Autosomal STRs Provide Genetic Evidence for the Hypothesis That Tai People Originate from Southern China

Tai people are widely distributed in Thailand, Laos and southwestern China and are a large population of Southeast Asia. Although most anthropologists and historians agree that modern Tai people are from southwestern China and northern Thailand, the place from which they historically migrated remains controversial. Three popular hypotheses have been proposed: northern origin hypothesis, southern origin hypothesis or an indigenous origin. We compared the genetic relationships between the Tai in China and their “siblings” to test different hypotheses by analyzing 10 autosomal microsatellites. The genetic data of 916 samples from 19 populations were analyzed in this survey. The autosomal STR data from 15 of the 19 populations came from our previous study (Lin et al., 2010). 194 samples from four additional populations were genotyped in this study: Han (Yunnan), Dai (Dehong), Dai (Yuxi) and Mongolian. The results of genetic distance comparisons, genetic structure analyses and admixture analyses all indicate that populations from northern origin hypothesis have large genetic distances and are clearly differentiated from the Tai. The simulation-based ABC analysis also indicates this. The posterior probability of the northern origin hypothesis is just 0.04 [95%CI: (0.01–0.06)]. Conversely, genetic relationships were very close between the Tai and populations from southern origin or an indigenous origin hypothesis. Simulation-based ABC analyses were also used to distinguish the southern origin hypothesis from the indigenous origin hypothesis. The results indicate that the posterior probability of the southern origin hypothesis [0.640, 95%CI: (0.524–0.757)] is greater than that of the indigenous origin hypothesis [0.324, 95%CI: (0.211–0.438)]. Therefore, we propose that the genetic evidence does not support the hypothesis of northern origin. Our genetic data indicate that the southern origin hypothesis has higher probability than the other two hypotheses statistically, suggesting that the Tai people most likely originated from southern China.     

The genetic divergence of three populations

This paper considers the effect of the genetic divergence on the genetic composition of three samples drawn from three populations at some time after the populations had split. It generalizes the two-sample case studied earlier by Watterson (1985a). Under the assumptions that (i) mating is at random, (ii) the genes at a locus can be any of infinitely many alleles and all mutants are assumed to be new alleles, and (iii) no selective differences exist, we find the probability distribution of the sample gene configurations. From this distribution the single-sample allelic distribution after one-step and two-step bottlenecks and the allelic distribution in the two-sample case can be obtained as marginal distributions. Some numerical results on the number of alleles in common in the three samples are compared with those obtained by Watterson's simulation method; the agreement is excellent. Also, the probability that the three samples are monomorphic for the same allele is found, and numerical examples are given.     

Spatio-temporal population genetics of the Danish pine marten (Martes martes)

A spatio-temporal study of genetic variation in the Danish pine marten ( Martes martes ) populations from the Jutland peninsula and from the island of Sealand was performed using 11 microsatellite markers. Samples obtained from 1892 to 2003 were subdivided into historical (prior to 1970) and recent (from 1970) groups. As compared with the historical samples, there was a significant loss of genetic variation in the recent Jutland population, but not in Sealand. Effective population sizes were estimated using Bayesian-based software (TMVP). Historical effective population sizes were 5897 (90% highest probability density, HPD, limits: 1502–6849) in Jutland and 1300 (90% HPD limits: 224–5929) in Sealand, whereas recent effective population sizes were 14.7 (90% HPD limits: 10.9–23.5) in Jutland and 802 (90% HPD limits: 51.8–5510) in Sealand. Significant genetic differentiation ( F _ST) was found between the two historical samples, between the two recent samples, and between the historical and the recent sample in Jutland; whereas the F _ST value between the historical and the recent sample in Sealand was not significant. The significant genetic differentiation between the historical and the recent samples indicates changes in the genetic compositions over time, and the higher F _ST values between the two recent samples, as compared with the two historical samples, indicates that the populations in Sealand and Jutland have drifted apart within a short time span. No deviation from Hardy–Weinberg equilibrium was found within populations, indicating no further substructuring.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 93 , 457–464.     

