Ecological Diversification in an Adaptive Radiation of Plants: The Role of De Novo Mutation and Introgression

Molecular Biology and Evolution, Journal Year: 2024, Volume and Issue: 41(1)

Published: Jan. 1, 2024

Abstract Adaptive radiations are characterized by rapid ecological diversification and speciation events, leading to fuzzy species boundaries between ecologically differentiated species. therefore key systems for understanding how formed maintained, including the role of de novo mutations versus preexisting variation in adaptation genome-wide consequences hybridization events. For example, adaptive introgression, where beneficial alleles transferred lineages through hybridization, may fuel facilitate new environments. In this study, we employed whole-genome resequencing data investigate evolutionary origin hummingbird-pollinated flowers characterize patterns phylogenetic discordance introgression Penstemon subgenus Dasanthera, a small diverse radiation plants. We found that magenta hummingbird-adapted have apparently evolved twice from ancestral blue-violet bee-pollinated within radiation. These shifts flower color accompanied variety inactivating anthocyanin pathway enzyme, suggesting independent loss-of-function underlie parallel evolution trait. Although were heterogenous across genome, strong effect gene density suggests that, general, natural selection opposes maintains genetic differentiation gene-rich genomic regions. Our results highlight importance both mutation as sources change indicate driving radiations.

Language: Английский

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High quality genome assembly of the brown hare (Lepus europaeus) with chromosome-level scaffolding

Peer Community Journal, Journal Year: 2024, Volume and Issue: 4

Published: March 5, 2024

We present here a high-quality genome assembly of the brown hare (Lepus europaeus Pallas), based on fibroblast cell line male specimen from Liperi, Eastern Finland. This represents first Finnish contribution to European Reference Genome Atlas pilot effort generate reference genomes for biodiversity. The was assembled using 25X PacBio HiFi sequencing data and scaffolded utilizing Hi-C chromosome structure capture approach. After manual curation, length 2,930,972,003 bp with N50 scaffold 125.8 Mb. 93.16% could be assigned 25 identified chromosomes (23 autosomes plus X Y), matching published karyotype. were numbered according size. has high degree completeness BUSCO score (mammalia_odb10 database), Complete: 96.1% [Single copy: 93.1%, Duplicated: 3.0%], Fragmented 0.8%, Missing 2.9%. mitochondrial sequenced separately. final annotated 30,833 genes which 21,467 code polypeptide. is particularly interesting as this species readily hybridizes mountain timidus L.) at contact zone in northern Eurasia, producing fertile offspring resulting gene flow between two species. In addition providing useful comparison population studies, can offer insight into chromosomal evolution among Glires general Lagomorpha particular. also demonstrates that not acquired karyotypic changes during culture.

Language: Английский

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Species-specific variation in mitochondrial genome tandem repeat polymorphisms in hares (Lepus spp., Lagomorpha, Leporidae) provides insight into their evolution

Gene, Journal Year: 2024, Volume and Issue: 926, P. 148644 - 148644

Published: June 6, 2024

The non-coding regions of the mitochondrial DNAs (mtDNAs) hares, rabbits, and pikas (Lagomorpha) contain short (∼20 bp) long (130-160 tandem repeats, absent in related mammalian orders. In presented study, we provide in-depth analysis for mountain hare (Lepus timidus) brown (L. europaeus) mtDNA regions, together with a species- population-level repeat variation. Mountain repeats (SRs) as well other analyzed species consist two conserved 10 bp motifs, only hares exhibiting single, more variable motif. Long (LRs) also differ sequence copy number between species. have four to seven LRs, median value five, while exhibit five nine six. Interestingly, introgressed obtained an intermediate LR length distribution, being same conspecific mtDNA. contrast, transfer into cultured mtDNA-less cells maintained original number, whereas reciprocal caused instability, suggesting that cellular environment rather than nuclear genomic background plays role maintenance. Due their dynamic nature separation from known elements on region genomes, likely represent signatures ancient genetic rearrangements. clarifying dynamics these rearrangements may shed light possible NCR repeated mitochondria evolution.

