Comparative analysis of STR and SNP polymorphism in the populations of sockeye salmon (<Emphasis Type="Italic">Oncorhynchus nerka</Emphasis>) from Eastern and Western Kamchatka

Sockeye salmon samples from five largest lacustrine-riverine systems of Kamchatka Peninsula were tested for polymorphism at six microsatellite (STR) and five single nucleotide polymorphism (SNP) loci. Statistically significant genetic differentiation among local populations from this part of the species range examined was demonstrated. The data presented point to pronounced genetic divergence of the populations from two geographical regions, Eastern and Western Kamchatka. For sockeye salmon, the individual identification test accuracy was higher for microsatellites compared to similar number of SNP markers. Pooling of the STR and SNP allele frequency data sets provided the highest accuracy of the individual fish population assignment.     

Variability of size-age indices and genetic variability of sockeye salmon <Emphasis Type="Italic">Oncorhynchus nerka</Emphasis> from the Western Coast of Kamchatka: Comparative analysis of methods of differentiation of local populations

Study of variability of size-age indices and polymorphism of 6 microsatellite loci, 5 loci of SNP, and accidentally amplified polymorphic DNA (RAPD) of sockeye salmon Oncorhynchus nerka of three largest populations from the western coast of Kamchatka Peninsula was performed. The efficiency of using different types of markers for the differentiation of populations and determination of the population belonging of sockeye salmon from lake-river systems of western Kamchatka was analyzed. Significant interpopulation differences were revealed from the frequencies of alleles of genetic markers and from a set of biological indices. It was established that genetic markers are characterized by a better differentiating capacity, as compared to biological characteristics. The most satisfactory results during determination of population belonging of sockeye salmon were obtained using an integrated data base of allele frequencies of microsatellite and SNP loci.     

Genetic variability and population structure of sockeye salmon from the Asian Coast of Pacific Ocean

Variability of six microsatellite loci and 45 single nucleotide polymorphism (SNP) loci was analyzed in 17 samples of sockeye salmon from 10 major spawning watersheds on the Asian coast of the Pacific Ocean. On the basis of the analysis of SNP loci variability of sockeye salmon in the examined part of the range, five population groups were identified, including local stocks from the Palana, Okhota, and Kamchatka rivers, as well as the population groups of Southwestern Kamchatka, and Northeastern Kamchatka and Chukotka. Rather different pattern of samples differentiation was obtained by estimating variability of six microsatellite DNA loci. Regional complexes of the eastern and western coasts of Kamchatka were identified. Moreover, sockeye salmon from the Palana River fell into the cluster of Western Kamchatka populations, while the population from the Okhota River and Meynypilgin lake–river system (Chukotka), confined to the subperiphery of the range, where the most differentiated from the others. The possible reasons for the discrepancies and high divergence of the Palana River and the Okhota River sockeye salmon populations, inferred from the SNP markers analysis, are discussed.     

Intra- and interpopulation variability of southwestern Kamchatka sockeye salmon Oncorhynchus nerka inferred from the data on single nucleotide polymorphism

The variability of 45 single nucleotide polymorphism (SNP) loci was studied in nine samples of the sockeye salmon Oncorhynchus nerka from the rivers of southwestern Kamchatka. The Wahlund effect, gametic disequilibrium at some loci, and a decrease in interpopulation genetic diversity indices observed in samples from the Bolshaya River outlet can be attributed to the samples’ heterogeneity. Partitioning of the mixed samples using some biological characteristics of the individuals led to a noticeable decrease in the frequency of these phenomena. It was demonstrated that the allelic diversity between the populations within the river accounted for the larger part of genetic variation, as compared to the differentiation between the basins. The SNP loci responsible for intra- and interpopulation differentiation of sockeye salmon from the rivers of southwestern Kamchatka were identified. Some recommendations for field population genetic studies of Asian sockeye salmon were formulated.     

Precision and accuracy of divergence time estimates from STR and SNPSTR variation

Inference of intraspecific population divergence patterns typically requires genetic data for molecular markers with relatively high mutation rates. Microsatellites, or short tandem repeat (STR) polymorphisms, have proven informative in many such investigations. These markers are characterized, however, by high levels of homoplasy and varying mutational properties, often leading to inaccurate inference of population divergence. A SNPSTR is a genetic system that consists of an STR polymorphism closely linked (typically < 500 bp) to one or more single-nucleotide polymorphisms (SNPs). SNPSTR systems are characterized by lower levels of homoplasy than are STR loci. Divergence time estimates based on STR variation (on the derived SNP allele background) should, therefore, be more accurate and precise. We use coalescent-based simulations in the context of several models of demographic history to compare divergence time estimates based on SNPSTR haplotype frequencies and STR allele frequencies. We demonstrate that estimates of divergence time based on STR variation on the background of a derived SNP allele are more accurate (3% to 7% bias for SNPSTR versus 11% to 20% bias for STR) and more precise than STR-based estimates, conditional on a recent SNP mutation. These results hold even for models involving complex demographic scenarios with gene flow, population expansion, and population bottlenecks. Varying the timing of the mutation event generating the SNP revealed that estimates of divergence time are sensitive to SNP age, with more recent SNPs giving more accurate and precise estimates of divergence time. However, varying both mutational properties of STR loci and SNP age demonstrated that multiple independent SNPSTR systems provide less biased estimates of divergence time. Furthermore, the combination of estimates based separately on STR and SNPSTR variation provides insight into the age of the derived SNP alleles. In light of our simulations, we interpret estimates from data for human populations.     