Genetic differentiation among European whitefish ecotypes based on microsatellite data

The amount of genetic differentiation at DNA microsatellite loci in European whitefish (Coregonus lavaretus) was assessed among ecotypes, populations and run-timing types. The magnitude of genetic changes potentially caused by hatchery broodstock rearing were also compared with those observed in corresponding natural populations. A total of 35 populations were studied, including 33 Coregonus lavaretus populations and two samples of Coregonus peled. Five of the six whitefish ecotypes in Finland were represented within C. lavaretus populations. Genetic diversity among C. lavaretus populations proved to be high compared to two C. peled populations. The genetic D(A) distance between these two species was as high as 0.86. The genetic differentiation among ecotypes was generally low and thus gives support for the hypothesis of one native European whitefish species in Scandinavia. Among the ecotypes the northern, large sparsely-rakered, bottom-dwelling whitefish was most unique. Thus, observed genetic differences in quantitative traits have either developed independently of phylogenetic lineages, or have mixed and later changed according to environments and selection pressures. Overall genetic distances between the anadromous whitefish populations along the Finnish coast, especially in the Bothnian Bay area, were small. Populations of this area have been heavily influenced by human activities, and they also have the highest probability of mixing by natural means. In two cases, the Rivers Iijoki and Tornionjoki, statistically significant genetic differences could be observed between summer- and autumn-run spawning-time types. Wild populations had slightly higher allelic diversity than hatchery-reared populations of corresponding rivers. Although some reduction in genetic diversity during hatchery rearing is possible, it is an important aid in maintaining endangered populations.     

Definition of the USDA103 strain of channel catfish (Ictalurus punctatus)

Although there are differences in performance between genetic groups of channel catfish, identification and management of these groups is difficult because catfish strains look alike and individuals cannot be tagged efficiently. Thus, US catfish producers have not been able to objectively identify fish from different strains or populations, and it has been difficult for them to maintain the genetic purity of populations on the farm. We have developed a multiplexed microsatellite genotyping system to define catfish populations based on allelic frequency and exclusion. A commercial catfish genotype database was developed using catfish samples collected from 24 processing plants in the four main US catfish-producing states. The utility of the system was tested by the molecular characterization of the USDA103 research strain. Using eight microsatellite loci, the probability of falsely classifying an individual non-USDA103 catfish as a USDA103 was 0.0065. From a sample of 50 fish from a putative USDA103 pond, the probability of falsely including two non-USDA103 fish was 1 x 10(-105), and the conservative probability of falsely excluding two USDA103 fish was 1 x 10(-6). This genotyping system provides channel catfish producers with an objective mechanism for identification and management of genetically selected fish.     

Genetic structure of the clonal herb Tanakaea radicans (Saxifragaceae) at multiple spatial scales,revealed by nuclear and mitochondrial microsatellite markers

The genus Tanakaea is a plant genus that consists of one or two evergreen herbaceous species in Japan and China. As rithophytic plant species occur on shaded rocks, the populations are usually isolated and sporadically found in disjunct areas. To evaluate the genetic structure of the species at multiple spatial scales, 10 nuclear and mitochondrial microsatellite markers were developed. The novel markers showed high genetic variations (two to 15 alleles and H_e from 0.400 to 0.894). Clonal samples were identified with the probability of identity of 9.0E‐8. When evaluated with 11 populations in Japan, significant genetic differentiation between regional population groups was detected (F_ST = 0.313 between Shikoku and Honshu islands), suggesting they have long been isolated from each other. Overall, these markers will be useful for population genetic research to investigate clonal structure and genetic diversity and levels of genetic differentiation between the geographically isolated populations.     

Pooling hair samples to increase DNA yield for PCR

Hairs are useful non-invasive sources of DNA, but the DNA yield can be very small, thus promoting genotyping errors. Using multiple hairs can counter this problem, but may introduce multiple contributors to a sample if collected remotely. With microsatellite genotyping, samples representing multiple animals are obvious if three or more alleles are detected at any locus: these samples can then be removed from any analyses. However, some multiple-individual samples may have only one or two alleles at each of the loci examined. We investigated the probability of failing to identify mixed pooled samples by simulating pooled samples (10 000 replicates) from microsatellite data from the northern and southern hairy-nosed wombats (NHNW, Lasiorhinus krefftii; SHNW, L. latifrons), species with low and high genetic diversity respectively. The majority (81.7%) of the 40 000 simulated samples had three or four alleles, so were readily identified as mixed. In the remaining 1-or-2-allele SHNW samples, forensic science software (DNAMIX) correctly identified mixed versus single-individual samples for all cases when the probability of locus failure was low (P _(LF) = 0.1), and 99% of samples when locus failure was high (P _(LF) = 0.5). For NHNW however, the probability of failing to identify a mixed sample was too high for population size estimation (0.05), even when the probability of locus failure was low. In cases such as this, pooled samples may be adequate for less demanding tasks, such as estimation of allele proportions. However, for animal populations with at least average levels of genetic variation, pooling of samples could safely be utilised for most applications. This revised version was published online in July 2006 with corrections to the Cover Date.     

