Development of 11 polymorphic microsatellite markers in a macrophyte of conservation concern, Vallisneria americana Michaux (Hydrocharitaceae)

Vallisneria americana Michaux (wild celery) is currently a target of submersed aquatic vegetation restoration efforts in the Chesapeake Bay watershed. To aid these efforts, we have developed 11 polymorphic microsatellite markers to assess the distribution and degree of genetic diversity in both restored and naturally occurring populations in the Chesapeake Bay. In 59 individuals from two populations, we detected two to 10 total alleles per locus. Observed heterozygosity ranged from 0.125 to 0.929, and two loci exhibited significant deviations from Hardy-Weinberg equilibrium in at least one of the populations assayed.     

Isolation and characterization of novel dinucleotide repeat microsatellites in the Jamaican click beetle Pyrophorus plagiophthalamus (Coleoptera: Elateridae)

We report 10 polymorphic microsatellite loci for the Jamaican click beetle, Pyrophorus plagiophthalamus. A survey of 36 individuals from three populations in Jamaica showed that these are highly variable, with three to 17 alleles per locus. Observed heterozygosity ranged from 0.250 to 0.917, and mean heterozygosity from 0.601 to 0.747. Most loci were in Hardy–Weinberg equilibrium, although excess of homozygotes was observed in four tests (out of 20), suggesting the possibility of null alleles. Significant linkage disequilibrium was observed for only one pair. These newly developed markers will be useful in understanding the population structure of click beetles in Jamaica, and in identifying possible selective factors responsible for bioluminescent colour variation.     

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.     

Ribosomal DNA variation within and among individuals ofLisianthius (Gentianaceae) populations

Restriction endonuclease fragment analysis of nuclear ribosomal DNA (rDNA) was completed on 25 individuals each from seven populations of theLisianthius skinneri (Gentianaceae) species complex in Panama. Seven restriction enzymes were used to determine the amount and type of rDNA variation within and among individuals of the populations. No restriction site variation was seen within populations or individuals although site differences were seen among populations. Spacer length variation within and among individuals of populations was mapped to the internal transcribed spacer (ITS) region between the 18S and 5.8S rRNA genes, a region inLisianthius rDNA that previously was shown to exhibit length differences among populations. This is the first reported case of such variation within and among individuals of populations for the ITS region. Presence or absence of ITS spacer length variation is not correlated with levels of isozymic heterozygosity within populations. No detectable length variation within individuals or populations was seen in the larger intergenic spacer (IGS). Although populations varied with respect to IGS length, all individuals of a given population had a single and equivalent IGS length.     

Microsatellite markers isolated from saltgrass (Distichlis spicata)

Twelve polymorphic microsatellite DNA loci were isolated from saltgrass (Distichlis spicata) and optimized for future studies of its breeding system. The loci were screened for variability among 24 individuals from two populations. The primers amplified loci with numbers of alleles ranging from four to 14 per locus and polymorphic information content from 0.481 to 0.951. Observed heterozygosity varied from 0.227 to 0.958.     

Microsatellite markers isolated from barn swallows (Hirundo rustica)

Fifteen polymorphic microsatellite DNA loci were isolated from barn swallow (Hirundo rustica) and optimized for future studies of radiation‐induced mutations in populations from Ukraine. The loci were screened for variability among 25 individuals from two populations. The primers amplified loci with relatively high numbers of alleles ranging from five to 32 alleles per locus and polymorphic information content from 0.481 to 0.951. Observed heterozygosity varied from 0.458 to 0.960. None of the loci showed deviations from Hardy–Weinberg equilibrium in either population.     

Development of nine polymorphic microsatellite markers for the phytoparasitic nematode Xiphinema index, the vector of the grapevine fanleaf virus

We report isolation, characterization and cross-species amplification of nine microsatellite loci from the phytoparasitic nematode Xiphinema index, the vector of grapevine fanleaf virus. Levels of polymorphism were evaluated in 62 individuals from two X. index populations. The number of alleles varies between two and 10 depending on locus and population. Observed heterozygosity on loci across both populations varied from 0.32 to 0.857 (mean 0.545). The primers were tested for cross-species amplification in three other species of phytoparasitic nematodes of the Xiphinema genus. These nine microsatellite loci constitute valuable markers for population genetics and phylogeographical studies of X. index.     

