Polymorphism of the 12S rRNA gene and phylogeography of the Central Asian tortoises Agrionemys horsfieldii gray, 1844

Based on intraspecific polymorphism of 12S rRNA gene, genetic variation of isolated populations of the Central Asian tortoise, Agrionemys horsfieldii, was for the first time investigated on a large part of the species distribution range, encompassing Uzbekistan, southern Kazakhstan, and northern and eastern Iran. In 59 tortoises, four haplotypes were discovered, including two (AH1 and AH2), described earlier. Haplotype AH1 was detected in 52 tortoises, inhabiting southern Kazakhstan and Uzbekistan. Haplotype AH2 was found in four tortoises from the border territory between Uzbekistan, Tajikistan, and Afghanistan. Two novel haplotypes, AH3 and AH4, were detected in the three tortoises from Iran. Based on nucleotide substitutions in the 12S rDNA sequence, the possible divergence time between the tortoises from different parts of the range was estimated. Possible pathways of the formation of modern intraspecific groups of A. horsfieldii are discussed.     

Phylogenetic relationships of intraspecific forms of the house mouse Mus musculus: Analysis of variability of the control region (D-loop) of mitochondrial DNA

Analysis of the control region of mitochondrial DNA (mtDNA) or D-loop of 96 house mice (Mus musculus) from Russia, Moldova, Armenia, Azerbaijan, Kazakhstan, and Turkmenistan has been used to reconstruct the phylogenetic relationships and phylogeographic patterns of intraspecific forms. New data on the phylogenetic structure of the house mouse are presented. Three phylogroups can be reliably distinguished in the eastern part of the M. musculus species range, the first one mainly comprising the haplotypes of mice from Transcaucasia (Armenia); the second one, the haplotypes of mice from Kazakhstan; and the third one, the haplotypes of mice from Siberia and some other regions. The morphological subspecies M. m. wagneri and M. m. gansuensis have proved to be genetically heterogeneous and did not form discrete phylogroups in the phylogenetic tree.     

Secondary contact between two divergent lineages of charrs of the genus <Emphasis Type="Italic">Salvelinus</Emphasis> in the Northwest Pacific

The present-day contact zone between the Beringian and Arctic phylogenetic lineages of charrs of the genus Salvelinus in the Northwest Pacific is documented. A comparative analysis of the genetic differentiation and divergence indices for allopatric and sympatric populations of charrs and phylogenetic and genealogical analyses of the mtDNA haplotypes indicate that Lake Achchen and the Lake Pekulineiskoe are the zones of secondary contact between S. m. malma and S. taranetzi; Lake Nachikinskoe, between S. m. malma and Salvelinus sp. 4; and Lake Dal’nee, between S. m. malma and S. krogiusae. The level of divergence between phylogenetic groups of haplotypes considerably exceeds the range of intraspecific variability of S. m. malma and could not have been achieved after colonization of the lakes in conditions of sympathy. The obtained data suggest that the territory of Kamchatka was colonized by the common ancestor of the Arctic phylogroup of Taranetz charr.     

Is <Emphasis Type="Italic">Testudo werneri</Emphasis> a distinct species?

Sequence variation of a 1066 bp long mtDNA fragment (cytochrome b gene, adjacent part of tRNA-Thr gene) of four known-locality samples of Testudo kleinmanni (Tripolitania, Libya) and of four samples of T. werneri (Negev, Israel) is compared with additional five sequences of pet trade tortoises allegedly representing T. kleinmanni. Four haplotypes, differing in one to four mutation steps occur. The most common haplotype was shared by all known-locality samples of T. kleinmanni and three T. werneri. Sequence variation within each nominal species and in the pooled sample of T. kleinmanni, T. werneri and pet trade tortoises is the lowest known for any Testudo species. We conclude there is no support for the validity of T. werneri Perälä, 2001.     