Heterologous amplification and characterization of microsatellite markers in the Neotropical fish Leporinus friderici

Leporinus friderici, native to the Amazon Basin and popularly known as "piau-três-pintas", has great ecological and economic importance; it is widely fished and consumed throughout much of tropical South America. Knowledge of the genetic diversity of this native species is important to support management and conservation programs. We evaluated microsatellite loci amplification, using heterologous primers, in 31 individuals of L. friderici. These samples were collected from natural populations of the Araguaia River basin, in central Brazil, and the DNA was extracted from samples of muscle tissue. Eight loci were successfully analyzed. Six of them were polymorphic, and the number of alleles ranged from three to 10. Values of expected heterozygosities for these polymorphic loci ranged from 0.488 to 0.795. Exclusion probability (0.983), the identity probability (0.000073), and the mean genetic diversity values were high, showing that these microsatellite markers are suitable for assessing the genetic variability of L. friderici populations. There is a growing interest in studies that evaluate the genetic variability of natural populations for various purposes, such as conservation. Here, we showed that a viable alternative to the costly development of specific primers for fish populations is simply testing for heterologous amplification of microsatellite markers available from research on other species.     

Population genetics of Biomphalaria straminea in Hong Kong. A neotropical schistosome-transmitting snail recently introduced into China

Since its introduction in the early 1970s Biomphalaria straminea (Gastropoda: Planorbidae) has spread rapidly and is locally the most abundant fresh water snail in Hong Kong. Studies of 19 electrophoretically detected loci in four populations show that the colonists retain high levels of variability (P = 0.26, H = 0.056 - 0.097), comparable with those found in autochthonous samples of related species. Genotype frequencies at the five polymorphic loci, and a comparison of maternal and progeny genotypes of individual field-collected snails, revealed no evidence for self-fertilization in these functional hermaphrodites. F statistics indicated minimal genetic structuring, presumably because of outcrossing and recency of origin of the populations. Geographic distribution of various alleles and their frequencies suggest that two southern populations were derived from the original colonists by dispersal but that a northern population represents a second introduction in about 1982. This interpretation (based on genetics) is consistent with the known history of the various populations. The Asian populations of this South American snail are interpreted as being in the "flush" phase of the colonization process. Finally, the probability of the secondary spread of this snail from Hong Kong, and the probability of its parasite, the human blood fluke Schistosoma mansoni, being introduced to Asia are discussed.     

Genetic identification of two sibling species of Lutzomyia longipalpis (Diptera: Psychodidae) that produce distinct male sex pheromones in Sobral,Ceará State,Brazil

Lutzomyia longipalpis, the main sandfly vector for New World visceral leishmaniasis is a complex of an as yet undefined number of sibling species. At present, there is no consensus on the status (single species vs. species complex) of Brazilian populations. We applied five microsatellite loci to test the hypothesis that L. longipalpis occurs as two sympatric cryptic species in Sobral, Ceará State, Brazil as predicted by male sex pheromone chemotypes described previously for field specimens from this site [S-9-methyl-germacrene-B (9MGB) and a cembrene compound]. Abdominal spot morphology corresponds with pheromone type at this locality (9MGB in '1 spot' males and cembrene in '2 spot' males). Genotype data from 190 wild-caught L. longipalpis specimens collected in October 1999 and April 2001 were used to estimate genetic differentiation between the two sex pheromone populations and sampling dates. No significant (P > 0.05) genetic differences were found between the 1999 and 2001 9MGB samples (theta = 0.018; RST = -0.005), and genetic differentiation was low between the cembrene collections (theta = 0.037, P < 0.05; RST = -0.043, P > 0.05). By contrast, highly divergent allelic frequencies (largely at two microsatellite loci) corresponded to significant (P > 0.05) genetic differentiation (theta = 0.221; RST = 0.215) for all comparisons between samples with different pheromones. When pheromone samples were pooled across sample date, genetic differentiation was high (theta = 0.229; P < 0.001; Nem = 0.84). The allele frequency distribution at each of the five microsatellite loci was similar for males and females from the two collection years. Two of these loci showed highly divergent allele frequencies in the two sex pheromone populations. This was reflected in the highly significant genetic differentiation obtained from the male genotypes, between populations producing different pheromones (theta = 0.229-0.268; P < 0.0001 for the 2001 and theta = 0.254-0.558; P < 0.0001 for the 1999 collections, respectively). Similar results were obtained when the females, assigned to a pheromone type, were included in the analysis. Both a Bayesian analysis of the data set and a population assignment test provided strong evidence for two distinct populations corresponding to pheromone type. Given its genotype, the probability of assigning a 9MGB male to the original 9MGB population was 100% once the two years' collections were pooled. For cembrene-producing '2 spot' males this probability although still high, was lower than for 9MGB males, at 86%. This microsatellite data together with previously reported reproductive isolation between the two Sobral populations confirm that premating barriers are important in speciation of L. longipalpis.     

