Browsing by Subject "POPULATION-STRUCTURE"

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  • Horesh, Gal; Blackwell, Grace A.; Tonkin-Hill, Gerry; Corander, Jukka; Heinz, Eva; Thomson, Nicholas R. (2021)
    Escherichia coli is a highly diverse organism that includes a range of commensal and pathogenic variants found across a range of niches and worldwide. In addition to causing severe intestinal and extraintestinal disease, E. coli is considered a priority pathogen due to high levels of observed drug resistance. The diversity in the E. coli population is driven by high genome plasticity and a very large gene pool. All these have made E. coli one of the most well- studied organisms, as well as a commonly used laboratory strain. Today, there are thousands of sequenced E. coli genomes stored in public databases. While data is widely available, accessing the information in order to perform analyses can still be a challenge. Collecting relevant available data requires accessing different sources, where data may be stored in a range of formats, and often requires further manipulation and processing to apply various analyses and extract useful information. In this study, we collated and intensely curated a collection of over 10 000 E. coli and Shigella genomes to provide a single, uniform, high- quality dataset. Shigella were included as they are considered specialized pathovars of E. coli. We provide these data in a number of easily accessible formats that can be used as the foundation for future studies addressing the biological differences between E. coli lineages and the distribution and flow of genes in the E. coli population at a high resolution. The analysis we present emphasizes our lack of understanding of the true diversity of the E. coli species, and the biased nature of our current understanding of the genetic diversity of such a key pathogen.
  • Guo, Baocheng; Fang, Bohao; Shikano, Takahito; Momigliano, Paolo; Wang, Cui; Kravchenko, Alexandra; Merilä, Juha (2019)
    Hybridization and convergent evolution are phenomena of broad interest in evolutionary biology, but their occurrence poses challenges for reconstructing evolutionary affinities among affected taxa. Sticklebacks in the genus Pungitius are a case in point: evolutionary relationships and taxonomic validity of different species and populations in this circumpolarly distributed species complex remain contentious due to convergent evolution of traits regarded as diagnostic in their taxonomy, and possibly also due to frequent hybridization among taxa. To clarify the evolutionary relationships among different Pungitius species and populations globally, as well as to study the prevalence and extent of introgression among recognized species, genomic data sets of both reference genome-anchored single nucleotide polymorphisms and de novo assembled RAD-tag loci were constructed with RAD-seq data. Both data sets yielded topologically identical and well-supported species trees. Incongruence between nuclear and mitochondrial DNA-based trees was found and suggested possibly frequent hybridization and mitogenome capture during the evolution of Pungitius sticklebacks. Further analyses revealed evidence for frequent nuclear genetic introgression among Pungitius species, although the estimated proportions of autosomal introgression were low. Apart from providing evidence for frequent hybridization, the results challenge earlier mitochondrial and morphology-based hypotheses regarding the number of species and their affinities in this genus: at least seven extant species can be recognized on the basis of genetic data. The results also shed new light on the biogeographical history of the Pungitius-complex, including suggestion of several trans-Arctic invasions of Europe from the Northern Pacific. The well-resolved phylogeny should facilitate the utility of this genus as a model system for future comparative evolutionary studies.
  • Calboli, Federico C. F.; Byström, Pär; Merilä, Juha (2016)
    Specialization for the use of different resources can lead to ecological speciation. Accordingly, there are numerous examples of ecologically specialized pairs of fish species in postglacial lakes. Using a polymorphic panel of single nucleotide variants, we tested for genetic footprints of within-lake population stratification in nine-spined sticklebacks (Pungitius pungitius) collected from three habitats (viz. littoral, benthic, and pelagic) within a northern Swedish lake. Analyses of admixture, population structure, and relatedness all supported the conclusion that the fish from this lake form a single interbreeding unit.
  • Smaragdov, Michael G.; Kudinov, Andrei A.; Uimari, Pekka (2018)
    Holstein bulls and semen have been imported to Russia from Western countries since the 1970s. The objective of our study was to examine the effect of this introgression on genetic diversity between various commercial Holstein herds in the Leningrad region. A total of 803 Holstein cows from 13 herds were genotyped using the Illumina BovineSNP50 v.2 array. The pairwise Hudson's estimator of F-st values between 13 herds varied from 0.002 to 0.015, which is less than values usually obtained between dairy cattle breeds (> 0.1). The mean of these pairwise F-st values revealed differences between herds depending, mainly, on the proportion of common sires shared between the herds. In addition, we investigated the cause of negative F-st values. Based on our results, these negative values could be interpreted as an excess of within-herd genetic diversity over the between-herds genetic diversity. Our results show that introgressions of Holstein genes into Russian Black and White cattle of the Leningrad region have created genetic separation between herds similar with those for Jersey cows in USA, Australia and New Zealand.