New data on the distribution of <Emphasis Type="Italic">Cylindera</Emphasis> (s. str.) <Emphasis Type="Italic">dokhtourowi</Emphasis> (V.E. Jakovlev, 1884) (Coleoptera,Carabidae: Cicindelinae)

The data on the distribution of Cylindera (s. str.) dokhtourowi (V.E. Jakovlev, 1884) are discussed. Records of this species from Kazakhstan and Uzbekistan are not supported by the material available, while its distribution in China (Xinjiang Uyghur Autonomous Region and Qinghai Province) is confirmed.     

New Data on MtDNA Variability of Pond Smelt <Emphasis Type="Italic">Hypomesus olidus</Emphasis> (Osmeridae) from the Commander Islands in Comparison with Other Populations of the Species

Sequencing of two regions of mitochondrial DNA, CytB (1124 bp) and COI (629 bp), is conducted for the first time for pond smelt Hypomesus olidus (Osmeridae) from the Commander Islands. The haplotypes identified, H1 and H2, differ by one mutation in the region of the COI gene. Haplotype H1 that belongs to the pond smelt from the Commander Islands was previously massively found in pond smelt of Azabache Lake. Haplotype H2 was not found previously and is probably unique to pond smelt from the Commander Islands.     

Polymorphism of Chloroplast DNA and Phylogeography of Green Alder (<Emphasis Type="Italic">Alnus alnobetula</Emphasis> (Ehrh.) K. Koch s. l.) in Asiatic Russia

This paper studies the phylogeography of Alnus alnobetula s. l. in the Asian part of the Russian range with the use of chloroplast DNA (cpDNA) sequences (intergenic spacers trnH-psbA, trnS-trnG, and psaA-trnS). Nine haplotypes were identified as a result of a combination of polymorphism of all sites in 241 plants in 20 populations of A. alnobetula. High interpopulation differentiation (G_ST = 0.914, N_ST = 0.928) and a significant phylogeographic structure (N_ST > G_ST, p < 0.05) were found. Reconstruction of genealogical relationships of green alder haplotypes revealed five highly divergent genetic lineages: one geographically widespread throughout Siberia and the Urals and several allopatric lines in the Far East of Russia, namely, the Chukotka Peninsula and the mouth of the Yana River, Magadan oblast, Primorye and the central part of Sakhalin Island, and the southern part of Sakhalin Island. Our data confirm that in the past the range of this species in the Far East was fragmented in several refugia that were isolated for a long time in various ice-free regions. This could have contributed to a high level of intraspecific polymorphism of green alder as a result of the divergence of endemic haplotypes, with almost non-overlapping distribution. However, the level of their molecular divergence does not correspond to the level of morphological differences.     

Comparative cytogenetic analysis of four species of <Emphasis Type="Italic">Dendropsophus</Emphasis> (Hylinae) from the Brazilian Atlantic forest

We conducted a cytogenetic study of four hyline frog species (Dendropsophus elegans, D. microps, D. minutus and D. werneri) from southern Brazil. All species had 2n = 30 chromosomes, with interspecific and intraspecific variation in the numbers of metacentric, submetacentric, subtelocentric and telocentric chromosomes. C-banding and fluorochrome staining revealed conservative GC-rich heterochromatin localized in the pericentromeric regions of all species. The location of the nucleolus organizer regions, as confirmed by fluorescent in situ hybridization, differed between species. Telomeric probes detected sites that were restricted to the terminal regions of all chromosomes and no interstitial or centromeric signals were observed. Our study corroborates the generic synapomorphy of 2n = 30 chromosomes for Dendropsophus and adds data that may become useful for future taxonomic revisions and a broader understanding of chromosomal evolution among hylids.     