Two complementary perspectives on inter-individual genetic distance

This paper examines population structure through the prism of pairwise genetic distances. Two complementary perspectives, framed as two simple questions, are explored: Q1: What is the probability that a random pair of individuals from the same local population is more genetically dissimilar than a random pair from two distinct populations? Q2: On average, how genetically different are two individuals from the same local population, in comparison with two individuals chosen from any two distinct populations? Models are developed to provide quantitative answers for the two questions, given allele frequencies across any number of markers from two diploid populations. The probability from Q1 is shown to drop to zero with increasing number of genetic markers even for very closely-related populations and rare alleles. The average genetic dissimilarity of two individuals from distinct populations diverges from the average dissimilarity of two individuals from the same population by a percentage dependent on estimates of population differentiation. This perspective also suggests a measure of population distance based on the intuitive notion of pairwise genetic distance, along with a simple method of estimation. Results from recent empirical research on inter-individual genetic distance in human populations are analyzed in the context of the theoretical framework.     

Genetic variation within and relatedness among wood and plains bison populations.

There are two recognized subspecies of bison, wood (Bison bison athabascae) and plains (Bison bison bison) bison. The establishment of most bison populations from a small number of individuals has raised concerns about their genetic variation. To this end, 11 bison populations were surveyed with 11 microsatellite loci in order to calculate genetic variation and genetic distances. Mean number of alleles ranged between 3.18 at Antelope Island State Park (Utah) and 6.55 at Wood Buffalo National Park (Alberta and Northwest Territories). Mean heterozygosity ranged from 0.295 at Antelope Island State Park to 0.669 at Custer State Park (South Dakota). The amount of genetic variability present in the bison populations as measured by mean number of alleles and overall probability of identity was found to correlate with the number of founders for all sampled populations. The G-test for heterogeneity revealed some evidence for the existence of subpopulations at Wood Buffalo National Park, however very small genetic distances between these subpopulations suggest that nuclear material from the plains bison introduced into Wood Buffalo National Park has diffused throughout the park. Genetic distances between the sampled populations were generally larger between than within the two bison subspecies.     

Effective population size and temporal genetic change in stream resident brown trout (Salmo trutta, L.)

Temporal genetic data may be used forestimating effective population size (N _e) and for addressing the `temporal stability' of population structure, two issues of central importance for conservation and management. In this paper we assess the amount of spatio-temporal genetic variation at 17 di-allelic allozyme loci and estimate current N _e in two populations of stream resident brown trout (Salmo trutta) using data collected over 20 years. The amount ofpopulation divergence was found to bereasonably stable over the studied time period.There was significant temporal heterogeneitywithin both populations, however, and N _e was estimated as 19 and 48 for the twopopulations. Empirical estimates of theprobability of detecting statisticallysignificant allele frequency differencesbetween samples from the same populationseparated by different numbers of years wereobtained. This probability was found to befairly small when comparing samples collectedonly a few years apart, even for theseparticular populations that exhibit quiterestricted effective sizes. We discuss someimplications of the present results for browntrout population genetics and conservation, andfor the analysis of temporal genetic change inpopulations with overlapping generations ingeneral.     