Genetic differentiation of sockeye salmon Oncorhynchus nerka (Walbaum, 1792) populations of eastern Kamchatka

The interpopulation differentiation of the sockeye salmon Oncorhynchus nerka (Walbaum) from the Olyutorskiy and Karaginskiy districts and from the Kamchatka River basin was examined based on the allelic variation at eight microsatellite loci (Ots107, Oki1a, Oki1b, One104, One109, OtsG68, OtsG85, and Oki6). The genetic diversity of samples from the northern rivers was lower, compared to samples from the Kamchatka River basin. Significant heterogeneity was found in the allele-frequency distribution at microsatellite loci of sockeye salmon from the investigated localities. The degree of genetic similarity of populations corresponded to their geographic closeness. The differences between population groups greatly exceeded the level of interpopulation differentiation. The analyzed samples formed four relatively separate groups: Lake Azabachye, Kamchatka River basin, Karaginskiy area (including the Navyrinvayam River in the south of the Olyutorskiy district), and northern Olyutorskiy area. The identification likelihood estimates of eastern Kamchatkan sockeye salmon in mixed aggregations at the level of population groups were fairly high (67.2–81.8%), greatly exceeding the accuracy of identification of individual populations.     

Single-nucleotide polymorphism in populations of sockeye salmon Oncorhynchus nerka from Kamchatka Peninsula

The genetic variability of 45 single-nucleotide polymorphism loci was examined in the four largest wild populations of sockeye salmon Oncorhynchus nerka from drainages of the Asian coast of the Pacific Ocean (Eastern and Western Kamchatka). It was demonstrated that sockeye salmon from the Palana River were considerably different from all other populations examined. The most probable explanation of the observed differences is the suggestion on possible demographic events in the history of this population associated with the decrease in its effective number. To study the origin, colonization patterns, and evolution of Asian sockeye salmon, as well as to resolve some of the applied tasks, like population assignment and genetic identification, a differential approach to SNP-marker selection was suggested. Adaptively important loci that evolve under the pressure of balancing (stabilizing) selection were identified, owing to this fact the number of loci that provide the baseline classification error rates in the population assignment tests was reduced to 30. It was demonstrated that SNPs located in the MHC2 and GPH genes were affected by diversifying selection. Procedures for selecting single-nucleotide polymorphisms for phylogenetic studies of Asian sockeye salmon were suggested. Using principal-component analysis, 17 loci that adequately reproduce genetic differentiation within and among the regions of the origin of Kamchatka sockeye salmon were selected.     

Outlier SNPs show more genetic structure between two Bay of Fundy metapopulations of Atlantic salmon than do neutral SNPs

Atlantic salmon of Eastern Canada were once of considerable importance to aboriginal, recreational, and commercial fisheries, yet many populations are now in decline, particularly those of the inner Bay of Fundy (iBoF), which were recently listed as endangered. We investigated whether nonneutral SNPs could be used to assign individual Atlantic salmon accurately to either the iBoF or the outer Bay of Fundy (oBoF) metapopulations because this has been difficult with existing neutral markers. We first searched for markers under diversifying selection by genotyping eight captively bred Bay of Fundy (BoF) populations for 320 SNP loci with the Sequenom MassARRAY? system and then analysed the data set with four different F(ST) outlier detection programs. Three outlier loci were identified by both BayesFST and BayeScan whereas seven outlier loci, including the three previously mentioned, were identified by both Fdist and Arlequin. A subset of 14 nonneutral SNPs was more accurate (85% accuracy) than a subset of 67 neutral SNPs (75% accuracy) at assigning individual salmon back to their metapopulation. We then chose a subset of nine outlier SNP markers and used them to inexpensively genotype archived DNA samples from seven wild BoF populations using Invader? chemistry. Hierarchical AMOVA of these independent wild samples corroborated our previous findings of significant genetic differentiation between iBoF and oBoF salmon metapopulations. Our research shows that identifying and using outlier loci is an important step towards achieving the goal of consistently and accurately distinguishing iBoF from oBoF Atlantic salmon, which will aid in their conservation.     

