Determination of population structure and stock composition of chum salmon (Oncorhynchus keta) in Russia determined with microsatellites

Variation at 14 microsatellite loci was examined in 34 chum salmon (Oncorhynchus keta) populations from Russia and evaluated for its use in the determination of population structure and stock composition in simulated mixed-stock fishery samples. The genetic differentiation index (Fst) over all populations and loci was 0.017, and individual locus values ranged from 0.003 to 0.054. Regional population structure was observed, and populations from Primorye, Sakhalin Island, and northeast Russia were the most distinct. Microsatellite variation provided evidence of a more fine-scale population structure than those that had previously been demonstrated with other genetic-based markers. Analysis of simulated mixed-stock samples indicated that accurate and precise regional estimates of stock composition were produced when the microsatellites were used to estimate stock compositions. Microsatellites can be used to determine stock composition in geographically separate Russian coastal chum salmon fisheries and provide a greater resolution of stock composition and population structure than that previously provided with other techniques.

Microsatellite multiplex panels for genetic studies of gray snapper (Lutjanus griseus) and lane snapper (Lutjanus synagris)

Microsatellites are codominantly inherited nuclear-DNA markers (Wright and Bentzen, 1994) that are now commonly used to assess both stock structure and the effective population size of exploited fishes (Turner et al., 2002; Chistiakov et al., 2006; Saillant and Gold, 2006). Multiplexing is the combination of polymerase chain reaction (PCR) amplification products from multiple loci into a single lane of an electrophoretic gel (Olsen et al., 1996; Neff et al., 2000) and is accomplished either by coamplification of multiple loci in a single reaction (Chamberlain et al., 1988) or by combination of products from multiple single-locus PCR amplifications (Olsen et al., 1996). The advantage of multiplexing micro-satellites lies in the significant reduction in both personnel time (labor) and consumable supplies generally required for large genotyping projects (Neff et al., 2000; Renshaw et al., 2006).

A Brief Interpretation of Summer Flounder, Paralichthys dentatus, Movements and Stock Structure with New Tagging Data on Juveniles

Summer flounder, Paralichthys dentatus, are managed as a single stock along the Atlantic coast from the U.S.– Canada border to the southern border of North Carolina. Justification of the single-stock approach is based on lack of genetic evidence for multiple stocks and the difficulty presented by managing the species from Cape Hatteras to the U.S.–Canada border. In this review, we present an interpretation of various morphometric, meristic, biochemical, and tagging studies, published and unpublished, that indicate the presence of two, or possibly three, distinct stocks in the management area. In addition, we have included new data from a tagging study that was conducted on juveniles from Virginia that aids in defining the stock(s) north of Cape Hatteras. Summer flounder, overfished for the past two decades, is recovering, and reconsideration of proposed stock structure could have direct implications for management policy decisions.

Red snapper (Lutjanus campechanus) demographic structure in the northern Gulf of Mexico based on spatial patterns in growth rates and morphometrics

Red snapper (Lutjanus campechanus) in the United States waters of the Gulf of Mexico (GOM) has been considered a single unit stock since management of the species began in 1991. The validity of this assumption is essential to management decisions because measures of growth can differ for nonmixing populations. We examined growth rates, size-at-age, and length and weight information of red snapper collected from the recreational harvests of Alabama (n=2010), Louisiana (n=1905), and Texas (n =1277) from 1999 to 2001. Ages were obtained from 5035 otolith sections and ranged from one to 45 years. Fork length, total weight, and age-frequency distributions differed significantly among all states; Texas, however, had a much higher proportion of smaller, younger fish. All red snapper showed rapid growth until about age 10 years, after which growth slowed considerably. Von Bertalanffy growth models of both mean fork length and mean total weight-at-age predicted significantly smaller fish at age from Texas, whereas no differences were found between Alabama and Louisiana models. Texas red snapper were also shown to differ significantly from both Alabama and Louisiana red snapper in regressions of mean weight at age. Demographic variation in growth rates may indicate the existence of separate management units of red snapper in the GOM. Our data indicate that the red snapper inhabiting the waters off Texas are reaching smaller maximum sizes at a faster rate and have a consistently smaller total weight at age than those collected from Louisiana and Alabama waters. Whether these differences are environmentally induced or are the result of genetic divergence remains to be determined, but they should be considered for future management regulations.

