Adaptive Introgression across Semipermeable Species Boundaries between Local Helicoverpa zea and Invasive Helicoverpa armigera Moths

Molecular Biology and Evolution, Год журнала: 2020, Номер 37(9), С. 2568 - 2583

Опубликована: Апрель 23, 2020

Abstract Hybridization between invasive and native species has raised global concern, given the dramatic increase in range shifts pest outbreaks due to anthropogenic dispersal. Nevertheless, secondary contact sister lineages of local provides a natural laboratory understand factors that determine introgression maintenance or loss barriers. Here, we characterize early evolutionary outcomes following Helicoverpa armigera H. zea Brazil. We carried out whole-genome resequencing moths from Brazil two temporal samples: during outbreak 2013 2017. There is evidence for burst hybridization widespread into coinciding with expansion 2013. However, armigera, admixture proportion length introgressed blocks were significantly reduced 2017, suggesting selection against admixture. In contrast genome-wide pattern, there was striking adaptive single region zea, including an insecticide resistance allele increased frequency over time. summary, despite extensive gene flow after contact, boundaries are largely maintained except containing insecticide-resistant locus. document worst-case scenario species, which now instead one, acquired pyrethroid insecticides through introgression.

Язык: Английский

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The wild species genome ancestry of domestic chickens

BMC Biology, Год журнала: 2020, Номер 18(1)

Опубликована: Фев. 12, 2020

Abstract Background Hybridisation and introgression play key roles in the evolutionary history of animal species. They are commonly observed within several orders wild birds. The domestic chicken Gallus gallus domesticus is most common livestock More than 65 billion chickens raised annually to produce meat 80 million metric tons egg for global human consumption by commercial sector. Unravelling origin its genetic diversity has major application sustainable breeding improvement programmes. Results In this study, we report genome-wide analyses signatures between indigenous village four We first assess phylogeny divergence time across genus . Genome-wide sequence analysis supports a sister relationship Grey junglefowl G. sonneratii Ceylon lafayettii Both species form clade that Red , with Green varius ancient lineage genus. reveal extensive bidirectional much lesser extent junglefowl. identify single case introgression. These introgressed regions include genes biological functions related development immune system. Conclusions Our study shows while main ancestral species, introgressive hybridisation episodes have impacted genome contributed chicken, although likely at different levels geographic range.

Язык: Английский

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Ancient and recent introgression shape the evolutionary history of pollinator adaptation and speciation in a model monkeyflower radiation (Mimulus section Erythranthe)

PLoS Genetics, Год журнала: 2021, Номер 17(2), С. e1009095 - e1009095

Опубликована: Фев. 22, 2021

Inferences about past processes of adaptation and speciation require a gene-scale genome-wide understanding the evolutionary history diverging taxa. In this study, we use capture nuclear gene sequences, plus skimming organellar to investigate phylogenomics monkeyflowers in Mimulus section Erythranthe (27 accessions from seven species). Taxa within Erythranthe, particularly parapatric putatively sister species M. lewisii (bee-pollinated) cardinalis (hummingbird-pollinated), have been model system for investigating ecological genetics over five decades. Across >8000 loci, multiple methods resolve predominant tree which groups with other hummingbird-pollinated taxa (37% trees), rather than being (32% trees). We independently corroborate single evolution hummingbird pollination syndrome by demonstrating functional redundancy genetic complementation tests floral traits hybrids; together, these analyses overturn textbook case pollination-syndrome convergence. Strong asymmetries allele sharing (Patterson's D-statistic related tests) indicate that discordance reflects ancient recent introgression incomplete lineage sorting. Consistent abundant blurring divergence, low-recombination adaptation-associated regions support new tree, while high-recombination generate phylogenetic evidence status cardinalis. Population-level sampling core also revealed two instances chloroplast capture, Sierran Southern Californian parishii each carrying organelle genomes nested respective sympatric clades. A transfer cardinalis, an outcrosser where selfish cytonuclear dynamics are more likely, may account unexpected cytoplasmic male sterility effects selfer organelles hybrids lewisii. Overall, our phylogenomic results reveal extensive reticulation throughout classic monkeyflower radiation, suggesting natural selection (re-)assembles maintains species-diagnostic barriers face flow. Our findings further underline challenges, even reproductively isolated species, distinguishing re-use adaptive alleles true convergence emphasize value framework reconstructing speciation.