Population structure of chum salmon Oncorhynchus keta in the Russian Far East, as revealed by microsatellite markers

Chum salmon populations in the Russian Far East have a complex multi-level genetic structure. A total of 53 samples (2446 fish) were grouped into five major regional clusters: the southern Kurils, eastern Sakhalin, southwestern Sakhalin, the Amur River, and a northern cluster. The northern cluster consists of chum salmon populations from a vast geographical region, including Chukotka, Kamchatka, and the continental coast of the Sea of Okhotsk. However, the degree of its genetic differentiation is low, 1.9%. In contrast, the southern population cluster exhibits much higher variation; for example, differentiation between chum salmon groups within Sakhalin Island reaches 4.6%, and the differentiation between Iturup Island and Sakhalin Island chum salmon is 7.7%. This suggests that southern populations of Asian chum salmon have a more ancient evolutionary history than northern populations. In contrast to the available data, our study indicates a great deviation of southwestern Sakhalin populations from other Sakhalin chum salmon. The Russian Far East chum salmon are genetically diverse and show statistically significant differentiation even within small geographic localities. This can be used to assign samples of unknown origins to definite local populations.     

Genetic diversity in a small population of sockeye salmon, Oncorhynchus nerka (Walbaum) from the Ola river (northern coast of the Okhotsk sea)]

The genetic structure of a small sockeye salmon population from the Ola River (Tauyskaya Inlet, the Okhotsk Sea) was shown to exhibit high heterogeneity. Significant differences of LDH-B2* and ALAT-2* gene frequencies were detected not only among samples within the spawner and juvenile groups but also between spawners and juveniles as a whole. The average heterozygosity of sockeye salmon from the Ola River was considerably lower than the corresponding values for other Asian populations. The Ola sockeye salmon is genetically similar to the population from the Pakhach River of the northwestern Kamchatka Peninsula but different from other Kamchatka populations and the Okhota River population. A hypothesis explaining the genetic differentiation of Asian sockeye populations is advanced.     

Genetic Diversity in a Small Population of Sockeye Salmon Oncorhynchus nerkaWalbaum from the Ola River (the Northern Coast of the Okhotsk Sea)

The genetic structure of a small sockeye salmon population from the Ola River (Tauyskaya Inlet, the Okhotsk Sea) was shown to exhibit high heterogeneity. Significant differences of LDH-B2*and ALAT-2*gene frequencies were detected not only among samples within the spawner and juvenile groups but also between spawners and juveniles as a whole. The average heterozygosity of sockeye salmon from the Ola River was considerably lower than the corresponding values for other Asian populations. The Ola sockeye salmon is genetically similar to the population from the Pakhach River of the northwestern Kamchatka Peninsula but different from other Kamchatka populations and the Okhota River population. A hypothesis explaining the genetic differentiation of Asian sockeye populations is advanced.     

Seasonal and interannual variations of sockeye salmon (Oncorhynchus nerka) microsatellite DNA in two Kamchatka lake-river systems

Seasonal and interannual variations in the sockeye salmon populations from two lake-river systems of the East and West Kamchatka were studied. Stability of allele and genotypic frequencies of six microsatellite DNA loci in the adjacent generations and spawning populations of the sockeye salmon of the Bol'shaya River was confirmed experimentally. The pairwise intersample differentiation (F(st)) of the local sockeye salmon populations from the southwestern Kamchatka coast (Ozernaya and Bol'shaya Rivers)was almost 7 times higher than the corresponding values for the spawning populations of the Bol'shaya River sockeye salmon of the adjacent years; 15 times, for the adjacent Bol'shaya River sockeye salmon generations; and four times, for the seasonal races within the Kamchatka River.     

Allelic polymorphism of six microsatellite DNA Loci in populations of Sakha (Yakutia)

The allele frequency distributions of six STR loci (D3S1358, D16S539, THOI, D8S1179, LPL, and HUMvWFII) used in forensic practice were analyzed in populations of Sakha (Yakutia): three ethnogeographical groups of Sakha (Yakuts), Evenks, Yukagirs, Dolgans, and Russians. There were significant differences between Russians and all other populations by five markers. The total discriminating power (PD) of the locus system studied was assessed for each population. The interpopulation genetic difference (F _ST) was 0.005. Data on the allelic polymorphism of the above STR loci were used to analyze phylogenetic relationships among the populations of Sakha and those of other regions: East Europe, South Siberia, Chukotka, and Kamchatka.     

