitable exploring almost any dataset. Scripts implement described available at http://github.com/simonhmartin/twisst.

Language: Английский

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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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Insect genomes: progress and challenges

Insect Molecular Biology, Journal Year: 2019, Volume and Issue: 28(6), P. 739 - 758

Published: May 23, 2019

Abstract In the wake of constant improvements in sequencing technologies, numerous insect genomes have been sequenced. Currently, 1219 genome‐sequencing projects registered with National Center for Biotechnology Information, including 401 that genome assemblies and 155 an official gene set annotated protein‐coding genes. Comparative genomics analysis showed expansion or contraction families was associated well‐studied physiological traits such as immune system, metabolic detoxification, parasitism polyphagy insects. Here, we summarize progress sequencing, emphasis on how this impacts research pest control. We begin a brief introduction to basic concepts assembly, annotation metrics evaluating quality draft assemblies. then provide overview information species, highlighting examples from prominent model organisms, agricultural pests disease vectors. also introduce major databases. The increasing availability genomic resources is beneficial developing alternative control methods. However, many opportunities remain data‐mining tools make maximal use available resources. Although rapid has achieved, challenges field genomics.

Language: Английский

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Single master regulatory gene coordinates the evolution and development of butterfly color and iridescence

Proceedings of the National Academy of Sciences, Journal Year: 2017, Volume and Issue: 114(40), P. 10707 - 10712

Published: Sept. 18, 2017

Significance The optix gene is well known for its genetic association with wing pattern variation in butterflies; however, actual function has never been directly confirmed. Using CRISPR genome editing multiple butterfly species, we show that this plays a fundamental and deeply conserved role the family Nymphalidae, where it acts as an activator of color. We were also surprised to discover simultaneously controls blue iridescence some species well, providing example how single can act switch coordinate between structural pigmentary coloration.

Language: Английский

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Supergene Evolution Triggered by the Introgression of a Chromosomal Inversion

Current Biology, Journal Year: 2018, Volume and Issue: 28(11), P. 1839 - 1845.e3

Published: May 24, 2018

Language: Английский

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Agouti-related peptide 2 facilitates convergent evolution of stripe patterns across cichlid fish radiations

Science, Journal Year: 2018, Volume and Issue: 362(6413), P. 457 - 460

Published: Oct. 26, 2018

The color patterns of African cichlid fishes provide notable examples phenotypic convergence. Across the more than 1200 East rift lake species, melanic horizontal stripes have evolved numerous times. We discovered that regulatory changes gene agouti-related peptide 2 (agrp2) act as molecular switches controlling this evolutionarily labile phenotype. Reduced agrp2 expression is convergently associated with presence stripe across species flocks. However, cis-regulatory mutations are not predictive radiations, suggesting independent mechanisms. Genetic mapping confirms link between locus and patterns. crucial role further supported by a CRISPR-Cas9 knockout reconstitutes in nonstriped cichlid. Thus, we unveil how single affects convergent evolution complex pattern.

Language: Английский

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