Allozyme variation in populations, full-sib families and selfed lines in Betula pendula Roth

Changes in genetic variability in populations (stand origins), full-sib (FS) families and three generations of selfed lines of Betula pendula were observed based on 15 allozyme loci. Growth vigour, measured as stem volume, and its relationship with heterozygosity was studied to determine the effect of inbreeding. Pooled FS families showed a higher percentage of polymorphic loci (P) and allelic numbers per locus (A) than those of natural populations, but no difference in heterozygosity. There was no difference in allozyme variability between fast-and slow-growing family groups, and heterozygosity was not correlated with stem volume among FS families. Allozyme variability was significantly decreased in advancing generations of selfing, and the further the selfing generation, the lower the heterozygosity and the slower the growth. Observed heterozygosity after advancing generations of inbreeding was increasingly higher than expected, indicating overdominance effects or, alternatively, selection against deleterious homozygotes.     

Microsatellite markers for the native Texas perennial grass, Panicum hallii (Poaceae)

? Premise of the study: We developed microsatellites for Panicum hallii for studies of gene flow, population structure, breeding experiments, and genetic mapping. ? Methods and Results: Next-generation (454) genomic sequence data were used to design markers. Eighteen robust markers were discovered, 15 of which were polymorphic across six accessions of P. hallii var. hallii. Fourteen of the markers cross-amplified in a P. capillare accession. For the 15 polymorphic markers, the total number of alleles per locus ranged from two to 26 (mean: 11.0) across six populations (11-19 individuals per population). Observed heterozygosity (mean: 0.031) was 13.7 times lower than the expected heterozygosity (mean: 0.426). ? Conclusions: The deficit of heterozygous individuals is consistent with P. hallii having a high rate of self-fertilization. These markers will be useful for studies in P. hallii and related species.     

Genetic diversity in natural Cupressus sempervirens L. populations in Turkey

Nine polymorphic out of 13 isoenzymes (Gdh-A, Lap-A, Mdh-B, Mdh-C, Ndh-A, 6Pgd-B, Pgi-B, Pgm-A and Pgm-B) were used to assess genetic diversity in seven natural Cupressus sempervirens populations in South-western Anatolia. Except for Pgi-B, all loci were in Hardy–Weinberg equilibrium. A high level of genetic diversity was observed within populations. The mean number of alleles was 2.3±0.08, the effective number of alleles was 1.53±0.10, the percentage of polymorphic loci was 82.6±8.7%, expected heterozygosity was 0.350±0.039, observed heterozygosity was 0.326±0.039, and the fixation index was 0.049. Interpopulation differentiation was moderate, with differentiation indices of G_ST=0.073 and δ=0.104. A UPGMA tree and differentiation (D_j) showed that Kumluca, Kemer and Kas were the most differentiated populations. Pgm-B was one of the loci contributing most to interpopulation differentiation (G_ST=0.119; D_i=0.201), clearly distinguishing Eastern populations, as indicated by a highly significant correlation coefficient between D_j and longitude (R²=0.88^**). No other significant correlation was found between genetic measures and geographical traits for the Turkish cypress populations. A metanalysis of these and other cypress populations from Crete and the Aegean islands, that had been characterised previously using the same isoenzymes, showed no significant relationship between altitude and genetic measures (within-population differentiation or δ_T, observed heterozygosity, fixation index and D_j). Observed heterozygosity and latitude were negatively correlated. Longitude was found to be correlated with heterozygosity, fixation index and differentiation. Genetic and geographic distances were positively correlated over loci. Deviations from selective neutrality by Ewens–Watterson test were observed for Pgm-B, Ndh-A and 6Pgd-B.     

Nineteen novel microsatellites in Chinese lake gudgeon Sarcocheilichthys sinensis Bleeker, 1971

Nineteen polymorphic microsatellites isolated from a partial genomic DNA library of Sarcocheilichthys sinensis enriched for CA repeats were developed. Variability was tested on 48 unrelated individuals collected from Jiangsu province, China. Observed heterozygosity ranged from 0.200 (Ss236) to 1.00 (Ss223, Ss224), whereas the expected heterozygosity ranged from 0.213 (Ss232) to 0.939 (Ss224). Shannon's information index ranged from 0.405 (Ss236) to 2.988 (Ss224). Sixteen of the 19 microsatellites conformed to Hardy–Weinberg equilibrium. These microsatellites can be used for the evaluation of genetic parameters in populations to supply valuable information for conservation management.     

