Genome‐wide single nucleotide polymorphisms reveal recurrent waves of speciation in niche‐pockets, in Europe's most venomous snake

Molecular Ecology, Journal Year: 2023, Volume and Issue: 32(13), P. 3624 - 3640

Published: March 31, 2023

Within the Balkan Peninsula, topographic and climatic agents have promoted biodiversity shaped speciation history of many ectotherms. Here, we targeted an iconic European reptile, nose-horned viper species-complex (Vipera ammodytes), explored its spatial temporal evolution. We (i) utilized genome-wide single nucleotide polymorphisms to infer genetic structure build a time-calibrated species-tree, (ii) applied species distribution modelling with niche-divergence tests among major phylogenomic clades. Geographically structured diversity was found. Cycles recurrent isolation expansion during glacial-interglacial periods led allopatric secondary contacts formation multiple hybrid zones throughout Peninsula. Deep divergence is still detected populations separated by old imminent biogeographical barriers (Pindos Mountain Range, Cyclades islands, etc.), but in most cases incomplete. At other end continuum, recognize two well-differentiated lineages, currently lacking any evidence gene flow; one distributed Northwestern Balkans Southeastern Balkans, further expanding into Asia. Despite their split 5 million years ago, there no ecological divergence, as probably occurred niche-pockets analogous environments. These lineages represent different species, while V. transcaucasiana does not merit status. By comparing genomic phylogenies updated mitochondrial one, propose evolutionary scenario that resolves all mitonuclear conflicts, according which ammodytes complex processes, including event introgressive hybridization asymmetric capture.

Language: Английский

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Mitonuclear discordance results from incomplete lineage sorting, with no detectable evidence for gene flow, in a rapid radiation of Todiramphus kingfishers

Molecular Ecology, Journal Year: 2023, Volume and Issue: 32(17), P. 4844 - 4862

Published: July 29, 2023

Abstract Many organisms possess multiple discrete genomes (i.e. nuclear and organellar), which are inherited separately may have unique even conflicting evolutionary histories. Phylogenetic reconstructions from these can yield different patterns of relatedness, a phenomenon known as cytonuclear discordance. In many animals, mitonuclear discordance discordant histories between the mitochondrial genomes) has been widely documented, but its causes often considered idiosyncratic inscrutable. We show that case in Todiramphus kingfishers be explained by extensive genome‐wide incomplete lineage sorting (ILS), likely result explosive diversification history this genus. For kingfishers, quartet frequencies reveal genome is dominated topologies, with none internal branches our consensus tree recovered >50% gene trees. Meanwhile, lack inter‐species shared ancestry, non‐significant pairwise tests for flow, little evidence meaningful migration edges species, leads to conclusion flow cannot explain we observe. This combined discordance, hallmark ILS, us conclude observe results specifically deep coalescence genome. Based on study, hypothesize similar demographic other ‘great speciator’ taxa across Indo‐Pacific predispose groups high levels ILS likelihoods

Language: Английский

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Integrated phylogenomic analyses unveil reticulate evolution inParthenocissus(Vitaceae), highlighting speciation dynamics in theHimalayan–HengduanMountains

New Phytologist, Journal Year: 2022, Volume and Issue: 238(2), P. 888 - 903

Published: Oct. 28, 2022

Summary Hybridization caused by frequent environmental changes can lead both to species diversification (speciation) and speciation reversal (despeciation), but the latter has rarely been demonstrated. Parthenocissus , a genus with its trifoliolate lineage in Himalayan–Hengduan Mountains (HHM) region showing perplexing phylogenetic relationships, provides an opportunity for investigating dynamics based on integrated evidence. We investigated discordance reticulate evolution rigorous analyses of plastome transcriptome data. focused reticulations HHM using population‐level genome resequencing dataset, incorporating evidence from morphology, distribution, elevation. Comprehensive confirmed multiple introgressions within robust temporal–spatial framework. Around region, at least three hybridization hot spots were identified, one which showed ongoing reversal. present solid case study integrative methodological approach investigate evolutionary history underlying mechanisms plants. It demonstrates example through hybridizations new perspectives mountainous areas strong topographic heterogeneity.

