Comparative phylogeography of salmonid fishes (Salmonidae) reveals late to post-Pleistocene exchange between three now-disjunct river basins in Siberia

Abstract. We use a comparative phylogeographical framework to evaluate the hypothesis of hydrological exchange during the Pleistocene among the now disjunct Lena, Amur, and Enisei basins in Siberia, and to provide evidence on the causal mechanism of their present day faunal dissimilarities. Approximately 600 bases of the mitochondrial control region were sequenced in five distinct lineages among three genera of salmonid fishes, Hucho, Brachymystax and Thymallus. All three basins were fixed for divergent (2–5.4%) lineages of Thymallus whereas a single shared haplotype was present in all three basins for Hucho taimen ( Pallas, 1773 ) and one shared haplotype between the Lena and Amur basins out of a total of five for blunt‐snouted and one out of five for sharp‐snouted Brachymystax lenok ( Pallas, 1773 ). For both blunt‐ and sharp‐snouted lenok the haplotypes found within each basin did not form clades, so no relationship between genotypes and geographical occurrence was found. Our data support relatively recent hydrological mixing of the major river drainage systems in eastern and far‐eastern Siberia, congruent with the hypothesis of large‐scale palaeo‐hydrological exchange stemming from glacial advance, retreat and melting during Pleistocene climate fluctuations. Furthermore, these results in conjunction with a comparison of overall faunal composition suggest that environmental differences rather than historical contingency may be responsible for the faunal dissimilarities of the Amur, Lena, and Enisei river basins.     

额尔齐斯河流域不同来源哲罗鲑形态及COⅠ基因比较研究

为对哲罗鲑(Hucho)的引种放流和土著物种的保护提供科学依据, 研究采集了数尾来源于天然水域的哲罗鲑(Hucho BHB和Hucho BEJ), 与引进的哲罗鲑(Hucho HLJ)一起进行了形态特点观察描述, 同时对COⅠ基因扩增测序并从GenBank下载哲罗鲑属COⅠ基因构建系统发育树、计算遗传距离进行分子生物学比较研究。结果显示, Hucho BEJ和Hucho HLJ形态特点相一致, Hucho BHB与其他两种来源的哲罗鲑在体色、斑点大小等均有差异。基于COⅠ基因的系统发育树显示几种不同来源的哲罗鲑均与太门哲罗鲑(H. taimen)聚为一个大的分枝, 但在这个分枝下, Hucho BEJ和Hucho HLJ与俄罗斯阿穆尔河(中国称黑龙江)的哲罗鲑聚为一枝, 而Hucho BHB单独形成一支。基于COⅠ基因的遗传矩阵显示, Hucho BEJ和Hucho HLJ与俄罗斯阿穆尔河的哲罗鲑遗传距离较近(0—0.0044), 而Hucho BHB与Hucho BEJ、Hucho HLJ及俄罗斯阿穆尔河的哲罗鲑遗传距离较远(0.0057—0.0082)。这说明Hucho BHB在形态和基因序列上与Hucho HLJ及俄罗斯阿穆尔河的哲罗鲑具有较大差异, 可能是不同的生态地理类型, Hucho BEJ和Hucho HLJ在形态和基因序列上基本一致, 我们推测Hucho BEJ是放流或养殖场逃逸的哲罗鲑。     

Blackflies (Diptera,Simuliidae) in eastern Trans-Baikal: Taxonomic composition and physiographic distribution

The blackfly fauna and biodiversity of some physiographic regions in eastern Trans-Baikal have been described. The structural characteristics of blackfly communities in the highlands and lowlands in the southern and northern territories of the region have been reported. A regional list of forty seven species in five genera of the Simuliidae family has been produced for the first time. The species distribution in three major river basins, Upper Amur, Lena, and Yenisei, are examined. A comparative cluster analysis of the similarities in species composition between the blackflies in the observed area and the adjacent regions is carried out. The blackfly species composition of the Upper Amur basin is more similar to the population of the Selenga River basin and significantly differs from the fauna in the middle and lower reaches of the Amur River; only three blackfly species typical for the Far East fauna have been indicated.     

