L. N. Spiridonova

Genetic and Taxonomic Diversity of the House Mouse Mus musculus from the Asian Part of the Former Soviet Union

Genetic diversity of the house mouse Mus musculus from 12 local populations (n = 65) of the central and eastern parts of the former Soviet Union was examined using RAPD–PCR. About 400 loci were identified, encompassing approximately 500 kb of the mouse genome. Genetic diversity was assessed using NTSYS, POPGENE, TFPGA, and TREECON software programs. In general, the house mouse sample from the regions examined was characterized by moderate genetic variation: polymorphism P = 95.6%, P99 = 60.7%, P95 = 24.2%; heterozygosity H = 0.089; the mean observed number of alleles na = 1.97; effective number of alleles ne = 1.13; intrapopulation differentiation δS = 0.387; gene diversity h = 0.09. Individual local populations displayed different levels of genetic isolation: the genetic subdivision index Gst varied from 0.086 to 0.324 at gene flow Nm varying from 5.3 to 1.05, while the interpopulation genetic distance DN ranged from 0.059 to 0.186. Most of the genetic diversity of the total sample resided within the local populations: HS = 0.06, total gene diversity HT = 0.09. The exact test for differentiation, however, did not confirm the affiliation of all the mice examined to one population: χ2 = 1446, d.f. = 724, P = 0.000. Molecular markers specific to four subspecies (musculus, castaneus, gansuensis, and wagneri) were identified. Moreover, in some cases the populations and individual animals exhibited traits of different subspecies, suggesting their introgressive hybridization. It was demonstrated that the house mouse fauna on the territories investigated was characterized by the prevalence of musculus-specific markers, while gansuensis-specific markers ranked second. The castaneus-specific markers were highly frequent in the Far East, but almost absent in Central Asia, where wagneri-specific markers were detected. It was suggested that house mice from Turkmenistan could belong to one of the southern subspecies, which had not deeply penetrated into the Asian fauna of the former Soviet Union. In phenogenetic (UPGMA) and phylogenetic (NJ) reconstructions this form with the high bootstrap support was placed at the tree base, while the isolation of other clusters was not statistically significant. It is thus likely that the house mice from Turkmenistan are closest to the ancestral form of the genus Mus on the territory of the former Soviet Union.

RAPD-PCR Analysis of Ground Squirrels from the Tobol-Ishim Interfluve: Evidence for Interspecific Hybridization between Ground Squirrel Species Spermophilus major and S. erythrogenys

Populations of two ground squirrel species, Spermophilus major and S. erythrogenys, from the interfluvial area of the Tobol and Ishim rivers, where their ranges overlap, have been examined using RAPD-PCR. We have identified 253 loci, which included taxon-specific markers for S. major and S. erythrogenys as well as markers for geographic populations. Estimation of genetic diversity and construction of phylogenetic relationships were performed using software programs POPGENE, TEPGA, and TREECON. In all, based on morphological traits, animals from the Tobol-Ishim interfluve were assigned to the two parental morphotypes and showed similar levels of genetic variability (H, na, ne). However, the total polymorphism level proved to be higher in ground squirrels with the major morphotype (P = 40.32%,P95 = 27.27%) than in animals with the erythrogenys morphotype (P = 32%,P95 = 22.13%). Nevertheless, the number of rare alleles was high in both cases, constituting about 70% of the total number. Interpopulation differentiation was considerably higher in S. major δ = 0.50) than in S. erythrogenys δ = 0.41). The genetic differentiation between local samples from the Tobol-Ishim interfluvial area was lower than that between the parental species. A significant part of the genetic diversity of the species examined and animals from the zone of overlapping ranges was accounted for by intrapopulation variability. Animals from the northern and southern parts of the Tobol-Ishim interfluve were charac-terized by the core traits of S. major and S. erythrogenys, respectively, falling into two distinct clusters in the UPGMA and NJ reconstructions. In addition to three hybrid individuals, identified by the bioacoustic method, three hybrid animals were distinguished using RAPD analysis. These animals earlier were thought to be “pure” species and formed their own clusters in phylogenetic reconstructions. Thus, the RAPD-PCR results directly showed the existence of stable hybridization (20% genetic hybrids) between S. major and S. erythrogenys in the Tobol-Ishim interfluvial area, which is more extensive than inferred previously from morphological and bioacoustic data.

