Population genetic structure and effective population size of ayu (Plecoglossus altivelis), an amphidromous fish

The temporal and spatial population genetic structure of ayu Plecoglossus altivelis (Salmoniformes: Plecoglossidae), an amphidromous fish, was examined using analysis of variation at six microsatellite DNA loci. Intracohort genetic diversities, as measured by the number of alleles and heterozygosity, were similar among six cohorts (2001–2006) within a population (Nezugaseki River), with the mean number of alleles per cohort ranging from 11·0 to 12·5 and the expected heterozygosity ranging from 0·74 to 0·77. Intrapopulational genetic diversities were also similar across the three studied populations along the 50 km coast, with the mean number of alleles and the expected heterozygosity ranging from 11·33 to 11·67 and from 0·75 to 0·76, respectively. The authors observed only one significant difference in pair-wise population differentiation ( F _ST-value) between the cohorts within a population and among three populations. Estimates of the effective population size ( N _e) based on maximum-likelihood method yielded small values (ranging from 94·8 to 135·5), whereas census population size ranged from c. 4800 to 24 000. As a result, the ratio of annual effective population sizes to census population size ( N _e/ N ) ranged from 0·004 to 0·023. These estimates of N _e/ N agree more closely with estimates for marine fishes than that of the larger estimates for freshwater fishes. The present study suggests that ayu which is highly fecund and shows low survival during the early life stages is also characterized by having low value of N _e/ N , similar to marine species with a pelagic life cycle.     

Population structure of lake‐type and river‐type sockeye salmon in transboundary rivers of northern British Columbia

The population structure of 'lake‐type' and 'river‐type' sockeye salmon Oncorhynchus nerka , primarily in transboundary rivers in northern British Columbia, was examined with a survey of microsatellite variation. Variation at 14 microsatellite loci was surveyed from c . 3000 lake‐type and 3200 river‐type sockeye salmon from 47 populations in six river drainages in British Columbia. The mean F _ST for the 14 microsatellite loci and 47 populations was 0·068, and 0·034 over all river‐type populations. River‐type sockeye salmon were more genetically diverse than lake‐type sockeye salmon, with expected heterozygosity of river‐type sockeye salmon 0·72 and with an average 12·7 alleles observed per locus, whereas expected heterozygosity of lake‐type sockeye salmon was 0·65 with and average 10·5 alleles observed per locus. River drainage of origin was a significant unit of population structure. There was clear evidence of genetic differentiation among river‐type populations of sockeye salmon from different drainages over a broad geographic range in British Columbia.     

Cloning and characterization of microsatellite loci in channel catfish, Ictalurus punctatus

Short tandem repeat (microsatellite) loci were cloned from the channel catfish, Ictalurus punctatus , genome for use as molecular markers for genetic improvement of this important agricultural species. Plasmid clones containing catfish genomic DNA inserts were identified, by hybridization with tandem repeat DNA probes, and sequenced using automated laser fluorescence. A feral population of catfish displayed levels of heterozygosity greater than 0·7 for 13 of 22 loci and heterozygosity greater than 0·5 for 20 of 22 loci. Allelic polymorphism ranged from three to 17 alleles per locus in the feral population. Populations of domestic, farm-raised catfish and a research strain displayed levels of heterozygosity similar to the feral population. Non-invasive tissue sampling provided abundant material for the polymerase chain reaction-based genotype assay. The microsatellite loci will be useful in the molecular characterization and genetic improvement of channel catfish populations.     

Genic diversity in Red River pupfish Cyprinodon rubrofluviatilis (Atheriniformes: Cyprinodontidae) and its implications for the conservation genetics of the species

Starch gel electrophoresis of proteins was used to study geographic variation at 26 gene loci in the Red River pupfish ( Cyprinodon rubrofluviatílís ), a species restricted to west Texas and Oklahoma. Marked differences were detected between populations in the Red and Brazos river drainages, with fixed or nearly fixed differences occurring at five gene loci. In addition, mean heterozygosity was uniformly high for the Red River form ( = 0·076–0·101) while samples of the Brazos River form were genetically depauperate ( =0·00–0·017). Introduced populations in the South Canadian and Colorado river drainages appear to have been derived from the Red River drainage. The presence of alleles diagnostic of the Red and Brazos river forms supports the suggestion from previous work that they may represent cryptic species. Regardless of taxonomy, however, the presence of two genetically distinct forms must be taken into consideration by those concerned with maintenance of biotic diversity.     

