Recombination-Aware Phylogenomics Reveals the Structured Genomic Landscape of Hybridizing Cat Species

Molecular Biology and Evolution, Journal Year: 2019, Volume and Issue: 36(10), P. 2111 - 2126

Published: June 10, 2019

Current phylogenomic approaches implicitly assume that the predominant phylogenetic signal within a genome reflects true evolutionary history of organisms, without assessing confounding effects postspeciation gene flow can produce mosaic signals interact with recombinational variation. Here, we tested validity this assumption analysis 27 species cat family, local recombination rate on tree inference and divergence time estimation across their genomes. We found prevailing autosomes is not always representative most probable speciation history, due to ancient hybridization throughout felid evolution. Instead, was concentrated regions low recombination, notably enriched large X chromosome cold spots exhibited recurrent patterns strong genetic differentiation selective sweeps mammalian orders. By contrast, high were for signatures flow, these sequences inflated crown-lineage times by ∼40%. conclude existing infer Tree Life may be highly misleading considering genomic architecture relative its interplay historical hybridization.

Language: Английский

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Reproductive transitions in plants and animals: selfing syndrome, sexual selection and speciation

New Phytologist, Journal Year: 2019, Volume and Issue: 224(3), P. 1080 - 1094

Published: July 23, 2019

The evolution of predominant self-fertilisation frequently coincides with the a collection phenotypes that comprise 'selfing syndrome', in both plants and animals. Genomic features also display selfing syndrome. Selfing syndrome traits often involve changes to male female reproductive characters were subject sexual selection conflict obligatorily outcrossing ancestor, including gametic phase for Rapid traits, due relaxed directional under new status selfing, lays genetic groundwork isolation. Consequently, shifts pressures coupled transitions provide powerful paradigm investigating speciation process. Plant animal studies, however, emphasise distinct selective forces influencing reproductive-mode transitions: transmission advantage or assurance outweighing costs inbreeding depression vs males meiosis. Here, I synthesise links between selection, speciation, particular focus on identifying commonalities differences plant systems pointing areas warranting further synergy.

Language: Английский

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Comparative studies on speciation: 30 years since Coyne and Orr

Evolution, Journal Year: 2021, Volume and Issue: 75(4), P. 764 - 778

Published: Jan. 25, 2021

Understanding the processes of population divergence and speciation remains a core question in evolutionary biology. For nearly hundred years geneticists have characterized reproductive isolation (RI) mechanisms specific barriers to gene flow required for species formation. The seminal work Coyne Orr provided first comprehensive comparative analysis speciation. By combining phylogenetic hypotheses range data with estimates genetic multiple RI across Drosophila, Orr's influential meta-analyses answered fundamental questions motivated new analyses that continue push field forward today. Now 30 later, we revisit five addressed by Orr, identifying results remain well supported others seem less robust data. We then consider future research, emphasis on areas where novel methods motivate potential progress. While literature biased towards Drosophila other model systems, are enthusiastic about field.

Language: Английский

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How Important Are Structural Variants for Speciation?

Genes, Journal Year: 2021, Volume and Issue: 12(7), P. 1084 - 1084

Published: July 17, 2021

Understanding the genetic basis of reproductive isolation is a central issue in study speciation. Structural variants (SVs); that is, structural changes DNA, including inversions, translocations, insertions, deletions, and duplications, are common broad range organisms have been hypothesized to play role Recent advances molecular statistical methods identified variants, especially underlying ecologically important traits; thus, suggesting these mutations contribute adaptation. However, contribution between species—and mechanism by which most often speciation—remain unclear. Here, we review (i) different mechanisms can generate or maintain isolation; (ii) patterns expected with mechanisms; (iii) relevant empirical examples each. We also summarize available sequencing bioinformatic detect variants. Lastly, suggest approaches new research directions help obtain more complete assessment

Language: Английский

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A genetic switch for male UV iridescence in an incipient species pair of sulphur butterflies

Proceedings of the National Academy of Sciences, Journal Year: 2022, Volume and Issue: 119(3)

Published: Jan. 10, 2022

Significance Incipient species are at an intermediate stage of speciation where reproductive isolation is counteracted by the homogenizing effects gene flow. Human activity sometimes leads such to reunite, as seen in Orange Sulphur butterfly, which forms large hybridizing populations with Clouded alfalfa fields. Here we show that sex chromosomes maintain these distinct, while rest their genome admixed. Sex notably determine males display females a bright, iridescent UV signal on wings. Genetic mapping, antibody stainings, and CRISPR knockouts collectively indicate bric brac controls whether UV-iridescent nanostructures develop each species, illustrating how master switch modulates male courtship signal.

