MitoFinder: Efficient automated large‐scale extraction of mitogenomic data in target enrichment phylogenomics

Molecular Ecology Resources, Journal Year: 2020, Volume and Issue: 20(4), P. 892 - 905

Published: April 3, 2020

Abstract Thanks to the development of high‐throughput sequencing technologies, target enrichment nuclear ultraconserved DNA elements (UCEs) now allows routine inference phylogenetic relationships from thousands genomic markers. Recently, it has been shown that mitochondrial (mtDNA) is frequently sequenced alongside targeted loci in such capture experiments. Despite its broad evolutionary interest, mtDNA rarely assembled and used conjunction with markers capture‐based studies. Here, we developed MitoFinder, a user‐friendly bioinformatic pipeline, efficiently assemble annotate mitogenomic data hundreds UCE libraries. As case study, ants (Formicidae) for which 501 libraries have whereas only 29 mitogenomes are available. We compared efficiency four different assemblers (IDBA‐UD, MEGAHIT, MetaSPAdes, Trinity) assembling both loci. Using show metagenomic assemblers, particular well suited UCEs mtDNA. Mitogenomic signal was successfully extracted all libraries, allowing us confirm species identification using CO1 barcoding. Moreover, our automated procedure retrieved 296 cases genome single contig, thus increasing number available ant by an order magnitude. By utilizing power MitoFinder provides efficient tool extract complementary testing potential mitonuclear discordance. Our approach potentially applicable other sequence methods, transcriptomic whole shotgun diverse taxa. The software GitHub ( https://github.com/RemiAllio/MitoFinder ).

Language: Английский

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Triticum population sequencing provides insights into wheat adaptation

Nature Genetics, Journal Year: 2020, Volume and Issue: 52(12), P. 1412 - 1422

Published: Oct. 26, 2020

Language: Английский

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The evolutionary history of Neanderthal and Denisovan Y chromosomes

Science, Journal Year: 2020, Volume and Issue: 369(6511), P. 1653 - 1656

Published: Sept. 25, 2020

Y chromosome evolution in Neanderthals The genomes of archaic hominins have been sequenced and compared with that modern humans. However, most individuals high-quality sequences available female. Petr et al. performed targeted sequencing the paternally inherited chromosomes from three two Denisovans (see Perspective by Schierup). Comparisons diverse human indicated that, similar to maternally mitochondria, Neanderthal were more closely related each other Denisovan chromosome. This result supports conclusion interbreeding between early humans selection replaced ancient Denisovian-like mitochondria Neanderthals. Science , this issue p. 1653 ; see also 1565

Language: Английский

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The genomic impact of historical hybridization with massive mitochondrial DNA introgression

Genome biology, Journal Year: 2018, Volume and Issue: 19(1)

Published: July 17, 2018

The extent to which selection determines interspecific patterns of genetic exchange enlightens the role adaptation in evolution and speciation. Often reported extensive introgression could be selection-driven, but also result from demographic processes, especially cases invasive species replacements, can promote at their invasion front. Because selective sweeps similarly mold variation, population genetics evidence for only gathered an explicit framework. Iberian hare, Lepus granatensis, displays its northern range mitochondrial DNA L. timidus, arctic/boreal that it replaced locally after last glacial maximum. We use whole-genome sequencing infer geographic genomic nuclear fit a neutral model replacement with hybridization, allowing us evaluate how influenced genome-wide, including mtDNA.Although average mtDNA contrast strongly, they single post-glacial timidus by granatensis. Outliers elevated include several genes related immunity, spermatogenesis, metabolism. Introgression is reduced on X chromosome low recombining regions.General explained purely processes. Hybrid incompatibilities interplay between recombination modulate levels introgression. Selection promoted some involved conflicts, either (parasites) or possibly cytonuclear. In latter case, mitigate potential negative effects alien metabolism male-specific traits.

Language: Английский

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Insights into invasive species from whole‐genome resequencing

Molecular Ecology, Journal Year: 2021, Volume and Issue: 30(23), P. 6289 - 6308

Published: May 27, 2021

Studies of invasive species can simultaneously inform management strategies and quantify rapid evolution in the wild. The role genomics invasion science is increasingly recognised, growing availability reference genomes for paving way whole-genome resequencing studies a wide range systems. Here, we survey literature to assess application data biology. For some applications, such as reconstruction routes time space, sequencing whole genome many individuals increase accuracy existing methods. In other cases, population genomic approaches haplotype analysis permit entirely new questions be addressed technologies applied. To date has only been used handful systems, but these have confirmed importance processes balancing selection hybridization allowing reuse adaptations rapidly overcome challenges foreign ecosystem. use does not constitute paradigm shift per se, by leveraging theory, tools, technologies, provide unprecedented insight into basic applied aspects science.