The geographic basis for population structure in Fraser River chinook salmon (Oncorhynchus tshawytscha)

We surveyed variation at 13 microsatellite loci in approximately 7400 chinook salmon sampled from 52 spawning sites in the Fraser River drainage during 1988–98 to examine the spatial and temporal basis of population structure in the watershed. Genetically discrete chinook salmon populations were associated with almost all spawning sites, although gene flow within some tributaries prevented or limited differentiation among spawning groups. The mean FST value over 52 samples and 13 loci surveyed was 0.039. Geographic structuring of populations was apparent: distinct groups were identified in the upper, middle, and lower Fraser River regions, and the north, south, and lower Thompson River regions. The geographically and temporally isolated Birkenhead River population of the lower Fraser region was sufficiently genetically distinctive to be treated as a separate region in a hierarchial analysis of gene diversity. Approximately 95% of genetic variation was contained within populations, and the remainder was accounted for by differentiation among regions (3.1%), among populations within regions (1.3%), and among years within populations (0.5%).Analysis of allelic diversity and private alleles did not support the suggestion that genetically distinctive populations of chinook salmon in the south Thompson were the result of postglacial hybridization of ocean-type and stream-type chinook in the Fraser River drainage. However, the relatively small amount of differentiation among Fraser River chinook salmon populations supports the suggestion that gene flow among genetically distinct groups of postglacial colonizing groups of chinook salmon has occurred, possibly prior to colonization of the Fraser River drainage.

Population structure of king mackerel (Scomberomorus cavalla) around peninsular Florida, as revealed by microsatellite DNA

A total of 1006 king mackerel (Scomberomorus cavalla) representing 20 discrete samples collected between 1996 and 1998 along the east (Atlantic) and west (Gulf) coasts of Florida and the Florida Keys were assayed for allelic variation at seven nuclear-encoded microsatellites. No significant deviations from Hardy-Weinberg equilibrium expectations were found for six of the microsatellites, and genotypes at all microsatellites were independent. Allele distributions at each microsatellite were independent of sex and age of individuals. Homogeneity tests of spatial distributions of alleles at the microsatellites revealed two weakly divergent “genetic” subpopulations or stocks of king mackerel in Florida waters—one along the Atlantic coast and one along the Gulf coast. Homogeneity tests of allele distributions when samples were pooled along seasonal (temporal) boundaries, consistent with the temporal boundaries used currently for stock assessment and allocation of the king mackerel resource, were nonsignificant. The degree of genetic divergence between the two “genetic” stocks was small: on average, only 0.19% of the total genetic variance across all samples assayed occurred between the two regions. Cluster analysis, assignment tests, and spatial autocorrelation analysis did not generate patterns that were consistent with either geographic or spatial-temporal boundaries. King mackerel sampled from the Florida Keys could not be assigned unequivocally to either “genetic” stock. The genetic data were not consistent with current spatial-temporal boundaries employed in stock assessment and allocation of the king mackerel resource. The genetic differences between king mackerel in the Atlantic versus those in the Gulf most likely stem from reduced gene flow (migration) between the Atlantic and Gulf in relation to gene flow (migration) along the Atlantic and Gulf coasts of peninsular Florida. This difference is consistent with findings for other marine fishes where data indicate that the southern Florida peninsula serves (or has served) as a biogeographic boundary.

An examination of spatial and temporal genetic variation in walleye pollock (Theragra chalcogramma) using allozyme, mitochondrial DNA, and microsatellite data

We used allozyme, microsatellite, and mitochondrial DNA (mtDNA) data to test for spatial and interannual genetic diversity in wall-eye pollock (Theragra chalcogramma) from six spawning aggregations representing three geographic regions: Gulf of Alaska, eastern Bering Sea, and eastern Kamchatka. Interpopulation genetic diversity was evident primarily from the mtDNA and two allozyme loci (SOD-2*, MPI*). Permutation tests ˆindicated that FST values for most allozyme and microsatellite loci were not significantly greater than zero. The microsatellite results suggested that high locus polymorphism may not be a reliable indicator of power for detecting population differentiation in walleye pollock. The fact that mtDNA revealed population structure and most nuclear loci did not suggests that the effective size of most walleye pollock populations is large (genetic drift is weak) and migration is a relatively strong homogenizing force. The allozymes and mtDNA provided mostly concordant estimates of patterns of spatial genetic variation. These data showed significant genetic variation between North American and Asian populations. In addition, two spawning aggregations in the Gulf of Alaska, in Prince William Sound, and off Middleton Island, appeared genetically distinct from walleye pollock spawning in the Shelikof Strait and may merit management as a distinct stock. Finally, we found evidence of interannual genetic variation in two of three North American spawning aggregations, similar in magnitude to the spatial variation among North American walleye pol-lock. We suggest that interannual genetic variation in walleye pollock may be indicative of one or more of the following factors: highly variable reproductive success, adult philopatry, source-sink metapopulation structure, and intraannual variation (days) in spawning timing among genetically distinct but spatially identical spawning aggregates.