Language: Английский

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Thrushes in Love: Extensive Gene Flow, With Differential Resistance and Selection, Obscures and Reveals the Evolutionary History of a Songbird Clade

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

Published: Jan. 2, 2025

ABSTRACT The application of high‐throughput sequencing to phylogenetic analyses is allowing authors reconstruct the true evolutionary history species. This work can illuminate specific mechanisms underlying divergence when combined with gene flow, recombination and selection. We conducted a phylogenomic analysis Catharus , songbird genus considerable potential for variation in migratory behaviour genomic resources. documented discordance among trees constructed mitochondrial, autosomal sex (Z) chromosome partitions. Two were recovered on Z. Both differed from autosomes, one matched mitochondria, other was unique Gene flow species likely generated much this discordance; substantial admixture between ustulatus remaining linked at least two historic events. tree Z reflects ; local same regions reduced recombination. Genes previously connected migration enriched these suggesting transitions non‐migratory states helped generate divergence. Migratory (vs. nonmigratory) formed monophyletic clade subset regions. elevated some adaptive introgression may have occurred, but dominant pattern balancing selection maintaining ancestral polymorphisms important olfaction perhaps, by extension, adaptation temperate climates. illuminates an model speciation demonstrates how differential resistance affect patterns.

Language: Английский

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Incomplete lineage sorting and ancient admixture, and speciation without morphological change in ghost-worm cryptic species

PeerJ, Journal Year: 2021, Volume and Issue: 9, P. e10896 - e10896

Published: Feb. 9, 2021

Morphologically similar species, that is cryptic may be or quasi-similar owing to the deceleration of morphological evolution and stasis. While factors underlying stasis in species remain unknown, decades research field paleontology on punctuated equilibrium have originated clear hypotheses. Species are expected morphologically identical scenarios shared genetic variation, such as hybridization incomplete lineage sorting, where bottlenecks reduce variation constrain morphology. Here, focusing three

Language: Английский

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Museum Skins Enable Identification of Introgression Associated with Cytonuclear Discordance

Systematic Biology, Journal Year: 2024, Volume and Issue: 73(3), P. 579 - 593

Published: April 5, 2024

Abstract Increased sampling of genomes and populations across closely related species has revealed that levels genetic exchange during after speciation are higher than previously thought. One obvious manifestation such is strong cytonuclear discordance, where the divergence in mitochondrial DNA (mtDNA) differs from for nuclear genes more (or less) expected differences between mtDNA (nDNA) population size mutation rate. Given genome-scale data sets coalescent modeling, we can now confidently identify cases discordance test specifically historical or recent introgression as cause. Using sampling, combining exon capture museum specimens recently collected tissues showcase how genomic tools resolve complex evolutionary histories brachyotis group rock-wallabies (Petrogale). In particular, applying phylogenomic approaches assess role demographic processes driving patterns a ancient hybridization. We find described well supported monophyletic taxa nDNA genes, but not mtDNA, with involving at least 4 operational taxonomic units which diverged 183–278 kya. ABC modeling gene trees supports some taxon pairs discordance. substantial body involved, this evidence flow surprising. Heterogenous were identified do appear to be associated chromosome species. These previous results suggest dynamic past climates monsoonal tropics could have promoted reticulation among

Language: Английский

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Diversification, Introgression, and Rampant Cytonuclear Discordance in Rocky Mountains Chipmunks (Sciuridae: Tamias)