Genetic diversity of sockeye salmon <Emphasis Type="Italic">Oncorhynchus nerka</Emphasis> Walbaum of Kamchatka and the Commander Islands based on analysis of the variability of microsatellite DNA

The genetic diversity of the resident and migratory forms of sockeye salmon is investigated in 14 populations from various water bodies of Kamchatka and the Commander Islands by ten loci of microsatellite DNA. There are considerable differences in the frequencies of alleles among the populations of kokanee from Lake Kronotskoe, the residual form of sockeye salmon from Lake Kopylie, and other populations analyzed. Clustering of samples corresponds to their geographic position. No differences in the frequencies of alleles of the investigated loci are found between two forms of resident sockeye salmon from Kronotskoe Lake. In the sockeye salmon from the Commander Islands, a relatively low genetic diversity is found, as well as the greatest remoteness from the other Kamchatka group.     

Seasonal and interannual variations of sockeye salmon (<Emphasis Type="Italic">Oncorhynchus nerka</Emphasis>) microsatellite DNA in two Kamchatka lake-river systems

Seasonal and interannual variations in the sockeye salmon populations from two lake-river systems of the East and West Kamchatka were studied. Stability of allele and genotypic frequencies of six microsatellite DNA loci in the adjacent generations and spawning populations of the sockeye salmon of the Bol’shaya River was confirmed experimentally. The pairwise intersample differentiation (F _st) of the local sockeye salmon populations from the southwestern Kamchatka coast (Ozernaya and Bol’shaya Rivers) was almost 7 times higher than the corresponding values for the spawning populations of the Bol’shaya River sockeye salmon of the adjacent years; 15 times, for the adjacent Bol’shaya River sockeye salmon generations; and four times, for the seasonal races within the Kamchatka River.     

Comparative study of the population structure and population assignment of sockeye salmon Oncorhynchus nerka from West Kamchatka based on RAPD-PCR and microsatellite polymorphism

Using two types of molecular markers, a comparative analysis of the population structure of sockeye salmon from West Kamchatka as well as population assignment of each individual fish were carried out. The values of a RAPD-PCR-based population assignment test (94-100%) were somewhat higher than those based on microsatellite data (74-84%). However, these results seem quite satisfactory because of high polymorphism of the microsatellite loci examined. The UPGMA dendrograms of genetic similarity of three largest spawning populations, constructed using each of the methods, were highly reliable, which was demonstrated by high bootstrap indices (100% in the case of RAPD-PCR; 84 and 100%, in the case of microsatellite analysis), though the resultant trees differed from one another. The different topology of the trees, in our view, is explained by the fact that the employed methods explored different parts of the genome; hence, the obtained results, albeit valid, may not correlate. Thus, to enhance reliability of the results, several methods of analysis should be used concurrently.     

Comparative study of the population structure and population assignment of sockeye salmon Oncorhynchus nerka from West Kamchatka based on RAPD-PCR and microsatellite polymorphism

Using two types of molecular markers, a comparative analysis of the population structure of sockeye salmon from West Kamchatka as well as population assignment of each individual fish were carried out. The values of a RAPD-PCR-based population assignment test (94–100%) were somewhat higher than those based on microsatellite data (74–84%). However, these results seem quite satisfactory because of high polymorphism of the microsatellite loci examined. The UPGMA dendrograms of genetic similarity of three largest spawning populations, constructed using each of the methods, were highly reliable, which was demonstrated by high bootstrap indices (100% in the case of RAPD-PCR; 84 and 100%, in the case of microsatellite analysis), though the resultant trees differed from one another. The different topology of the trees, in our view, is explained by the fact that the employed methods explored different parts of the genome; hence, the obtained results, albeit valid, may not correlate. Thus, to enhance reliability of the results, several methods of analysis should be used concurrently.     

SNP芯片数据估计动物个体基因组品种构成的方法及应用

自然和人工选择、地理隔离和遗传漂移等原因使动物基因组中许多位点的等位基因频率在群体间会产生差异。源于不同品种(祖先)杂交(交配)的动物个体,其基因组与这些品种(祖先)的基因频率(基因型)会存在一定的相关性。因此采用合适的统计模型和分析方法,可以估计出每个品种(祖先)对于个体基因组的遗传贡献比例,又称为个体的基因组品种构成(genomic breed composition, GBC)。本文介绍了利用SNP芯片数据估计动物个体GBC的原理、方法及步骤,并且通过对198头待鉴定的日本红毛和牛GBC的评估,演示了用回归模型和混合分布模型估计动物个体GBC的具体步骤,其中包括SNP子集的筛选、参考群体中动物个体选择以及待测定动物GBC的计算。参考动物群体选自日本红毛和牛(Akaushi)、安格斯牛(Angus)、海福特牛(Hereford)、荷斯坦牛(Holstein)和娟珊牛(Jersey) 5个品种共36 574头,每个个体有40K或50K芯片数据。本文在现有商用 SNP芯片基础上筛选用于品种鉴定和估计动物个体GBC的SNP子集,是对现有SNP芯片功能的拓展和深入开发利用。此外,在基因组选择中如何利用SNP基因型估计动物个体GBC的结果,提高纯种和杂种动物的预测准确度,也是值得深入研究的领域。