Genetic diversity of <Emphasis Type="Italic">Haemaphysalis qinghaiensis</Emphasis> (Acari: Ixodidae) in western China

Haemaphysalis qinghaiensis as an endemic species in China mainly infests domestic animals and causes great harm to animals and humans in Northwestern plateau. However, there is no information about genetic diversity within the recently established populations of this tick species. Therefore, the present study analyzed the fragments of mitochondrial 16S rDNA, COI and the nuclear gene ITS1 of 56 H. qinghaiensis ticks across four regions of China which are main endemic areas of this species. Analysis showed 98.1–100% (16S rDNA), 97.9–100% (COI), 99.7–100% (ITS1) identity within individuals. For these sequences, 9, 15 and 8 haplotypes were found for 16S rDNA, COI and ITS1, respectively. Ticks from Yongjing were the most variable group, followed by Lintan, Huangyuan, and Tianzhu. Based on parallel analysis of the mitochondrial and nuclear genetic diversity of H. qinghaiensis, our results indicated that mitochondrial markers (especially COI) were much more useful than nuclear ITS for intraspecific genetic variability analysis.     

Spatial patterns and intraspecific diversity of the glacial relict legume species <Emphasis Type="Italic">Vavilovia formosa</Emphasis> (Stev.) Fed. in Eurasia

Vavilovia formosa is one of five genera in tribe Fabeae, (Fabaceae, Leguminosae) with close phylogenetic relationships to Pisum. It grows in subalpine and alpine levels in Armenia, Azerbaijan, Georgia, Iran, Iraq, Lebanon, Russia and Turkey and is recognized as an endangered and protected plant. This study was conducted to reveal its intraspecific variability, as well as to predict the past, extant and future species distribution range. We analysed 51 accessions with common phylogenetic markers (trnF-trnL, trnS-trnG, matK, rbcL, psbA-trnH and ITS). These represent in total up to 2551 bp of chloroplast and 664 bp of nuclear sequences per sample. Two populations from Turkey and Armenia were analysed for genetic diversity by AFLP. Leaf morphometry was conducted on 1457 leaflets from 43 specimens. Extracted bioclimatic parameters were used for niche-modelling approach. Analysis of cpDNA revealed two haplotypes, 12 samples from Armenia, Daghestan, Nakhichevan and Iran belonged to H1 group, while 39 samples of all Turkish and part of Armenian were in H2 group. The mean intrapopulation diversity based on AFLP was low (H _E = 0.088) indicating limited outcrossing rate. A significantly positive correlation between geographical latitude and leaf area (\(\rho\) = 0.527, p < 0.05) was found. Niche modelling has shown temporal variation of predicted occurrence across the projected time periods. Vavilovia formosa has suffered a range reduction following climate warming after last glacial maximum, which classify this species as cold-adapted among the Fabeae species as well as a glacial relict.     

Genetic diversity and population structure in the narrow endemic Chinese walnut <Emphasis Type="Italic">Juglans hopeiensis</Emphasis> Hu: implications for conservation

The conservation of narrow endemic species relies on accurate information regarding their population structure. Juglans hopeiensis Hu (Ma walnut), found only in Hebei province, Beijing, and Tianjin, China, is a threatened tree species valued commercially for its nut and wood. Sequences of two maternally inherited mitochondrial markers and two maternally inherited chloroplast intergenic spacers, three nuclear DNA sequences, and allele sizes from 11 microsatellites were obtained from 108 individuals of J. hopeiensis, Juglans regia, and Juglans mandshurica. Haplotype networks were constructed using NETWORK. Genetic diversity, population differentiation, and analysis of molecular variance (AMOVA) were used to determine genetic structure. MEGA was used to construct phylogenetic trees. Genetic diversity of J. hopeiensis was moderate based on nuclear DNA, but low based on uniparentally inherited mitochondrial DNA and chloroplast DNA. Haplotype networks showed that J. hopeiensis haplotypes were different than haplotypes found in J. regia and J. mandshurica. Allelic variants in nuclear genes that were shared among J. hopeiensis populations were not found in J. regia or J. mandshurica. Sampled populations of J. hopeiensis showed clear genetic structure. The maximum parsimony (MP) tree showed J. hopeiensis to be distinct from J. mandshurica but threatened by hybridization with J. regia and J. mandshurica. J. hopeiensis populations are strongly differentiated from sympatric Juglans species, but they are threatened by small population sizes and hybridization.     

