Divergence and gene flow history at two large chromosomal inversions underlying ecotype differentiation in the long‐snouted seahorse

Molecular Ecology, Год журнала: 2024, Номер 33(24)

Опубликована: Янв. 27, 2024

Abstract Chromosomal inversions can play an important role in divergence and reproductive isolation by building maintaining distinct allelic combinations between evolutionary lineages. Alternatively, they take the form of balanced polymorphisms that segregate within populations until one arrangement becomes fixed. Many questions remain about how inversion arise, are maintained over long term, ultimately, whether contribute to speciation. The long‐snouted seahorse ( Hippocampus guttulatus ) is genetically subdivided into geographic lineages marine‐lagoon ecotypes, with shared structural variation underlying lineage ecotype divergence. Here, we aim characterize variants reconstruct their history suspected formation. We generated a near chromosome‐level genome assembly described genome‐wide patterns diversity through analysis 112 whole‐genome sequences from Atlantic, Mediterranean, Black Sea populations. By also analysing linked‐read sequencing data, found evidence for two chromosomal were several megabases length showed contrasting allele frequency ecotypes across species range. reveal these represent ancient intraspecific polymorphisms, likely being divergent selection other pseudo‐overdominance. A possible selective coupling was further supported absence specific haplotype putative functional interaction reproduction. Lastly, detected gene flux eroding inverted alleles at varying levels inversions, impact on dynamics contribution

Язык: Английский

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Introgression dynamics of sex-linked chromosomal inversions shape the Malawi cichlid adaptive radiation

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Июль 29, 2024

Abstract Chromosomal inversions contribute to adaptive speciation by linking co-adapted alleles. Querying 1,375 genomes of the species-rich Malawi cichlid fish radiation, we discovered five large segregating in benthic subradiation that each suppress recombination over more than half a chromosome. Two were transferred from deepwater pelagic Diplotaxodon via admixture, while others established early deep clade. Introgression haplotypes lineages inside and outside radiation coincided with bursts species diversification. Inversions show evidence for transient sex linkage striking excess protein changing substitutions points towards selection on neuro-sensory, physiological reproductive genes. We conclude repeated interplay between depth adaptation sex-specific has been central evolution this iconic system.

Язык: Английский

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Limited genomic signatures of population collapse in the critically endangered black abalone (Haliotis cracherodii)

Molecular Ecology, Год журнала: 2024, Номер unknown

Опубликована: Апрель 29, 2024

The black abalone, Haliotis cracherodii, is a large, long-lived marine mollusc that inhabits rocky intertidal habitats along the coast of California and Mexico. In 1985, populations were impacted by bacterial disease known as withering syndrome (WS) wiped out >90% individuals, leading to closure all U.S. abalone fisheries since 1993. Current conservation strategies include restoring diminished translocating healthy individuals. However, population collapse on this scale may have dramatically lowered genetic diversity strengthened geographic differentiation, making translocation-based recovery contentious. Additionally, current prevalence WS remains unknown. To address these uncertainties, we sequenced analysed genomes 133 individuals from across their present range. We observed no spatial structure among with exception single chromosomal inversion increases in frequency latitude. Outside inversion, differentiation between sites minimal does not either distance or environmental dissimilarity. Genetic appears uniformly high Demographic inference indicate severe bottleneck beginning just 15 generations past, but decline short lived, present-day size far exceeding pre-bottleneck status quo. Finally, find agent equally sampled range, only 10% lack structure, uniform bacteria indicates translocation could be valid low-risk means restoration for species' recovery.

Язык: Английский

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Genomic structural variation contributes to evolved changes in gene expression in high-altitude Tibetan sheep

Proceedings of the National Academy of Sciences, Год журнала: 2024, Номер 121(27)

Опубликована: Июнь 24, 2024

Tibetan sheep were introduced to the Qinghai Tibet plateau roughly 3,000 B.P., making this species a good model for investigating genetic mechanisms of high-altitude adaptation over relatively short timescale. Here, we characterize genomic structural variants (SVs) that distinguish from closely related, low-altitude Hu sheep, and examine associated changes in tissue-specific gene expression. We document differentiation between two breeds frequencies SVs with genes involved cardiac function circulation. In identified high-frequency total 462 genes, including EPAS1 , PAPSS2 PTPRD . Single-cell RNA-Seq data luciferase reporter assays revealed had cis -acting effects on expression levels these three specific tissues cell types. chromosomal inversion exhibited modified chromatin architectures relative noninverted allele predominates sheep. The harbors several altered patterns related heart protection, brown adipocyte proliferation, angiogenesis, DNA repair. These findings indicate represent an important source variation may have contributed

