The mandarin vole, Lasiopodomys mandarinus, is one of the most intriguing species among mammals with non-XX/XY sex chromosome system. It combines polymorphism in diploid chromosome numbers, variation in the morphology of autosomes, heteromorphism of X chromosomes, and several sex chromosome systems the origin of which remains unexplained. Here we elucidate the sex determination system in Lasiopodomys mandarinus vinogradovi using extensive karyotyping, crossbreeding experiments, molecular cytogenetic methods, and single chromosome DNA sequencing. Among 205 karyotyped voles, one male and three female combinations of sex chromosomes were revealed. The chromosome segregation pattern and karyomorph-related reproductive performances suggested an aberrant sex determination with almost half of the females carrying neo-X/neo-Y combination. The comparative chromosome painting strongly supported this proposition and revealed the mandarin vole sex chromosome systems originated due to at least two de novo autosomal translocations onto the ancestral X chromosome. The polymorphism in autosome 2 was not related to sex chromosome variability and was proved to result from pericentric inversions. Sequencing of microdissection derived of sex chromosomes allowed the determination of the coordinates for syntenic regions but did not reveal any Y-specific sequences. Several possible sex determination mechanisms as well as interpopulation karyological differences are discussed.

Whole-chromosome fusions play a major role in the karyotypic evolution of reptiles. It has been suggested that certain chromosomes tend to fuse with sex chromosomes more frequently than others. However, the comparative genomic synteny data are too scarce to draw strong conclusions. We obtained and sequenced chromosome-specific DNA pools of Sceloporus malachiticus , an iguanian species which has experienced many chromosome fusions. We found that four of seven lineage-specific fusions involved sex chromosomes, and that certain syntenic blocks which constitute the sex chromosomes, such as the homologues of the Anolis carolinensis chromosomes 11 and 16, are repeatedly involved in sex chromosome formation in different squamate species. To test the hypothesis that the karyotypic shift could be associated with changes in recombination patterns, we performed a synaptonemal complex analysis in this species and in Sceloporus variabilis (2 n = 34). It revealed that the sex chromosomes in S. malachiticus had two distal pseudoautosomal regions and a medial differentiated region. We found that multiple fusions little affected the recombination rate in S. malachiticus . Our data confirm more frequent involvement of certain chromosomes in sex chromosome formation, but do not reveal a connection between the gonosome–autosome fusions and the evolution of recombination rate. This article is part of the theme issue ‘Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part II)’.

Polyploid species represent a challenge for both cytogenetic and genomic studies due to their high chromosome numbers and the morphological similarity between their paralogous chromosomes. This paper describes the use of low-coverage high-throughput sequencing to identify the 14 most abundant tandemly arranged repetitive elements in the paleotetraploid genome of the crucian carp (Carassius carassius, 2n = 100). These repetitive elements were then used for molecular cytogenetic studies of a closely related functionally triploid form of the Prussian carp (Carassius gibelio, 3n = 150 + Bs) and a relatively distant diploid species, the tench (Tinca tinca, 2n = 48). According to their distribution on the chromosomes of the 3 aforementioned species, the repetitive elements here identified can be divided into 5 groups: (1) those specific to a single genomic locus in both Carassius species, despite the recent carp-specific genome duplication; (2) those located in a single genomic locus of T. tinca, but amplified in one or both Carassius species; (3) those massively amplified in the B chromosomes of C. gibelio; (4) those located in a single locus in C. gibelio, but amplified in many blocks in C. carassius; and (5) those located in multiple pericentromeric loci in both Carassius species. Our data indicate that some of the repetitive elements are highly conserved in cyprinoid species and may serve as good cytogenetic and genomic markers for discriminating paralogous chromosomes, while others are evolutionarily recent, and their amplification may be related to the last whole-genome duplication event.

The brown bear (Ursus arctos) is an iconic carnivoran species of the Northern Hemisphere. Its population history has been studied extensively using mitochondrial markers, which demonstrated signatures of multiple waves of migration, arguably connected with glaciation periods. Among Eurasian brown bears, Siberian populations remain understudied. We have sequenced complete mitochondrial genomes of four ancient (~4.5–40 kya) bears from South Siberia and 19 modern bears from South Siberia and the Russian Far East. Reconstruction of phylogenetic relationships between haplotypes and evaluation of modern population structure have demonstrated that all the studied samples belong to the most widespread Eurasian clade 3. One of the ancient haplotypes takes a basal position relative to the whole of clade 3; the second is basal to the haplogroup 3a (the most common subclade), and two others belong to clades 3a1 and 3b. Modern Siberian bears retain at least some of this diversity; apart from the most common haplogroup 3a, we demonstrate the presence of clade 3b, which was previously found mainly in mainland Eurasia and Northern Japan. Our findings highlight the importance of South Siberia as a refugium for northern Eurasian brown bears and further corroborate the hypothesis of several waves of migration in the Pleistocene.