Development of polymorphic microsatellite loci in Nothapodytes nimmoniana, a medicinally important tree from the Western Ghats, India

Nothapodytes nimmoniana is a medicinally important tree species that occur in the Western Ghats, a megadiversity hotspot in southern India. Inner stem bark of the tree contains an important anti-cancer alkaloid, camptothecin for which the natural population of the tree is heavily harvested. In this paper, we report the isolation and characterization of eight polymorphic microsatellite loci using enrichment hybridization protocol. Analysis of 36 individuals representing two populations revealed three to 12 alleles per locus. Observed heterozygosity ranged from 0.21 to 0.94 for the two populations. None of the loci tested showed linkage disequilibrium. These markers are invaluable for evaluating the genetic structure and assessing the genetic impacts of harvesting of N. nimmoniana in the Western Ghats to formulate strategies for conservation of the species.     

HETEROZYGOSITY AND GROWTH IN MARINE BIVALVES: FURTHER DATA AND POSSIBLE EXPLANATIONS

In a natural population of two-year-old mussels, shell length was correlated with degree of heterozygosity. There was no correlation between an individual's glycogen level and its degree of heterozygosity, but when individuals were grouped in heterozygosity classes a near-significant correlation was observed between degree of heterozygosity and mean glycogen level corrected for the effects of sex and stage of gonad development. There was no correlation between degree of heterozygosity and index of gonad development. Such a correlation would have provided support for the hypothesis (Zouros and Foltz, 1984) that dependence of time of spawning on heterozygosity may explain the observed heterozygote-deficiency. The causes of heterozygote-deficiency, a common phenomenon in populations of marine bivalves, remain obscure. The observed heterozygosity-growth correlation is examined in the light of the controversy of whether allozymes act as markers in linkage association with genetic conditions that are responsible for the differences in growth among individuals or are themselves the agents of the correlation. The observations that 1) the contributions of individual loci to the correlation vary among populations, 2) the correlation is observed in samples from natural populations but not among progeny from pair matings, and 3) the correlation is nearly always accompanied with heterozygote-deficiency in the population are more compatible with the first explanation and suggest that the growth-heterozygosity correlation results mostly from associative overdominance and to a lesser extent from the direct contributions of scored loci to growth.     

A mating system conundrum: hybridization in Apocynum (Apocynaceae)

Based upon an intermediate morphology, Apocynum x-floribundum Greene has long been considered a hybrid involving A. androsaemifolium and A. cannabinum. The floral morphology in this genus, however, appears to prohibit both import and export of pollen, and observations of numerous insect visitors reveal that pollen is not routinely carried from flower to flower. Furthermore, reproductive success as measured by fruit set is very low in most populations. Hybridization was thus called into question, with allozyme evidence used to test the hypothesis of a hybrid origin for A. x-floribundum. Six diagnostic loci, as well as two loci exhibiting highly disparate allele frequencies, were resolved for each parent. All examined populations of A. x-floribundum were heterozygous at these loci, thus supporting the hypothesis of hybridization. Evidence from additional loci indicated that all populations tend to be strongly clonal. Observed heterozygosity was very low in the parental species, suggesting a history of inbreeding or a severe bottleneck. There was no support for earlier assumptions that some intermediates are derived from backcrosses or "secondary hybrids." Statistical analyses of plant height, leaf shape, petal length, sepal length, follicle length, seed length, and seed number per follicle supported these conclusions. The persistence and vegetative spread of hybrid clones may contribute to the illusion that hybridization is common.     

微卫星DNA标记分析野生鲤鱼群体的遗传多样性

利用30个微卫星分子标记对海南鲤(HN)、长江鲤(CY)、月亮湖鲤(YL)、黑龙江鲤(FY)、呼伦湖鲤(ZL)、贝尔湖鲤(BR)6个野生鲤鱼群体的观测杂合度(Ho)、期望杂合度(He)、多态信息含量(PIC)和有效等位基因数(Ae)等进行了遗传检测,根据基因频率计算遗传相似系数和Nei氏标准遗传距离,χ2检验估计Hardy-Weinberg平衡,用近交系数(FST)和基因流(Nm)分析群体的遗传分化及其来源。同时,使用PHYLIP3.63软件绘制基于Nei氏标准遗传距离的UPGMA进化树。6个群体共检测到8,136个扩增片段,长度在125bp～414bp,30个基因座扩增出等位基因数从3～13个不等,共计210个等位基因,平均每个基因座扩增得到7个等位基因。结果显示:(1)6个野鲤群体的多态性指标均适中,多态信息含量依次0.44、0.52、0.53、0.57、0.63和0.64,有效等位基因数1.04～4.72个不等,平均有效等位基因数依次为2.19、2.60、2.42、2.43、2.45和2.33,无偏期望杂合度平均值为0.50、0.59、0.56、0.56、0.57和0.54;(2)遗传相似系数BR与ZL最高(0.8511),BR与HN最低(0.6688),聚类结果与地理分布呈一定相关性。     