Genetic Variation of the Siberian Sturgeon (<Emphasis Type="Italic">Acipenser baerii</Emphasis> Brandt, 1869) in Aquaculture

Genetic variation of aquaculture broodstocks of the Siberian sturgeon of different origin from 13 farms across the Russian Federation was assessed at five tetraploid microsatellite loci and the mitochondrial DNA control region. At present, in aquaculture stocks of Siberian sturgeon originating from the Lena and Ob rivers, a sharp decline of haplotype diversity is observed. The most part of aquaculture individuals carry two major haplotypes characteristic of the European part of Russia (the Lena aquaculture) and two haplotypes characteristic of the western part of Siberia (the Ob aquaculture). According to the results of the microsatellite analysis, in sturgeon aquaculture stock originating from the Lena River, two genetic clusters can be distinguished. One of these clusters is represented by the stocks composed of inbred individuals and, because of this, is characterized by depleted allelic variation and the loss of rare alleles.     

Ecologically Tolerable Levels of Abiotic Factors. Study of Freshwater Bodies in Asiatic Part of Russia and Uzbekistan

Ecologically tolerable levels (ETL) of environmental factors have been determined for freshwater ecosystems in Asiatic part of Russia and neighboring countries (basins of Ob, Yenisei, Lena, Amur, and Syr-Darya rivers). Inobservance of ecologically tolerable levels degrades ecological status of the ecosystems manifested as deviation from normal saprobic indices of phytoplankton, zooplankton, and periphyton as well as biotic indices of zoobenthos. The basins were compared by the calculated ETL values for over 40 physicochemical indices. The revealed ecologically tolerable levels were compared with the standard maximum allowable concentrations.     

The Pechora Pipit (<Emphasis Type="Italic">Anthus gustavi</Emphasis>, Passeriformes,Motacillidae) in Northeastern Asia

The data on the distribution and ecology of the Pechora pipit in northeastern Asia were updated on the basis of published data and the results of studies performed in the period from 1977 to 2016 in the basins of the Olenek, Lena, Yana, Indigirka, and Alazeya rivers. In contrast to the Ob and Yenisei watersheds, as well as to Chukotka and Kamchatka, in the basins of the above-mentioned rivers and in the mid-Kolyma basin, the Pechora pipit inhabits the northern taiga and shows less preference for the tundra zone. Compact breeding grounds are largely confined to large river valleys, and only in the Vilyui River basin can they be found in the watershed wetlands. The breeding range is predominately fragmented. The continuous distribution area of this species encompasses Kamchatka and, apparently, the Koryak Highlands and Southern Chukotka. Westwards, in the Yana and Kolyma basins between 66° N and 69° N, in the Lena valley between 68° N and 70° N, in the interfluve between the Vilyui and Olenek rivers between 63° N and 66° N, and in the Khatanga and Yenisei basins between 63° N and 72° N, a discontinuous distribution zone has formed. In the interfluve between the Vilyui and Olenek rivers and in the Alazeya River valley, the population density reaches its highest values observed in the species optimum in Kamchatka. The nesting sites of the Pechora pipit nests in grass associations, forages mostly in meadows and swamps, and feeds mainly on amphibiont invertebrates.     

Ichthyofauna of the Lena River (Laptev Sea Basin): Modern composition and historical formation

The modern ichthyofauna of the Lena River includes 46 species and subspecies: 45 bony fishes and one lamprey. In the upper reaches, 24 species have been recorded, 38 in the middle reaches, 36 in the lower reaches, and 24 in the delta. Four of the seven species intentionally introduced into water bodies of the Lena River basin have successfully naturalized; the presence of the others is unconfirmed. All areas of the river are dominated by fishes of the orders Salmoniformes and Cypriniformes. The ranges of the Amur carp Cyprinus rubrofuscus, common bream Abramis brama, ide Leuciscus idus, roach Rutilus rutilus, pike Esox lucius, and perch Perca fluviatilis have expanded over the last few years. The causes and possible ways of the historical formation of the Lena River fish population are discussed in the light of data on the Pleistocene paleogeographical events and patterns of the distribution of species in the river and in adjacent basins.     