Genetic differentiation of subspecies of the house mouse Mus musculus and their taxonomic relationships inferred from RAPD-PCR data

Genetic differentiation of six subspecies of the house mouse Mus musculus (Mus musculus musculus, M. m. domesticus, M. m. castaneus, M. m. gansuensis, M. m. wagneri, and M. m. ssp. (bactrianus?) was examined using RAPD-PCR analysis. In all, 373 loci of total length of about 530 kb were identified. Taxonspecific molecular markers were detected and the levels of genetic differences among the subspecies were estimated. Different degree of subspecific genetic differentiation was shown. The most similar subspecies pairs were M. m. castaneus-M. m. domesticus and M. m. musculus-M. m. gansuensis. In our phylogenetic reconstruction, M. m. wagneri proved to be most different from all the other subspecies. Genetic distances between it and other subspecies were two-to threefold higher than those between the “good”species of the subgenus Mus (e.g., between M. m. musculus and M. spicilegus, M. musculus and M. abbotti). The estimates of genetic similarity and the phylogenetic relationships between six house mouse subspecies inferred from RAPD partially conformed to the results based on cytogenetic and allozyme data. However, they were considerably different from phylogenetic reconstructions based on sequencing of the control mtDNA region, which reflects mutual inconsistency of different systems of inheritance.

Intraspecific genetic differentiation of the Siberian Rubythroat (Luscinia calliope): Data of sequencing the mtDNA cytochrome b gene

For the first time, genetic diversity and intraspecific structure of Luscinia calliope was studied according to the data of the mtDNA cytochrome b gene sequencing. The strong differentiation of haplotypes of the Siberian Rubythroat into western and eastern groups, which include subspecies according to their geographical attachment, was revealed. A high-haplotypic (Hd = 0.986) and nucleotide (π= 0.00875) variety was shown for the species as a whole. We revealed considerable genetic distances (D = 0.016) between the western and eastern haplotypes that were four times higher than the intraspecific distances in terms of cytochrome b for passerines (D = 0.004). For three birds from Transbaikal, significant genetic divergence was detected, which could indirectly indicate the existence of the hybrid zone of several subspecies in this part of the area.

Discordance in the distribution of markers of different inheritance systems (nDNA, mtDNA, and Chromosomes) in the superspecies complex Mus musculus as a result of extensive hybridization in primorye

The genetic structure of eight Mus musculus L. populations in Primorskii krai was studied with the use of taxon-specific markers of different inheritance systems: nDNA (RAPD), mtDNA (D-loop), and chromosomes. The results obtained demonstrate that although the compared nuclear marker characteristics (nDNA and chromosomes) have the same basis they are not linke with each other and, moreover, are often mutually inconsistent. Discordance in the inheritance of the marker characteristics in most of the animals studied is a result of extensive hybridization involving two to four house mouse subspecies. To identify taxonspecific nuclear markers revealed by RAPD, some RAPD PCR products were cloned, and their localization on chromosomes was determined. It was found that some fragments similar in size consist of two different comigrating sequences that are localized on different chromosomes and belong to different subspecies. All sequenced anonymous markers are localized in protein-coding genes. The functions of genes containing the marker sequences have been established. Differences in the taxon-specific RAPD fragments are associated with changes in the structure of important functional genes, and this can be considered as a significant genetic marker.

Genetic diversity of the house mouse Mus musculus and geographic distribution of its subspecies-specific RAPD markers on the territory of Russia

Genetic diversity and geographic distribution of taxon-specific RAPD markers was examined in ten local populations of the house mouse Mus musculus (n = 42). The house mice were generally characterized by moderate genetic variation: polymorphism P99 = 60%, P95 = 32.57%; heterozygosity H = 0.12; the observed allele number na = 1.6; the effective allele number ne = 1.18; the within-population differentiation ϑs = 0.388; and Shannon index I = 0.19. The degree of genetic isolation of individual local populations was greatly variable. The genetic subdivision index Gst varied from 0.162 to 0.770 at the gene flow of Nm = 2.58−0.149, while the among-population distances DN varied from 0.026 to 0.178. The largest part of the genetic diversity was found among the populations (HT = 0.125), while the within-population diversity was twice lower (HS = 0.06). The samples examined were well discriminated relative to the sets of RAPD markers. The character distribution pattern provided conditional subdivision of the mice into the “western” and the “eastern” groups with the putative boarder along the Baikal Lake. The first group was characterized by the prevalence of the markers typical of M. m. musculus and M. m. domesticus. The second group was characterized by the prevalence of the markers typical of M. m. musculus, M. m. gansuensis, M. m. castaneus, M. m. domesticus, and M. m. wagneri. The genotype of the nominative subspecies M. m. musculus was background for all populations. In the populations examined some of earlier described subspecies-specific molecular markers were found at different frequencies, pointing to the involvement of several subspecies of M. musculus in the process of hybridization.