On the taxonomic rank of <Emphasis Type="Italic">ciscaucasicus</Emphasis> and its relationships with the pygmy wood mouse <Emphasis Type="Italic">Sylvaemus uralensis</Emphasis> inferred from the mtDNA cytochrome b gene sequence

To specify the taxonomic rank of form ciscaucasicus (independent species Sylvaemus ciscaucasicus, or intraspecific form of pygmy wood mouse, S. uralensis), a 402-bp the mtDNA cytochrome b gene fragment (402 bp) was examined in ciscaucasicus individuals from six geographic localities of the Caucasus and Ciscaucasus (Krasnodar krai and Adygeya Republic) and 17 S. uralensis individuals from seven localities of the Russian Plain (Saratov oblast, Smolensk oblast, Voronezh oblast, Tula oblast, Moscow oblast, Tver’ oblast, and northern Krasnodar krai). For comparison, the cytochrome b gene was partly sequenced in the samples of yellow necked, S. flavicollis (n = 2, Samara oblast), and Caucasian, S. ponticus (n = 6, Krasnodar krai), wood mice. One Mus musculus specimen from Western Europe, whose nucleotide sequences were deposed in the GenBank, was used as intergeneric outgroup. Phylogenetic trees for the forms examined were constructed based on the mtDNA sequence variation and using the neighbor joining and maximum parsimony methods. The network of the cytochrome b haplotypes was also constructed. The level of genetic divergence was evaluated using Kimura’s two-parameter algorithm. Based on the data on the sequence variation in a 402-bp mtDNA cytochrome b gene fragment, the hypothesis on the species status of the ciscaucasicus form was. The mean intergroup distances (d) between the geographic groups of S. uralensis varied from 0.0036 to 0.0152. At the same time, the distances between the pygmy wood mice and the group of S. flavicollis-S. ponticus varies in the range from 0.0860 to 0.0935, and the level of intergeneric genetic differentiation (Sylvaemus-Mus) is higher than the latter index (d = 0.142). Ciscaucasicus should be considered as geographic substitution form of S. uralensis. Furthermore, the Caucasian populations of S. uralensis (= ciscaucasicus) were characterized by a threefold lower value of intergroup genetic divergence (d = 0.0062) than the East European populations (d = 0.0179). This finding pointed to some isolation of Caucasian populations of pygmy wood mouse and depletion of their gene pool. However other molecular genetic data (similarity of nucleotide composition and consistence of the levels of intra-and intergroup distances) suggest the absence of geographic subdivision between Caucasian and East European populations of S. uralensis relative to the molecular marker examined.     

<Emphasis Type="Italic">Scalaspira</Emphasis> (Gastropoda) from the Paleogene of the Transcaspian Region

The composition and distribution of the species of the genus Scalaspira Conrad, 1862 in the Eocene-Oligocene of western Kazakhstan are revised. Following Tembrock we assign this genus to Buccinidae and synonymize Aquilofusus Kautsky, 1925 with it. The stratigraphic interval studied contains at least eight species. Three species are new: S. alexeevi (Middle? and Upper Eocene, Chegan Formation), S. korobkovi, and S. kumsuatensis (Upper Oligocene, Karatomak Beds).     

