Genomics of Evolutionary Novelty in Hybrids and Polyploids

Frontiers in Genetics, Journal Year: 2020, Volume and Issue: 11

Published: July 28, 2020

It has long been recognized that hybridization and polyploidy are prominent processes in plant evolution. Although classically as significant speciation adaptation, recognition of the importance interspecific gene flow dramatically increased during genomics era, concomitant with an unending flood empirical examples, or without genome doubling. Interspecific is thus increasingly thought to lead evolutionary innovation diversification, via adaptive introgression, homoploid hybrid allopolyploid speciation. Less well understood, however, suite genetic genomic mechanisms set motion by merger differentiated genomes, temporal scale over which recombinational complexity mediated might be expressed exposed natural selection. We focus on these issues here, considering types molecular saltational event between two diverged species, either doubling, how various can contribute novel phenotypes. Genetic include infusion new alleles genesis structural variation including translocations inversions, homoeologous exchanges, transposable element mobilization insertional effects, presence-absence copy number variation. Polyploidy generates massive transcriptomic regulatory alteration, presumably disrupted stoichiometries factors, small RNAs other interactions cascade from single-gene expression change up through entire networks transformed modules. highlight both combinatorial possibilities range scales such generated, selection drift.

Language: Английский

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The genic view of hybridization in the Anthropocene

Evolutionary Applications, Journal Year: 2021, Volume and Issue: 14(10), P. 2342 - 2360

Published: March 13, 2021

Human impact is noticeable around the globe, indicating that a new era might have begun: Anthropocene. Continuing human activities, including land-use changes, introduction of non-native species and rapid climate change, are altering distributions countless species, often giving rise to human-mediated hybridization events. While interbreeding different populations or can detrimental effects, such as genetic extinction, it be beneficial in terms adaptive introgression an increase diversity. In this paper, I first review mechanisms outcomes anthropogenic based on literature from last five years (2016-2020). The most common leading previously isolated taxa include habitat change (51% studies) (34% intentional 19% unintentional). These human-induced events result (80%). high incidence exchange between hybridizing indicates application genic view speciation (and introgression) provide crucial insights how address This perspective considers genome dynamic collection loci with distinct evolutionary histories, heterogenous genomic landscape differentiation introgression. First, understanding lead better selection diagnostic markers characterize hybrid populations. Second, describing patterns vary across help predict likelihood negative processes, demographic swamping, well positive outcomes, It especially important not only quantify much material introgressed, but also what has been exchanged. Third, comparing pre-Anthropocene current cases novel into swamping collapse during event. However, comparative approach remains tested before applied practice. Finally, combined conservation studies determine legal status hybrids take appropriate measures manage interplay genomics will constant ideas these fields which improve our knowledge origin conserve protect them.

Language: Английский

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Genome chaos: Creating new genomic information essential for cancer macroevolution

Seminars in Cancer Biology, Journal Year: 2020, Volume and Issue: 81, P. 160 - 175

Published: Nov. 13, 2020

Language: Английский

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Sex chromosomes in meiotic, hemiclonal, clonal and polyploid hybrid vertebrates: along the ‘extended speciation continuum'

Philosophical Transactions of the Royal Society B Biological Sciences, Journal Year: 2021, Volume and Issue: 376(1833), P. 20200103 - 20200103

Published: July 25, 2021

We review knowledge about the roles of sex chromosomes in vertebrate hybridization and speciation, exploring a gradient divergences with increasing reproductive isolation (speciation continuum). Under early divergence, well-differentiated meiotic hybrids may cause Haldane-effects introgress less easily than autosomes. Undifferentiated are more susceptible to introgression form multiple (or new) chromosome systems hardly predictable dominance hierarchies. increased most vertebrates reach complete intrinsic isolation. Slightly earlier, some (linked ‘the extended speciation continuum') exhibit aberrant gametogenesis, leading towards female clonality. This facilitates evolution various allodiploid allopolyploid clonal (‘asexual’) hybrid vertebrates, where ‘asexuality' might be A comprehensive list ‘asexual' shows that they all evolved from parents were greater at intraspecific level (K2P-distances 5–22% based on mtDNA). These taxa inherited genetic determination by mostly undifferentiated chromosomes. Among few known sex-determining ‘asexuals', heterogamety (ZW) occurred twice as often male (XY). hypothesize pre-/meiotic aberrations all-female ZW-hybrids present promoting their evolution. Understanding preconditions produce or allopolyploids appears crucial for insights into sex, polyploidy. article is part theme issue ‘Challenging paradigm evolution: empirical theoretical focus (Part II)’.

Language: Английский

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Diverging patterns of introgression from Schistosoma bovis across S. haematobium African lineages

PLoS Pathogens, Journal Year: 2021, Volume and Issue: 17(2), P. e1009313 - e1009313

Published: Feb. 5, 2021

Hybridization is a fascinating evolutionary phenomenon that raises the question of how species maintain their integrity. Inter-species hybridization occurs between certain Schistosoma can cause important public health and veterinary issues. In particular hybrids haematobium S . bovis associated with humans animals respectively are frequently identified in Africa. Recent genomic evidence indicates some populations show signatures introgression from Here, we conducted comparative study investigated relationships , using 19 isolates originating wide geographical range over Africa, including samples initially classified as (n = 11), 6) x 2). Based on whole sequencing approach, developed 56,181 SNPs allowed clear differentiation cluster all natural haematobium-bovis hybrid. All except isolate Madagascar harbored Isolates Corsica, Mali Egypt -like Invadolysin gene, an introgressed tract has been previously detected Niger. Together our results highlight fact widespread across observed unidirectional.

