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.     

Species structure, contemporary distribution and status of the Siberian surgeon Acipenser baerii

A detailed analysis of the historical and contemporary range of the Siberian sturgeon, Acipenser baerii, shows that the contemporary status of its populations and forms can be described as threatened or endangered. Recently, the abundance of the nominal subspecies, A. b. baerii, which inhabits mainly the Ob River basin, decreased sharply. Due to construction of hydroelectric dams, up to 40% of the spawning grounds became inaccessible for migrating sturgeon of this subspecies. The Lake Baikal subspecies, A. baerii baicalensis, is extremely rare and was included in the Russian Federation Red Data Book in 1983. The abundance of the east Siberian subspecies, A. baerii stenorrhynchus, inhabiting the basins of the east Siberia rivers, has also significantly decreased during the last few years. Its range in the Yenisey and Lena River basins is gradually being reduced. Gametogenesis is anomalous in a high number of females from all populations of this subspecies (in the Kolyma and Indigirka river stocks 80–100% of females were anomalous in 1987–1989). These anomalies seem to be caused by high levels of water pollution.     

Variability of siberian sculpin <Emphasis Type="Italic">Cottus sibiricus</Emphasis> (Cottidae,Sorpaeniformes)

The morphometric characteristic is composed and special traits of the biology of seven populations of the Siberian sculpin Cottus sibiricus from three large river basins of Siberia are considered (the Lena, Yenisei, and Ob basins). The studied populations demonstrate a rather wide range of variation of biological characteristics and exterior characters. The fish from different water bodies differ in longevity, growth rate, term of maturation, and, as a consequence, in definite size. However, there is no geographic regularity in this variation. Morphometric investigations also demonstrated the absence of clear geographic variation at a relatively high intrapopulational polymorphism. With consideration of the obtained data, it may be concluded that in spite of internal heterogeneity there are no reasons for subdivision of the Siberian sculpin into geographic forms (subspecies).     

Microsatellite multiplex assay for the analysis of Atlantic sturgeon populations

We have developed a multiplex assay covering 16 microsatellite loci, amplified in four polymerase chain reaction (PCR) assays, and loaded on the ABI DNA Analyzer in two separate panels. The assay was tested on 603 individuals originating from wild populations and hatchery stocks of Atlantic sturgeon. The assay was also tested on 12 individuals of European sturgeon and appeared to be almost equally useful. The multiplex assay designed in this study can be successfully applied in studies requiring high genetic resolution, such as relatedness analysis, selective breeding programs, and stock identification of Atlantic sturgeon.     

Features of inheritance of several morphological characters in the hybrids between Siberian sturgeon <Emphasis Type="Italic">Acipenser baerii</Emphasis> and beluga <Emphasis Type="Italic">A. huso</Emphasis> (Acipenseridae) and in gynogenetic individuals of Siberian sturgeon

Comparative analysis of several morphological characters is conducted in experimentally obtained hybrids between Siberian sturgeon Acipenser baerii and beluga A. huso, in parental species, and in gynogenetic progeny of Siberian sturgeon. The gynogenetic individuals are similar to Siberian sturgeon by all characters used for differentiation between Siberian sturgeon and beluga that supports gynogenetic origin of these individuals. Based on the data obtained on the hybrid specimens, the features of inheritance of the studied characters in sturgeons and their variation in postlarval ontogeny are discussed.     

Siberian Roe Deer (<Emphasis Type="Italic">Capreolus pygargus</Emphasis> Pallas, 1771) in Ukraine: Analysis of the Mitochondrial and Nuclear DNA

A molecular-genetic analysis of the nucleotide sequences of the cytochrome b gene (1140 base pairs) of the mitochondrial DNA and 17 microsatellite loci of eight samples of roe deer from the Samara forest of Dnipropetrovsk oblast (Ukraine) was carried out. For comparison, 212 corresponding mtDNA sequences of the Siberian and European roe deer and data on the variability of microsatellite markers in 49 representatives of these species were included in the study. It was noted that all the analyzed mitochondrial sequences of individuals from the Samara forest are characteristic of the Siberian roe Capreolus pygargus Pallas, 1771. Four haplotypes were described, all of which belonged to the haplogroup typical for the western part of the range of C. pygargus. A fragment analysis of the microsatellite loci of nuclear DNA confirmed the identification of the investigated group with the Siberian species.     