Study on chloroplast DNA diversity of cultivated and wild pears (<Emphasis Type="Italic">Pyrus</Emphasis> L.) in Northern China

Eight pairs of chloroplast DNA (cpDNA) universal primers selected from 34 pairs were used to assess the genetic diversity of 132 pear accessions in Northern China. Among them, six amplified cpDNA fragments showed genetic diversity. A total of 24 variable sites, including 1 singleton variable site and 23 parsimony informative sites, as well as 21 insertion-deletion fragments, were obtained from the combined cpDNA sequences (5309–5535 bp). Two trnL-trnF-487 haplotypes, five trnL-trnF-413 haplotypes, five rbcL haplotypes, six trnS-psbC haplotypes, eight accD-psaI haplotypes and 12 rps16-trnQ haplotypes were identified among the individuals. Twenty-one haplotypes were identified based on the combined fragments. The values of nucleotide diversity (P_i), average number of nucleotide differences (k) and haplotype diversity (H_d) were 0.00070, 3.56408 and 0.7960, respectively. No statistical significance was detected in Tajima’s D test. Remarkably, the important cpDNA haplotypes and their representing accessions were identified clearly in this study. H_19 was considered as one of the ancient haplotypes and was a divergent centre. H_16 was the most common haplotype of the wild accessions. H_2 was the haplotype representing the most pear germplasm resources (46 cultivars and two wild Ussurian Pear accessions), followed by haplotype H_5 (30 cultivars, two wild Ussurian Pear accessions and four sand pears in outgroups) representing the cultivars ‘Dangshan Suli’ and ‘Yali’, which harbour the largest and the second largest cultivation areas in China. More importantly, this study demonstrated, for the first time, the supposed evolution routes of Pyrus based on cpDNA divergence in the background of pear phylogeny in Northern China.     

Phylogeography of mitochondrial DNA in South Asian Dolly Varden char <Emphasis Type="Italic">Salvelinus curilus</Emphasis> Pallas, 1814 (Salmoniformes,Salmonidae): Mediated gene introgression?

In 41 individuals of South Asian Dolly Varden char Salvelinus curilus, nucleotide sequences of tRNA-Pro gene fragment (27 bp) and mtDNA control region (483–484 bp) were analyzed. The fish were collected in 20 localities covering virtually the whole range of the species: Kuril Islands, Sakhalin Island, and Primorye. In addition, six individuals of three other char species (S. albus, S. malma, and S. leucomaenis), which are closely related to S. curilus and inhabit the Russian Far East, were examined. In all, we detected 12 different variants of mtDNA haplotypes that formed three distinct groups differing in 14–20 nucleotide positions. The first group consisted of six haplotypes found in S. curilus in Kuril Islands, Sakhalin, and Primorye (mtDNA phylogroup OKHOTSKIA). The second group comprised four haplotypes representing the mtDNA phylogroup BERING, which had been described earlier (Brunner et al, 2001); they were found in S. curilus in Kuril Islands and Sakhalin, as well as in S. albus and S. malma in Kamchatka and northern Kurils. The third group included two haplotypes detected in S. leucomaenis. The existence of two mtDNA lineages (OKHOTSKIA and BERING) in S. curilus from Kurils and Sakhalin was explained by hybridization and mtDNA transfer from S. malma to S. curilus. The absence of the BERING haplotypes in S. curilus from Primorye water reservoirs is related to the physical isolation of the Sea of Okhotsk and Sea of Japan basins in past epochs. On the basis of comparing phylogenetic trees, constructed from the data on allozyme and mtDNA variation, we suggest that in this case, a mediated transfer of mtDNA in Alpinoid chars → S. malma → S. curilus chain could occur.     

