Genetic diversity and divergence among clam <Emphasis Type="Italic">Cyclina sinensis</Emphasis> populations assessed using amplified fragment length polymorphism

ABSTRACT:   The genetic diversity and population structure of Cyclina sinensis were assessed using amplified fragment length polymorphism (AFLP). Three hundred and fifty-four AFLP loci were analyzed in 160 individuals collected from Lvshun, Lianyungang, Yueqing and Dongxing of coastal China. High levels of genetic diversity were detected, where the percentage of polymorphic loci and average expected heterozygosity ranged 88.4–98.9% and 0.304–0.365, respectively. Analysis of molecular variance showed that variation among populations (24.4%) was highly significant ( P  < 0.001). Accordingly, the global fixation index ( θ _B) averaged over loci was high (0.205). The large genetic differences among populations indicate restricted gene flow, congruent with limited dispersal capability of C. sinensis . The unweighted pair group method with arithmetic mean (UPGMA) tree topology constructed on the basis of Nei's genetic distances between populations showed a clear separation of the northern two populations from the southern two populations, suggesting that gene flow between the northern and southern regions is extremely low. This finding is additionally supported by the separate clustering of the four populations in the results of principal coordinate analysis. The useful information obtained in this study will offer insights to fine-tune conservation and fishery management measures in the future.     

Genetic diversity and relatedness estimates for captive barramundi (Lates calcarifer,Bloch) broodstock informs efforts to form a base population for selective breeding

Aquaculture of barramundi or Asian seabass (Lates calcarifer) is growing in both Australia and Southeast Asia and there is substantial interest to improve production efficiency through selective breeding. The establishment of a large and genetically diverse base population is a prerequisite for a sustainable and long‐term productive breeding program. Before selective breeding programs can begin for Australian barramundi it is important to assess the overall genetic diversity of current captive broodstock populations. To address this question, 407 captive barramundi broodstock from eight separate Australian broodstock populations were genotyped using 16 polymorphic microsatellite DNA markers. A Bayesian STRUCTURE analysis indicated that captive Australian broodstock are broadly divided into two genetic stocks. Multivariate analysis between broodstock individuals and pairwise F_ST between broodstock populations also supported the existence of two stocks. Comparisons with data obtained from natural stocks suggested that hatchery individuals were either sourced from the two stocks or represented an admixture between them. Genetic diversity was low within each broodstock population (allelic richness ranged from 2.67 to 3.42 and heterozygosity ranged from 0.453 to 0.537) and relatedness estimates within hatcheries were generally low (average r was equal to 0.141). We recommend sourcing captive individuals according to high levels of neutral genetic diversity and low levels of relatedness for the establishment of a base population. We also make recommendations about including genetically diverse wild individuals.     

Common pearl oysters in China, Japan, and Australia are conspecific: evidence from ITS sequences and AFLP

ABSTRACT:   To elucidate the species status of Pinctada fucata in China, P. fucata martensii in Japan and P. imbricata in Australia, one population of each taxon was studied using internal transcribed spacer 1 and 2 (ITS1, and ITS2) and amplified fragment length polymorphism (AFLP) markers. ITS1 and ITS2 were 401–405 and 229–237 bp long, respectively. Twenty-nine ITS1 and 15 ITS2 unique genotypes were obtained from 44 and 34 individuals, respectively, with some genotypes shared by two or three populations. In AFLP analysis, each individual exhibited a distinct phenotype. No population had diagnostic markers. Mean genetic divergences within and among the three populations were very low and overlapped (between-population: 0.7–0.9% for ITS1, 0.9–1.3% for ITS2, and 53.3–55.6% for AFLP; within-population: 0.5–0.9% for ITS1, 0.8–1.2% for ITS2, and 50.4–53.6% for AFLP). Low levels of genetic differentiation were observed among the three populations while the Australian population is partially genetically isolated. Under an infinite allele model, genetic differentiation among populations was not significant based on a permutation test. Under an infinite site model, most F _ST values were not significant for ITS data although they were significant for AFLP data. Network analysis using ITS data indicated that individuals from the same population did not cluster together. Analysis of molecular variance ( amova ) demonstrated that > 94% variation was contributed by within-population variation. These findings suggest that the three taxa are conspecific and Pinctada fucata is the correct name.     

