Differentiation of large-scaled redfin <Emphasis Type="Italic">Tribolodon hakonensis</Emphasis> (Pisces,Cyprinidae) in the Russian part of the range as inferred from the data of karyological analysis and PCR-RFLP analysis of mitochondrial DNA

Considerable differences in karyotypes of Tribolodon hakonensis from Primorye and the rivers of the Sea of Okhotsk drainage were demonstrated. These differences raise doubts that these fishes belong to one species and point to the necessity of more precise definition of the species status of the southern form of T. hakonensis. The karyological evidence is consistent with the data of mtDNA PCR-RFLP analysis on genetic independence of the southern and the northern forms of T. hakonensis. In the northern form of T. hakonensis, variation of the chromosomal arm number was revealed. Specifically, the number of chromosomes was constant (2n = 50), whereas the number of chromosomal arms (NF) constituted 88, 92, and 94, which suggests genetic heterogeneity of the northern form. PCR-RFLP analysis of mtDNA showed that haplotypes of northern T. hakonensis split into two groups with 100% support. Based on comparative phylogenetic and karyological analyses of the Tribolodon species, independent divergence of the southern and the northern forms of T. hakonensis was suggested.     

Speciation and dispersal of Tribolodon species (Pisces,Cyprinidae) around the Sea of Japan

Gene products of 22 protein coding loci from 29 populations of a uniquely sea-going cyprinid genus Tribolodon, T. hakonensis (anadromous and/or river-resident), T. brandtii (anadromous), T. ezoe (freshwater) and T. nakamurai (freshwater), were analyzed in order to infer the genetic divergence and dispersal of Tribolodon species around the Sea of Japan. According to the genetic distance, T. brandtii is located near the center between T. hakonensis and T. ezoe-T. nakamurai cluster. The outgroup root (Pseudaspius leptocephalus, Rhynchocypris lagowskii and Leuciscus waleckii) is attached between T. hakonensis-T. brandtii and the T. ezoe-T. nakamurai clusters. The origin of the genus Tribolodon and its salinity tolerance may date back to the Miocene Sea-of-Japan Lake and the Pliocene Paleo-Sea-of-Japan, respectively, as judged from the divergence time between Tribolodon and the outgroups. The genetic relationships and distribution pattern of Tribolodon species suggest they speciated on the Sakhalin-Japan side, and the continental populations of T. hakonensis and T. brandtii originated from anadromous colonizers. A new faunal element of Japanese freshwater fishes, the Sakhalin-Japan sub-element, is proposed for Tribolodon and some other fishes.     

Phylogeographic analysis reveals two periods of divergence in large-scaled redfin Tribolodon hakonensis (Pisces, Cyprinidae)

Analysis of mtDNA variation in one of the amphidromic Far Eastern redfins, Tribolodon hakonensis, revealed the presence of three considerably genetically different mtDNA phylogroups in the individuals from the Russian part of the range. These data suggest the presence of the two periods of divergent evolution in the history of the species examined. Comparison of the haplotype distributions from different phylogroups over the species range revealed geographic localization of only one phylogroup in the population samples from southern continental coastal regions of the Sea of Japan. At the same time, two other phylogroups were found in almost equal ratios in northern continental samples and near the Sakhalin Island. These results suggest that the first stage of the divergent evolution, which occured between Pliocene and Pleistocene, resulted in the formation of genetically isolated form (probably, a species) in the region of the Sea of Japan. The second, later period of divergence, probably associated with the separation of the Sea of Okhotsk from the Pacific Ocean then ended with the integration of earlier genetically separated forms into one species with the common gene pool.     

Identification of Hybrids between the Far Eastern Redfins Tribolodon hakonensis and T. brandtii Based on the Cephalic Lateral-Line System and Four Molecular Genetic Markers

Journal of Ichthyology - Three species of the genus Tribolodon (T.&nbsp;hakonensis, T.&nbsp;brandtii, and T.&nbsp;sachalinensis) and hybrids between T.&nbsp;hakonensis and...     