  • Smaragdov, M. G.; Kudinov, A. A. (2020)
    Background Due to the advent of SNP array technology, a genome-wide analysis of genetic differences between populations and breeds has become possible at a previously unattainable level. The Wright's fixation index (F-st) and the principal component analysis (PCA) are widely used methods in animal genetics studies. In paper we compared the power of these methods, their complementing each other and which of them is the most powerful. Results Comparative analysis of the power Principal Components Analysis (PCA) and F-st were carried out to reveal genetic differences between herds of Holsteinized cows. Totally, 803 BovineSNP50 genotypes of cows from 13 herds were used in current study. Obtained F-st values were in the range of 0.002-0.012 (mean 0.0049) while for rare SNPs with MAF 0.0001-0.005 they were even smaller in the range of 0.001-0.01 (mean 0.0027). Genetic relatedness of the cows in the herds was the cause of such small F-st values. The contribution of rare alleles with MAF 0.0001-0.01 to the F-st values was much less than common alleles and this effect depends on linkage disequilibrium (LD). Despite of substantial change in the MAF spectrum and the number of SNPs we observed small effect size of LD - based pruning on F-st data. PCA analysis confirmed the mutual admixture and small genetic difference between herds. Moreover, PCA analysis of the herds based on the visualization the results of a single eigenvector cannot be used to significantly differentiate herds. Only summed eigenvectors should be used to realize full power of PCA to differentiate small between herds genetic difference. Finally, we presented evidences that the significance of F-st data far exceeds the significance of PCA data when these methods are used to reveal genetic differences between herds. Conclusions LD - based pruning had a small effect on findings of F-st and PCA analyzes. Therefore, for weakly structured populations the LD - based pruning is not effective. In addition, our results show that the significance of genetic differences between herds obtained by F-st analysis exceeds the values of PCA. Proposed, to differentiate herds or low structured populations we recommend primarily using the F-st approach and only then PCA.
  • Mäklin, Tommi; Kallonen, Teemu; Alanko, Jarno; Samuelsen, Ørjan; Hegstad, Kristin; Mäkinen, Veli; Corander, Jukka; Heinz, Eva; Honkela, Antti (2021)
    Genomic epidemiology is a tool for tracing transmission of pathogens based on whole-genome sequencing. We introduce the mGEMS pipeline for genomic epidemiology with plate sweeps representing mixed samples of a target pathogen, opening the possibility to sequence all colonies on selective plates with a single DNA extraction and sequencing step. The pipeline includes the novel mGEMS read binner for probabilistic assignments of sequencing reads, and the scalable pseudoaligner Themisto. We demonstrate the effectiveness of our approach using closely related samples in a nosocomial setting, obtaining results that are comparable to those based on single-colony picks. Our results lend firm support to more widespread consideration of genomic epidemiology with mixed infection samples.
  • Momigliano, Paolo; Florin, Ann-Britt; Merilä, Juha (2021)
    Testing among competing demographic models of divergence has become an important component of evolutionary research in model and non-model organisms. However, the effect of unaccounted demographic events on model choice and parameter estimation remains largely unexplored. Using extensive simulations, we demonstrate that under realistic divergence scenarios, failure to account for population size (N-e) changes in daughter and ancestral populations leads to strong biases in divergence time estimates as well as model choice. We illustrate these issues reconstructing the recent demographic history of North Sea and Baltic Sea turbots (Scophthalmus maximus) by testing 16 isolation with migration (IM) and 16 secondary contact (SC) scenarios, modeling changes in N-e as well as the effects of linked selection and barrier loci. Failure to account for changes in N-e resulted in selecting SC models with long periods of strict isolation and divergence times preceding the formation of the Baltic Sea. In contrast, models accounting for N-e changes suggest recent (
  • Voronova, Angelika; Rendón-Anaya, Martha; Ingvarsson, Pär; Kalendar, Ruslan; Ruņģis, Dainis (2020)
    Sequencing the giga-genomes of several pine species has enabled comparative genomic analyses of these outcrossing tree species. Previous studies have revealed the wide distribution and extraordinary diversity of transposable elements (TEs) that occupy the large intergenic spaces in conifer genomes. In this study, we analyzed the distribution of TEs in gene regions of the assembled genomes of Pinus taeda and Pinus lambertiana using high-performance computing resources. The quality of draft genomes and the genome annotation have significant consequences for the investigation of TEs and these aspects are discussed. Several TE families frequently inserted into genes or their flanks were identified in both species' genomes. Potentially important sequence motifs were identified in TEs that could bind additional regulatory factors, promoting gene network formation with faster or enhanced transcription initiation. Node genes that contain many TEs were observed in multiple potential transposable element-associated networks. This study demonstrated the increased accumulation of TEs in the introns of stress-responsive genes of pines and suggests the possibility of rewiring them into responsive networks and sub-networks interconnected with node genes containing multiple TEs. Many such regulatory influences could lead to the adaptive environmental response clines that are characteristic of naturally spread pine populations.