Loss of genetic variability in the captive stocks of tambaqui,Colossoma macropomum (Cuvier, 1818), at breeding centres in Brazil,and their divergence from wild populations

The loss of variability in farmed populations and the risks of interactions with wild populations support the need for the genetic monitoring of species farmed throughout the world. In Brazil, the tambaqui is the most widely farmed native fish species. Despite this, there are no data on the pedigree of the farmed stocks, and the potential for interactions with wild populations in the Amazon basin has raised concerns with regard to the genetic variability of these stocks. The present study analysed sequences of the mitochondrial Control Region and 12 microsatellites to characterize the genetic variability of seven historically important commercial tambaqui breeding centres located in four different regions of Brazil, and compared these sequences with those obtained from individuals collected from a wild population. High levels of genetic diversity were found in the wild population, whereas genetic diversity was reduced in both markers in most captive populations, except for the broodstock located near the Amazon River. High F_ST and D_EST indices were recorded between the wild population and most of the captive stocks analysed. The drastic reduction in genetic diversity found in most captive stocks and the difference between these stocks and the wild population may have been the result of the small size of the founding populations and the absence of breeding management. The renewal of the broodstocks and the application of breeding management techniques are recommended. In the Amazon region, in addition, the use of broodstocks that are genetically very different from local wild populations should be avoided.     

Genetic and morphological divergences between wild and captive‐bred populations of Salmo trutta abanticus

Salmo trutta abanticus is a non‐anadromous trout species native to Lake Abant and Seven Lakes in Turkey. A restocking programme by captive breeding was initiated in 1999 to support S. trutta abanticus population. Reared 2‐year‐old juveniles from randomly caught wild parental individuals in Maçka breeding farm were introduced into Lake Abant. We aimed to compare genetic and morphological divergences between wild‐ and captive‐bred populations using seven microsatellite loci and geometric morphometric measurements. A significant genetic and morphological divergences were detected between all population in F_st and canonical variate analysis based on geometric morphometric with 10 homolog landmark. Eighty‐six microsatellites alleles were recorded across loci. Number of private alleles, observed alleles and observed heterozygosity are statistically significant higher in Maçka captive‐bred population than Lake Abant and Seven Lakes populations. Of 42 tests, three departures from Hardy–Weinberg equilibrium were detected in all populations after Bonferroni correction. Two pairs of loci (Ssa85 – Str73 and Str73‐Str543) in Maçka, one pairs of loci (Ssa85‐Str73) in Abant and two pairs of loci (Ssa85‐Str60 and Str73‐Str543) in Seven Lakes populations show linkage disequilibrium. Population structure analysed with Structure software showed three genetic groups (?K = 3) in our studied populations. Relatedness estimates show higher mean relatedness values (r = 0.220 ± 0.230) for Maçka captive‐breed population than wild populations of Abant Lake and Seven Lakes (r = 0.140 ± 0.210 and r = 0.170 ± 0.200 respectively).     

Evaluation of genetic characteristics of wild and cultured populations of the Japanese pearl oyster <Emphasis Type="Italic">Pinctada fucata martensii</Emphasis> by using AFLP markers

Genetic characteristics of four wild (Mie, Fukui, Shimane and Nagasaki) and five cultured populations (selectively bred for 12 years with an origin of Ehime population) of the Japanese pearl oyster, Pinctada fucata martensii, were evaluated by using AFLP markers. Six primer pairs generated 1019 loci in total, among which 45.2–55.1 % was polymorphic among populations. Although there was no significant difference in gene diversity between wild (0.170–0.174) and cultured (0.158–0.173) populations, genetic relatedness in cultured populations (0.316–0.450) was about three times higher than that in wild populations (0.110–0.165). In addition, genetic differentiation was about twenty times larger in cultured populations (Nei’s distance: 0.0111) than in wild populations (Nei’s distance: 0.0005). These results mean that selective breeding can cause marked inbreeding as well as large genetic differentiation among cultured populations in a short period. On the other hand, it was suggested that genetic homogenization in the wild, probably due to a large-scale transport of cultured oysters, had progressed in the sea around Japan. In conclusion, it is necessary to prevent inbreeding by the reconsideration of the style of selective breeding in cultured populations, while the escape of gametes or spats of cultured strains in the wild should be avoided for the preservation of genetic characteristics in native populations of P. f. martensii.     

