Structural Variants and Speciation: Multiple Processes at Play

Cold Spring Harbor Perspectives in Biology, Год журнала: 2023, Номер 16(3), С. a041446 - a041446

Опубликована: Дек. 5, 2023

Emma L. Berdan1,2, Thomas G. Aubier3,4, Salvatore Cozzolino5, Rui Faria6,7, Jeffrey Feder8, Mabel D. Giménez9,10, Mathieu Joron11, Jeremy B. Searle12 and Claire Mérot13 1Department of Marine Sciences, Gothenburg University, 40530, Sweden 2Bioinformatics Core, Department Biostatistics, Harvard T.H. Chan School Public Health, Medical School, Boston, Massachusetts 02115, USA 3Laboratoire Évolution & Diversité Biologique, Université Paul Sabatier Toulouse III, UMR 5174, CNRS/IRD, 31077 Toulouse, France 4Department Biology, University North Carolina at Chapel Hill, 27599, 5Department Naples Federico II, Complesso Universitario di Monte S. Angelo, 80126 Napoli, Italia 6CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Universidade do Porto, Vairão, Portugal 7BIOPOLIS Program in Genomics, Biodiversity Land Planning, CIBIO, 4485-661 8Department Biological Notre Dame, Indiana 46556, 9Consejo Nacional Investigaciones Científicas y Técnicas (CONICET), Instituto Genética Humana Misiones (IGeHM), Parque la Salud Provincia "Dr. Ramón Madariaga," N3300KAZ Posadas, Misiones, Argentina 10Facultad Ciencias Exactas, Químicas Naturales, Universidad N3300LQH 11Centre d'Ecologie Fonctionnelle et Evolutive, Montpellier, CNRS, EPHE, IRD, 12Department Ecology Evolutionary Cornell Ithaca, New York 14853, 13CNRS, 6553 Ecobio, OSUR, Rennes, 35000 Correspondence: claire.merot{at}gmail.com; emma.berdan{at}gmail.com

Язык: Английский

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Sex‐biased gene content is associated with sex chromosome turnover in Danaini butterflies

Molecular Ecology, Год журнала: 2024, Номер 33(24)

Опубликована: Янв. 5, 2024

Sex chromosomes play an outsized role in adaptation and speciation, thus deserve particular attention evolutionary genomics. In particular, fusions between sex autosomes can produce neo-sex chromosomes, which offer important insights into the dynamics of chromosomes. Here, we investigate origin previously reported Danaus chromosome within tribe Danaini. We assembled annotated genomes Tirumala septentrionis (subtribe Danaina), Ideopsis similis (Amaurina), Idea leuconoe (Euploeina) Lycorea halia (Itunina) identified their Z-linked scaffolds. found that resulting from fusion a Z autosome corresponding to Melitaea cinxia (McChr) 21 arose common ancestor Danaina, Amaurina Euploina. also two additional as W further fused with synteny block McChr31 I. independent occurred ancestral McChr12 L. halia. tested possible sexually antagonistic selection turnover by analysing genomic distribution sex-biased genes The McChr21 involved are significantly enriched female- male-biased genes, respectively, could have hypothetically facilitated fixation This suggests sexual antagonism Lepidoptera. neo-Z both appear fully compensated somatic tissues, but extent dosage compensation for varies across tissues species.

Язык: Английский

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A punctuated burst of massive genomic rearrangements by chromosome shattering and the origin of non-marine annelids

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Май 20, 2024

The genomic basis of cladogenesis and adaptive evolutionary change has intrigued biologists for decades. unique insights gained from a genome-level perspective have revealed striking pattern conserved macrosynteny within chromosomes across huge phylogenetic distances in animals, yet progress many lineages been hampered by the absence data. Here, we show that tectonics genome evolution clitellates, clade composed most freshwater all terrestrial species phylum Annelida, is characterised extensive genome-wide scrambling resulted massive loss between marine annelids to point ancient bilaterian linkage groups (ie, genes inherited as block phyla) are fully disrupted. These rearrangements included formation putative neocentromeres with newly acquired transposable elements, preceded further period reshaping events including whole-genome duplications macrosyntenic reshuffling clitellate lineages, potentially triggered involved stability homeostasis cell division. Notably, while these broke short-range interactions observed Hox annelids, they were reformed long-range clitellates. led relocation new chimeric genetic both which may contributed adaptation clitellates environments. Our findings provide evidence at 2D 3D levels, suggest synteny not limit structural this animal lineage. study thus suggests landscape Clitellata rare burst changes ended long persists large distances.