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 .     

Genetic variation and relationships of seven sturgeon species and ten interspecific hybrids

Background

Sturgeon cultivation is important for both industry and aquaculture in China. To date, more than 17 species or strains have been farmed for fillets and caviar production. Crossbreeding among different sturgeon species is frequent and the F2 hybrids are fertile. However, large-scale farming can have negative impacts on wild populations i.e. escape of exotic sturgeons and must be taken into consideration. Escape of exotic sturgeons can cause severe ecological problems, including threatening native sturgeon species once the exotic varieties become established or hybridize with native individuals. However, little is known about their genetic resources and variation.

Methods

Genetic diversity and introgression of seven sturgeon species were analyzed using mitochondrial DNA cytochrome oxidase subunit I (COI) and nine microsatellite markers. This study included 189 individuals from seven sturgeon species and 277 individuals from ten lineages of F2 hybrid strains.

Results

MtDNA COI sequences (632 bp long) were generated from 91 individuals across the 17 sturgeon strains and produced 23 different haplotypes. Haplotype diversity was high (h = 0.915 ± 0.015) and nucleotide diversity was low (π = 0.03680 ± 0.00153) in the seven sturgeon species and ten interspecific hybrids. Phylogenetic analyses resulted in almost identical tree topologies, and different haplotype structures were mainly related with sturgeons of different female parents. Analysis of molecular variance revealed that 81.73% of the genetic variance was due to matrilineal differences, while 9.40% resulted from strain variation. Pairwise Fst values obtained with POLYSAT software, were high among strains and ranged from 0.031 to 0.164. Admixture analysis assigned seven distinct groups and ten genotypes of admixed clusters composed of hybrid strains using STRUCTURE when assuming K = 7.

Conclusions

The interspecific mtDNA gene tree corresponded to the expected taxonomic divisions. These relationships were also supported by the results from the microsatellite analysis and contributed to unambiguously identify seven sturgeon species and ten F2 hybrid strains from sturgeon farms in China. Moreover, we found that introgressive hybridization is pervasive, exists in both purebred and hybrid sturgeons, and may reflect widespread mismanagement in sturgeon breeding in China.     

First evidence of hybridization between endangered sterlets (Acipenser ruthenus) and exotic Siberian sturgeons (Acipenser baerii) in the Danube River

Most natural populations of Eurasian sturgeons have declined dramatically during recent decades, reaching historic low levels today. During the same period, sturgeon has become very popular in European aquaculture. Because many hatcheries are located near rivers, their unintentional escape is often documented, especially during floods. Until now, no cases of successful hybridization of these escaped fish with wild stocks have been reported. In this study, the genetic structure of a highly threatened population of sterlets (Acipenser ruthenus) from the Upper Danube was analysed as a requirement for their conservation. Surprisingly, we observed genotypes and morphotypes of Siberian sturgeon (Acipenser baerii), as well as hybrids between this species and native sterlets. This hybridization poses a serious threat for the survival of this isolated sterlet population in the upper part of the Danube. For the first time, natural reproduction is documented for Siberian sturgeon outside their natural range in Europe. This finding demonstrates the risk of extinction by hybridisation of endangered populations. We would like to stress that taking into consideration the risks for native sturgeon populations, farmed sturgeon should not be released into the wild, and all measures should be taken to prevent their accidental escape.     

On the Gene Pool of Roe Deer (<Emphasis Type="Italic">Capreolus</Emphasis>) of Eastern Europe: Analysis of the Cyt <Emphasis Type="Italic">b</Emphasis> Gene Sequence Variability

Sequence analysis of the mtDNA cytochrome b gene (974 bp) was performed using 139 roe deer specimens from different regions of the European part of Russia and Ukraine. The data obtained showed that, at present, both European and Siberian roe deer inhabit this part of the range with predominance of the later: about 60% of individuals carry various Siberian haplotypes, most of which are similar to those in the populations of Capreolus pygargus from the Urals, Siberia, and the Far East. A great variety of mtDNA haplotypes of Siberian roe deer in Eastern Europe is undoubtedly caused by the heterogeneity of founder individuals (immigrants) that were imported from different parts of Asia. Some problems of coexistence of closely related species are discussed.     

