selscan 2.0: scanning for sweeps in unphased data

Bioinformatics, Год журнала: 2024, Номер 40(1)

Опубликована: Янв. 1, 2024

Abstract Summary Several popular haplotype-based statistics for identifying recent or ongoing positive selection in genomes require knowledge of haplotype phase. Here, we provide an update to selscan which implements a re-definition these use unphased data. Availability and implementation Source code binaries are freely available at https://github.com/szpiech/selscan, implemented C/C++, supported on Linux, Windows, MacOS.

Язык: Английский

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Evolutionary genomics of oceanic island radiations

Trends in Ecology & Evolution, Год журнала: 2023, Номер 38(7), С. 631 - 642

Опубликована: Март 2, 2023

Язык: Английский

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A Bird’s-Eye View of Chromosomic Evolution in the Class Aves

Cells, Год журнала: 2024, Номер 13(4), С. 310 - 310

Опубликована: Фев. 7, 2024

Birds (Aves) are the most speciose of terrestrial vertebrates, displaying Class-specific characteristics yet incredible external phenotypic diversity. Critical to agriculture and as model organisms, birds have adapted many habitats. The only extant examples dinosaurs, emerged ~150 mya >10% currently threatened with extinction. This review is a comprehensive overview avian genome (“chromosomic”) organization research based mostly on chromosome painting BAC-based studies. We discuss traditional contemporary tools for reliably generating chromosome-level assemblies analyzing multiple species at higher resolution wider phylogenetic distance than previously possible. These results permit more detailed investigations into inter- intrachromosomal rearrangements, providing unique insights evolution speciation mechanisms. ‘signature’ karyotype likely arose ~250 remained largely unchanged in groups including extinct dinosaurs. Exceptions include Psittaciformes, Falconiformes, Caprimulgiformes, Cuculiformes, Suliformes, occasional Passeriformes, Ciconiiformes, Pelecaniformes. reasons this remarkable conservation may be greater diploid number variation (the driver natural selection) through possible combination gametes and/or an increase recombination rate. A deeper understanding genomic structure permits exploration fundamental biological questions pertaining role evolutionary breakpoint regions homologous synteny blocks.

Язык: Английский

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A genomic basis of vocal rhythm in birds

Nature Communications, Год журнала: 2024, Номер 15(1)

Опубликована: Апрель 23, 2024

Abstract Vocal rhythm plays a fundamental role in sexual selection and species recognition birds, but little is known of its genetic basis due to the confounding effect vocal learning model systems. Uncovering could facilitate identifying genes potentially important speciation. Here we investigate genomic underpinnings non-learning Pogoniulus tinkerbirds using 135 individual whole genomes distributed across southern African hybrid zone. We find speed associated with two that are also affect human speech, Neurexin-1 Coenzyme Q8A. Models leveraging ancestry reveal these candidate loci impact rhythmic stability, trait linked motor performance which an indicator quality. Character displacement stability suggests possible reinforcement against hybridization, supported by evidence asymmetric assortative mating producing faster, more stable rhythms. Because omnipresent animal communication, identified here may shape birds other vertebrates.

Язык: Английский

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selscan 2.0: scanning for sweeps in unphased data

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2021, Номер unknown

Опубликована: Окт. 24, 2021

Abstract Summary Several popular haplotype-based statistics for identifying recent or ongoing positive selection in genomes require knowledge of haplotype phase. Here we provide an update to selscan which implements a re-definition these use unphased data. Availability and Implementation Source code binaries freely available at https://github.com/szpiech/selscan , implemented C/C++ supported on Linux, Windows, MacOS. Contact [email protected] Supplemental Information Online supplemental information

Язык: Английский

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How structural variants shape avian phenotypes: Lessons from model systems

Molecular Ecology, Год журнала: 2024, Номер 33(11)

Опубликована: Апрель 23, 2024

Despite receiving significant recent attention, the relevance of structural variation (SV) in driving phenotypic diversity remains understudied, although advances long-read sequencing, bioinformatics and pangenomic approaches have enhanced SV detection. We review role SVs shaping phenotypes avian model systems, identify some general patterns type, length their associated traits. found that most so far identified are short indels chickens, which frequently with changes body weight plumage colouration. Overall, we relatively more detected, likely due to a combination prevalence compared large SVs, detection bias, stemming primarily from widespread use short-read sequencing analytical methods. commonly involve non-coding regions, especially introns, when inheritance were reported, dominant discrete summarise several examples convergence across different species, mediated by same or genes types gene can lead various phenotypes. Complex rearrangements supergenes, simultaneously affect link genes, tend pleiotropic effects. Additionally, co-occur single-nucleotide polymorphisms, highlighting need consider all genetic understand basis end summarising expectations for technologies become implemented non-model birds, leading an increase discovery characterisation. The growing interest this subject suggests our understanding effects upcoming years.