Genetic differentiation of charrs in the Russian north and far east

Genetic differences and relationships within charrs Salvelinus alpinus , northern and southern S. malma, S. taranetzi, S. levanidovi and S. leucomaenis , were studied by examination of 31–35 allozyme loci and PCR-RFLP analysis of mtDNA segment (about 2600 bp) including the cytochrome b gene and D-loop. Data for mtDNA were also obtained for samples of S. drjagini, S. albus and for European samples of S. alpinus. Generally allozyme and mtDNA segment analyses produced similar pictures of genetic divergence and relationships. The southern S. malma exhibited the greatest genetic variability (allozyme heterozygosity and mtDNA haplotype diversity). S. alpinus, S. malma, S. levanidovi and S. leucomaenis had fixed differences from one another at various allozyme loci, and differed in fixed (but polymorphic in S. malma ) individual mtDNA haplotypes produced with MspI restrictase. Such genetic individuality is typical of distinct taxa. S. taranetzi is closest genetically to allopatric S. alpinus , but exhibited fixed differences from the northern S. malma in sympatry. In all samples of S. alpinus the only mtDNA haplotype was shared with S. drjagini. S. albus shared its single haplotype with the northern S. malma from the same locality. S. leucomaenis is differentiated from the other species to the greatest extent, possibly reflecting an early evolutionary divergence. Some evolutionary and taxonomic implications of the genetic relationships of charrs studied are discussed.     

Genetic divergence of Far Eastern dace species belonging to the genus Tribolodon (Pisces,Cyprinidae) and closely related taxa

Based on a biochemical-genetic approach, heterozygosity and divergence of structural genes of 30 enzyme loci were analyzed in six dace species. In addition, intra- and interspecific divergence of gene expression was analyzed based on a sample of 12 to 15 loci. Mean heterozygosities per individual varied as follows: Tribolodon species, Hobs = 0.007 +/- 0.007 and Hexp = 0.007 +/- 0.007; T. ezoe, Hobs = 0.045 +/- 0.016 and Hexp = 0.067 +/- 0.029. Several variants of genetic distances were estimated. Standard Nei's distances (DN) varied from 0.145 to 0.284 in four dace species studied. As related to Tribolodon dace species, the following genetic distances were obtained for two members of other genera: Pseudaspius leptocephalus, DN = 0.269; Leuciscus waleckii, DN = 0.769. Based on the distance matrices, different clustering algorithms were realized. The main feature shared by different dendrograms was a separate position of the cluster joining Far-Eastern dace species, to which P. leptocephalus and L. waleckii are successively added. Among the species studied, the proportion of loci similar by expression (E) varied from 87 to 100%. The greatest difference was found between anadromous and nonanadromous ecotypes of T. hakonensis, E = 67%. The following conclusions can be made: (1) Four studied species of the genus Tribolodon are rather well genetically differentiated. Diagnostic loci are available. (2) A nominal dace species, T. species, should be considered the fourth isolated species of this genus, which is confirmed by its recent zoological acceptance of this species. (3) The origin and divergence of dace species belonging to the genus Tribolodon are relatively late (1 to 3 Myr ago) historical events. (4) Taxonomically, the genus Tribolodon belong to the tribe Pseudaspinini together with P. leptocephalus, which is confirmed by genetic data. (5) Data on heterozygosity and the divergence of structural and regulatory elements of genome, along with the proposed scheme of speciation types, suggest the following speciation modes for the species studied: for four species, adaptive divergence and for two species, genetic transformation.     

Phylogenetic analysis of Altai osmans of the genus Oreoleuciscus (Pisces, Cyprinidae, Leuciscinae), based on the analysis of the cytochrome oxidase 1 gene (Co-1) sequence

Molecular genetic analysis of Altai osmans of the genus Oreoleuciscus from two different parts of the range was carried out. In this study, based on the mitochondrial Co-1 gene sequence, a total of 25 fish specimens belonging to four genera were examined: (1) O. humilis, 2 specimens; O. potanini, 13 specimens; (2) Pseudaspius leptocephalus, 1 specimen; (3) Tribolodon brandtii, T. hakonensis, and T. sachalinensis from the GenBank database, 8 speciens; and (4) Leuciscus waleckii, 1 specimen (used as an outgroup). The p-distances were very low both within and between the species: (1) 0.20 +/- 0.03%; (2) 0.40 +/- 0.12%; and (1-2) 0.80 +/- 0.04%. To visualize the relationships among all of the species examined, the neighbor joining (NJ), maximum parsimony (MP), Bayesian (BA), and maximum likelihood (ML) trees were constructed. The results obtained using these methods were very similar. It was demonstrated that species assignment of the individuals (barcoding) with the help Co-1 gene was effective, despite of very low divergence of the two osman taxa, which was comparable with typical intraspecific values in other animal groups. Taxonomic status of O. potanini and O. humilis requires further investigation with paying attention to low genetic distances between these species along with the lack of material from sympatric parts of the ranges.     

