Phylogenomics and species delimitation in the Lepidophyma sylvaticum complex (Squamata: Xantusiidae) using ddRADseq and morphological data

Molecular Phylogenetics and Evolution, Journal Year: 2025, Volume and Issue: unknown, P. 108288 - 108288

Published: Jan. 1, 2025

Language: Английский

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Repeated Mitochondrial Capture With Limited Genomic Introgression in a Lizard Group

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

Published: April 16, 2025

ABSTRACT Mitochondrial introgression is common among animals and often first identified through mitonuclear discordance—discrepancies between evolutionary relationships inferred from mitochondrial DNA (mtDNA) nuclear (nuDNA). Over recent decades, genomic data have also revealed extensive in many animal groups, with implications for genetic phenotypic diversity. However, the extent to which mtDNA corresponds nuDNA varies. Here, we investigated historical Gehyra nana ‐occidentalis clade, a complex group of Australian geckos documented cases discordance suggestive repeated introgression. We hypothesised that this clade reflects substantial Despite evidence introgression, however, found little no using exon capture genome‐wide single nucleotide polymorphism (SNP) data. gene flow at modern contact zones detected only early generation hybrid. Unsurprisingly, given these results, transgressive, intermediate, or more variable morphological phenotypes taxa introgressed mtDNA. These findings suggest hybridisation system has, least some cases, resulted This pattern aligns other studies showing limited discordance, highlighting potentially broader trend radiations.

Language: Английский

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Biases in ARG-based inference of historical population size in populations experiencing selection

Molecular Biology and Evolution, Journal Year: 2024, Volume and Issue: 41(7)

Published: June 14, 2024

Inferring the demographic history of populations provides fundamental insights into species dynamics and is essential for developing a null model to accurately study selective processes. However, background selection sweeps can produce genomic signatures at linked sites that mimic or mask signals associated with historical population size change. While theoretical biases introduced by effects have been well established, it unclear whether ancestral recombination graph (ARG)-based approaches inference in typical empirical analyses are susceptible misinference due these effects. To address this, we developed highly realistic forward simulations human Drosophila melanogaster populations, including empirically estimated variability gene density, mutation rates, purifying, positive selection, across different scenarios, broadly assess impact on using genealogy-based approach. Our results indicate minimally although could cause similar genome architecture parameters experiencing more frequent recurrent sweeps. We found accurate D. ARG-based methods compromised presence pervasive alone, leading spurious inferences recent expansion, which may be further worsened sweeps, depending proportion strength beneficial mutations. Caution additional testing species-specific needed when inferring non-human avoid selection.

Language: Английский

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Holocene Climate Change Promoted Allopatric Divergence and Disjunct Geographic Distribution in a Bee Orchid Species

Journal of Biogeography, Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 2, 2024

ABSTRACT Aim Species with disjunct geographic distributions provide natural opportunities to investigate incipient or recent allopatric divergence. The combination of both genetic and ecological data may be fruitful decipher the causes such patterns: (i) actual vicariance, (ii) successful colonisation from one source a new range (dispersal, biological introduction) (iii) parallel convergent evolution. Location Southern France Northern Spain. Taxon bee orchid Ophrys aveyronensis (and its two recognised subspecies O. a. subsp. vitorica ) displays distribution subranges separated by 600 km on sides Pyrenees mountain range. Methods As divergence is often complex document in wild, we used population genomics niche modelling (ENM) this intriguing biogeographic pattern. Results genomic demonstrate that all studied populations exhibit similar patterns diversity dramatic decrease effective size compared ancestral population. Significant differentiation reciprocal monophyly exist between , despite very time as young ca. 1500 generations ago. Moreover, paleo‐ENM analyses support consistent split broad range, contraction distinct longitudinal latitudinal shifts response climate warming during Holocene. Main Conclusion congruence results obtained ENM approaches documents how continental initiated speciation system. provides promising opportunity study onset reproductive isolation evolution following an initial stage separation group high diversification rate.

Language: Английский

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The long and short of hyperdivergent regions

Trends in Genetics, Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 1, 2024

Language: Английский

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