The use of microsatellite loci for identification of sturgeon species (Acipenseridae) and hybrid forms

The genetic polymorphism of ten sturgeon species that inhabit the territory of the Russian Federation (Russian sturgeon, Siberian sturgeon, Amur sturgeon, Sakhalin sturgeon, Persian sturgeon, ship sturgeon, sterlet, stellate sturgeon, beluga, and kaluga) was examined at five microsatellite loci (Afug41, Afug51, An20, AoxD161, AoxD165) (in total, 3821 individuals). The examined loci were successfully amplified with the same primer set in all species tested and demonstrated a high level of variation. Alleles specific to different species have been identified, which allows them to be used to identify species of sturgeon and their food products. In addition, the possibility of identifying hybrid forms was demonstrated. The assignment test performed in the STRUCTURE software program showed a high probability of correctly assigning each individual to its species based on genotyping with five microsatellite loci examined (96–98%, on average). However, for Russian and Persian sturgeon, the rate of proper species assignment was considerably lower (75 and 84%, respectively).

     

Characterisation of 12 microsatellite loci in the Vietnamese commercial clam <Emphasis Type="Italic">Lutraria rhynchaena</Emphasis> Jonas 1844 (Heterodonta: Bivalvia: Mactridae) through next-generation sequencing

The marine clam Lutraria rhynchaena is gaining popularity as an aquaculture species in Asia. Lutraria populations are present in the wild throughout Vietnam and several stocks have been established and translocated for breeding and aquaculture grow-out purposes. In this study, we demonstrate the feasibility of utilising Illumina next-generation sequencing technology to streamline the identification and genotyping of microsatellite loci from this clam species. Based on an initial partial genome scan, 48 microsatellite markers with similar melting temperatures were identified and characterised. The 12 most suitable polymorphic loci were then genotyped using 51 individuals from a population in Quang Ninh Province, North Vietnam. Genetic variation was low (mean number of alleles per locus = 2.6; mean expected heterozygosity = 0.41). Two loci showed significant deviation from Hardy–Weinberg equilibrium (HWE) and the presence of null alleles, but there was no evidence of linkage disequilibrium among loci. Three additional populations were screened (n = 7–36) to test the geographic utility of the 12 loci, which revealed 100 % successful genotyping in two populations from central Vietnam (Nha Trang). However, a second population from north Vietnam (Co To) could not be successfully genotyped and morphological evidence and mitochondrial variation suggests that this population represents a cryptic species of Lutraria. Comparisons of the Qang Ninh and Nha Trang populations, excluding the 2 loci out of HWE, revealed statistically significant allelic variation at 4 loci. We reported the first microsatellite loci set for the marine clam Lutraria rhynchaena and demonstrated its potential in differentiating clam populations. Additionally, a cryptic species population of Lutraria rhynchaena was identified during initial loci development, underscoring the overlooked diversity of marine clam species in Vietnam and the need to genetically characterise population representatives prior to microsatellite development. The rapid identification and validation of microsatellite loci using next-generation sequencing technology warrant its integration into future microsatellite loci development for key aquaculture species in Vietnam and more generally, aquaculture countries in the South East Asia region.     

African DNA Lineages in the Mitochondrial Gene Pool of Europeans

Mitochondrial DNA (mtDNA) nucleotide sequences of African origin are found in various European populations at a low frequency (on average, less than 1%). Data on mtDNA variation in Eurasian and African populations have been analyzed, and African mtDNA lineages have been found in Europeans. It has been demonstrated that, despite the high diversity of mtDNA haplotypes of African origin in Europeans, few monophyletic clusters of African lineages are characterized by long-term diversity formed in Europe. Only two such mtDNA clusters (from haplogroups L1b and L3b) have been found, their evolutionary age not exceeding 6500 years. European and African populations have been compared with respect to the frequency distributions of the alleles of autosomal microsatellite loci found in Russian carriers of African mtDNA haplotypes. It has been demonstrated that alleles typical of Europeans are characteristic of the autosomal genotypes of these Russian individuals.     