  • Monzon-Argueello, Catalina; Consuegra, Sofia; Gajardo, Gonzalo; Marco-Rius, Francisco; Fowler, Daniel M.; De Faveri, Jacquelin; de Leaniz, Carlos Garcia (2014)
  • Radenkovic, Snezana; Zoric, Ljiljana Sasic; Djan, Mihajla; Vidakovic, Dragana Obreht; Acanski, Jelena; Ståhls, Gunilla; Velickovic, Nevena; Markov, Zlata; Petanidou, Theodora; Tubic, Natasa Kocis; Vujic, Ante (2018)
    The Merodon aureus group is characterized by high endemism and the presence of morphologically cryptic species. Within one of its subgroups, M.bessarabicus, seven species and four more species complexes have been described to date. One of these complexes, the M.luteomaculatus, comprises new taxa that are the subject of the present study. Its members have allopatric ranges restricted to the Balkan Peninsula and Aegean islands. This complex exhibits morphological variability that could not be characterized using a traditional morphological approach. Thus, we used integrative taxonomy with independent character sets (molecular, geometric morphometric, distributional) to delimit species boundaries. Data on three molecular markers (COI, 28S rRNA, and ISSR) and geometric morphometry of the wing and male genitalia, together with distributional data, enabled recognition of six cryptic species within the complex: M.andriotes sp. n., M.euri sp. n., M.erymanthius sp. n., M.luteomaculatus sp. n., M.naxius sp. n., and M.peloponnesius sp. n. We discuss the possible influence of Aegean paleogeographical history on the speciation of this complex.
  • Van Steenberge, Maarten; Raeymaekers, Joost Andre Maria; Hablützel, Pascal Istvan; Vanhove, Maarten Pieterjan Maria; Koblmüller, Stephan; Snoeks, Jos (2018)
    BackgroundSpecies delineation is particularly challenging in taxa with substantial intra-specific variation. In systematic studies of fishes, meristics and linear measurements that describe shape are often used to delineate species. Yet, little is known about the taxonomic value of these two types of morphological characteristics. Here, we used Tropheus (Teleostei, Cichlidae) from the southern subbasin of Lake Tanganyika to test which of these types of characters best matched genetic lineages that could represent species in this group of stenotypic rock-dwelling cichlids. We further investigated intra-population variation in morphology. By linking this to a proxy of a population's age, we could assess the evolutionary stability of different kinds of morphological markers.ResultsMorphological data was collected from 570 specimens originating from 86 localities. An AFLP approach revealed the presence of five lineages in the southern subbasin: T. moorii, T. brichardi, T. sp. maculatus', T. sp. Mpimbwe' and T. sp. red', which we consider to represent distinct species. Although both types of morphological data supported this classification, a comparison of P-ST-values that describe inter-population morphological differentiation, revealed a better correspondence between the taxon delineation based on AFLP data and the patterns revealed by an analysis of meristics than between the AFLP-based taxon delineation and the patterns revealed by an analysis of shape. However, classifying southern populations of Tropheus was inherently difficult as they contained a large amount of clinal variation, both in genetic and in morphological data, and both within and among species. A scenario is put forward to explain the current-day distribution of the species and colour varieties and the observed clinal variation across the subbasin's shoreline. Additionally, we observed that variation in shape was larger in populations from shallow shores whereas populations from steep shores were more variable in meristics. This difference is explained in terms of the different timescales at which small and large scale lake level fluctuations affected populations of littoral cichlids at steep and shallow shores.ConclusionsOur results showed meristics to be more evolutionary stable, and of higher taxonomic value for species delimitation in Tropheus, than linear measurements that describe shape. These results should be taken into account when interpreting morphological differences between populations of highly stenotypic species, such as littoral cichlids from the Great East African Lakes.