Язык: Английский

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Mechanisms of Intrinsic Postzygotic Isolation: From Traditional Genic and Chromosomal Views to Genomic and Epigenetic Perspectives

Cold Spring Harbor Perspectives in Biology, Год журнала: 2023, Номер 15(10), С. a041607 - a041607

Опубликована: Сен. 11, 2023

Radka Reifová1, S. Lorena Ament-Velásquez2, Yann Bourgeois3, Jenn Coughlan4, Jonna Kulmuni5,6, Agnieszka P. Lipinska7,8, Genta Okude9, Laurie Stevison10, Kohta Yoshida9 and Jun Kitano9 1Department of Zoology, Faculty Science, Charles University, 128 00 Prague, Czech Republic 2Department Stockholm 106 91 Stockholm, Sweden 3DIADE, University Montpellier, CIRAD, IRD, 34090 France 4Department Ecology & Evolutionary Biology, Yale New Haven, Connecticut 06520, USA 5Institute for Biodiversity Ecosystem Dynamics, Department Population Amsterdam, 1012 The Netherlands 6Organismal Biology Research Programme, Helsinki, 00100 Finland 7Department Algal Development Evolution, Max Planck Institute 72076 Tuebingen, Germany 8CNRS, UMR 8227, Integrative Marine Models, Sorbonne Université, Station Biologique de Roscoff, 29680 9Department Genomics National Genetics, Mishima, Shizuoka 411-8540, Japan 10Department Biological Sciences, Auburn Auburn, Alabama 36849, Correspondence: radka.reifova{at}natur.cuni.cz; jkitano{at}nig.ac.jp

Язык: Английский

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Combining Molecular, Macroevolutionary, and Macroecological Perspectives on the Generation of Diversity

Cold Spring Harbor Perspectives in Biology, Год журнала: 2024, Номер 16(9), С. a041453 - a041453

Опубликована: Март 19, 2024

Charles Darwin presented a unified process of diversification driven by the gradual accumulation heritable variation. The growth in DNA databases and increase genomic sequencing, combined with advances molecular phylogenetic analyses, gives us an opportunity to realize Darwin's vision, connecting generation variation lineages. rate evolution is correlated across animals plants, but relationship between genome change speciation complex: Mutation rates evolve response life history niche; substitution are influenced mutation, selection, population size; acquisition reproductive isolation vary populations; traits, niches, distribution can influence rates. connection mutation one part complex varied story speciation, which has theoretical importance for understanding biodiversity also practical impacts on use understand dynamics over macroevolutionary timescales.

Язык: Английский

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Cytogenetic insights into Sosippinae (Araneae, Lycosidae) reveal pronounced diploid number reduction in Aglaoctenus and elevated number of rDNA loci in two unrelated species

Zoology, Год журнала: 2025, Номер 170, С. 126269 - 126269

Опубликована: Апрель 17, 2025

Язык: Английский

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Hierarchical architecture of neo-sex chromosomes and accelerated adaptive evolution in tortricid moths