Assessment of cattle genetic introgression into domestic yak populations using mitochondrial and microsatellite DNA markers

Hybridization between yak Poephagus grunniens and taurine Bos taurus or indicine B. indicus cattle has been widely practiced throughout the yak geographical range, and gene flow is expected to have occurred between these species. To assess the impact of cattle admixture on domestic yak, we examined 1076 domestic yak from 29 populations collected in China, Bhutan, Nepal, India, Pakistan, Kyrgyzstan, Mongolia and Russia using mitochondrial DNA and 17 autosomal microsatellite loci. A cattle diagnostic marker-based analysis reveals cattle-specific mtDNA and/or autosomal microsatellite allele introgression in 127 yak individuals from 22 populations. The mean level of cattle admixture across the populations, calculated using allelic information at 17 autosomal microsatellite loci, remains relatively low (mY(cattle) = 2.66 +/- 0.53% and Q(cattle) = 0.69 +/- 2.58%), although it varies a lot across populations as well as among individuals within population. Although the level of cattle admixture shows a clear geographical structure, with higher levels of admixture in the Qinghai-Tibetan Plateau and Mongolian and Russian regions, and lower levels in the Himalayan and Pamir Plateau region, our results indicate that the level of cattle admixture is not significantly correlated with the altitude across geographical regions as well as within geographical region. Although yak-cattle hybridization is primarily driven to produce F-1 hybrids, our results show that the subsequent gene flow between yak and cattle took place and has affected contemporary genetic make-up of domestic yak. To protect yak genetic integrity, hybridization between yak and cattle should be tightly controlled.

Genetic studies of human diversity in East Asia

East Asia is one of the most important regions for studying evolution and genetic diversity of human populations. Recognizing the relevance of characterizing the genetic diversity and structure of East Asian populations for understanding their genetic his

Genetic analysis of east and west coast populations of Penaeus monodon from India based on random amplified polymorphic DNA

The east and west coast populations of wild Penaeus monodon in India were genetically characterized by RAPD analysis using six highly polymorphic primers reported earlier. The average genetic similarities within populations, based on profiles generated by all the six primers, were 0.828 and 0.851 for the east and west coast populations, respectively, values with individual primers ranging from 0.744 to 0.889. The average genetic similarity between populations across all the primers was 0.774. The number of bands found to be polymorphic were 38 (51.35%) and 37 (50.68%) in the east and west coast populations, respectively. Primer 5 yielded the highest level of polymorphism (63.63%) in the east coast population whereas primer 3 yielded the lowest level of polymorphism (36.36%) in the west coast population. The study reveals the existence of genetic variation in P. monodon stocks providing scope for genetic improvement through selective breeding. It also provides baseline data for future work on population structure analysis of P. monodon.

Mitochondrial diversity and phylogeographic structure of Chinese domestic goats

China has numerous native domestic goat breeds, but so far there has been no extensive study on genetic diversity, population demographic history, and origin of Chinese goats. Here, we examined the genetic diversity and phylogeographic structure of Chinese domestic goats by determining a 481-bp fragment of the first hypervariable region of mitochondrial DNA (mtDNA) control region from 368 individuals representing 18 indigenous breeds. Phylogenetic analyses revealed that there were four mtDNA lineages (A-D) identified in Chinese goats, in which lineage A was predominant, lineage B was moderate, and lineages C and D were at low frequency. These results further support the multiple maternal origins of domestic goats. The pattern of genetic variation in goat mtDNA sequences indicated that the two larger lineages A and B had undergone population expansion events. In a combined analysis of previously reported sequences and our sequences belonging to lineage B, we detected two subclades, in which one was unique to eastern Asia and another was shared between eastern and southern Asia. A larger genetic variation in eastern Asia than southern Asia and the pattern of phylogeographic variation in lineage B suggest that at least one subclade of lineage B originated from eastern Asia. There was no significant geographical structuring in Chinese goat populations, which suggested that there existed strong gene flow among goat populations caused by extensive transportation of goats in history. (c) 2005 Elsevier Inc. All rights reserved.