Polymorphism and divergence of karyotypes in taimens of the Hucho genus

Karyotypes of Siberian taimen Hugo taimen from the Manoma River (Amur basin) were investigated. The karyotypes examined differed in chromosome number from 2n = 82 to 2n = 83; chromosome arm number was NF = 112. These differences, as well as the difference in the karyotype of Siberian taimen from the lower flow of the Amur River (2n = 84) described earlier, are due to Robertsonian polymorphism of one pair of large submetacentric chromosomes. The nucleolus organizer regions are located on the short arms of one or two subtelocentric chromosomes of different pairs. The probable sequence of karyotype divergence in taimens of the Hugo genus is discussed.     

The complete mitochondrial genome of the taimen, Hucho taimen, and its unusual features in the control region

The whole mitochondrial genome of Hucho taimen was firstly sequenced and characterized. The genome is 16,833 bp in length and contains 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and a noncoding control region. Twelve protein-coding genes on the heavy strand showed that the content of A+T was higher than that of G+C, whereas the nd6 protein-coding gene on the light strand displayed an opposite pattern. We described the secondary structure of the origin of light strand (oriL) replication and found that the conserved 5'-GCCGG-3' sequence motif is variable in H. taimen and some other salmonids. We conclude that the control region is variable in length and represents the high A+T content, compared with other mitochondrial control regions available in Salmonidae and other non-salmonids. Additionally, another interesting feature of H. taimen mitogenome is that a T-type mononucleotide microsatellite and an 82 bp tandem repeat were identified in the control region.     

(S)he who dares, grows! A cross‐population study of growth and behaviour in three‐spined sticklebacks

Three‐spined sticklebacks ( Gasterosteus aculeatus ) exhibit considerable inter‐population variation in behaviour, morphology and life history characteristics. Such population‐level variation can be generated directly by environmental characteristics of the water body they inhabit ( e.g . temperature regimes, which directly influence growth rates) but local genetic adaptation is also important. By performing 'common garden' experiments, in which laboratory‐bred individuals from separate populations are raised under standardized controlled laboratory conditions, it is possible to identify genetically‐based population‐level phenotype variation. Here we present the results of two studies, carried out using juvenile three‐spined sticklebacks bred from parental stock from five geographically isolated UK populations and reared under standard laboratory ('common garden') conditions. Firstly we report the results of a study examining population‐level variation in patterns of early growth, in which we tracked the growth of replicate groups of full‐sibs from all five populations, from hatching to 126d. Secondly we report the results of an experimental behavioural study, designed to examine population‐level variation in the exploratory or 'boldness' behaviour of laboratory‐bred and reared juvenile three‐spined sticklebacks from the same five populations. We discuss how adaptive genetically based patterns of behaviour and growth may co‐vary across populations.     

The complete mitochondrial genome of the Sichuan taimen (Hucho bleekeri): repetitive sequences in the control region and phylogenetic implications for Salmonidae

The complete mitochondrial DNA genome of the Sichuan taimen (Hucho bleekeri) was determined by the long and accurate polymerase chain reaction (LA-PCR) and primer walking sequence method. The entire mitochondrial genome of this species is 16,997 bp in length, making it the longest among the completely sequenced Salmonidae mitochondrial genomes. It consists of two ribosomal RNA (rRNA) genes, 13 protein-coding genes, 22 transfer RNA (tRNA) genes, and one control region (CR). The gene arrangement, nucleotide composition, and codon usage pattern of the mitochondrial genome are similar to those of other teleosts. A T-type mononucleotide microsatellite and an 82 bp tandem repeat were identified in the control region, which were almost identical among the three H. bleekeri individuals examined. Both phylogenetic analyses based on 12 concatenated protein-coding genes of the heavy strand and on just the control region show that H. bleekeri is a basal species in Salmoninae. In addition, Salmo, Salvelinus and Oncorhynchus all represent monophyletic groups, respectively. All freshwater species occupied basal phylogenetic positions, and also possessed various tandem repeats in their mitochondrial control regions. These results support established phylogenetic relationships among genera in Salmonidae based on morphological and molecular analyses, and are consistent with the hypothesis that Salmonidae evolved from freshwater species.     