Язык: Английский

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A supergene controls facultative diapause in the crop pest Helicoverpa armigera

Cell Reports, Год журнала: 2024, Номер 43(11), С. 114939 - 114939

Опубликована: Ноя. 1, 2024

Many insect species, including the economically important pest Helicoverpa armigera, avoid unfavorable conditions by suspending development. This form of phenotypic plasticity-facultative diapause-is a complex trait, though its evolution and intricate genetic architecture remain poorly understood. To investigate how such polygenic trait could be locally adapted, we explore architecture. We map large-effect diapause-associated locus to Z chromosome crossing high- low-latitude populations. By generating multiple chromosome-scale assemblies, identify an ∼5.93-Mb chromosomal inversion that constitutes locus. Within this inversion, 33 genes harbor divergent non-synonymous mutations, notably three circadian rhythm genes: Period, Clock, Cycle. CRISPR-Cas9 knockout experiments confirm each gene is independently essential for pupal diapause. Thus, diapause supergene arose within H. armigera via enabling local climatic adaptation in crop pest.

Язык: Английский

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Genetic characterization and phylogenetic analysis of common house crows (Corvus splendens)

Scientific Reports, Год журнала: 2025, Номер 15(1)

Опубликована: Фев. 10, 2025

The Common House Crow (Corvus splendens) exhibits remarkable ecological adaptability, enabling its rapid expansion across continents. However, despite wide distribution, there is a need for genetic studies to clarify evolutionary history and population structure. This research employs DNA barcoding, focusing on the mitochondrial gene cytochrome oxidase subunit I (Cox1), which effective species identification phylogenetic analysis. Blood samples were collected from 70 C. splendens specimens seven cities in Punjab, Pakistan: Lahore, Kasur, Sialkot, Narowal, Pakpattan, Gujranwala, Bahawalpur. Genomic extraction was performed, partial sequence of COX1 amplified using PCR techniques. Sequencing Cox1 marker 10 randomly selected revealed nine distinct variants. Interspecific analysis positioned our sequences alongside various Corvus available GenBank, while intraspecific identified total 15 These variants showed nucleotide identity rates ranging 98.7 99.8%, with distances between 0.002 0.013. indicated that group consists single heterogeneous clade multiple countries, including Pakistan, Tanzania, Nepal, South Africa, Malaysia, Sri Lanka, Bangladesh, Kenya, Australia, Singapore. study significantly enhances understanding diversity relationships within populations, highlighting necessity inform conservation strategies. Further employing advanced molecular techniques broader geographic sampling essential assess dynamics this adaptable species.

Язык: Английский

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Evolutionary Inferences on the Chromosomal Diversity of Anseriformes (Neognathae; Galloanseres) by Microsatellite Mapping

Birds, Год журнала: 2025, Номер 6(2), С. 20 - 20

Опубликована: Апрель 15, 2025

Anseriformes represent a basal order in the phylogeny of neognath birds and are particular interest cytogenetic research due to their distinctive chromosomal features. However, aspects evolution, such as distribution organization microsatellite sequences, remain poorly understood. Given role these dynamic repetitive sequences chromosome organization, differentiation, we analyzed three Anatidae species, each representing different subfamily: Amazonetta brasiliensis-Brazilian Teal (Anatinae), Coscoroba coscoroba-Coscoroba Swan (Anserinae), Dendrocygna viduata-White-faced Whistling Duck (Dendrocygninae). This is first karyotypic description for White-faced (2n = 78) Brazilian 80), whereas Swan, previously analyzed, exhibits notably high diploid number 98). Despite sharing similar macrochromosome morphology, showed differences numbers distribution. Extensive accumulation was found both autosomal sex chromosomes (Z W) while displays minimal hybridization signals an absence microsatellites on chromosomes. The specific microsatellites, (CAC)10 (GAG)10, centromeric pericentromeric regions suggests association with transposable elements, potentially driving evolution. Notably, substantial Z W but not Duck, supports hypothesis that sequence expansion occurs species-specific manner, contributing differentiation. These findings highlight mapping valuable tool understanding evolution genomic differentiation Anseriformes.

Язык: Английский

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Integrating spatial analyses of genomic and physiological data to understand avian responses to environmental change

Integrative and Comparative Biology, Год журнала: 2024, Номер unknown

Опубликована: Июнь 3, 2024

Projected rates of climate change over the next century are expected to force species shift ranges, adapt or acclimate evade extinction. Predicting which these scenarios may be most likely is a central challenge for conserving biodiversity in immediate future. Modeling frameworks that take advantage intraspecific variation across environmental gradients can particularly important meeting this challenge. While space-for-time approaches essential climatic and genomic modeling approaches, mechanistic models incorporate ecological physiology data into assessing vulnerabilities rarely include variation. A major reason gap general lack empirical on geographic avian physiological traits. In review, we outline evidence processes shaping We use example evaporative water loss underscore research even traits cooling costs birds. demonstrate how shifting focus facilitate greater integration with emerging genomics approaches. Finally, steps an integrative approach advance understanding adaptation within species. Addressing knowledge gaps outlined review will contribute improved predictive framework synthesizes environmental, morphological, physiological, assess specific warming planet.

Язык: Английский

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