基于线粒体控制区的许氏平鲉养殖群体与野生群体比较研究

为研究许氏平鲉养殖群体与野生群体遗传结构及遗传多样性状况,采用PCR扩增获得许氏平鲉线粒体DNA控制区高变区片段,并对其进行比对分析。结果显示,在长度为451 bp的线粒体控制区片段中,养殖群体单倍型多样度(0.540±0.067~0.815±0.021)明显低于野生群体(0.883±0.053~0.944±0.028),而核苷酸多样度(0.001±0.001~0.007±0.004)与野生群体(0.004±0.003~0.007±0.004)相差不大,遗传多样性水平均较低。在52个单倍型中,养殖群体仅占12个,且有6个单倍型与野生群体共享。群体间遗传分化指数和AMOVA分析结果显示,养殖群体和野生群体之间以及养殖群体之间的遗传分化较大,而野生群体间遗传变异较小,组群间的遗传分化较小且不显著(ΦCT=-0.013;P0.05)。单倍型最小跨度树和NJ系统发育树均未检测到明显的谱系结构。     

Survey of genetic variation at three microsatellite loci in captive populations of endangered Japanese minnow <Emphasis Type="Italic">Aphyocypris chinensis</Emphasis> with implications for reduction of inbreeding

The Japanese population of the cyprinid minnow Aphyocypris chinensis is nearing extinction in the wild. The genetic diversity of three microsatellite loci in five captive populations was investigated, and an effective breeding strategy to reduce inbreeding from pairwise relatedness (R _xy ) between each captive line is discussed. The average number of alleles ranged 2.33–4.67 and the average heterozygosity ranged 0.283–0.602. The pairwise relatedness observed in most combinations showed a significant decrease between the populations. It is suggested that exchange of individuals between different breeding lines should effectively stop inbreeding. Studies show that the effective population size (N _e ) estimated from the number of parental individuals was 8.54 in one captive population, which is insufficient to maintain genetic diversity. It is recommended that more parental individuals should be used, and to exchange fish in a rotating mating mode between institutions participating in captive breeding of A. chinensis.     

Comparison of mortality of wild and released reared 0-group turbot, Scophthalmus maximus, on an exposed beach (Ría de Vigo, NW Spain) and a study of the population dynamics and ecology of the natural population

Abstract  Marked reared turbot, Scophthalmus maximus (L.) (594) were released onto an exposed beach nursery ground together with marked wild fish (438) of approximately the same size (4–6 cm TL) and were sampled at intervals for 38 days. A consistent ratio of marked wild: unmarked wild indicated that marking did not increase mortality. The wild 0-group turbot population size was estimated at 1540 at the time of release, indicating that hatchery-reared individuals could theoretically make a significant contribution to the local population size. However, the absolute and relative catches of the marked, reared fish were lower than those of the marked wild fish, and no reared fish were caught after 23 days. The higher mortality rate was attributed to both a smaller size and their hatchery-reared origin. The population dynamics of the 1994–1995 year-classes of wild turbot were also studied. Recruitment of post-larvae (3 cm) to the beach started in March and continued until October. Population size peaked over the August–October period. Juvenile turbot remained on the nursery beach until June of the following year when they presumably emigrated to deeper water. During this 15-month period their length increased from 3 to 12–15 cm.     

中国海南三亚大珠母贝不同年代种群的遗传变异研究

利用10个多态微卫星标记对中国海南三亚海域大珠母贝（Pinctada maxima）3个不同年代（2007、2009和2010）群体的遗传变异进行了分析，每个群体30个样品。10个位点共扩增出60个等位基因，平均每个位点6（2—8）个，3个群体分别丢失了1、2和4个稀有等位基因。平均期望杂合度（Hc）、平均多态信息含量（PIC）、平均Shannon多样性指数均呈下降趋势。各群体均存在一定程度的杂合子缺失。30个数据中（3个种群×10个位点）有18个偏离了Hardy—Weinberg平衡。两两群体间的平均近交系数（FIS）介于0．2273～0．2601之间，平均遗传分化指数（FST）介于0．0204～0．0462，遗传分化显著（P〈0．01）。结果表明，3个年代群体遗传多样性水平已经出现了逐渐降低的趋势，遗传结构存在显著差异，近交程度增加，因此，人工繁育工作中应注意避免近亲繁殖和遗传多样性的降低。     

Accumulated snow and summer temperature – critical factors for recruitment to high mountain populations of brown trout (Salmo trutta L.)