Isolation and characterization of polymorphic microsatellite loci in the scarlet ibis (Eudocimus ruber— Threskiornithidae‐Aves)

Here we presented 10 polymorphic microsatellite loci obtained from scarlet ibis through an enriched genomic library. The analysis of 45 individuals from three Brazilian natural populations showed allelic diversity ranged from three to 17 alleles, observed heterozygosity ranged from 0.03 to 0.92, and expected heterozygosity ranged from 0.06 to 0.92. These highly variable microsatellite loci can provide means for assessing overall genetic variation in its remnant natural populations, which may help the development of effective conservation programs.     

Loss of genetic variation in hatchery-reared Indian major carp, Catla catla

The hypothesis that effective population sizes are low in hatchery-reared catla ( Catla catla ) from Bangladesh, possibly leading to inbreeding and loss of variation, was tested. The study was based on analysis of seven microsatellite loci in three samples of hatchery-reared catla and four samples representing wild populations. Pair-wise estimates of genetic differentiation between samples were low between wild samples (θ ranging from 0·012 to 0·034), but high between hatchery samples (θ ranging from 0·153 to 0·185), suggesting strong genetic drift in hatcheries. Genetic variation, both in terms of expected heterozygosity and allelic richness, was significantly lower in hatchery samples than in samples of wild catla. Application of a method for reconstructing families among offspring without parental genetic data showed that the hatchery samples consisted of very few half- and full-sib families, whereas the wild samples consisted of a high number of families, suggesting that most individuals were unrelated. Finally, estimation of the effective number of parents ( N _b) in the largest sample of hatchery fish confirmed that effective population size was low ( N _b= 14·9 for multiallelic loci and N _b= 10·6 if alleles were pooled into two composite alleles). The results show that low effective population sizes leading to loss of variation and possibly inbreeding depression should be a matter of serious concern in aquaculture production of catla.     

Ten new microsatellite loci for analysis of genetic diversity in isolated populations of the Alpine land snail <Emphasis Type="Italic">Cylindrus obtusus</Emphasis>

In this study we characterized 10 polymorphic microsatellite markers for the land snail Cylindrus obtusus, an endemism of the Austrian Alps with a distribution in isolated populations above approximately 1,600 m. The microsatellite loci were analyzed in 44 individuals from two populations. Number of alleles per locus ranged between two and eight. Observed heterozygosity ranged between 0.00 and 1.00, and expected heterozygosity between 0.09 and 0.72. No significant linkage disequilibrium was found between pairs of loci. One of the sampled populations (Dachstein) showed no deviation from Hardy–Weinberg equilibrium and no presence of null alleles, whereas the other one (Schneeberg) did. These diverging results probably reflect differences in population structure rather than characteristics of the microsatellite loci and underline the usefulness of these markers for studying genetic diversity, population structure and differentiation in C. obtusus.     

Polymorphic dinucleotide microsatellite loci in the clonal ascidian Diplosoma listerianum: predominance of compound and highly interrupted imperfect repeats

We report the isolation of the first dinucleotide microsatellite loci from the clonal ascidian, Diplosoma listerianum. Most repeats were compound and highly interrupted, with flanking sequences containing many small interspersed repetitive regions. Consequently, most primers detected polymerase chain reaction products outside the expected size range, and only five out of 15 primers detected polymorphic single‐locus markers. Characterization of five variable loci from two UK populations revealed three to seven alleles per locus, with observed heterozygosity of 0.00–0.86 and expected heterozygosity of 0.10–0.66. Three loci showed significant heterozygote deficits either because of inbreeding, population substructure or the presence of null alleles.     

Isolation and characterization of 11 polymorphic trinucleotide microsatellite markers in the stonefly Arcynopteryx compacta (Plecoptera: Perlodidae)

We describe the isolation of 11 polymorphic trinucleotide microsatellite loci from the stonefly Arcynopteryx compacta. Loci were highly variable with 3 to 14 alleles (mean = 6.45). Observed heterozygosity ranged from 0 to 0.867. Seven loci showed significant deviation from Hardy–Weinberg equilibrium across both populations. There was no evidence for null alleles, and thus, Hardy–Weinberg departures could have resulted from genetic structure between populations or subpopulations. No linkage between loci was found. The 11 loci should prove highly informative for population genetic studies.     

Development and characterization of microsatellite markers to study population genetic diversity of Przewalski's naked carp Gymnocypris przewalskii in China

Two populations of Przewalski's naked carp Gymnocypris przewalskii, 30 individuals per population, were screened for 10 microsatellite loci. Moderate allele variation was found in these loci with two to eight alleles per locus. The expected and observed heterozygosity ranged from 0·019 to 0·805 and from 0·160 to 0·575, respectively.     