Revision of the species composition of the wood mice from the genus Sylvaemus from the territory of Rostov oblast using karyological, allozyme and molecular genetic analysis

Using karyological, allozyme, and molecular genetic analysis, habitation of the four Sylvaemus wood mice species, pygmy wood mouse (S. uralensis), wood mouse (S. sylvaticus), yellow-necked mouse (S. flavicollis), and yellow-bellied mouse (S. fulvipectus) in Rostov oblast was demonstrated. Sylvaemus uralensis was distributed nearly over nearlythe whole territory of the oblast; S. sylvaticus was found in the central and western parts of the oblast on the right bank area of Don River; S. flavicollis inhabited northern and central parts of the right bank area of Don River; S. fulvipectus was found in the southern parts of the oblast, in the left bank area of Don River. Using the chromosome C-banding technique, it was demonstrated that the pygmy wood mice living in Rostov oblast in the right bank areas of Manych River and Don River in its low course, belonged to the eastern European chromosomal form of S. uralensis. The mice from the outskirts of the town of Salsk, the left bank area of Manych River, were probably hybrids between eastern European and southern European chromosomal forms. Based on the mitochondrial DNA cytochrome b gene fragment sequencing and chromosome C-banding, it was suggested that the wood mice inhabiting Rostov oblast belonged to the southern lineage of S. sylvaticus, living on Apennine Peninsula, Balkan Peninsula, and nearly throughout Ukraine.     

Phylogeography of southern Asian Dolly Varden char <Emphasis Type="Italic">Salvelinus malma krascheninnikovi</Emphasis>: Genealogical analysis of mitochondrial DNA

Phylogeography of southern Asian Dolly Varden char was studied using the data on mtDNA variation (regions ND1/ND2, ND5/ND6, and Cytb/D loop) obtained using PCR-RFLP analysis. Analysis of contemporary population genetic structure showed that Salvelinus malma krascheninnikovi throughout the whole species range was characterized by high population differentiation in combination with rather small differences between the populations from remote regions. The genealogy of mtDNA haplotypes was reconstructed and nested clade analysis of geographical distances was performed. Geographical distribution of mtDNA haplotypes of S. m. krascheninnikovi was explained by population genetic processes (restricted gene flow), as well as by historical demographic events (range expansion and fragmentation). It was demonstrated that the main demographic events were associated with cyclic processes of the geological formation of the Sea of Japan and adjacent territories. Furthermore, genealogical tree of S. m. krascheninnikovi contained the traces of secondary contact between isolated phylogeographical lineages.     

Comparative morphological analysis of big-scaled redfin <Emphasis Type="Italic">Tribolodon hakonensis</Emphasis> Günther, 1877 (Cyprinidae,Cypriniformes) from Sakhalin and southern Primorye

Comparative analysis of plastic and meristic characteristics of big-scaled redfin Tribolodon hakonensis from Sakhalin and southern Primorye has been performed. The considerable differences revealed are supported by results of genetic studies. The results of comparison of morphology of big-scaled and Pacific T. brandtii redfins with the purpose of assessing the probability of the previously advanced hypothesis on the origin of the “southern” form of big-scaled redfin are provided.     