Unidirectional hybridization of kaluga <Emphasis Type="Italic">Acipenser dauricus</Emphasis> Georgi, 1775 and Amur sturgeon <Emphasis Type="Italic">Acipenser schrenckii</Emphasis> Brandt, 1869, inferred from the mitochondrial DNA genotyping of their natural hybrids

In 2009 through 2011, among 730 individuals of kaluga and Amur sturgeon collected in the lower reaches of the Amur River and the Amursky Liman, 17 morphologically intermediate individuals (hybrids) with the body length of 56 to 202 cm (median, 81 cm) were identified, including 11 individuals (4.6%) found in 2009, three individuals (1.6%) found in 2010, and three individuals (1.1%), in 2011. In 16 hybrids, 819 bp of the mtDNA control regions were sequences and 11 haplotypes were identified. Since all these haplotypes were from the mtDNA lineages of kaluga, it was concluded that hybridization occurred in one direction, kaluga (♀) × Amur sturgeon (♂). This asymmetry could be caused by the large size differences between these species. Since the earlier examined morphologically typical Amur sturgeons showed the absence of alien haplotypes (Shedko et al., 2015), the absence of the mtDNA introgression is claimed. This can be caused by low viability or sterility of the backcross females (kaluga (♀) × Amur sturgeon (♂)) × Amur sturgeon (♂). The samples of hybrids and typical kaluga individuals demonstrated no differences in the frequency spectra of the mtDNA haplotypes. However, haplotype and nucleotide diversity in the first sample was somewhat higher than in the second one (0.950 versus 0.927 and 0.0054 versus 0.0044, respectively). The data obtained will be useful for population monitoring of kaluga and Amur sturgeon, Amur River endemics, which are classified as critically endangered by the IUCN Red List of Threatened Species.     

Managing polyploidy in ex situ conservation genetics: the case of the critically endangered Adriatic sturgeon (Acipenser naccarii)

While the current expansion of conservation genetics enables to address more efficiently the management of threatened species, alternative methods for genetic relatedness data analysis in polyploid species are necessary. Within this framework, we present a standardized and simple protocol specifically designed for polyploid species that can facilitate management of genetic diversity, as exemplified by the ex situ conservation program for the tetraploid Adriatic sturgeon Acipenser naccarii. A critically endangered endemic species of the Adriatic Sea tributaries, its persistence is strictly linked to the ex situ conservation of a single captive broodstock currently decimated to about 25 individuals, which represents the last remaining population of Adriatic sturgeon of certain wild origin. The genetic variability of three F1 broodstocks available as future breeders was estimated based on mitochondrial and microsatellite information and compared with the variability of the parental generation. Genetic data showed that the F1 stocks have only retained part of the genetic variation present in the original stock due to the few parent pairs used as founders. This prompts for the urgent improvement of the current F1 stocks by incorporating new founders that better represent the genetic diversity available. Following parental allocation based on band sharing values, we set up a user-friendly tool for selection of candidate breeders according to relatedness between all possible parent-pairs that secures the use of non-related individuals. The approach developed here could also be applied to other endangered tetraploid sturgeon species overexploited for caviar production, particularly in regions lacking proper infrastructure and/or expertise.     

Generative and somatic production of female sturgeon at a research farm in Primorsky Krai as a basis for manufacturing gastronomic caviar

The generative and somatic characteristics of female sturgeon of five species and three hybrid forms, which were reared at the TINRO Center’s warm-water cage farm at the north of Primorsky Krai and used in caviar production, are considered. Data on the somatic growth, roe output, functional fecundity, mean egg weight, and gonadosomatic index of the female Amur Sturgeon, Kaluga, Siberian Sturgeon of the Lena and the Baikal populations, Sterlet of the Volga population, hybrids of Russian Sturgeon and Siberian Sturgeon, hybrids of Siberian Sturgeon and Amur Sturgeon, and hybrids of Kaluga and Amur Sturgeon are analyzed. The sexual maturity age and interspawning intervals are defined in the studied females. Domesticated females of all the species are shown to mature a few years earlier than those in natural conditions and to have a greater body weight. The interspawning intervals shorten by a few years in domesticated females. Most female Sterlet and some females from both populations of Siberian Sturgeon spawn annually, while the remainder spawn once in 2 years. The interspawning intervals in two species of sturgeon that inhabit the Amur River and in hybrid forms usually last for 2 years. With age, values of characteristics such as roe amount, fecundity, mean egg weight, and roe output relative to body weight grow in females spawning for the second time in the warm-water farm. The maximum roe output is found in female Kalugas at the second spawning. Then the species follow in the order of decreasing of roe output: Amur Sturgeon, hybrids of Amur Sturgeon with Kaluga, hybrids of Siberian Sturgeon with Amur Sturgeon, hybrids of Russian Sturgeon with Siberian Sturgeon, Siberian Sturgeon of the Baikal population, Siberian Sturgeon of the Lena population, and Sterlet. The hybrid between the Russian Sturgeon and Siberian Sturgeon shows the best processability and survivability characteristics; the Amur Sturgeon and Sterlet follow.     