Язык: Английский

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Nanopore sequencing-based genome assembly and evolutionary genomics of circum-basmati rice

Genome biology, Год журнала: 2020, Номер 21(1)

Опубликована: Фев. 5, 2020

The circum-basmati group of cultivated Asian rice (Oryza sativa) contains many iconic varieties and is widespread in the Indian subcontinent. Despite its economic cultural importance, a high-quality reference genome currently lacking, group's evolutionary history not fully resolved. To address these gaps, we use long-read nanopore sequencing assemble genomes two varieties.We generate high-quality, chromosome-level that represent 12 chromosomes Oryza. assemblies show contig N50 6.32 Mb 10.53 for Basmati 334 Dom Sufid, respectively. Using our highly contiguous assemblies, characterize structural variations segregating across genomes. We discover repeat expansions observed japonica-the most closely related to circum-basmati-as well as presence absence variants over 20 Mb, one which circum-basmati-specific deletion gene regulating awn length. further detect strong evidence admixture between circum-aus groups. This flow has greatest effect on chromosome 10, causing both variation single-nucleotide polymorphism deviate from genome-wide history. Lastly, population genomic analysis 78 shows three major geographically structured genetic groups: Bhutan/Nepal, India/Bangladesh/Myanmar, Iran/Pakistan.The availability allows functional analyses providing circum-basmati, describes nature variation, reveals presence/absence this important variety group.

Язык: Английский

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Something old, something borrowed: admixture and adaptation in human evolution

Current Opinion in Genetics & Development, Год журнала: 2018, Номер 53, С. 1 - 8

Опубликована: Июнь 9, 2018

Язык: Английский

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The global diversity of Haemonchus contortus is shaped by human intervention and climate

Nature Communications, Год журнала: 2019, Номер 10(1)

Опубликована: Окт. 22, 2019

Abstract Haemonchus contortus is a haematophagous parasitic nematode of veterinary interest. We have performed survey its genome-wide diversity using single-worm whole genome sequencing 223 individuals sampled from 19 isolates spanning five continents. find an African origin for the species, together with evidence parasites spreading during transatlantic slave trade and colonisation Australia. Strong selective sweeps surrounding β-tubulin locus, target benzimidazole anthelmintic drug, are identified in independent populations. These further supported by signals diversifying selection enriched genes involved response to drugs other anthelmintic-associated biological functions. also identify some candidate that may play role ivermectin resistance. Finally, genetic signatures climate-driven adaptation described, revealing gene acting as epigenetic regulator components dauer pathway. results begin define climate nematode.

Язык: Английский

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The Persistence of Polymorphisms across Species Radiations

Trends in Ecology & Evolution, Год журнала: 2020, Номер 35(9), С. 795 - 808

Опубликована: Май 11, 2020

Язык: Английский

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Interspecific introgression mediates adaptation to whole genome duplication

Nature Communications, Год журнала: 2019, Номер 10(1)

Опубликована: Ноя. 18, 2019

Abstract Adaptive gene flow is a consequential phenomenon across all kingdoms. Although recognition increasing, there no study showing that bidirectional mediates adaptation at loci manage core processes. We previously discovered concerted molecular changes among interacting members of the meiotic machinery controlling crossover number upon to whole-genome duplication (WGD) in Arabidopsis arenosa . Here we conduct population genomic test hypothesis WGD has been mediated by adaptive between A. and lyrata find underwent more recently than , suggesting pre-adapted alleles have rescued nascent but also detect opposite direction functionally under most extreme levels selection. These data indicate allowed for survival after WGD, merger these species greater sum their parts.

Язык: Английский

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Selective sweeps on novel and introgressed variation shape mimicry loci in a butterfly adaptive radiation

PLoS Biology, Год журнала: 2020, Номер 18(2), С. e3000597 - e3000597

Опубликована: Фев. 6, 2020

Natural selection leaves distinct signatures in the genome that can reveal targets and history of adaptive evolution. By analysing high-coverage sequence data from 4 major colour pattern loci sampled nearly 600 individuals 53 populations, we show pervasive on wing patterns Heliconius radiation. The strongest correspond to with greatest phenotypic effects, consistent visual by predators, are found geographically restricted distributions. These recent sweeps similar between co-mimics indicate turn-over events despite strong stabilising selection. Using simulations, compare sweep expected under classic hard those resulting introgression, an important aspect mimicry evolution butterflies. Simulated recipient populations a 'volcano' peaks increased genetic diversity around selected target, characteristic introgressed variation some populations. Our genomic surprisingly dynamic co-evolution this

Язык: Английский

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

Molecular Ecology, Год журнала: 2021, Номер 30(23), С. 6036 - 6071

Опубликована: Май 19, 2021

Characterizing the population history of a species and identifying loci underlying local adaptation is crucial in functional ecology, evolutionary biology, conservation agronomy. The constant improvement high-throughput sequencing techniques has facilitated production whole genome data wide range species. Population genomics now provides tools to better integrate selection into historical framework, take account when reconstructing demographic history. However, this come with profusion analytical that can confuse discourage users. Such confusion limits amount information effectively retrieved from complex genomic sets, impairs diffusion most recent fields such as biology. It may also lead redundancy among methods. To address these isssues, we propose an overview more than 100 state-of-the-art methods deal data. We summarize strategies they use infer selection, discuss some their limitations. A website listing available at www.methodspopgen.com.

Язык: Английский

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