Phylogeographic analysis reveals two periods of divergence in large-scaled redfin <Emphasis Type="Italic">Tribolodon hakonensis</Emphasis> (Pisces,Cyprinidae)

Analysis of mtDNA variation in one of the amphidromic Far Eastern redfins, Tribolodon hakonensis, revealed the presence of three considerably genetically different mtDNA phylogroups in the individuals from the Russian part of the range. These data suggest the presence of the two periods of divergent evolution in the history of the species examined. Comparison of the haplotype distributions from different phylogroups over the species range revealed geographic localization of only one phylogroup in the population samples from southern continental coastal regions of the Sea of Japan. At the same time, two other phylogroups were found in almost equal ratios in northern continental samples and near the Sakhalin Island. These results suggest that the first stage of the divergent evolution, which occured between Pliocene and Pleistocene, resulted in the formation of genetically isolated form (probably, a species) in the region of the Sea of Japan. The second, later period of divergence, probably associated with the separation of the Sea of Okhotsk from the Pacific Ocean then ended with the integration of earlier genetically separated forms into one species with the common gene pool.     

Arsenic accumulation in organs of the fresh water fish Tribolodon hakonensis.

The fish Tribolodon hakonensis lives in good health in Lake Usoriko, which has been acidified and naturally contaminated with arsenic by volcanic activities. We have determined the contents of various metals in various fish organs of T. hakonensis, collected at Lake Usoriko. We found that a large amount of arsenic was accumulated in the eye, especially in the choroid-retina part. The arsenic concentrations in the liver and kidneys were about 0.4 microgram/g (wet), whereas the muscle contained less arsenic. The arsenic accumulation in the skin was also observed, especially in the epaxial part. Zinc and arsenic contents in various fish organs correlated well.     

Mitochondrial DNA variation in Russian populations of Stavropol krai,Orel and Saratov oblasts

Mitochondrial DNA (mtDNA) polymorphism was examined in three Russian populations from the European part of Russia (Stavropol krai, Orel oblast, and Saratov oblast). This analysis showed that mitochondrial gene pool of Russians was represented by the mtDNA types belonging to haplogroups H, V, HV*, J, T, U, K, I, W, and X. A mongoloid admixture (1.5%) was revealed in the form of mtDNA types of macrohaplogroup M. Comparative analysis of the mtDNA haplogroup frequency distribution patterns in six Russian populations from the European part of Russia indicated the absence of substantial genetic differences between them. However, in Russian populations from the southern and central regions the frequency of haplogroup V (average frequency 8%) was higher than in the populations from more northern regions. Based on the data on mtDNA HVS1 sequence variation, it was shown that the diversity of haplogroup V in Russians (h = 0.72) corresponded to the highest h values observed in Europe. The reasons for genetic differentiation of the Russian population (historical, ecological, and adaptive) are discussed.     

Revision of the species composition of the wood mice from the genus <Emphasis Type="Italic">Sylvaemus</Emphasis> from the territory of Rostov oblast using karyological,allozyme and molecular genetic analysis

Using karyological, allozyme, and molecular genetic analysis, habitation of the four Sylvaemus wood mice species, pygmy wood mouse (S. uralensis), wood mouse (S. sylvaticus), yellow-necked mouse (S. flavicollis), and yellow-bellied mouse (S. fulvipectus) in Rostov oblast was demonstrated. Sylvaemus uralensis was distributed nearly over the whole territory of the oblast; S. sylvaticus was found in the central and western parts of the oblast on the right bank area of Don River; S. flavicollis inhabited northern and central parts of Rostov oblast on the right bank area of Don River; S. fulvipectus was found in the southern parts of the oblast, in the left bank area of Don River. Using the chromosome C-banding technique, it was demonstrated that the pygmy wood mice living in Rostov oblast in the right bank areas of Manych River and Don River in its low course, belonged to the eastern European chromosomal form of S. uralensis. The pygmy wood mice from the outskirts of the town of Salsk, the left bank area of Manych River, were probably hybrids between eastern European and southern European chromosomal forms. Based on the mitochondrial DNA cytochrome b gene fragment sequencing and chromosome C-banding, it was suggested that the wood mice inhabiting Rostov oblast belonged to the southern lineage of S. sylvaticus, living on Apennine Peninsula, Balkan Peninsula, and nearly throughout Ukraine.     

