Biology subjects

Djansugurova, L.

Publications and source records attributed to Djansugurova, L..

3 recordsLinked to original sources

bioRxiv2025

Evolutionary history and recurrent host adaptation in ancient Salmonella enterica

Salmonella enterica subsp. enterica is an extremely diverse bacterial pathogen causing frequent infections and foodborne disease among human populations. More than 1500 different bacterial strains (serovars) have been described, many with a wide host range. A small number of serovars are adapted to infect specific hosts: of these, serovars Typhi and Paratyphi A, B, and C cause primate-specific systemic infections (typhoid and paratyphoid fever). Although Paratyphi C is one of the rarest human-specific serovars today, it was once widespread, and all ancient Salmonella genomes published to date belong to or are ancestral to this lineage. Here, we present 53 new ancient Salmonella genomes spanning Eurasia and dating between 3500 BCE and 1300 CE. This rich genomic dataset allows us to reconstruct the evolutionary history of this pathogen in unprecedented detail. We identify multiple extinct prehistoric lineages that caused infections throughout Eurasia. Multiple lineage replacement events are observed throughout prehistoric and historic times, and Bayesian phylogenetic analysis is used to date and identify host adaptation events within this lineage. We find that host-adapted sublineages Paratyphi C, Choleraesuis, and Typhisuis continued to evolve host specificity independently from each other. We reconstruct signals of convergent host adaptation in the studied lineages and other host-adapted strains by analysing shared pseudogenes and recurrent gene gain and loss events. This analysis demonstrates a role for host interactions as a particular target of selection, highlighting the gradual adaptation of this S. enterica lineage to humans that coincides with the intensification of animal husbandry in pastoralist and sedentary farming societies.

genetics↗

bioRxiv2024

Advanced median-based genetic similarity analysis in Kazakh Tazy dogs: A novel approach for breed conformity assessment

The breed conformity evaluation is crucial for the preservation of the traits that characterise each dog breed. The use of genetic markers for this purpose provides a precision and objectivity that can surpass the reliability of phenotypic evaluations. In this study, we present a new simple algorithm for assessing breed conformity. The algorithm creates a similarity matrix based on genotypic data and then uses the median to calculate the percentage of genetic similarity that an individual has in relation to the genetic diversity of the breed. To validate the proposed algorithm, we applied it to the genotypic data of 18 microsatellites and 43,691 single nucleotide polymorphisms (SNPs) of the Kazakh Tazy dog, a breed of great cultural and historical importance to Kazakhstan that is now threatened with extinction due to crossbreeding. The algorithm showed a moderate correlation between the microsatellite and SNP genotyping methods, reflecting the different aspects of genetic similarity. In particular, the SNP-based evaluations agreed better with the expert judgements, highlighting their potential for accurate analysis of breed conformity. The proposed algorithm provides easily interpretable results, is flexible, adapts to different genetic markers and may provide an evaluation mechanism for breed conformity in situations where there is no reference population, incomplete pedigrees, unidentified meta-founders and high genetic diversity in the population. Author summaryOur research was initiated by the urgent concern for the possible extinction of the Kazakh Tazy dog, a breed with deep historical roots and cultural significance in Kazakhstan. Information at the DNA level may lead to faster genetic improvement of the breed than relying only on phenotypic data and pedigrees. Genotypic data can be processed to provide valuable insights into genetic diversity, relatedness and ancestry. However, existing methods do not provide a measure of percentage similarity that can be used to assess how closely a particular individual matches the typical genetic composition of the breed. These challenges have led us to propose an approach that overcomes the limitations of existing methods and allows genetic similarity to be assessed based on genotypes. It is based on a median-based approach to analyze genetic data and has been applied to microsatellite and SNP markers but can also be adapted to other genetic markers. This method provides results even in the absence of a defined reference population, complete pedigrees or identified meta-pedigrees and during high genetic diversity within a breed. It can provide breeders and researchers with a tool to maintain the genetic purity of unique breeds.

genomics↗

bioRxiv2018

Characterizing the genetic history of admixture across inner Eurasia

The indigenous populations of inner Eurasia, a huge geographic region covering the central Eurasian steppe and the northern Eurasian taiga and tundra, harbor tremendous diversity in their genes, cultures and languages. In this study, we report novel genome-wide data for 763 individuals from Armenia, Georgia, Kazakhstan, Moldova, Mongolia, Russia, Tajikistan, Ukraine, and Uzbekistan. We furthermore report genome-wide data of two Eneolithic individuals ({bsim}5,400 years before present) associated with the Botai culture in northern Kazakhstan. We find that inner Eurasian populations are structured into three distinct admixture clines stretching between various western and eastern Eurasian ancestries. This genetic separation is well mirrored by geography. The ancient Botai genomes suggest yet another layer of admixture in inner Eurasia that involves Mesolithic hunter-gatherers in Europe, the Upper Paleolithic southern Siberians and East Asians. Admixture modeling of ancient and modern populations suggests an overwriting of this ancient structure in the Altai-Sayan region by migrations of western steppe herders, but partial retaining of this ancient North Eurasian-related cline further to the North. Finally, the genetic structure of Caucasus populations highlights a role of the Caucasus Mountains as a barrier to gene flow and suggests a post-Neolithic gene flow into North Caucasus populations from the steppe.

genomics↗