Abstract –  In lake Krokavatn, 1236 m a.s.l., only six strong year-classes of brown trout appeared during the period 1970–2003. Eleven year-classes were missing during the same period. The observed recruitment failure depended significantly on the accumulated snow depth in April, whereas the mean August temperature in the year of birth was significant for the appearance of strong year-classes. Size of the young-of-the-year (YOY) trout at onset of the winter seemed to be crucial for survival. Also little snow and low temperatures during the winter may have led to recruitment failure, as small nursery streams may freeze completely under such conditions, as happened during the winter of 1995/1996. Thus, the recruitment to brown trout populations in western high mountain areas of Norway seemed to be strongly affected by accumulated snow depth and summer temperatures. A climate change with more winter precipitation, as predicted for the present century, may therefore be detrimental to recruitment. However, warmer summers may increase recruitment to levels that lead to overpopulation, but also to establishment of brown trout populations at higher elevations than today.     

辽宁沿海海蜇与沙海蜇遗传多样性的AFLP分析

海蜇和沙海蛰均为腔肠动物门的大型食用水母,采用AFLP分子标记技术对辽宁沿海的海蜇野生群体、养殖群体和沙海蜇野生群体共90个个体进行了遗传多样性分析.10对引物共得到560个稳定扩增位点.3个群体的多态性位点比例为海蜇野生群体82.05%.海蜇养殖群体78.46%,沙海蜇野生群体74.10%;平均杂合度分别为0.2072,0.1850和0.2116,Shannon多样性指数分别为0.3248、0.2954和0.3262,海蜇野生群体与海蜇养殖群体和沙海蜇野生群体的遗传距离分别为0.0300和0.2702.分析结果表明,3个群体的遗传多样性均保持了相对较高的水平.     

马氏珠母贝大亚湾和三亚野生种群内自繁及种群间杂交一代的RAPD分析

运用RAPD技术分析了广东大亚湾野生种群内繁殖一代DDl群体和海南三亚野生种群内繁殖一代SSl、两野生种群间杂交一代DS1群体各18个个体的遗传多样性。筛选的28个含10碱基的随机引物中，其中11个随机引物可产生稳定和可重复的多态扩增结果，共检测出86个位点，其中DDl群体有74个基因位点，其中56个表现多态，多态比例为75．68％；SSl群体79个基因位点，其中57个表现多态，多态比例是72．15％；DSl群体有72个基因位点，其中64个表现多态，多态比例为88．89％。用修正的Shannon表型多态性指数量化3个群体的遗传多态性，DDl、SSl和DS13个群体的遗传多态性分别为0．2280，0．2ll5和0．2456。不同地理种群间杂交能够增加子代的遗传多态性。     

Can conservation‐oriented,captive breeding limit behavioural and growth divergence between offspring of wild and captive origin Atlantic salmon (Salmo salar)?

Captive rearing is being used increasingly to maintain demographics and genetic diversity of threatened fish populations and species, but its effectiveness can be hindered by domestication, that is, inadvertent selection for performance in captivity at the cost of that in the wild. Some captive rearing programmes have begun to take steps to limit such domestication, but the results are ambiguous, as the degree of generational exposure to captivity is often difficult to control. Using an endangered population of Atlantic salmon (Salmo salar) currently undergoing conservation‐oriented captive rearing, we tested for domestication effects on dominance (dyadic trials) and growth (seminatural stream channels with differing densities and group proportions) of juvenile offspring of wild and captive origin parents. Pedigree data afforded the ability to compare these effects among three specific study groups: wild, single‐generation captives and two to three generation captives. Our results indicate that, despite conservation breeding practices, a divergence in growth can occur in as little as one generation without divergence in dominance behaviour. Further, evidence suggests that trait divergence did not increase with generations in captivity. Given the experimental design, results and supporting literature, we conclude that this contemporary divergence is likely genetic and driven by a combination of factors, including variation in selective histories influencing behaviour.     

Molecular analysis of grass carp (<Emphasis Type="Italic">Ctenopharyngodon idella</Emphasis>) by SRAP and SCAR molecular markers