Mitochondrial DNA Variation in Russian Populations of Stavropol Krai, Orel and Saratov Oblasts

Mitochondrial DNA (mtDNA) polymorphism was examined in three Russian populations from the European part of Russia (Stavropol krai, Orel oblast, and Saratov oblast). This analysis showed that mitochondrial gene pool of Russians was represented by the mtDNA types belonging to haplogroups H, V, HV*, J, T, U, K, I, W, and X. A mongoloid admixture (1.5%) was revealed in the form of mtDNA types of macrohaplogroup M. Comparative analysis of the mtDNA haplogroup frequency distribution patterns in six Russian populations from the European part of Russia indicated the absence of substantial genetic differences between them. However, in Russian populations from the southern and central regions the frequency of haplogroup V (average frequency 8%) was higher than in the populations from more northern regions. Based on the data on mtDNA HVS1 sequence variation, it was shown that the diversity of haplogroup V in Russians (h= 0.742) corresponded to the highest h values observed in Europe. The reasons for genetic differentiation of the Russian population (historical, ecological, and adaptive) are discussed.     

Genetic Variation in Wild and Hatchery Stocks of Suminoe Oyster (Crassostrea ariakensis) Assessed by PCR-RFLP and Microsatellite Markers

Genetic variation in wild Asian populations and U.S. hatchery stocks of Crassostrea ariakensis was examined using polymerase chain reactions with restriction fragment length polymorphism (PCR-RFLP) analysis of both the mitochondrial COI gene and the nuclear internal transcribed spacer (ITS) 1 region and using 3 microsatellite markers. Hierarchical analysis of molecular variance and pairwise comparisons revealed significant differentiation (P < 0.05) between samples from the northern region, represented by collections from China and Japan, and 2 of 3 samples from southern China. PCR-RFLP patterns were identified that were diagnostic for the northern (N-type) and southern (S-type) groups. Microsatellite marker profiles were used to assign each oyster to one of the two northern or two southern populations. Results for more than 97% of the oysters were consistent with the PCR-RFLP patterns observed for each individual in that oysters with N-type patterns were assigned to one of the northern populations and those with S-type patterns to one of the southern populations. At one site of the Beihai (B) region in southern China a mix of individuals with either the N-type or S-type PCR-RFLP genotypes was found. No heterozygotes at the nuclear ITS-1 locus were found in the sample, possibly indicating reproductive isolation in sympatry. Microsatellite assignment test results of the B individuals were also consistent with identifications as either the N-type or S-type based on PCR-RFLP patterns. The parental population for one hatchery stock was this B sample, which initially was composed of almost equal numbers of northern and southern genetic types. After hatchery spawns, however, more than 97% of the progeny fell into the northern genetic group by PCR-RFLP and microsatellite assignment test analyses, indicating that the individuals with the southern genotype contributed little to the spawn, owing to gametic incompatibility, differential larval survival, or a difference in timing of sexual maturity. Overall, results suggested that oysters collected as C. ariakensis in this study, and likely in other studies as well, include two different sympatric species with some degree of reproductive isolation.     

A study of the systematics of cyprinid fishes by two-dimensional gel electrophoresis

This study was carried out to shed light on confused subfamilial groupings in the Cyprinidae from the biochemical viewpoint at the molecular level, specifically by using two-dimensional gel electrophoresis of liver proteins. Six pairs of cypriniform fishes, which are different from one another at familial, subfamilial, generic, specific, subspecific, and individual levels, were compared. The genetic distances between pairs of fishes increased as taxonomic ranks of the pairs became higher, confirming the reliable usefulness of this technique. Four species representing the different subfamilies, Cyprininae, Gobioninae, Acheilognathinae, and Leuciscinae, were compared to give new insight into relationships at the subfamilial level. Cyprinus carpio (Cyprininae) and Pseudogobio esocinus esocinus (Gobioninae) gave the smallest genetic distance and the largest values were obtained between either one of the above species and Acheilognathus melanogaster (Acheilognathinae), suggesting that the former two subfamilies compose the most closely related group that is in turn distantly related to Acheilognathinae. Tribolodon hakonensis (Leuciscinae) had almost equal genetic distances to the three other species.     