Phylogeography and intraspecific genetic variation of prochilodontid fishes endemic to rivers of northern South America

Phylogeography and intraspecific genetic variation were studied in prochilodontids endemic to the Orinoco, Essequibo and Amazon River basins of northern South America. Portions of two protein‐encoding mitochondrial (mt) DNA genes, ND4 and COI, were examined using single‐strand conformational polymorphisms (SSCPs) and nucleotide sequencing. Phylogeographic analysis indicated that the geographically widespread Prochilodus rubrotaeniatus is paraphyletic, with individuals from the Orinoco sharing most recent common ancestry with co‐occurring Prochilodus mariae . A second Prochilodus rubrotaeniatus clade was composed of haplotypes found in the Rio Cuyuní(Essequibo Basin) and tributaries of the Rio Negro (Amazon Basin). Intraspecific genetic analysis suggested that a complex set of processes have influenced patterns of genetic variation in prochilodontid lineages. Prochilodus rubrotaeniatus is monomorphic at both loci in the Rio Negro and probably recently colonized this basin from the Rio Essequibo. Only two of 55 P. mariae exhibited variant haplotypes, and both had resulted from non‐synonymous changes in the ND4 region. These observations were counter to neutral expectation and consistent with the action of natural selection on the mitochondrion. Overall, these analyses implicate vicariance, demography and selection for driving diversification of prochilodontids in northern South America.     

Identification of reproductively isolated lineages of Amur grayling (Thymallus grubii Dybowski 1869): concordance between phenotypic and genetic variation

We analysed variation at maternally (mitochondrial DNA control region sequences) and bi-parentally (10 microsatellites) inherited genetic markers, as well as across 12 meristic characters in 7 populations of Amur grayling, Thymallus grubii, from eastern Siberia. All three data sets were concordant in supporting the existence of three diagnosable, reciprocally monophyletic, and most probably reproductively isolated, lineages of grayling within the Amur drainage. There was a significant correlation between genetic and phenotypic divergence, both within and among lineages. Two phenotypically distinct forms (with and without an orange spot on the posterior portion of the dorsal fin), found in sympatry in the lower Amur, most likely result from secondary contact, as they demonstrate 4.6% sequence divergence at the mitochondrial DNA control region. This divergence, together with the existence of at least one nearby population of orange spot grayling outside the Amur drainage (0.8% divergence) underscore the palaeo-hydrological complexity of the system, which presumably promoted genetic divergence in a shifting allopatric framework throughout the Pleistocene. Grayling from the upper Amur, corresponding to the type locality for the species, formed a sister group (1.4-1.6% divergent) to the orange spot lineage perhaps diverging in the early Pleistocene (1.4-1.6 Ma).     

Distribution of Masu Salmon <Emphasis Type="Italic">Oncorhynchus masou</Emphasis> (Salmonidae) in Amur River Basin

The presented data on the distribution of the masu salmon Oncorhynchus masou in the Amur River Basin are collected in 1976–2015. In the analyzed region the species’ spawning range includes the lower part of the Amur River basin from the rivers flowing into the Amur estuary to the basins of the Anyui and Amgun’ Rivers in their middle courses. The information on the catch of a masu salmon specimen in the Khor River Basin (approximately 1300 km from the Amur River mouth) in 2015 is presented. It is assumed that the total Amur population does not exceed several thousand of adult anadromous fish.     

