The Impact of Chromosomal Rearrangements in Speciation: From Micro- to Macroevolution

Cold Spring Harbor Perspectives in Biology, Journal Year: 2023, Volume and Issue: 15(11), P. a041447 - a041447

Published: Aug. 21, 2023

Kay Lucek1, Mabel D. Giménez2,3, Mathieu Joron4, Marina Rafajlović5,6, Jeremy B. Searle7, Nora Walden8, Anja Marie Westram9,10 and Rui Faria11,12 1Biodiversity Genomics Laboratory, Institute of Biology, University Neuchâtel, 2000 Switzerland 2Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto Genética Humana Misiones (IGeHM), Parque la Salud Provincia "Dr. Ramón Madariaga," N3300KAZ Posadas, Misiones, Argentina 3Facultad Ciencias Exactas Químicas Naturales, Universidad N3300LQH 4Centre d'Ecologie Fonctionnelle et Evolutive, Université Montpellier, CNRS, EPHE, IRD, 34293 France 5Department Marine Sciences, Gothenburg, 405 30 Sweden 6Centre for Evolutionary 7Department Ecology Cornell University, Ithaca, New York 14853, USA 8Centre Organismal Studies, Heidelberg, 69117 Germany 9Institute Science Technology Austria (ISTA), 3400 Klosterneuburg, 10Faculty Biosciences Aquaculture, Nord 8026 Bodø, Norway 11CIBIO, Centro Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, CIBIO, Campus Vairão, Universidade do Porto, 4485-661 Portugal 12BIOPOLIS Program in Genomics, Biodiversity Land Planning, Correspondence: kay.lucek{at}unine.ch; ruifaria{at}cibio.up.pt

Language: Английский

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Coupling of Barriers to Gene Exchange: Causes and Consequences

Cold Spring Harbor Perspectives in Biology, Journal Year: 2024, Volume and Issue: 16(8), P. a041432 - a041432

Published: Jan. 8, 2024

Erik B. Dopman1, Kerry L. Shaw2, Maria R. Servedio3, Roger K. Butlin4,5 and Carole M. Smadja6 1Department of Biology, Tufts University, Medford, Massachusetts 02155, USA 2Department Neurobiology Behavior, Cornell Ithaca, New York 14853, 3Department University North Carolina, Chapel Hill, Carolina 27599, 4Ecology Evolutionary School Biosciences, The Sheffield, Western Bank, Sheffield S10 2TN, United Kingdom 5Department Marine Sciences, Gothenburg, Gothenburg 40530, Sweden 6Institut des Sciences de l'Evolution Montpellier ISEM, Universite Montpellier, CNRS, IRD, 34095, France Correspondence: erik.dopman{at}tufts.edu

Language: Английский

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​​Fusion, fission, and scrambling of the bilaterian genome in Bryozoa

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Feb. 16, 2024

Abstract Groups of orthologous genes are commonly found together on the same chromosome over vast evolutionary distances. This extensive physical gene linkage, known as macrosynteny, is seen between bilaterian phyla divergent Chordata, Echinodermata, Mollusca, and Nemertea. Here, we report a unique pattern genome evolution in Bryozoa, an understudied phylum colonial invertebrates. Using comparative genomics, reconstruct chromosomal history five bryozoans. Multiple ancient fusions followed by mixing led to near-complete loss linkage groups ancestor extant A second wave rearrangements, including fission, then occurred independently two bryozoan classes, further scrambling genomes. We also discover at least derived fusion events shared bryozoans brachiopods, supporting traditional but highly debated Lophophorata hypothesis. Finally, show that fission processes partitioning from Hox clusters onto multiple chromosomes. Our findings demonstrate canonical structure has been lost across all studied representatives entire phylum; reveal group can occur very frequently specific lineages; provide powerful source phylogenetic information.