Mitochondrial DNA variation, but not nuclear DNA, sharply divides morphologically identical chameleons along an ancient geographic barrier

The Levant is an important migration bridge, harboring border-zones between Afrotropical and palearctic species. Accordingly, Chameleo chameleon, a common species throughout the Mediterranean basin, is morphologically divided in the southern Levant (Israel) into two subspecies, Chamaeleo chamaeleon recticrista (CCR) and C. c. musae (CCM). CCR mostly inhabits the Mediterranean climate (northern Israel), while CCM inhabits the sands of the north-western Negev Desert (southern Israel). AFLP analysis of 94 geographically well dispersed specimens indicated moderate genetic differentiation (PhiPT = 0.097), consistent with the classical division into the two subspecies, CCR and CCM. In contrast, sequence analysis of a 637 bp coding mitochondrial DNA (mtDNA) fragment revealed two distinct phylogenetic clusters which were not consistent with the morphological division: one mtDNA cluster consisted of CCR specimens collected in regions northern of the Jezreel Valley and another mtDNA cluster harboring specimens pertaining to both the CCR and CCM subspecies but collected southern of the Jezreel Valley. AMOVA indicated clear mtDNA differentiation between specimens collected northern and southern to the Jezreel Valley (PhiPT = 0.79), which was further supported by a very low coalescent-based estimate of effective migration rates. Whole chameleon mtDNA sequencing (∼17,400 bp) generated from 11 well dispersed geographic locations revealed 325 mutations sharply differentiating the two mtDNA clusters, suggesting a long allopatric history further supported by BEAST. This separation correlated temporally with the existence of an at least 1 million year old marine barrier at the Jezreel Valley exactly where the mtDNA clusters meet. We discuss possible involvement of gender-dependent life history differences in maintaining such mtDNA genetic differentiation and suggest that it reflects (ancient) local adaptation to mitochondrial-related traits.     

Mitochondrial DNA and Y chromosome variation provides evidence for a recent common ancestry between Native Americans and Indigenous Altaians

The Altai region of southern Siberia has played a critical role in the peopling of northern Asia as an entry point into Siberia and a possible homeland for ancestral Native Americans. It has an old and rich history because humans have inhabited this area since the Paleolithic. Today, the Altai region is home to numerous Turkic-speaking ethnic groups, which have been divided into northern and southern clusters based on linguistic, cultural, and anthropological traits. To untangle Altaian genetic histories, we analyzed mtDNA and Y chromosome variation in northern and southern Altaian populations. All mtDNAs were assayed by PCR-RFLP analysis and control region sequencing, and the nonrecombining portion of the Y chromosome was scored for more than 100 biallelic markers and 17 Y-STRs. Based on these data, we noted differences in the origin and population history of Altaian ethnic groups, with northern Altaians appearing more like Yeniseian, Ugric, and Samoyedic speakers to the north, and southern Altaians having greater affinities to other Turkic speaking populations of southern Siberia and Central Asia. Moreover, high-resolution analysis of Y chromosome haplogroup Q has allowed us to reshape the phylogeny of this branch, making connections between populations of the New World and Old World more apparent and demonstrating that southern Altaians and Native Americans share a recent common ancestor. These results greatly enhance our understanding of the peopling of Siberia and the Americas.     

Phylogenetic relationships between tuna species of the genus Thunnus (Scombridae: Teleostei): Inconsistent implications from morphology,nuclear and mitochondrial genomes

In order to infer phylogenetic relationships between tuna species of the genus Thunnus, partial sequences of the mitochondrial cytochrome b and ATPase genes were determined in all eight species. Supplemental restriction analysis on the nuclear rRNA gene was also carried out. Pacific northern bluefin tuna (Thunnus thynnus orientalis) was found to have mtDNA distinct from that of the Atlantic subspecies (T. t. thynnus) but very similar to that from the species albacore (T. alaluga). In contrast, no differentiation in nuclear genome was observed between the Atlantic and Pacific northern bluefin tunas. The Atlantic northern bluefin and southern bluefin tunas possessed mtDNA sequences very similar to species of yellowfin tuna group and not so similar to albacore and bigeye tunas which were morphologically assigned to the bluefin tuna group. The molecular data indicate that (1) mtDNA from albacore has been incorporated into the Pacific population of northern bluefin tuna and has extensively displaced the original mtDNA, and (2) albacore is the earliest offshoot, followed by bigeye tuna in this genus, which is inconsistent with the phylogenetic relationships between these tuna species inferred from morphology. Correspondence to: S. Chow