Isolation and characterization of eight microsatellite loci in the brook lamprey Lampetra planeri (Petromyzontiformes) using 454 sequence data

Eight polymorphic microsatellite loci were developed for the brook lamprey Lampetra planeri through 454 sequencing and their usefulness was tested in 45 individuals of both L. planeri and the river lamprey Lampetra fluviatilis. The number of alleles per loci ranged between two and five; the Italian and Irish populations had a mean expected heterozygosity of 0·388 and 0·424 and a mean observed heterozygosity of 0·418 and 0·411, respectively.     

Genetic divergence in Greek populations of the genus Leuciscus and its evolutionary and biogeographical implications

In 23 populations of Greek Leuciscus ( Squalius ), the percentage of polymorphic allozyme loci ranged between 0·034 and 0·379 (P=0·19) and expected heterozygosity was 0·011–0·166 (H_e=0·067). Current taxonomy is confusing and does not correspond to genetic data that support the presence in Greece of at least seven different species: L. cephalus , L. peloponnensis , L. prespensis , L. moreoticus , L. borysthenicus , L. keadicus and Leuciscus sp. from Euboea Island. The maximum Nei modified genetic distance was found among L. keadicus and the rest of subgenus Squalius populations D * Nei=0·446–0·705). Accepting the molecular clock hypothesis, speciation for the genus Leuciscus in Greece must have occurred during the Cenozoic period (between the Middle Miocene and the Later Pliocene). The two main biogeographical events causing speciation on mainland Greece were the Uplift of the Pindic cordillera and the isolation of the southern part of Peloponnesus. The faunistic composition of the lakes studied, in which new taxa are reconsidered, suggests the same faunistic origin in the Early Pliocene for Lakes Prespa and Stymphalia and a younger one in the Late Pliocene for Lake Trichonis. Euboea Island was not a zoogeographical unit during the Cenozoic. The isolation of all the freshwater fish fauna of Euboea has occurred since the Pliocene. The biogeographical model proposed here differs from classical hypotheses in considering of lesser importance the dispersion of L. cephalus on the Greek mainland during the Neogene and Quaternary.     

Characterization of eight polymorphic microsatellite loci from the Bengalese finch (Lonchura striata var. domestica)

Eight polymorphic microsatellite loci were isolated and characterized from the Bengalese finch (Lonchura striata var. domestica). In analyses of 25 individuals, the number of alleles ranged from two to four, and observed heterozygosity ranged between 0.05 and 0.73. At four loci, the observed heterozygosity of the Bengalese finches was significantly different from the expected heterozygosity. Primer sets were also tested in Javan munia (Lonchura leucogastroides), and the same eight loci were successfully amplified. In analyses of 20 unrelated individuals, the number of alleles ranged from one to seven, and the observed heterozygosity ranged from 0 to 0.56. In Javan munia, the observed heterozygosity differed significantly from the expected heterozygosity in only one locus.     

用微卫星标记分析皱纹盘鲍群体的遗传变异

利用微卫星标记技术, 对皱纹盘鲍山东长岛和辽宁獐子岛的两个野生群体以及山东崆峒岛一个养殖群体的遗传变异进行了分析。对6个微卫星基因座的多态性进行了评估, 各基因座的多态信息含量(PIC)值均大于0.5, 适合对鲍群体遗传结构的分析。结果表明, 这6个基因座在3个皱纹盘鲍群体中共获得57个等位基因, 等位基因数(A)平均为9.50, 有效等位基因数(N_e)平均为5.8572, 平均杂合度观测值(H_o)和期望值(^H_e)分别为0.6925和0.7966; 两个野生群体的杂合度观测值(H_o)和期望值(H_e)均高于养殖群体。上述结果为保护和利用皱纹盘鲍的遗传多样性提供了依据。     

Microsatellite variation in marine, freshwater and anadromous fishes compared with other animals

From a total of 524 microsatellite loci considered in nearly 40 000 individuals of 78 species, freshwater fish displayed levels of population genetic variation (mean heterozygosity, h=0·46, and mean numbers of alleles per locus, a=7·5) roughly similar to those of non-piscine animals (h=0·58 and a=7·1). In contrast, local population samples of marine fish displayed on average significantly higher heterozygosities (h=0·79) and nearly three times the number of alleles per locus (a=20·6). Anadromous fish were intermediate to marine and freshwater fish (h=0·68 and a=11·3). Results parallel earlier comparative summaries of allozyme variation in marine, anadromous, and freshwater fishes and probably are attributable in part to differences in evolutionarily effective population sizes typifying species inhabiting these realms.     