Genetic Diversity of the Carrion and Jungle Crows as Evidenced by RAPD–PCR Analysis

RAPD–PCR analysis of the genetic diversity of the carrion crow (Corvus corone) and jungle crow (C. macrorhynchos) living in the continental parts of their species ranges and on some Russian and Japanese Far Eastern islands has been performed. Taxon-specific molecular markers have been found for each species. The genetic diversity of the carrion crow is considerably less than that of the jungle crow at the same genetic distance (P95 = 68.2%, DN = 0.27 and P95 = 88.4%, DN = 0.24, respectively). In both species, the genetic polymorphism of island samples is almost two times greater than that of continental samples (62 and 31.8%, respectively, for C. corone and 81.5 and 47.2%, respectively, for C. macrorhynchos). In addition, differences in genetic diversity between males and females (P95 = 55.1 and 72.1, respectively) has been found in the carrion crow but not in the jungle crow. The gene diversity of C. macrorhynchos is greater than that of C. corone: the mean numbers of alleles per locus are 2 and 1.81, effective numbers of alleles are 1.62 and 1.43, and the mean expected heterozygosities are 0.39 and 0.30, respectively. The phenograms and phylograms significantly segregate the clusters of the carrion and jungle crows. The clustering patterns of carrion crows corresponds to the intraspecies taxonomic and geographic differentiation: subspecies C. c. corone and C. c. orientalis living in the western and eastern parts of the species range, respectively, form different subclusters. The cluster of the jungle crow does not exhibit differentiation into subspecies C. m. mandshuricus and C. m. japonensis; molecular genetic differences between them are small.

Molecular genetic relationships among east Palaerctic ground squirrels of the genus Spermophilus (Sciuridae, Rodentia)

AbstactGenetic diversity in the four east Palearctic ground squirrel species of the genus Spermophilus—S. undulatus, S. parryi (subgenus Urocitellus), S. dauricus, and S. relictus (subgenus Citellus)—was investigated using RAPD PCR with ten random primers. Siberian chipmunk, Tamias sibiricus, was used as an out-group. Molecular markers for different taxonomic ranks were identified, including those for the genera Spermophilus and Tamias, subgenera Urocitellus and Citellus, as well as for each of the four species, S.undulatus, S. parryi, S. dauricus, and S. relictus. For the ground squirrel species and subgenera, genetic differentiation indices (Ht, Hs, Dst, Gst,Nm, and D) were calculated. In addition, for these groups the NJ phylogenetic reconstructions and UPGMA dendrograms of genetic similarity of the individuals and combined populations were constructed. Comparative molecular genetic analysis revealed a high genetic differentiation between S. undulatus, S. dauricus, S. relictus, and S. parryi (Gst= 0.58 to 0.82; D= 0.53 to 1.06), along with a low level of genetic differentiation of the subgenera Citellus and Urocitellus (Gst = 0.33; D= 0.27), distinguished in accordance with the existing taxonomic systems of the genus Spermophilus

Nuclear mtDNA pseudogenes as a source of new variants of the mtDNA cytochrome b haplotypes: A case study of Siberian rubythroat Luscinia calliope (Muscicapidae, Aves)

Sequence polymorphism of the mitochondrial DNA cytochrome b gene fragment was analyzed in 21 specimens of subspecies Luscinia calliope calliope (Pallas, 1776) and two specimens of L. c. anadyrensis (Portenko, 1939). On sequence chromatograms, in 19 specimens of L. c. calliope, double peaks of heteroplasmy type in the taxon-specific positions were revealed. Moreover, two clone variants were identified. The first variant was the calliope mitochondrial cyt b gene and the second was the nuclear cyt b pseudogene, similar to the mitochondrial haplotype anadyrensis-camtschatkensis. In L. c. anadyrensis, four clone variants, represented by the mitochondrial calliope and anadyrensis-camtschatkensis cyt b genes and nuclear calliope and sachalinensis cyt b pseudogenes, were identified. Some nuclear cyt b pseudogenes were highly similar (98–99%) to the mitochondrial genes of the subspecies L. c. anadyrensis, L. c. camtschatkensis, and L. c. sachalinensis. In the same time, the majority of nuclear pseudogene sequences were characterized by a high level of polymorphism, caused by nonsynonymous substitutions (up to five substitutions per sequence), the presence of indels in some of the clones, and TAA and TGA stop codons. In our opinion, the mitochondrial haplotypes anadyrensis-camtschatkensis and sachalinensis occurred as a result of intergenomic homologous recombination. This finding provides a new insight into the colonization history of the northeastern part of the range by L. calliope, according to which populating the territory of Chukotka, Kamchatka, and Sakhalin took place at different times and along the independent pathways.

Nuclear mtDNA pseudogenes as a source of new variants of mitochondrial genes: A case study of Siberian rubythroat Luscinia calliope (muscicapidae, aves)

First evidence for the presence of copies of mitochondrial cytochrome b gene of the subspecies group Luscinia calliope anadyrensis–L. c. camtschatkensis in the nuclear genome of nominative L. c. calliope was obtained, which indirectly indicates the nuclear origin of the subspecies-specific mitochondrial haplotypes in Siberian rubythroat. This fact clarifies the appearance of mitochondrial haplotypes of eastern subspecies by exchange between the homologous regions of the nuclear and mitochondrial genomes followed by fixation by the founder effect. This is the first study to propose a mechanism of DNA fragment exchange between the nucleus and mitochondria (intergenomic recombination) and to show the role of nuclear copies of mtDNA as a source of new taxon-specific mitochondrial haplotypes, which implies their involvement in the microevolutionary processes and morphogenesis.