Isolation and characterization of microsatellite loci from Silene tatarica

Five new microsatellite loci were isolated from the perennial plant, Silene tatarica. We characterized S. tatarica individuals originating from two riverbank populations in northern Finland and observed between four and nine alleles per locus. Observed heterozygosity was consistently lower than gene diversity (H_O: 0.0450–0.2385, H_E: 0.1919–0.6187). This deficiency of heterozygous genotypes was observed in most locus/population combinations, and is presumably caused by spatial genetic structuring due to restricted seed flow within subpopulations. The markers presented here are the first microsatellites reported for S. tatarica.     

Microsatellite loci for studies on population differentiation and connectivity of the red‐bellied yellow tail fusilier,Caesio cuning (Caesionidae)

Ten polymorphic microsatellites were isolated from the red‐bellied yellow tail fusilier Caesio cuning, a reef‐associated fish which occurs widely in the Indo‐Pacific region. The species is exploited by both small‐scale and commercial fisheries. Fifty individuals from six populations were genotyped using primers that reliably amplified 10 polymorphic loci. The number of alleles per locus ranged from three to 11. Observed heterozygosity (H_O) and expected heterozygosity (H_E) ranged between 0.400 to 0.880 and 0.337 to 0.843, respectively. These microsatellite loci may be used to study population structure, genetic diversity and connectivity of C. cuning in the range of its distribution.     

Genetic diversity of north-east Asian cattle based on microsatellite data

In order to assess the genetic variability and population structure of north-east Asian cattle, 13 microsatellite loci were analysed for a total of 200 individuals including Korean, Chinese, Japanese Black and European Holstein cattle. Observed and expected heterozygosity, two estimators (F(ST) and G(ST)) of gene differentiation, and Nei's DA distance were evaluated. Based on expected mean heterozygosity, the lowest genetic diversity was exhibited in Japanese Black cattle (H(E)=0.471), and the highest in Chinese cattle (H(E)=0.744). Korean cattle revealed a relatively high degree of genetic diversity (H(E)=0.728). Average proportion of genetic variation because of interpopulation subdivision among north-east Asian cattle varied between 10.9 and 9.9%, depending on the estimator used. N-J tree based on Nei's DA genetic distance showed that Korean and Chinese cattle are closely related, whereas Japanese Black cattle are clearly distinct from the other two populations, forming a north-east Asian outgroup.     

Characterization of polymorphic microsatellite DNA markers in Hakea oldfieldii Benth. (Proteaceae)

A genomic library was constructed and 13 polymorphic microsatellite markers were developed for Hakea oldfieldii, a woody shrub endemic to southwest Western Australia. Polymorphism was investigated for these markers in 28 individuals from a single population located in restricted habitat at the base of the Whicher Range south of Busselton. Expected heterozygosity ranged from 0.279 to 0.770 and averaged 0.633. Observed heterozygosity ranged from 0.321 to 0.786 and averaged 0.598. The number of alleles per locus ranged from 2.0 to 6.0 and averaged 4.5. These markers will be used to assay genetic diversity and pollen dispersal in this species.     

Heterozygosity in an Isolated Population of a Large Mammal Founded by Four Individuals Is Predicted by an Individual-Based Genetic Model

Background

Within-population genetic diversity is expected to be dramatically reduced if a population is founded by a low number of individuals. Three females and one male white-tailed deer Odocoileus virginianus, a North American species, were successfully introduced in Finland in 1934 and the population has since been growing rapidly, but remained in complete isolation from other populations.

Methodology/Principal Findings

Based on 14 microsatellite loci, the expected heterozygosity H was 0.692 with a mean allelic richness (AR) of 5.36, which was significantly lower than what was found in Oklahoma, U.S.A. (H = 0.742; AR = 9.07), demonstrating that a bottleneck occurred. Observed H was in line with predictions from an individual-based model where the genealogy of the males and females in the population were tracked and the population''s demography was included.

Conclusion

Our findings provide a rare within-population empirical test of the founder effect and suggest that founding a population by a small number of individuals need not have a dramatic impact on heterozygosity in an iteroparous species.