Language: Английский

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Evolutionary history of New World crakes (Aves: Rallidae) with emphasis on the tribe Laterallini

Zoologica Scripta, Journal Year: 2023, Volume and Issue: 52(4), P. 394 - 412

Published: April 7, 2023

Abstract New World crakes are intriguing, poorly known birds with cursorial cryptic habits; they belong to two unrelated tribes: Laterallini and Pardirallini. Recent genetic studies contributed the phylogenetic knowledge of these tribes, but a complete reconstruction is still missing. Here, we present most taxonomically dated gene‐based phylogeny crakes, an emphasis on Laterallini, including for first time sequences Coturnicops notatus , Laterallus levraudi L. jamaicensis tuerosi xenopterus . We used multilocus (mtDNA + nucDNA) analyses interpreted our results in light natural history group. Our novel show that: (1) sister leucopyrrhus ; (2) j. spilonota (3) C. clade that groups remaining black ( tuerosi, rogersi spilopterus ); (4) melanophaius conform recently diverged clade. Thus, indicate polyphyly this group, particularly and, time, some discrepancies previous stem from misidentified samples or Anurolimnas fasciatus. Finally, provide new preliminary insights into species limits taxa, specifically set stage integrative taxonomic assessments at generic level by incorporating (gene‐based) data.

Language: Английский

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Ephemeral Speciation in a New Guinean Honeyeater Complex (Aves: Melidectes)

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

Published: April 11, 2025

Speciation is a fundamental concept in evolutionary biology, and understanding the mechanisms driving speciation remains foremost research topic within this field. Hybridisation often involved can influence its rates, potentially accelerating, decelerating or even reversing process. This study investigates history of New Guinean bird genus Melidectes, consisting six species that inhabit various montane regions at different elevations. While most Melidectes have allopatric distributions, two overlap central mountain range hybridise. However, plumage differences elevational adaptations are assumed to maintain species' boundaries. Utilising specimens from natural collections comprehensive genomic analyses, including de novo genome assembly, we characterise patterns highlight how future could be driven by climate change. Contrary previous hypotheses, our findings suggest distributionally overlapping species, phenotypic do not prevent gene flow. We find limited acoustic differentiation extensive admixture across their distributions. Divergence levels conform poorly current taxonomy follow geographical pattern which isolated populations ends distributions divergent show least admixture. contrast, mitochondrial genomes group accordance with identity, namely, into deeply lineages. propose system demonstrates ephemeral nature speciation, incipient started mixing extensively as they came secondary contact, resulting nearly complete fusion single lineage.

Language: Английский

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Genomic Footprints of Ancient Multi‐Species Introgression Events Among Allopatric Australo‐Papuan Butcherbird Species

Journal of Biogeography, Journal Year: 2025, Volume and Issue: unknown

Published: April 11, 2025

ABSTRACT Aim Climate change has influenced the evolution of world's biota, shaping species distributions, promoting diversification and causing extinctions. The turbulent climatic oscillations Pleistocene, which caused repeated periods isolation secondary contact, have left lasting signatures on genomes across world. resultant reticulate histories are difficult to untangle, yet offer unique insights, capturing responses climate that would otherwise be undetected providing empirical case‐studies impact introgression tens thousands years later. Here, we explore such dynamics using three currently allopatric Australian butcherbirds. We specifically test long‐standing biogeographic hypotheses concerning role intermittent Pleistocene land‐bridges in facilitating contact. Location Australia New Guinea. Taxon Silver‐backed Butcherbird Cracticus argenteus , Black‐backed mentalis Grey torquatus (Passeriformes: Artamidae). Methods generated genomic data from museum specimens infer relationships, taxonomic boundaries elucidate history gene flow this complex. Results uncovered evidence multiple ancient introgressions into savannah‐adapted C. both more arid‐tolerant despite their current allopatry. This supports Arafura Shelf maintaining genetic connectivity between Guinea expansion aridity during glacial maxima range expansions species. Main Conclusions Our showcase how retained over generations can reveal unexpected insights about evolutionary history, as well expand our understanding guilds similarly adapted may responded concordantly paleoclimate change. These important implications for biodiversity conservation, increasing contact driven by might future.