Sturgeons in Greece: a review

In the past, sturgeons were practically unknown in Greece, both to the public and to scientists, the latter not having had the opportunity to study wild populations of the four native species. Populations of stellate sturgeon (Αcipenser stellatus Pallas, 1771), Adriatic sturgeon (Acipenser naccarii Bonaparte, 1836), and beluga sturgeon (Huso huso L., 1758) gradually collapsed by the end of the 1970s. Only the River Evros (Thrace, N.W. Greece) sustained a small fishery and caviar canning operation with European sturgeon (A. sturio L., 1758) until 1975. Collapse of stocks was mainly attributed to overfishing, pollution and damming. Sturgeons became widely known after initial farming efforts by the Municipal Hatchery at Lake Ioannina in 1992. Broodstock or fertilized eggs of species with high aquaculture potential, such as sterlet (Acipenser ruthenus L., 1758), Russian sturgeon (Acipenser gueldenstaedtii Brandt, 1833), bester hybrid (A. ruthenus ×H. huso), paddlefish (Polyodon spathula Walbaum, 1792), Siberian sturgeon (Acipenser baerii Brandt, 1869) and white sturgeon (Acipenser transmontanus Richardson, 1836) were imported into Greece between 1992 and 2004. Hatchery technology, larval rearing and production systems are reviewed in this paper and, despite problems, past and present efforts appear to meet a particular interest of the aquaculture sector as well as of those interested in the restoration of wild stocks.     

Dispermic androgenesis in sturgeons with the help of cryopreserved sperm: production of androgenetic hybrids between Siberian and Russian sturgeons

Dispermic androgenesis was used to produce, for the first time, an androgenetic progeny of the Siberian sturgeon (Acipenser baerii) and the androgenetic nuclear cytoplasmic hybrids (Siberian sturgeon, A. baerii x Russian sturgeon, A. gueldenstaedtii) using cryopreserved sperm. Microsatellite DNA analysis confirmed exclusively paternal inheritance in the androgenetic progeny of Siberian sturgeon. Heterozygotes for certain microsatellite loci were detected among the androgenetic hybrids, thereby confirming a dispermic nature of androgenesis. According to the data of comparative morphological analysis, the obtained androgenetic hybrid, by the age of 15 months old, was completely identical to the paternal species. Both a female and a male were detected in the androgenetic sturgeon progenies, which is of interest for producing bisexual progenies via androgenesis. The data of this study confirm the feasibility of dispermic androgenesis using cryopreserved sperm to preserve and recover the gene pools of endangered sturgeon species.     

利用微卫星遗传标记探讨达氏鳇的多倍体倍性

鲟形目(Acipenseriformes)鱼类是一类多倍体起源的鱼类,种问易于杂交,且由于存在大量微型染色体,其染色体数目和倍性也难于确定.到目前为止包括达氏鳇(Huso dauricus)在内的一些鲟鱼物种基因组大小和染色体倍性仍旧存在争议.本实验采用微卫星遗传标记技术,通过观察9个微卫星位点的等位基因数目,发现达氏鳇在大部分位点中显示的倍性大于二倍性,同时利用多倍体分析软件POLYSAT推断了26尾达氏鳇的个体倍性.结果表明,26尾达氏鳇中有20尾显示为六倍体,占总数的76.92％;4尾显示为八倍体,占总数的15.38％;2尾显示为四倍体,占总数的7.79％.因此,我们认为达氏鳇应该为八倍体物种,结果中出现的四倍体和六倍体个体,是由于这些个体在我们选取的微卫星位点中存在部分纯合等位基因,导致了多数个体显示为六倍体.这一结论与近年来支持达氏鳇为进化性八倍体物种的研究结果一致.