  • Cseh, András; Poczai, Péter; Kiss, Tibor; Balla, Kirsztina; Berki, Zita; Horváth, Ádám; Kúti, Csaba; Karsai, Ildikó (2021)
    Historical wheat landraces are rich sources of genetic diversity offering untapped reservoirs for broadening the genetic base of modern varieties. Using a 20K SNP array, we investigated the accessible genetic diversity in a Central European bread wheat landrace collection with great drought, heat stress tolerance and higher tillering capacity. We discovered distinct differences in the number of average polymorphisms between landraces and modern wheat cultivars, and identified a set of novel rare alleles present at low frequencies in the landrace collection. The detected polymorphisms were unevenly distributed along the wheat genome, and polymorphic markers co-localized with genes of great agronomic importance. The geographical distribution of the inferred Bayesian clustering revealed six genetically homogenous ancestral groups among the collection, where the Central European core bared an admixed background originating from four ancestral groups. We evaluated the effective population sizes (Ne) of the Central European collection and assessed changes in diversity overtime, which revealed a dramatic similar to 97% genetic erosion between 1955 and 2015.
  • Lees, John A.; Harris, Simon R.; Tonkin-Hill, Gerry; Gladstone, Rebecca A.; Lo, Stephanie W.; Weiser, Jeffrey N.; Corander, Jukka; Bentley, Stephen D.; Croucher, Nicholas J. (2019)
    The routine use of genomics for disease surveillance provides the opportunity for high-resolution bacterial epidemiology. Current whole-genome clustering and multilocus typing approaches do not fully exploit core and accessory genomic variation, and they cannot both automatically identify, and subsequently expand, clusters of significantly similar isolates in large data sets spanning entire species. Here, we describe PopPUNK (Population Partitioning Using Nucleotide K-mers), a software implementing scalable and expandable annotation-and alignment-free methods for population analysis and clustering. Variable-length k-mer comparisons are used to distinguish isolates' divergence in shared sequence and gene content, which we demonstrate to be accurate over multiple orders of magnitude using data from both simulations and genomic collections representing 10 taxonomically widespread species. Connections between closely related isolates of the same strain are robustly identified, despite interspecies variation in the pairwise distance distributions that reflects species' diverse evolutionary patterns. PopPUNK can process 10(3)-10(4) genomes in a single batch, with minimal memory use and runtimes up to 200-fold faster than existing model-based methods. Clusters of strains remain consistent as new batches of genomes are added, which is achieved without needing to reanalyze all genomes de novo. This facilitates real-time surveillance with consistent cluster naming between studies and allows for outbreak detection using hundreds of genomes in minutes. Interactive visualization and online publication is streamlined through the automatic output of results to multiple platforms. PopPUNK has been designed as a flexible platform that addresses important issues with currently used whole-genome clustering and typing methods, and has potential uses across bacterial genetics and public health research.
  • Kerminen, Sini; Havulinna, Aki S.; Hellenthal, Garrett; Martin, Alicia R.; Sarin, Antti-Pekka; Perola, Markus; Palotie, Aarno; Salomaa, Veikko; Daly, Mark J.; Ripatti, Samuli; Pirinen, Matti (2017)
    Coupling dense genotype data with new computational methods offers unprecedented opportunities for individual-level ancestry estimation once geographically precisely defined reference data sets become available. We study such a reference data set for Finland containing 2376 such individuals from the FINRISK Study survey of 1997 both of whose parents were born close to each other. This sampling strategy focuses on the population structure present in Finland before the 1950s. By using the recent haplotype-based methods ChromoPainter (CP) and FineSTRUCTURE (FS) we reveal a highly geographically clustered genetic structure in Finland and report its connections to the settlement history as well as to the current dialectal regions of the Finnish language. The main genetic division within Finland shows striking concordance with the 1323 borderline of the treaty of Noteborg. In general, we detect genetic substructure throughout the country, which reflects stronger regional genetic differences in Finland compared to, for example, the UK, which in a similar analysis was dominated by a single unstructured population. We expect that similar population genetic reference data sets will become available for many more populations in the near future with important applications, for example, in forensic genetics and in genetic association studies. With this in mind, we report those extensions of the CP + FS approach that we found most useful in our analyses of the Finnish data.