17There is a growing body of evidence that the common ancestor of vertebrates had a bimodal 18 karyotype, i.e. consisting of large macrochromosomes and small microchromosomes. This 19 type of karyotype organization is preserved in most reptiles. However, certain species 20 independently experience microchromosome fusions. The evolutionary forces behind this are 21 unclear. We investigated the karyotype of the green spiny lizard, Sceloporus malachiticus, an 22 iguana species which has 2n=22, whereas the ancestral karyotype of iguanas had 2n=36. We 23 obtained and sequenced flow-sorted chromosome-specific DNA samples and found that most 24 of the microchromosome fusions in this species involved sex chromosomes. We found that 25 certain ancestral squamate chromosomes, such as the homologue of the Anolis carolinensis 26 chromosome 11, are repeatedly involved in sex chromosome formation in different species. 27To test the hypothesis that the karyotypic shift could be associated with changes in 28 recombination patterns, and to study sex chromosome synapsis and recombination in meiosis, 29 we performed synaptonemal complex analysis in this species and in S. variabilis, a related 30 species with 2n=34. We found that in the species studied the recombination patterns correlate 31 more with phylogeny than with the structure of the karyotype. The sex chromosomes had two 32 distal pseudoautosomal regions and a medial differentiated region. 33 34 42 different lineages share high homology [4,5]. The unimodal organization originated 43 independently in different lineages by fusion of microchromosomes with each other and with 44 the macrochromosomes [6,7]. 45This parallel process is interesting in the context of the search for general patterns of 46 karyotype and genome evolution in animals. Fixation of chromosomal rearrangements is 47 recombine in a meiotic act. It has two components: the interchromosomal, which reflects 87 recombination via independent chromosome segregation, and the intrachromosomal, which 88 reflects crossover recombination. We also studied sex chromosome synapsis and 89 recombination to validate the FISH and sequencing data on their structure. 90 Materials and methods 91The male specimens of S. malachiticus and S. variabilis were obtained from the pet trade. To 92 confirm the species identification, the 5'-fragment of the mitochondrial COI gene was 93 sequenced using protocols and primers described previously [17]. 94The primary fibroblast cell cultures of S. malachiticus were obtained in the Laboratory of 95 Animal Cytogenetics, the Institute of Molecular and Cellular Biology, Russia, using the 96 protocols described previously [18,19]. All cell lines were deposited in the IMCB SB RAS 97 cell bank ("The general collection of cell cultures", 0310-2016-0002). Metaphase 98 chromosome spreads were prepared from chromosome suspensions obtained from early 99 passages of primary fibroblast cultures as described previously [20-22].100C-like DAPI staining was performed in the following way. The slides were incub...

The processes of domestication and subsequent distribution of animals in Eurasia are closely related to human migrations and intercultural exchanges starting from the end of the Pleistocene. The development of methods for the isolation and analysis of ancient DNA from archaeological and paleontological remains has made it possible to take a new look at both the presumed core regions of domestication and the geography and dynamics of livestock distribution. This paper discusses the reports on the reconstruction of the migration processes of domestic animals in Eurasia using the analysis of ancient DNA performed by leading specialists from Great Britain, France, Finland, Ireland, and Russia at the international symposium on Domestic Animal Archaeogenomics (Bolgar, Republic of Tatarstan, March 2020). In addition to discussing the demographic history of different species of domestic animals, special attention was given to the development of methods for working with ancient DNA and the peculiarities of sample storage and handling. Summarizing the results of the symposium, the authors identified priority areas for future research. The interdisciplinary nature of research and the need to create broad scientific network that includes specialists from different fields were emphasized.

This study focuses on expanding knowledge about the genetic diversity of the Altai horse native to Siberia. While studying modern horses from two Altai regions, where horses were subjected to less crossbreeding, we tested the hypothesis, formulated on the basis of morphological data, that the Altai horse is represented by two populations (Eastern and Southern) and that the Mongolian horse has a greater genetic proximity to Eastern Altai horses. Bone samples of ancient horses from different cultures of Altai were investigated to clarify the genetic history of this horse breed. As a genetic marker, we chose hypervariable region I of mitochondrial DNA. The results of the performed phylogenetic and population genetic analyses of our and previously published data confirmed the hypothesis stated above. As we found out, almost all the haplotypes of the ancient domesticated horses of Altai are widespread among modern Altai horses. The differences between the mitochondrial gene pools of the ancient horses of Altai and Mongolia are more significant than between those of modern horses of the respective regions, which is most likely due to an increase in migration processes between these regions after the Early Iron Age.