Language: 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, Journal Year: 2023, Volume and Issue: 15(10), P. a041607 - a041607

Published: Sept. 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

Language: Английский

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Fusion, fission, and scrambling of the bilaterian genome in Bryozoa

Genome Research, Journal Year: 2025, Volume and Issue: 35(1), P. 78 - 92

Published: Jan. 1, 2025

Groups of orthologous genes are commonly found together on the same chromosome over vast evolutionary distances. This extensive physical gene linkage, known as macrosynteny, is seen between bilaterian phyla divergent Chordata, Echinodermata, Mollusca, and Nemertea. Here, we report a unique pattern genome evolution in Bryozoa, an understudied phylum colonial invertebrates. Using comparative genomics, reconstruct chromosomal history five bryozoans. Multiple ancient fusions followed by mixing led to near-complete loss linkage groups ancestor extant A second wave rearrangements, including fission, then occurred independently two bryozoan classes, further scrambling genomes. We also discover at least derived fusion events shared bryozoans brachiopods, supporting traditional but highly debated Lophophorata hypothesis suggesting macrosynteny be potentially powerful source phylogenetic information. Finally, show that rearrangements dispersion from Hox clusters onto multiple chromosomes. Our findings demonstrate canonical structure has been lost across all studied representatives entire phylum, reveal group fission can occur very frequently specific lineages.

Language: Английский

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Unravelling genomic drivers of speciation in Musa through genome assemblies of wild banana ancestors

Nature Communications, Journal Year: 2025, Volume and Issue: 16(1)

Published: Jan. 23, 2025

Abstract Hybridization between wild Musa species and subspecies from Southeast Asia is at the origin of cultivated bananas. The genomes these cultivars are complex mosaics involving nine genetic groups, including two previously unknown contributors. This study provides continuous genome assemblies for six one which represents ancestor, identified as M. acuminata ssp. halabanensis . second ancestor partially present in a seventh assembly appears related to zebrina These provide key resources banana genetics improving cultivar assemblies, that emblematic triploid Cavendish. Comparative phylogenetic analyses reveal an ongoing speciation process within , characterised by large chromosome rearrangements centromere differentiation through integration different types repeated sequences, rDNA tandem repeats. may have been favoured reproductive isolation particular context climate land connectivity fluctuations Asian region.

Language: Английский

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SVCFit: Inferring structural variant cellular fraction in tumors

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 3, 2025

Abstract Many tumors evolve through cellular mutation and selection, where subpopulations of cells (subclones) with shared ancestry compete for dominance. Introduction next generation sequencing enables subclone identification using small somatic. However, there are several advantages to marking subclones structural variants: they have greater functional impact, play a crucial role in late-stage tumors, provide more complete view genomic instability driving tumor evolution. Here, we present SVCFit, scalable method estimate the prevalence somatic deletions, duplications inversions. We demonstrate that estimation can be improved by incorporating distinct read patterns each variant type. Additionally, this improvement is achieved without prior knowledge purity, which often inaccurate. Using combination simulated data patient-derived metastatic samples known mixture proportions, show our algorithm achieves significantly accuracy than state-of-the-art estimating variants (p<0.05). The speed SVCFit from cost-effective bulk whole-genome (WGS) makes it well-suited analyzing large cohorts sequenced samples, enhancing accessibility SV-based clonal reconstruction.

Language: Английский

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Chromosomal rearrangements drive diversity in arboreal rodents of the genus Oecomys

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

Published: Feb. 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.

Language: 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), Journal Year: 2024, Volume and Issue: unknown

Published: June 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.

Language: Английский

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Evolution of Hybrid Inviability Associated With Chromosome Fusions

Molecular Ecology, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 3, 2025

ABSTRACT Chromosomal rearrangements, such as inversions, have received considerable attention in the speciation literature due to their hampering effects on recombination. Less is known about how other chromosome fissions and fusions, can affect evolution of reproductive isolation. Here, we use crosses between populations wood white butterfly ( Leptidea sinapis ) with different karyotypes identify genomic regions associated hybrid inviability. We map inviability candidate loci by contrasting allele frequencies F 2 hybrids that survived until adult stage individuals same cohort succumbed incompatibilities. Hybrid high genetic differentiation parental populations, reduced recombination rates, are enriched near fusions. By analysing sequencing coverage, exclude aneuploidies a direct link Instead, our results point an indirect relationship possibly related fused chromosomes. Thus, postzygotic isolation chromosomal providing crucial empirical evidence for idea number differences taxa contribute speciation.

Language: Английский

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