Language: Английский

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“Ghost Introgression” As a Cause of Deep Mitochondrial Divergence in a Bird Species Complex

Molecular Biology and Evolution, Journal Year: 2019, Volume and Issue: 36(11), P. 2375 - 2386

Published: July 24, 2019

In the absence of nuclear-genomic differentiation between two populations, deep mitochondrial divergence (DMD) is a form mito-nuclear discordance. Such instances DMD are rare and might variably be explained by unusual cases female-linked selection, male-biased dispersal, "speciation reversal" or capture through genetic introgression. Here, we analyze in an Asian Phylloscopus leaf warbler (Aves: Phylloscopidae) complex. Bioacoustic, morphological, genomic data demonstrate close similarity taxa affinis occisinensis, even though previously led to their classification as distinct species. Using population comparative methods on 45 whole genomes, including historical reconstructions effective size, peaks linkage, infer that likely product westward expansion which it replaced now-extinct congener was donor its mtDNA small portions nuclear genome. This study provides strong evidence "ghost introgression" cause DMD, suggest may widely overlooked phenomenon nature.

Language: Английский

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Introgression drives repeated evolution of winter coat color polymorphism in hares

Proceedings of the National Academy of Sciences, Journal Year: 2019, Volume and Issue: 116(48), P. 24150 - 24156

Published: Nov. 11, 2019

Changing from summer-brown to winter-white pelage or plumage is a crucial adaptation seasonal snow in more than 20 mammal and bird species. Many of these species maintain nonwhite winter morphs, locally adapted less snowy conditions, which may have evolved independently. Mountain hares ( Lepus timidus ) Fennoscandia were introduced into the Faroe Islands 1855. While they initially winter-white, within ∼65 y all Faroese became winter-gray, morph that occurs source population at low frequency. The documented history makes this valuable model for understanding genetic basis evolution trait polymorphism. Through whole-genome scans differentiation single-nucleotide polymorphism (SNP) genotyping, we associated coat color genomic region pigmentation gene Agouti , previously linked introgression-driven variation snowshoe hare americanus ). Lower expression skin winter-gray individuals during autumn molt suggests regulatory changes underlie Variation shows signatures selective sweep population, suggesting positive selection drove fixation variant after introduction. Whole-genome analyses several revealed originated through introgression noncolor changing species, keeping with ancient hybridization between Our findings show recurrent role generating by repeatedly recruiting modulate change.

Language: Английский

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Ghost Introgression: Spooky Gene Flow in the Distant Past

BioEssays, Journal Year: 2020, Volume and Issue: 42(6)

Published: March 29, 2020

Abstract Evolution is a continuous trial and error process in which most lineages go extinct without leaving fossil remains. Many of these would be closely related occasionally hybridized with that gave rise to extant species. Hence, it likely one can find genetic signatures ancient introgression events present‐day genomes, so‐called ghost introgression. The increasing availability high‐quality genome assemblies for non‐model organisms the development more sophisticated methods detecting will undoubtedly reveal cases introgression, indicating Tree Life even reticulated than assumed. presence has important consequences study numerous evolutionary processes, including adaptation, speciation, macroevolutionary patterns. In addition, detailed studies introgressed regions could provide insights into morphology lineage, providing an unexpected link between genomics record. new take account need developed.

Language: Английский

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Subfamily evolution analysis using nuclear and chloroplast data from the same reads

Scientific Reports, Journal Year: 2025, Volume and Issue: 15(1)

Published: Jan. 3, 2025

The chloroplast (cp) genome is a widely used tool for exploring plant evolutionary relationships, yet its effectiveness in fully resolving these relationships remains uncertain. Integrating cp data with nuclear DNA information offers more comprehensive view but often requires separate datasets. In response, we employed the same raw read sequencing to construct genome-based trees and phylogenetic using Read2Tree, cost-efficient method extracting conserved gene sequences from data, focusing on Aurantioideae subfamily, which includes Citrus relatives. resulting were consistent existing derived high-throughput sequencing, diverged trees. To elucidate underlying complex processes causing discordances, implemented an integrative workflow that utilized multiple alignments of each generated by conjunction other phylogenomic methods. Our analysis revealed incomplete lineage sorting predominantly drives while introgression ancient also contribute topological discrepancies within certain clades. This study underscores cost-effectiveness both analyses understanding relationships.

Language: Английский

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Five millennia of mitonuclear discordance in Atlantic bluefin tuna identified using ancient DNA

Heredity, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 7, 2025

Mitonuclear discordance between species is readily documented in marine fishes. Such may either be the result of past natural phenomena or recent introgression from previously seperated after shifts their spatial distributions. Using ancient DNA spanning five millennia, we here investigate long-term presence Pacific bluefin tuna (Thunnus orientalis) and albacore alalunga) -like mitochondrial (MT) genomes Atlantic thynnus), a with extensive exploitation history observed abundance age structure. Comparing (n = 130) modern 78) MT most its range, detect no significant temporal population structure, which implies ongoing gene flow populations large effective sizes over millennia. Moreover, identify discordant haplotypes specimens up to 5000 years old find that frequency these has remained similar through time. We therefore conclude not driven by introgression. Our observations provide oldest example directly environment, highlighting utility obtain insights persistence such phenomena.

Language: Английский

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