Язык: Английский

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A whole-genome scan for evidence of recent positive and balancing selection in aye-ayes (Daubentonia madagascariensis) utilizing a well-fit evolutionary baseline model

Опубликована: Ноя. 11, 2024

The aye-aye (

Язык: Английский

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Genes and gene networks underlying spatial cognition in food-caching chickadees

Current Biology, Год журнала: 2024, Номер 34(9), С. 1930 - 1939.e4

Опубликована: Апрель 17, 2024

Язык: Английский

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High-recombining genomic regions affect demography inference based on ancestral recombination graphs

Genetics, Год журнала: 2025, Номер unknown

Опубликована: Янв. 10, 2025

Multiple methods of demography inference are based on the ancestral recombination graph. This powerful approach uses observed mutations to model local genealogies changing along chromosomes by historical events. However, underlying is difficult in regions with high rate relative mutation due lack representing genealogies. Despite prevalence high-recombining genomic some organisms, such as birds, its impact graphs has not been well studied. Here, we use population simulations investigate graphs. We demonstrate that effective size and time split events systematically affected when cover wide breadths chromosomes. Excluding can practically mitigate this impact, maps informative defining regions, yet estimated values may be utilized for decision. Finally, confirm relevance our findings empirical analysis contrasting inferences applied a bird species, Eurasian blackcap (Sylvia atricapilla), using different parts genome low rates. Our results suggest should carried out caution species whose genomes contain long stretches regions.

Язык: Английский

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Large inversions in Lake Malawi cichlids are associated with habitat preference, lineage, and sex determination

Опубликована: Янв. 31, 2025

Chromosomal inversions are an important class of genetic variation that link multiple alleles together into a single inherited block can have effects on fitness. To study the role large in massive evolutionary radiation Lake Malawi cichlids, we used long-read technologies to identify four and two tandem span half each respective chromosome, which encompass over 10% genome. Each inversion is fixed one states within seven major ecogroups, suggesting they played separation lake lineages specific habitats. One exception benthic sub-radiation, where both inverted non-inverted continue segregate group. The histories three six suggest transferred from pelagic Diplotaxodon group ancestors at time sub-radiation was seeded. remaining found subset species living deep waters. We show some these as XY sex-determination systems but also likely limited total species. Our work suggests been under sexual natural selection cichlids will be understanding how this adaptive evolved.

Язык: Английский

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Adaptation repeatedly uses complex structural genomic variation

Science, Год журнала: 2025, Номер 388(6744)

Опубликована: Апрель 17, 2025

Structural elements are widespread across genomes, but their complexity and role in repeatedly driving local adaptation remain unclear. In this work, we use phased genome assemblies to show that adaptive divergence cryptic color pattern a stick insect is underlain by structural variation, not simple chromosomal inversion. We found populations of insects on two mountains associated with translocations have also been inverted. These differ size origin each mountain, they overlap partially involve some the same gene regions. Moreover, variation subject divergent selection arose without introgression between species. Our results how provides mechanism for repeated bouts adaptation.

Язык: Английский

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Two pup vocalization types are genetically and functionally separable in deer mice

Current Biology, Год журнала: 2023, Номер 33(7), С. 1237 - 1248.e4

Опубликована: Март 8, 2023

Vocalization is a widespread social behavior in vertebrates that can affect fitness the wild. Although many vocal behaviors are highly conserved, heritable features of specific vocalization types vary both within and between species, raising questions why how some evolve. Here, using new computational tools to automatically detect cluster vocalizations into distinct acoustic categories, we compare pup isolation calls across neonatal development eight taxa deer mice (genus Peromyscus) them with laboratory (C57BL6/J strain) free-living, wild house (Mus musculus domesticus). Whereas Peromyscus Mus pups produce ultrasonic (USVs), also second call type features, temporal rhythms, developmental trajectories from those USVs. In mice, these lower frequency "cries" predominantly emitted postnatal days one through nine, whereas USVs primarily made after day 9. Using playback assays, show cries result more rapid approach by mothers than USVs, suggesting role for eliciting parental care early development. genetic cross two sister species exhibiting large, innate differences structure find variation rate, duration, pitch displays different degrees dominance cry USV be uncoupled second-generation hybrids. Taken together, this work shows evolve quickly closely related rodent which types, likely serving functions communication, controlled loci.

Язык: Английский

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