Genome Research, Год журнала: 2025, Номер 35(1), С. 66 - 77

Опубликована: Янв. 1, 2025

Sex chromosomes can expand through fusion with autosomes, thereby acquiring unique evolutionary patterns. In butterflies and moths (Lepidoptera), these sex chromosome–autosome (SA) fusions occur relatively frequently, suggesting possible advantages. Here, we investigated how SA affects chromosome features molecular evolution in leafroller (Lepidoptera: Tortricidae). Phylogenomic analysis showed that Tortricidae diverged ∼124 million years ago, accompanied by an between the Merian elements M(20 + 17) MZ. contrast to partial autosomal fusions, fused neo-Z Chromosome developed a hierarchical architecture, which three exhibit heterogeneous sequence Specifically, M17 part had distinct base composition chromatin domains. Unlike M20 MZ, was expressed at same levels as autosomes both sexes, compensating for lost gene dosage females. Concurrently, drove hotspot, accelerating of several genes related ecological adaptation (e.g., ABCC s) facilitating divergence closely species, whereas undercompensated did not show such effect. Thus, accelerated under novel pattern compensation may have favored adaptive radiation this group. This study demonstrates association karyotype variant explains recurrent Lepidoptera.

Язык: Английский

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Centromere diversity and its evolutionary impacts on plant karyotypes and plant reproduction

New Phytologist, Год журнала: 2025, Номер 245(5), С. 1879 - 1886

Опубликована: Янв. 6, 2025

Summary Karyotype changes are a formidable evolutionary force by directly impacting cross‐incompatibility, gene dosage, genetic linkage, chromosome segregation, and meiotic recombination landscape. These often arise spontaneously commonly detected within plant lineages, even between closely related accessions. One element that can influence drastic karyotype after only one (or few) generations is the alteration of centromere position, number, distribution, or its strength. Here, we briefly explore how these different configurations result in rearrangements, reproduction recombination.

Язык: Английский

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Chromosomal rearrangements drive diversity in arboreal rodents of the genus Oecomys

Scientific Reports, Год журнала: 2025, Номер 15(1)

Опубликована: Фев. 19, 2025

Oecomys (Rodentia, Sigmodontinae, Oryzomyini) is a taxonomically complex and cytogenetically diverse genus with controversial intraspecific phylogenetic relationship. Karyotypic analyses, using whole chromosome probes from Hylaeamys megacephalus (HME, in some taxonomic lineages of this have detected the rearrangements that shaped their karyotypes, addition to revealing relevant insights into status these taxa. Thus, investigate chromosomal evolution genus, we characterized karyotype rutilus (ORU) HME probes, establishing homology maps karyotypes other congeners. The phylogeny obtained by Maximum Parsimony analysis recovered as monophyletic, moderate bootstrap support (68%). This clade branches two large groups, first including O. followed catherinae—Rio de Janeiro catherinae—Pará; group includes auyantepui paricola cytotype C A + B. We taxa underwent intensive reorganization producing diversity were 15 pericentric inversions, 12 centric fusions, 11 fissions, 5 tandem 8 translocations addition/deletion constitutive heterochromatin on autosomes X chromosomes. However, despite high number found, identified entirely conserved syntenic blocks shared among all species analyzed. From data, hypothesized putative ancestral karyotype. also exclusive characteristics for ORU, 1/20/4 (ORU 1), (16,17)/3 2), 2/1 4), 2/7 5), 5/(9,10)/8 3), 19/12 9). provide an overview points show play important role radiation species.

Язык: Английский

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Population divergence manifested by genomic rearrangements in a keystone Arctic species with high gene flow

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Июнь 28, 2024

Abstract Genomic rearrangements have in recent years gained attention due to their evolutionary role processes related adaptation local environmental conditions as well diversification and speciation. In this study, we report on genomic the cold-water adapted polar cod ( Boreogadus saida ), a keystone Arctic fish species. By taking advantage of new chromosome-level genome assembly combination with whole-genome population sequencing data from specimens across northern Barents Sea adjacent regions, identified substantial number larger chromosomal inversions (n=20) characterized previously fusions (n=5). These features — encompassing over 20% exhibited genetic divergence, strong internal linkage disequilibrium, signals selection. Two were associated two described hemoglobin clusters, while third region was found differentiate between males females. Moreover, clustering analyses genotype frequencies revealed sub- structuring according five geographic sub-groups suggesting sub-populations and/or existence cryptic ecotypes. results provide novel insights into impact divergence thus, potentially adaptation, especially species high gene flow.

Язык: Английский

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