Evaluation of phylogenetic relationships in the genus <Emphasis Type="Italic">Mus</Emphasis> using <Emphasis Type="Italic">t</Emphasis>-specific microsatellite DNA markers

The t-complex includes a complex system of genes localized in the proximal region of chromosome 17 of house mouse Mus musculus. The results of microsatellite analysis of laboratory stocks of house mice carrying t ¹², t ^w5, t ^w12, and t ^w73 haplotypes and wild mice from natural populations of Russia (Volgograd, Rostov, Saratov oblasts, and Kalmykia), Armenia, Bulgaria, Iran, and Mongolia performed by the PCR method with the use of eight pairs of D17Mit primers (16, 21, 23, 28, 32, 57, 63, 78) are presented. These pairs of primers amplify microsatellite DNA sequences on mouse chromosome 17 in the region from 7.6 to 18.8 cM that correspond to inversions (In (17) 3.4). Each pair of primers recognized three to six variants of nucleotide sequences ranging in size from 90–120 bp (D17Mit 16) to 300–330 bp (D17Mit 57). In most cases, two variants of nucleotide sequences were detected in each individual, i. e., most individuals were heterozygous for the microsatellite loci under study. The highest similarity of the spectra of microsatellite DNA fragments was revealed in laboratory stocks of house mice carrying the t ^w5 and t ^w73 haplotypes. The spectra of animals from the Rostov and Volgograd oblasts appeard to be most similar to them. The microsatellite spectra of individuals from Iran closely resemble the spectrum of an individual from Armenia. It was demonstrated that amplified microsatellite fragments localized in the region of the t-complex can be used to identify representatives of the Mus genus from wild populations.     

A new species of the genus <Emphasis Type="Italic">Curimopsis</Emphasis> (Coleoptera,Byrrhidae) from southern Kazakhstan

A new pill-beetle species, Curimopsis kolovi sp. n., is described from the sandy desert on the left bank of the Ili River, southern Kazakhstan. This species differs from the closely related C. monticola Franz, 1967 and C. medvedevi Tshernyshev, 2002 in the 2-segmented antennal club, brown body, and shape of the aedeagus.     

Hytrosavirus genetic diversity and eco-regional spread in <Emphasis Type="Italic">Glossina</Emphasis> species

Background

The management of the tsetse species Glossina pallidipes (Diptera; Glossinidae) in Africa by the sterile insect technique (SIT) has been hindered by infections of G. pallidipes production colonies with Glossina pallidipes salivary gland hypertrophy virus (GpSGHV; Hytrosaviridae family). This virus can significantly decrease productivity of the G. pallidipes colonies. Here, we used three highly diverged genes and two variable number tandem repeat regions (VNTRs) of the GpSGHV genome to identify the viral haplotypes in seven Glossina species obtained from 29 African locations and determine their phylogenetic relatedness.

Results

GpSGHV was detected in all analysed Glossina species using PCR. The highest GpSGHV prevalence was found in G. pallidipes colonized at FAO/IAEA Insect Pest Control Laboratory (IPCL) that originated from Uganda (100%) and Tanzania (88%), and a lower prevalence in G. morsitans morsitans from Tanzania (58%) and Zimbabwe (20%). Whereas GpSGHV was detected in 25–40% of G. fuscipes fuscipes in eastern Uganda, the virus was not detected in specimens of neighboring western Kenya. Most of the identified 15 haplotypes were restricted to specific Glossina species in distinct locations. Seven haplotypes were found exclusively in G. pallidipes. The reference haplotype H1 (GpSGHV-Uga; Ugandan strain) was the most widely distributed, but was not found in G. swynnertoni GpSGHV. The 15 haplotypes clustered into three distinct phylogenetic clades, the largest contained seven haplotypes, which were detected in six Glossina species. The G. pallidipes-infecting haplotypes H10, H11 and H12 (from Kenya) clustered with H7 (from Ethiopia), which presumably corresponds to the recently sequenced GpSGHV-Eth (Ethiopian) strain. These four haplotypes diverged the most from the reference H1 (GpSGHV-Uga). Haplotypes H1, H5 and H14 formed three main genealogy hubs, potentially representing the ancestors of the 15 haplotypes.

Conclusion

These data identify G. pallidipes as a significant driver for the generation and diversity of GpSGHV variants. This information may provide control guidance when new tsetse colonies are established and hence, for improved management of the virus in tsetse rearing facilities that maintain multiple Glossina species.