Language: Английский

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Deep Ancestral Introgression Shapes Evolutionary History of Dragonflies and Damselflies

Systematic Biology, Journal Year: 2021, Volume and Issue: 71(3), P. 526 - 546

Published: July 27, 2021

Abstract Introgression is an important biological process affecting at least 10% of the extant species in animal kingdom. significantly impacts inference phylogenetic relationships where a strictly binary tree model cannot adequately explain reticulate net-like relationships. Here, we use phylogenomic approaches to understand patterns introgression along evolutionary history unique, nonmodel insect system: dragonflies and damselflies (Odonata). We demonstrate that pervasive force across various taxonomic levels within Odonata. In particular, show morphologically “intermediate” Anisozygoptera (one three primary suborders Odonata besides Zygoptera Anisoptera), which retain phenotypic characteristics other two suborders, experienced high likely coming from zygopteran genomes. Additionally, find evidence for multiple cases deep inter-superfamilial ancestral introgression. [Gene flow; Odonata; phylogenomics; evolution.]

Language: Английский

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Demographic History and Natural Selection Shape Patterns of Deleterious Mutation Load and Barriers to Introgression across Populus Genome

Molecular Biology and Evolution, Journal Year: 2022, Volume and Issue: 39(2)

Published: Jan. 10, 2022

Hybridization and resulting introgression are important processes shaping the tree of life appear to be far more common than previously thought. However, how genome evolution was shaped by various genetic evolutionary forces after hybridization remains unresolved. Here we used whole-genome resequencing data 227 individuals from multiple widespread Populus species characterize their contemporary patterns quantify genomic signatures past introgression. We observe a high frequency confirm that ambiguous in fact F1 hybrids. Seven were identified, which experienced different demographic histories resulted strikingly varied efficacy selection burdens deleterious mutations. Frequent has been found pervasive feature throughout speciation these species. The retained introgressed regions, generally, tend contain reduced load located regions recombination. also find pairs with substantial differences effective population size, inferred have undergone selective sweeps at greater expected frequencies lower suggesting likely higher potential provide beneficial variation for small populations. Our results, therefore, illustrate demography recombination interplayed both positive negative determining hybridization.

Language: Английский

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The Role of Hybridization in Species Formation and Persistence

Cold Spring Harbor Perspectives in Biology, Journal Year: 2024, Volume and Issue: 16(12), P. a041445 - a041445

Published: March 4, 2024

Joshua V. Peñalba1, Anna Runemark2, Joana I. Meier3,4, Pooja Singh5,6, Guinevere O.U. Wogan7, Rosa Sánchez-Guillén8, James Mallet9, Sina J. Rometsch10,11, Mitra Menon12, Ole Seehausen5,6, Jonna Kulmuni13,14,16 and Ricardo Pereira15,16 1Museum für Naturkunde, Leibniz Institute for Evolution Biodiversity Science, Center Integrative Discovery, 10115 Berlin, Germany 2Department of Biology, Lund University, 22632 Lund, Sweden 3Tree Life, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, United Kingdom 4Department Zoology, University Cambridge, CB2 3EJ, 5Department Aquatic Ecology, Ecology Evolution, Bern, 3012 Switzerland 6Center & Biogeochemistry, Swiss Federal Science Technology (EAWAG), CH-8600 Kastanienbaum, 7Department Oklahoma State Stillwater, 74078, USA 8Red de Biología Evolutiva, INECOL, Xalapa, Veracruz, CP 91073, Mexico 9Organismal Evolutionary Harvard Massachusetts 02138, 10Department Yale New Haven, Connecticut 06511, 11Yale Biospheric Studies, 12Department California Davis, 95616, 13Department Population Ecosystem Dynamics, Amsterdam, 1098 XH The Netherlands 14Organismal Biology Research Programme, Helsinki, Biocenter 3, Finland 15Department Museum Natural History Stuttgart, Stuttgart 70191, Correspondence: ricardojn.pereira{at}gmail.com ↵16 These authors contributed equally to this work.

Language: Английский

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Phylogenomic analyses re-evaluate the backbone of Corylus and unravel extensive signals of reticulate evolution

Molecular Phylogenetics and Evolution, Journal Year: 2025, Volume and Issue: 204, P. 108293 - 108293

Published: Jan. 23, 2025

Language: Английский

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Unraveling the extensive phylogenetic discordance and evolutionary history of spurless taxa within the Aquilegia ecalcarata complex

New Phytologist, Journal Year: 2025, Volume and Issue: unknown

Published: March 7, 2025

Parallel evolution of the same, or at least very similar, phenotype(s) in different lineages is often interpreted as evidence for action natural selection. However, caution required when inferring parallel based on uncertain potentially incorrect phylogenetic frameworks. Here, by conducting extensive phylogenomic and population genetic analyses, we aim to clarify evolutionary history spurless taxa within Aquilegia ecalcarata complex. We observed substantial discordance patterns across entire genome, primarily attributed ancient introgression incomplete lineage sorting. Additionally, identified several whose positions were distorted admixture events. Using a backbone tree demographic modeling, determined that these independently originated twice this group. Intriguingly, our investigation revealed experienced expansion during global cooling, while their spurred sister groups underwent contraction. The losses petal spurs, therefore, may be linked adaptations low-temperature conditions. These findings emphasize importance comprehensive population-level analyses inference provide valuable insights into dynamics trait loss its implications adaptive strategies.

Language: Английский

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