Language: Английский

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Phylogenomic cytonuclear discordance and evolutionary histories of plants and animals

Science China Life Sciences, Journal Year: 2023, Volume and Issue: 66(12), P. 2946 - 2948

Published: Nov. 1, 2023

Language: Английский

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Barcoding Fails to Delimit Species in Mongolian Oedipodinae (Orthoptera, Acrididae)

Insects, Journal Year: 2024, Volume and Issue: 15(2), P. 128 - 128

Published: Feb. 12, 2024

Mongolia, a country in central Asia, with its vast grassland areas represents hotspot for Orthoptera diversity, especially the Acrididae. For 128 Acrididae species have been documented so far, of which 41 belong to subfamily Oedipodinae (band-winged grasshoppers). Yet, few studies concerning distribution and diversity conducted this country. Molecular genetic data is almost completely absent, despite value identification discovery. Even, simplest most used data, DNA barcodes, far not generated local fauna. Therefore, we first barcode Mongolian band-winged grasshoppers investigated resolution marker delimitation. We were able assemble 105 (COI) sequences 35 from Mongolia adjacent countries. Based on reconstructed maximum likelihood Bayesian inference phylogenies. We, furthermore, automatic gap discovery Poisson tree process (PTP) Some was achieved at tribe genus level, but all delimitation methods failed differentiate by using COI region. This lack may multiple possible reasons, likely differ between taxa: Bryodemini be partially explained their massive genomes, implying potential presence large numbers pseudogenes, while within Sphingonotini incomplete lineage sorting incorrect taxonomy are more explanations signal. Further based larger number gene fragments, including nuclear DNA, needed distinguish also molecular level.

Language: Английский

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Utilizing museomics to trace the complex history and species boundaries in an avian-study system of conservation concern

Heredity, Journal Year: 2022, Volume and Issue: 128(3), P. 159 - 168

Published: Jan. 26, 2022

Abstract A taxonomic classification that accurately captures evolutionary history is essential for conservation. Genomics provides powerful tools delimiting species and understanding their relationships. This allows a more accurate detailed view on conservation status compared with other, traditionally used, methods. However, from practical ethical perspective, gathering sufficient samples endangered taxa may be difficult. Here, we use museum specimens to trace the boundaries in an Asian oriole clade. The silver has long been recognized as distinct based its unique coloration, but recent study suggested it might nested within maroon oriole-species complex. To evaluate designation, population connectivity, corresponding implications, assembled de novo genome used whole-genome resequencing of historical specimens. Our results show orioles form monophyletic lineage complex forms continued interbreed after initial divergence, do not signs gene flow. Using scan, identified genes basis color divergence act reproductive barriers. Taken together, our confirm highlight revision urgently needed. demonstrates how genomics Natural History Collections (NHC) can utilized shed light taxonomy natural populations such insights directly benefit practitioners when assessing wild populations.

Language: Английский

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Species limits in birds: Australian perspectives on interrelated challenges of allopatry, introgression of mitochondrial DNA, recent speciation, and selection

Ornithology, Journal Year: 2021, Volume and Issue: 138(2)

Published: April 6, 2021

Abstract Four main challenges that can underpin ongoing, intransigent debates about species limits in birds are reviewed: allopatry (population subdivision vs. speciation), geographically widespread introgression of mitochondrial DNA (mtDNA), recent speciation, and selection. Examples from the Australian region show how these challenges, their interplay, molecular-phenotypic discordance they generate clarify or mislead limits. phylogenetic frameworks help reject retain hypotheses under given. Although mtDNA’s strengths limitations well known, an underappreciated limitation mtDNA is homogenizes diversity across species, subspecies, population boundaries hundreds kilometers. The resulting between phenotype be profound. If undetected, setting evolutionarily significant units misled. An example shows genomic analyses detect solve problem. Other examples concern legacy mtDNA-only datasets. These often essentially unfinished studies leaving residual uncertainty illustrate when possibility large-scale needs to considered, scale data offer solutions. Researchers must carefully parse 3 questions: has there been and, if so, which genetics-based driver caused introgression, do need altering? Understanding allopatry, selection properly integrated robustly understood applied with maximum benefit downstream applications such as conservation management.

Language: Английский

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