薇菜SSR分子标记的开发及遗传多样性初步探讨

利用改良FIASCO法(Fast Isolation by AFLP Sequences COntaining repeats)开发出的9对多态性SSR引物评价了薇菜(Osmunda japonica Thunb.)2个野生居群(庐山和恩施)、1个栽培居群(恩施)的遗传多样性和遗传分化水平。结果显示,9个SSR标记在3个薇菜居群中共检测到47个等位基因,每个SSR位点的平均等位基因数为5.222个,观测杂合度和期望杂合度分别为0.000~0.944和0.577~0.834,香农指数为0.962~1.860,表明各SSR位点多态性较高;各居群的平均期望杂合度均大于平均观测杂合度且种内近交系数均为正值,说明3个薇菜居群中都存在非随机交配现象;对各居群的相关遗传多样性参数分析表明,恩施野生居群遗传多样性最高,而其栽培居群最低;庐山野生居群与恩施野生居群间遗传分化系数为0.092,说明两地野生薇菜居群的遗传分化程度较低,AMOVA分析也表明遗传变异主要存在于野生居群内部。     

Novel microsatellite loci in the grass snake (Natrix natrix) and cross-amplification in the dice snake (Natrix tessellata)

Six novel polymorphic microsatellite loci are presented for the grass snake (Natrix natrix), a species with declining populations in many regions. The number of alleles per locus ranged from two to seven. Four dice snake (Natrix tessellata) microsatellites were polymorphic in the grass snake with three to four alleles. At two loci, the expected heterozygosity differed significantly from observed heterozygosity. Cross-amplification of the grass snake markers in the dice snake showed two polymorphic microsatellites with two and four alleles.     

Factors affecting the distribution of genetic variability in the guppy, Poecilia reticulata

Previous studies on Trinidadian guppies have shown an apparent association of genetic variability, expressed as mean heterozygosity (Ho) at allozyme loci, with river order: fish from lowland sites exhibit higher mean Ho than their upland counterparts. Detailed genetic and behavioural observations were undertaken in the present study by repeated sampling throughout two river courses to examine population heterogeneity. Results show that the predation regime mediated mating behaviour of upland and lowland populations in the wild is not as divergent as previous laboratory observations have suggested. Furthermore, genetic variation at the eight loci variable in Trinidadian populations (p₁₀₀=0·13–O·88, H₀=O·03–0·23) appears to bear little association with predation regime, but is related to sub-structuring of populations by habitat features and geographic isolation. We therefore conclude that the observed patterns of genetic variability arise primarily as a consequence of stochastic as opposed to deterministic factors.     

Isolation and characterization of microsatellite loci from the endangered highlands scrub hypericum (Hypericum cumulicola)

We report the isolation of 19 primer pairs for amplification of polymorphic microsatellite loci for Hypericum cumulicola. These markers were evaluated in 24 individuals from one population; two to four alleles were detected per locus, and observed heterozygosity ranged from 0 to 0.5. Two loci demonstrated significant heterozygote deficiencies, possibly due to null alleles, and significant linkage disequilibrium was found between six pairs of loci. The remaining microsatellite loci will help determine if genetic differentiation is responsible for life‐history differences between natural and anthropogenically disturbed populations of H. cumulicola.     

A medium density microsatellite map of BTA10: reassignment of INRA69

We have developed a genetic map of BTA10 based on 8952 informative meioses for 13 microsatellite markers and the erythrocyte antigen Z. With the exception of OarAE64 , the support for the order of all loci in the map exceeded a LOD > 3·0. The length of the BTA10 genetic map was 87·0 centimorgans (cM). The 14-marker, sex-average map in Kosambi cM was: CSSM38 –8·9- BM1237 –5·2- HH8A –2·6- INRA69 –10·6- TGLA378 –0·8- BM6305 –17·2- TGLA102 –17·9- INRA96 –0·3- CSRM60 –9·2- DIK20 –3·0- EAZ –6·7- CSSM46 –3·7- SRCRSP3 –1·0- OarAE64 with an average interval of 6·70 cM. The microsatellite INRA69 was recently assigned to the pseudoautosomal region of the bovine X chromosome by linkage analysis. However, we found that twopoint support for linkage between INRA69 and 15 X-linked bovine microsatellites was LOD < 0·50 in 529 reciprocal backcross and F₂ fullsib progeny. We performed twopoint analyses of INRA69 against 275 markers distributed throughout the bovine genome and found significant associations with a LOD > 3·0 only between INRA69 and eight BTA10 microsatellite loci. Consequently, we excluded INRA69 from the genetic map of the X chromosome and reassign this microsatellite to BTA10.