The sequence-related amplified polymorphism (SRAP) technique was used to analyze the gene differentiation between two cultured populations [Freshwater Fisheries Research Center (FFRC) and Qianzhou populations] and one wild population (Hanjian population) of grass carp (Ctenopharyngodon idella). Some loci showed quite different genetic frequencies, attributable to artificial selection, which imply that these fragments are putative markers of germplasm identification. We developed a simple and effective method to further characterize these SRAP fragments. Specific SRAP bands were cut directly from polyacrylamide gels, re-amplified, cloned, and sequenced. Twenty-one putative genetic markers were sequenced, ranging from 137 to 357 bp. The sequences were submitted to the database of the Genome Sequence Survey. A BLAST analysis showed that eight SRAP fragments were highly similar to functional genes, whereas the other 13 had no similarity, indicating that these markers are tightly linked to the germ identification trait although only eight are functional genes. Three primers were designed according to this sequence information and used for PCR amplification of the three populations. A sequence-characterized amplified region (SCAR1) was positively amplified in the artificially cultured populations but not in the wild population. The frequency of the SCAR3 marker in the cultured populations was 87% (26/174), whereas it was only 6% (6/100) in the wild population. A specific band was isolated from all individuals in the wild population with the SCAR3 primers, whereas the specific band was amplified from only seven individuals in the FFRC population and from none of the Qianzhou population. The frequency of SCAR2 in the artificially cultured populations was 96.5%. These results indicate that SCAR1 could be used as a specific molecular marker for population identification. The SCAR markers used in this study offer a powerful, easy, and rapid method for genetic analysis and the discrimination of different populations.     

RAPD分析野生和养殖三角帆蚌的遗传多样性

用150个随机引物对野生三角帆蚌和养殖三角帆蚌进行随机扩增多态DNA(RAPD)分析，最终筛选出2．0个引物，分别能扩增出1-10条大小不等的片段，片段长度在500—2000bp之间。野生三角帆蚌和养殖三角粤蚌的种内相似系数分别为0．787和0．833，显示野生种群基因组发生的变异较养殖种群大。野生三角帆蚌和养殖三角帆蚌种群间遗传距离为0．054，表明三角帆蚌野生和养殖种群亲缘关系比较接近。     

3个不同群体罗氏沼虾线粒体16SrRNA基因序列分析及遗传差异

利用PCR技术扩增获得罗氏沼虾线粒体16SrRNA基因的部分片段,通过序列测定和用限制性内切酶MboI、AluI和TaqI分别对上述PCR产物进行限制性片段长度多态分析(RFLP),分析了取自缅甸引进种子代、广西养殖群体及江苏养殖群体3个不同群体罗氏沼虾的遗传差异。结果表明:在3个群体间序列同源性对比无变异,PCR-RFLP未发现有片段多态性,3个群体间不存在遗传结构差异。可能表明这3个群体的罗氏沼虾起源同一个种群,且分化较低。     

Population genetic structure and variability of Pacific herring <Emphasis Type="Italic">Clupea pallasii</Emphasis> in the stocking area along the Pacific coast of northern Japan

ABSTRACT:   The genetic diversity of wild and hatchery-released Pacific herring Clupea pallasii collected from three brackish lakes and two bays in Honshu and Hokkaido, Japan was examined with five microsatellite loci. All loci showed high genetic variability with expected heterozygosities ranging from 0.815 to 0.945. Significant differences in genotypic and allelic distributions were detected among all locations except for between the two bays in Honshu Island. Pairwise population analysis based on the F _ST values showed close genetic relationships among the locations in Hokkaido Island, and the hierarchical analyses of molecular variance showed significant genetic difference between the two islands. Those results suggest the existence of subpopulations due to natal homing. In addition, stocked fish showed as much genetic diversity as the wild fish. The pairwise population analyses also showed close relationships between the hatchery fish and the wild fish in respective stocking areas, showing that no effects of stocking programs on genetic diversity of wild populations were detected.     

Conservation genetics of the Mary River turtle (Elusor macrurus) in natural and captive populations

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Identification of differential broodstock contribution affecting genetic variability in hatchery stocks of Atlantic salmon (Salmo salar)

Supportive breeding of Atlantic salmon (Salmo salar) is commonly employed to maintain numbers of fish where the species has become locally endangered. Increasingly, one of the main aims of population management is the preservation of natural genetic diversity. If the stocks employed in supportive breeding exhibit reduced variation they can alter the natural pattern of genetic variation observed in wild populations. In northern Spain, wild adult salmon are caught every year from local rivers and artificially crossed in order to create supportive stocks. The offspring are hatchery reared until the juvenile stage, then released into the same river where their parents were caught. In the current study, our findings demonstrate that although adult broodstock exhibit a pattern of variation similar to the wild populations, variability at microsatellite loci was drastically reduced in the juveniles released into one of three rivers analyzed. The contribution of broodstock to this juvenile stock was examined by pedigree analysis. A restricted number of females contributing to the hatchery stock was identified as the main cause of loss in genetic variation, possibly due to overmaturity of some multi-sea-winter females. We suggest that better monitoring and control of parental contribution will help in solving the problem of loss of genetic diversity in hatchery populations.