Taxonomy and molecular phylogeny of Lethenteron lampreys in eastern Eurasia

Allozyme analyses of lampreys (genus Lethenteron ) in eastern Eurasia showed that samples of L. reissneri from the upper Amur River, Russia, possessed the diagnostic alleles of L. kessleri ( MDH‐3 *‐ 93 ). These samples were closely related to L. kessleri samples in the Ob, Lena and middle Amur Rivers and on Sakhalin and Hokkaido Islands. On the other hand, they were distantly related to samples of the northern and southern forms of L. reissneri in the Japanese Archipelago and the southern Korean Peninsula. The number of trunk myomeres in L. reissneri from the upper Amur (63–76) strongly overlapped the number in L. kessleri (64–73), but were markedly displaced from those of the northern (51–66) and southern forms (49–62). These results suggest that L. reissneri in the upper Amur basin is likely to be the same taxonomic entity as L. kessleri reported from eastern Eurasia. The genetic and morphological divergences from L. reissneri in the type locality make it appropriate to regard the northern and southern forms as distinct species, L . sp. N and sp. S. Despite the close relationships found among L. japonicum , the L. reissneri complex and L . sp. N, L . sp. S was highly divergent from other species of Lethenteron , Lampetra and Entosphenus . In the monophyletic group comprising L. japonicum , the L. reissneri complex and L . sp. N, the direction of life‐history evolution presumed from the most parsimonious character reconstruction on the molecular tree was inconsistent with the previous hypothesis that nonparasitic species arise from parasitic species, indicating the necessity of detailed assessment of characteristics. On the other hand, L . sp. S may be a relict species of the coancestor of Lethenteron , Lampetra and Entosphenus .     

Phylogeography and sympatric differentiation of the Arctic charr Salvelinus alpinus (L.) complex in Siberia as revealed by mtDNA sequence analysis

Sequence variation in the mtDNA control region of Arctic charr Salvelinus alpinus and Dolly Varden Salvelinus malma from 56 Siberian and North American populations was analysed to assess their phylogeographic relationships and the origins of sympatric forms. Phylogenetic trees confirm the integrity of phylogroups reported in previous mtDNA studies except that the Siberian group does not separate as a single cluster. Haplotype network analysis indicates the proximity of Siberian and Atlantic haplotypes. These are considered as one Eurasian group represented by the Atlantic, east Siberian (interior Siberia including Transbaikalia, Taimyr) and Eurosiberian (Finland, Spitsbergen, Taimyr) sub-groups. Salvelinus alpinus with presumably introgressed Bering group (malma) haplotypes were found along eastern Siberian coasts up to the Olenek Bay and the Lena Delta region, where they overlap with the Eurasian group and in the easternmost interior region. It is proposed that Siberia was colonized by S. alpinus in two stages: from the west by the Eurasian group and later from the east by the Bering group. The high diversity of Eurasian group haplotypes in Siberia indicates its earlier colonization by S. alpinus as compared with the European Alps. This colonization was rapid, proceeded from a diverse gene pool, and was followed by differential survival of ancestral mtDNA lineages in different basins and regions, and local mutational events in isolated populations. The results presented here support a northern origin of Transbaikalian S. alpinus , the dispersion of S. alpinus to the Lake Baikal Basin from the Lena Basin, segregation of S. alpinus between Lena tributaries and their restricted migration over the divides between sub-basins. These results also support sympatric origin of intralacustrine forms of S. alpinus .     

Finding a new form of the grayling Thymallus arcticus (thymallidae) in the basin of lake baikal

A dwarf form of the Arctic grayling Thymallus arcticus, inhabiting a group of small lakes at the origin of the Yakchii stream, which flows into the Verkhnyaya Angara River (basin of Lake Baikal), has been found in the northeastern watershed of the Baikal and Lena basins. The form is similar to upper Lena populations in body coloration and the pattern of dorsal fin. Our comparison by meristic characters indicated that the grayling of the Yakchii Lakes is more similar to the fish from Kutima River (basin of the upper courses of the Lena River) than to the black Baikal grayling T. arcticus baicalensis. The presence in Lake Baikal of a population similar to upper Lena graylings may have three causes: (1) possible drainage from Baikal to the pra-Lena via ancient valleys of the Barguzin and the Upper Angara; (2) appearance of transit zones as a result of glacial or tectonic events during the periods of watershed development between the Baikal and Lena basins; (3) the upper Lena grayling could be an endemic of the Baikal basin which was replaced by graylings penetrating from the Yenisei basin and remained in the form of relic populations in the upper courses of certain tributaries of the northern and northeastern parts of Lake Baikal.     