  • Pohjanmies, Tähti; Elshibli, Sakina; Pulkkinen, Pertti; Rusanen, Mari; Vakkari, Pekka; Korpelainen, Helena; Roslin, Tomas (2016)
    Populations at species' range margins are expected to show lower genetic diversity than populations at the core of the range. Yet, long-lived, widespread tree species are expected to be resistant to genetic impoverishment, thus showing comparatively high genetic diversity within populations and low differentiation among populations. Here, we study the distribution of genetic variation in the pedunculate oak (Quercus robur L.) at its range margin in Finland at two hierarchical scales using 15 microsatellite loci. At a regional scale, we compared variation within versus among three oak populations. At a landscape scale, we examined genetic structuring within one of these populations, growing on an island of ca 5 km(2). As expected, we found the majority of genetic variation in Q. robur to occur within populations. Nonetheless, differentiation among populations was markedly high (F-ST = 0.12) compared with values reported for populations of Q. robur closer to the core of its range. At the landscape level, some spatial and temporal sub-structuring was observed, likely explained by the history of land-use on the island. Overall, Q. robur fulfils the expectation of the central-marginal hypothesis of high differentiation among marginal populations, but the notable population differentiation has most likely been influenced also by the long, ongoing fragmentation of populations. Finnish oak populations may still be adjusting to the drastic habitat changes of the past centuries. Preservation of genetic variation within the remaining stands is thus an important factor in the conservation of Q. robur at its range margin.
  • Herrero, Annika; Klutsch, Cornelya F. C.; Holmala, Katja; Maduna, Simo N.; Kopatz, Alexander; Eiken, Hans Geir; Hagen, Snorre B. (2021)
    Conservation and management of large carnivores requires knowledge of female and male dispersal. Such information is crucial to evaluate the population's status and thus management actions. This knowledge is challenging to obtain, often incomplete and contradictory at times. The size of the target population and the methods applied can bias the results. Also, population history and biological or environmental influences can affect dispersal on different scales within a study area. We have genotyped Eurasian lynx (180 males and 102 females, collected 2003-2017) continuously distributed in southern Finland (similar to 23,000 km(2)) using 21 short tandem repeats (STR) loci and compared statistical genetic tests to infer local and sex-specific dispersal patterns within and across genetic clusters as well as geographic regions. We tested for sex-specific substructure with individual-based Bayesian assignment tests and spatial autocorrelation analyses. Differences between the sexes in genetic differentiation, relatedness, inbreeding, and diversity were analysed using population-based AMOVA, F-statistics, and assignment indices. Our results showed two different genetic clusters that were spatially structured for females but admixed for males. Similarly, spatial autocorrelation and relatedness was significantly higher in females than males. However, we found weaker sex-specific patterns for the Eurasian lynx when the data were separated in three geographical regions than when divided in the two genetic clusters. Overall, our results suggest male-biased dispersal and female philopatry for the Eurasian lynx in Southern Finland. The female genetic structuring increased from west to east within our study area. In addition, detection of male-biased dispersal was dependent on analytical methods utilized, on whether subtle underlying genetic structuring was considered or not, and the choice of population delineation. Conclusively, we suggest using multiple genetic approaches to study sex-biased dispersal in a continuously distributed species in which population delineation is difficult.
  • Galindo, Juan; Carvalho, Joao; Sotelo, Graciela; Duvetorp, Marten; Costa, Diana; Kemppainen, Petri; Panova, Marina; Kaliontzopoulou, Antigoni; Johannesson, Kerstin; Faria, Rui (2021)
    Low dispersal marine intertidal species facing strong divergent selective pressures associated with steep environmental gradients have a great potential to inform us about local adaptation and reproductive isolation. Among these, gastropods of the genus Littorina offer a unique system to study parallel phenotypic divergence resulting from adaptation to different habitats related with wave exposure. In this study, we focused on two Littorina fabalis ecotypes from Northern European shores and compared patterns of habitat-related phenotypic and genetic divergence across three different geographic levels (local, regional and global). Geometric morphometric analyses revealed that individuals from habitats moderately exposed to waves usually present a larger shell size with a wider aperture than those from sheltered habitats. The phenotypic clustering of L. fabalis by habitat across most locations (mainly in terms of shell size) support an important role of ecology in morphological divergence. A genome scan based on amplified fragment length polymorphisms (AFLPs) revealed a heterogeneous pattern of differentiation across the genome between populations from the two different habitats, suggesting ecotype divergence in the presence of gene flow. The contrasting patterns of genetic structure between nonoutlier and outlier loci, and the decreased sharing of outlier loci with geographic distance among locations are compatible with parallel evolution of phenotypic divergence, with an important contribution of gene flow and/or ancestral variation. In the future, model-based inference studies based on sequence data across the entire genome will help unravelling these evolutionary hypotheses, improving our knowledge about adaptation and its influence on diversification within the marine realm.
