Biology subjects

Yakupova, A.

Publications and source records attributed to Yakupova, A..

3 recordsLinked to original sources

bioRxiv2026

Sex-linked genomic variation reveals reproductive skew and male-biased dispersal in polygynous sea lions

Sex-biased dispersal and the resulting asymmetry in gene flow are important factors in evolution. However, their quantification in natural populations remains challenging, not least because sex-specific reproductive skew, as reflected in the mating system, further influences the relative contributions of males and females to the genetic pool of subsequent generations. Incorporating information from mitochondria (MT) and sex chromosomes (X, Y) alongside the more commonly used autosomal markers (AUT) provides a promising framework to partly disentangle confounding processes. Here, we exemplify this approach in two closely related, polygynous species with observational evidence for male-biased dispersal, the Galapagos sea lion (GSL) and the Steller sea lion (SSL). Using whole-genome resequencing data, we leveraged genetic variation among all four genomic compartments, representing genetic variation with female-only (MT), mixed (X, AUT) and male-only (Y) inheritance, to obtain information on the mating system and test for sex-specific migration across geographic and environmental boundaries. For GSL, genomic signatures were consistent with mild polygyny and a moderately elevated rate of male migration, particularly across habitat boundaries. In SSL, male reproductive skew was substantially greater, and male-biased migration was more pronounced and less habitat-dependent. Our results align with the species' life history and support a link between mating system and dispersal, but were also impacted by confounding biological processes and bioinformatic choices. This study highlights the value and challenges of population genomic approaches integrating multiple genomic compartments to infer variation in individual behaviours.

zoology↗

bioRxiv2025

Novel chromosome-length genome assemblies of three distinct subspecies of pine marten, sable, and yellow-throated marten (genus Martes, family Mustelidae)

The genus Martes consists of medium-sized carnivores within the family Mustelidae that are commonly known as martens, many of which exhibit extensive geographic variation and taxonomic uncertainty. Here, we report chromosome-length genome assemblies for three subspecies, each representing a different marten species: the Tobol sable (M. zibellina zibellina), the Ural pine marten (M. martes uralensis), and the Far East yellow-throated marten (M. flavigula aterrima). Using linked-read sequencing and Hi-C scaffolding, we generated assemblies with total lengths of 2.39-2.45 Gbp, N50 values of 137-145 Mbp, and high BUSCO scores (93.6-96.4%). We identified 19 chromosomal scaffolds for sable and pine marten, and 20 for yellow-throated marten, which agrees with the known karyotypes of these species (2n=38 and 2n=40, respectively). Annotation predicted ~20,000 protein-coding genes per genome, of which >90% were assigned functional names. Repeats encompass 36.9-40.4% of the assemblies, with a prevalence of LINEs and SINEs, and is conservative across the genus. Synteny analysis of our generated and available marten genome assemblies revealed assembly artifacts in previously published assemblies, which we confirmed through investigation of Hi-C contact maps. Among other rearrangements, we verified a sable-specific inversion on chromosome 11 using the published cytogenetic data. Our assemblies broaden the genomic resources available for Martes, extending coverage to geographically distant and taxonomically significant subspecies. Together, they provide a robust framework for assessing intraspecific genetic diversity, identifying signatures of hybridization, and refining the complex taxonomy of the genus. Beyond conservation and evolutionary applications, these references will facilitate comparative genomics across Mustelidae and other carnivorans.

genomics↗

bioRxiv2022

First mitogenome phylogeny of the sun bear Helarctos malayanus reveals a deep split between Indochinese and Sundaic lineages

The sun bear Helarctos malayanus is one of the most endangered ursids, and to date classification of sun bear populations has been based almost exclusively on geographic distribution and morphology. The very few molecular studies focusing on this species were limited in geographic scope. Using archival and non-invasively collected sample material, we have added a substantial number of complete or near-complete mitochondrial genome sequences from sun bears of several range countries of the species distribution. We here report 32 new mitogenome sequences representing sun bears from Cambodia, Thailand, Peninsular Malaysia, Sumatra and Borneo. Reconstruction of phylogenetic relationships revealed two matrilines that diverged [~]290 thousand years ago: one restricted to portions of mainland Indochina (China, Cambodia, Thailand; "Mainland clade"), and one comprising bears from Borneo, Sumatra, Peninsular Malaysia but also Thailand ("Sunda clade"). Generally recent coalescence times in the mitochondrial phylogeny suggest that recent or historical demographic processes have resulted in a loss of mtDNA variation. Additionally, analysis of our data in conjunction with shorter mtDNA sequences revealed that the Bornean sun bear, classified as a distinct subspecies (H. m. euryspilus), does not harbour a distinctive matriline. Further molecular studies of H. malayanus are needed, which should ideally include data from nuclear loci.

genomics↗