On the diversity and taxonomic status of graylings (Thymallus Thymallidae) from the Lena River

Two forms of graylings were distinguished in the Lena River, which differ in body coloration, the shape and pattern of the dorsal fin, and biological characteristics. With respect to these traits, the forms are divided between the upper and lower Lena. The first inhabits most of the basin, from the upper courses to the lower reaches, whereas the second inhabits the Lena delta and the adjacent arctic rivers and their tributaries. Comparative analysis of meristic traits revealed their low appropriateness for diagnosing Lena lineages as well as grayling populations inhabiting other northern rivers of Siberia. The body and fin coloration in the upper Lena form significantly differ from that found in forms and subspecies of graylings from the basins of the other rivers in the ranges of Eastern Siberian, Kamchatka, and Alaska. The lower Lena form should be classified with the Eastern Siberian subspecies T. arcticus pallasii and is closer to the populations of graylings from the rivers Anabar and Yana, and the rivers of the Chukot Peninsula and Alaska, and the upper courses of the Missouri. These results are supported by analysis of the mitochondrial DNA of graylings throughout the Paleoarctic. Further studies of these lineages and phylogenetic relationships between Arctic lineages are necessary for the final determination of the taxonomic status of the upper Lena form.     

Low genetic differentiation among morphologically distinct Labeobarbus species (Teleostei: Cyprinidae) in the Lake Victoria and Albertine basins,Uganda: insights from mitochondrial DNA

Labeobarbus altianalis and L. bynni bynni are hexaploid cyprinid fishes in the genus Labeobarbus. In the Great Lakes region of Africa, these two large-bodied barbs exhibit considerable morphological variations. Their intraspecific classification, currently based on geographical distribution and morphological variation, is of limited application due to the overlapping nature of the water systems. Patterns of genetic variation in the Albertine and Victoria drainage basins in Uganda were assessed using mitochondrial sequences of the control region (470 basepairs) and the cytochrome b gene (627 basepairs). At the control region 36 distinct haplotypes were observed in a total of 177 individuals. Relatively low overall nucleotide diversity (π = 0.010) was observed. Hierarchical analysis of the molecular variance revealed significant differentiation between populations in the total sample (F _ST = 0.172, p < 0.001), among populations within each basin (F _SC = 0.047, p < 0.001), but no significant subdivision among basins (F _CT = 0.131, p > 0.05). Phylogenetic analysis of the control region haplotypes resulted in a star-shaped phylogeny, with no clusters that reflect current taxonomic designation, morphotypes or basins. Phylogenetic analysis of cytochrome b gene sequences resulted in a tree topology similar to that observed for the control region. Thus the morphological characteristics separating the two species are intraspecific variation and the whole sample probably belongs to the same species.     

Natural genetic polymorphism and phylogeography of Siberian sturgeon <Emphasis Type="Italic">Acipenser baerii</Emphasis> Brandt, 1869

Five populations of Siberian sturgeon Acipenser baerii collected throughout the species distribution range (Lake Baikal, Lena, Yenisei, Kolyma, and Irtysh rivers) were examined for genetic polymorphism using five tetraploid microsatellite loci and the mitochondrial DNA control region. It was demonstrated that Siberian sturgeon was represented by genetically well-differentiated groups that corresponded to hydrographic basins, Ob–Irtysh, Baikal–Yenisei, Lena, and Kolyma. Population assignment of the Siberian sturgeon broodstock should be considered in the restocking programs.