Systematic Biology, Journal Year: 2020, Volume and Issue: 70(5), P. 908 - 921

Published: Dec. 19, 2020

Abstract Evidence from natural systems suggests that hybridization between animal species is more common than traditionally thought, but the overall contribution of introgression to standing genetic variation within remains unclear for most systems. Here, we use targeted exon capture sequence thousands nuclear loci and complete mitochondrial genomes closely related chipmunk in Tamias quadrivittatus group are distributed across Great Basin central southern Rocky Mountains North America. This recent radiation includes six overlapping, ecologically distinct (Tamias canipes, cinereicollis, dorsalis, T. quadrivittatus, rufus, umbrinus) show evidence widespread boundaries. Such has historically been derived a handful markers, typically focused on loci, describe patterns introgression; consequently, extent genes less well characterized. We conducted series phylogenomic species-tree analyses resolve phylogeny this group. In addition, performed several population-genomic characterize infer coancestry among individuals. Furthermore, used emerging quartets-based approaches simultaneously tree (SVDquartets) identify (HyDe). found that, spite rampant some pairs (and sometimes involving up three species), there appears be little no introgression. These findings mirror other genomic results where occurred absence appreciable gene flow. The underlying causes recurrent massive cytonuclear discordance remain unresolved DNA highly misleading population histories as whole. Collectively, it boundaries largely impermeable flow hybridization, while pervasive with respect mtDNA, likely played relatively minor role evolutionary history [Cytonuclear discordance; hyridization; introgression, phylogenomics; SVDquartets; Tamias.]

Language: Английский

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The evolutionary pathways for local adaptation in mountain hares

Molecular Ecology, Journal Year: 2022, Volume and Issue: 31(5), P. 1487 - 1503

Published: Jan. 7, 2022

Understanding the evolution of local adaptations is a central aim evolutionary biology and key for identification unique populations lineages conservation relevance. By combining RAD sequencing whole-genome sequencing, we identify genetic signatures adaptation in mountain hares (Lepus timidus) from isolated distinctive habitats its wide distribution: Ireland, Alps Fennoscandia. Demographic modelling suggested that split these occurred around 20 thousand years ago, providing opportunity to study adaptive over short timescale. Using genome-wide scans, identified extreme differentiation among distinct geographic areas overlap with area-specific selective sweeps, suggesting targets adaptation. Several candidate genes are associated traits related uniqueness different environments inhabited by three groups hares, including coat colour, ability live at high altitudes variation body size. In Irish variant ASIP, gene previously implicated introgression-driven winter colour snowshoe (L. americanus), may underlie brown coats, reinforcing repeated nature ASIP moulding seasonal colouration. Comparative genomic analyses across several hare species hares' variants appear predominantly species-specific. However, using coalescent simulations, also show instances where have been introduced via introgressive hybridization. Our shows standing variation, introgressed other species, was crucial component post-glacial dynamics species.

Language: Английский

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Divergence and introgression among the virilis group of Drosophila

Evolution Letters, Journal Year: 2022, Volume and Issue: 6(6), P. 537 - 551

Published: Nov. 29, 2022

Speciation with gene flow is now widely regarded as common. However, the frequency of introgression between recently diverged species and evolutionary consequences are still poorly understood. The virilis group Drosophila contains 12 that geographically widespread show varying levels prezygotic postzygotic isolation. Here, we use de novo genome assemblies whole-genome sequencing data to resolve phylogenetic relationships describe patterns divergence across group. We suggest consists three, rather than traditional two, subgroups. Some genes undergoing rapid sequence were involved in chemical communication desiccation tolerance, may be related evolution sexual isolation adaptation. found evidence pervasive discordance caused by ancient events distant lineages within group, more recent closely species. When assessing genome-wide pairs no consistent genomic a disproportionate role for X chromosome has been other systems. Our results how introgressions confuse reconstruction, but play an important during early radiation

Language: Английский

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Using Ultraconserved Elements to Unravel Lagomorph Phylogenetic Relationships

Journal of Mammalian Evolution, Journal Year: 2022, Volume and Issue: 29(2), P. 395 - 411

Published: Feb. 4, 2022

Language: Английский

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