Molecular genetic basis for the rhino mouse from Chinese KM subcolony

Both the rhino mouse and hairless mouse resulted from hairless gene mutation, but they show different phenotypes of skin physiology. The rhino mouse has more similar histological characters to human papular alopecia. Therefore rhino mouse is a good experimental animal model for human papular alopecia. This study reports a hairless mouse named rhino KIZ, arose from KM colony in Kunming Institue of Zoology, by systematic studies on morphology, skin histopathology, gene sequence, pedigree and protein domain analysis. The results demonstrate that a C-to-T transition in exon 11 of hr gene (The mutant gene has been applied for a Chinese patent (patent No. 03135280)) results in the rhino KIZ. The rhino KIZ with clear genetic mechanism will be a useful animal model.

Population structure and history in East Asia

Archaeological, anatomical, linguistic, and genetic data have suggested that there is an old and significant boundary between the populations of north and south China. We use three human genetic marker systems and one human-carried virus to examine the north/south distinction. We find no support for a major north/south division in these markers; rather, the marker patterns suggest simple isolation by distance.

Molecular phylogeography and population structure of a mid-elevation montane frog Leptobrachium ailaonicum in a fragmented habitat of southwest China

Leptobrachium ailaonicum is a vulnerable anuran restricted to a patchy distribution associated with small mountain streams surrounded by forested slopes at mid-elevations (approximately 2000-2600 m) in the subtropical Mount Wuliang and Mount Ailao ranges in southwest China (Yunnan Province) and northern Vietnam. Given high habitat specificity and lack of suitable habitat in lower elevations between these ranges, we hypothesized limited gene flow between populations throughout its range. We used two mitochondrial genes to construct a phylogeographic pattern within this species in order to test our hypothesis. We also examined whether this phylogeographic pattern is a response to past geological events and/or climatic oscillations. A total of 1989 base pairs were obtained from 81 individuals of nine populations yielding 51 unique haplotypes. Both Bayesian and maximum parsimony phylogenetic analyses revealed four deeply divergent and reciprocally monophyletic mtDNA lineages that approximately correspond to four geographical regions separated by deep river valleys. These results suggest a long history of allopatric separation by vicariance. The distinct geographic distributions of four major clades and the estimated divergence time suggest spatial and temporal separations that coincide with climatic and paleogeographic changes following the orogeny and uplift of Mount Ailao during the late Miocene to mid Pliocene in southwest China. At the southern distribution, the presence of two sympatric yet differentiated clades in two areas are interpreted as a result of secondary contact between previously allopatric populations during cooler Pleistocene glacial cycles. Analysis of molecular variance indicates that most of the observed genetic variation occurs among the four regions implying long-term interruption of maternal gene flow, suggesting that L ailaonicum may represent more than one distinct species and should at least be separated into four management units corresponding to these four geographic lineages for conservation. (C) 2009 Elsevier Inc. All rights reserved.

Analysis of genetic diversity in Glyptosternum maculatum (Sisoridae, Siluriformes) populations with AFLP markers

We determined the genetic diversity of geographic populations from three spawning grounds (Nyang River, Lhasa River, Shetongmon Reach of Yarlung Zangbo River) of Glyptosternum maculatum with amplified fragment length polymorphism (AFLP) markers. Five primer combinations detected 332 products, 51 of them (15.4%) were polymorphic in at least one population. The Shetongmon population was found to be the richest in genetic diversity as was indicated by the percentage of polymorphic loci and heterozygosity, followed by the Nyang population and the Lhasa population. The pair-wise genetic distance between populations were all very close, ranging from 0.0015 to 0.0042 with an average of 0.0024. The genetic distance was not proportional to the geographic distance. The analysis of molecular variance demonstrated that all variation occurred within populations. The average estimated fixation index (F (st)) of three populations across all polymorphic loci was -0.0184, indicating the absence of genetic differences among the three sampled populations. The differentiation among populations was not significant, and population structure was weak. Our observations will help identify the genetic relationship among populations as the first approach to understand the genetic diversity of Glyptosternum maculatum.