Language: Английский

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Gene flow mediates the role of sex chromosome meiotic drive during complex speciation

eLife, Journal Year: 2018, Volume and Issue: 7

Published: Dec. 13, 2018

During speciation, sex chromosomes often accumulate interspecific genetic incompatibilities faster than the rest of genome. The drive theory posits that are susceptible to recurrent bouts meiotic and suppression, causing evolutionary build-up divergent cryptic sex-linked systems and, incidentally, incompatibilities. To assess role during we combine high-resolution mapping X-linked hybrid male sterility with population genomics analyses divergence recent gene flow between fruitfly species, Drosophila mauritiana D. simulans. Our findings reveal a high density corresponding dearth on X chromosome. Surprisingly, find known element recently migrated species rather contributing divergence, caused strong reduction in local sequence undermining evolution sterility. Gene can therefore mediate effects selfish elements speciation.

Language: Английский

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Introduction: Sex chromosomes and speciation

Molecular Ecology, Journal Year: 2018, Volume and Issue: 27(19), P. 3745 - 3748

Published: Aug. 7, 2018

Language: Английский

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Hybrid Sterility, Genetic Conflict and Complex Speciation: Lessons From the Drosophila simulans Clade Species

Frontiers in Genetics, Journal Year: 2021, Volume and Issue: 12

Published: June 23, 2021

The three fruitfly species of the Drosophila simulans clade— D. simulans, mauritiana , and sechellia — have served as important models in speciation genetics for over 40 years. These are reproductively isolated by geography, ecology, sexual signals, postmating-prezygotic interactions, postzygotic genetic incompatibilities. All pairwise crosses between these conform to Haldane’s rule, producing fertile F 1 hybrid females sterile males. close phylogenetic proximity clade model organism, melanogaster has empowered analyses their differences, including reproductive But perhaps no phenotype been subject more continuous intensive scrutiny than male sterility. Here we review history, progress, current state our understanding sterility among species. Our aim is integrate available information from experimental population bearing on causes consequences We highlight numerous conclusions that emerged well issues remain unresolved. focus special role sex chromosomes, fine-scale architecture sterility, history gene flow biggest surprises emerge this work ( i ) conflicts may be an general force evolution incompatibility, ii polygenic with contributions complex epistasis, iii speciation, even geographically allopatric taxa, involved interplay flow, negative selection, positive selection. marked departures classical views modern evolutionary synthesis.

Language: Английский

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Population genomics provides insights into lineage divergence and local adaptation within the cotton bollworm

Molecular Ecology Resources, Journal Year: 2022, Volume and Issue: 22(5), P. 1875 - 1891

Published: Jan. 10, 2022

The cotton bollworm Helicoverpa armigera is a cosmopolitan pest and its diverse habitats plausibly contribute to the formation of lineages. Despite significant threat it poses economic crops worldwide, evolutionary history genetic basis local adaptation are poorly understood. In this study, we de novo assembled high-quality chromosome-level reference genome H. a. (contig N50 = 7.34 Mb), with 99.13% HaSCD2 assembly assigned 31 chromosomes (Z-chromosome + 30 autosomes). We constructed an ultradense variation map across 14 populations identified novel lineage in northwestern China. Historical inference showed that effective population size changes coincided global temperature fluctuation. nine differentiated genes three lineages (H. armigera, conferta new Chinese lineage), which per clk involved circadian rhythm. Selective sweep analyses series Gene Ontology categories related climate adaptation, feeding behaviour insecticide tolerance. Our findings reveal fundamental knowledge different will guide formulation management measures at scales.

Language: Английский

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A Chinese indicine pangenome reveals a wealth of novel structural variants introgressed from otherBosspecies

Genome Research, Journal Year: 2023, Volume and Issue: 33(8), P. 1284 - 1298

Published: Aug. 1, 2023

Chinese indicine cattle harbor a much higher genetic diversity compared with other domestic cattle, but their genome architecture remains uninvestigated. Using PacBio HiFi sequencing data from 10 across southern China, we assembled 20 high-quality partially phased genomes and integrated them into multiassembly graph containing 148.5 Mb (5.6%) of novel sequence. We identified 156,009 high-confidence nonredundant structural variants (SVs) 206 SV hotspots spanning ∼195 gene-rich detected 34,249 archaic introgressed fragments in covering 1.93 Gb (73.3%) the genome. inferred an average 3.8%, 3.2%, 1.4%, 0.5% sequence originating, respectively, banteng-like, kouprey-like, gayal-like, gaur-like

Language: Английский

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