  • Liu, Jiming; Gao, Shilun; Xu, Yuanyuan; Wang, Mianzhi; Ngiam, Jia Jun; Rui Wen, Nicholas Cho; Yi, Joan Jong Jing; Weng, Xuehuang; Jia, Liming; Salojarvi, Jarkko (2022)
    Sapindus is an important forest tree genus with utilization in biodiesel, biomedicine, and it harbors great potential for biochemical engineering applications. For advanced breeding of Sapindus, it is necessary to evaluate the genetic diversity and construct a rationally designed core germplasm collection. In this study, the genetic diversity and population structure of Sapindus were conducted with 18 expressed sequence tag-simple sequence repeat (EST-SSR) markers in order to establish a core germplasm collection from 161 Sapindus accessions. The population of Sapindus showed high genetic diversity and significant population structure. Interspecific genetic variation was significantly higher than intraspecific variation in the Sapindus mukorossi, Sapindus delavayi, and combined Sapindus rarak plus Sapindus rarak var. velutinus populations. S. mukorossi had abundant genetic variation and showed a specific pattern of geographical variation, whereas S. delavayi, S. rarak, and S. rarak var. velutinus showed less intraspecific variation. A core germplasm collection was created that contained 40% of genetic variation in the initial population, comprising 53 S. mukorossi and nine S. delavayi lineages, as well as single representatives of S. rarak and S. rarak var. velutinus. These results provide a germplasm basis and theoretical rationale for the efficient management, conservation, and utilization of Sapindus, as well as genetic resources for joint genomics research in the future.
  • Petersen, Jessica L.; Mickelson, James R.; Cothran, E. Gus; Andersson, Lisa S.; Axelsson, Jeanette; Bailey, Ernie; Bannasch, Danika; Binns, Matthew M.; Borges, Alexandre S.; Brama, Pieter; Machado, Artur da Camara; Distl, Ottmar; Felicetti, Michela; Fox-Clipsham, Laura; Graves, Kathryn T.; Guerin, Gerard; Haase, Bianca; Hasegawa, Telhisa; Hemmann, Karin; Hill, Emmeline W.; Leeb, Tosso; Lindgren, Gabriella; Lohi, Hannes; Lopes, Maria Susana; McGivney, Beatrice A.; Mikko, Sofia; Orr, Nicholas; Penedo, M. Cecilia T.; Piercy, Richard J.; Raekallio, Marja; Rieder, Stefan; Roed, Knut H.; Silvestrelli, Maurizio; Swinburne, June; Tozaki, Teruaki; Vaudin, Mark; Wade, Claire M.; McCue, Molly E. (2013)
  • Chertov, Nikita; Vasilyeva, Yulia; Zhulanov, Andrei; Nechaeva, Yu; Boronnikova, Svetlana; Kalendar, Ruslan (2021)
    The Ural Mountains and the West Eurasian Taiga forests are one of the most important centers of genetic diversity for Larix sibirica Ledeb. Forest fragmentation negatively impacts forest ecosystems, especially due to the impact of their intensive use on the effects of climate change. For the preservation and rational use of forest genetic resources, it is necessary to carefully investigate the genetic diversity of the main forest-forming plant species. The Larix genus species are among the most widespread woody plants in the world. The Siberian larch (Larix sibirica, Pinaceae) is found in the forest, forest-tundra, tundra (Southern part), and forest-steppe zones of the North, Northeast, and partly East of the European part of Russia and in Western and Eastern Siberia; in the Urals, the Siberian larch is distributed fragmentarily. In this study, eight pairs of simple sequence repeat (SSR) primers were used to analyse the genetic diversity and population structure of 15 Siberian larch populations in the Urals. Natural populations in the Urals exhibit indicators of genetic diversity comparable to those of Siberia populations (expected heterozygosity, He = 0.623; expected number of alleles, Ne = 4017; observed heterozygosity, Ho = 0.461). Genetic structure analysis revealed that the examined populations are relatively highly differentiated (Fst = 0.089). Using various algorithms for determining the spatial genetic structure, the examined populations formed three groups according to geographical location. The data obtained are required for the development of species conservation and restoration programs, which are especially important in the Middle Urals, which is the region with strong forest fragmentation.