Genetic variation in prehistoric Sardinia

We sampled teeth from 53 ancient Sardinian (Nuragic) individuals who lived in the Late Bronze Age and Iron Age, between 3,430 and 2,700 years ago. After eliminating the samples that, in preliminary biochemical tests, did not show a high probability to yield reproducible results, we obtained 23 sequences of the mitochondrial DNA control region, which were associated to haplogroups by comparison with a dataset of modern sequences. The Nuragic samples show a remarkably low genetic diversity, comparable to that observed in ancient Iberians, but much lower than among the Etruscans. Most of these sequences have exact matches in two modern Sardinian populations, supporting a clear genealogical continuity from the Late Bronze Age up to current times. The Nuragic populations appear to be part of a large and geographically unstructured cluster of modern European populations, thus making it difficult to infer their evolutionary relationships. However, the low levels of genetic diversity, both within and among ancient samples, as opposed to the sharp differences among modern Sardinian samples, support the hypothesis of the expansion of a small group of maternally related individuals, and of comparatively recent differentiation of the Sardinian gene pools. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

利用分子标记分析遗传多样性时的玉米群体取样策略研究

利用分子标记技术对玉米种质资源进行遗传多样性分析对种质资源的保存和利用具有重要的指导意义。但是,在对地方品种和育种群体这些开放授粉群体进行大规模遗传多样性分析时,取样方法将会严重影响到研究结果和工作效率。本研究用2个育种群体和3个地方品种为试材,利用微卫星(SSR)标记对每个群体100个个体及其组成的不同随机混合样品进行了分子检测。结果表明,不同群体的群体内遗传变异大小存在差异;相同数目的个体随机混合的不同样品间的检测结果基本相同;不同数目的个体混合的样品间存在一定程度的差异,并且与材料本身的遗传变异大小有一定关系。考虑到结果的科学性和工作的可行性,建议在利用分子标记(如SSR)进行地方品种和育种群体的遗传多样性评估时,随机选取30个个体组成混合样(或用15个个体组成2个混合样)来代表1个地方品种或育种群体进行分子鉴定。     

江苏常熟地区汉族人群47个微单倍型的遗传多态性及遗传结构分析

目的 探索江苏常熟地区汉族人群在47个常染色体微单倍型基因座的遗传多态性,评估应用效能及法庭科学参数。方法 采用MHSeqTyper47混合DNA鉴定试剂盒进行基因座复合扩增及文库构建,使用MiSeq FGx测序平台进行测序,测得的数据应用MHTyper数据分析软件进行分析,对获得的样本遗传信息进行评估,结合千人基因组数据（1000 Genomes Project phase 3,1KG）评估群体间遗传分化指数及遗传距离,并计算法庭科学参数。结果 江苏常熟地区汉族人群与1KG中的中国北京群体的遗传分化和遗传距离最小,并得到最接近的有效等位基因数（A_e）,累积随机匹配概率（combined matching probability,CMP）与1KG中东亚参考人群的5个群体均接近,为1.25×10^-36,累积非父排除概率达0.999 999 999 964 1。结论 本研究报告了47个微单倍型基因座在江苏常熟地区汉族人群中的等位基因频率及遗传多态性信息,为47个微单倍型在法医学应用中提供了数据基础。另外,比较了1KG参考人群与江苏常熟地区汉族人群的多态性差异,并揭示了47个微单倍型在江苏常熟地区汉族人群中的遗传结构。总的来说,1KG中的东亚人群参考数据更符合江苏常熟地区汉族人群的遗传特征。     

镜湖萼花臂尾轮虫（Brachionus calyciflorus）种群遗传多样性的季节变化

运用随机扩增多态DNA（RAPD）技术研究了于2005年春季和夏季采自芜湖市镜湖的萼花臂尾轮虫（Brachionus calyciflorus）种群基因组DNA多态性。从44个随机引物中筛选出10个谱带清晰、重复性好的引物。10个引物共检测到76个位点,其中65个位点显多态性,多态位点比例（P）为85.5%。对RAPD扩增结果进行聚类分析,基于遗传距离指数构建了萼花臂尾轮虫的UPGMA和ME系统树。经计算,各克隆平均遗传距离指数为0.5219,春季种群内遗传距离指数（0.4416）大于夏季种群内遗传距离指数（0.4304）;两季节种群间遗传距离指数为0.6010,明显大于季节种群内遗传距离指数。16个克隆分别聚在2个主要簇群中,在UPGMA系统树中,春季种群和夏季种群明显分聚在两个主要支系中;而在ME树中,除了夏季Su2克隆和春季种群聚到一个支系外,其它夏季种群则聚在一个独立支系中。上述结果表明,春季种群和夏季种群在遗传上具有较大的差异;镜湖萼花臂尾轮虫种群存在着明显的季节更替,而Su2克隆可能是春季和夏季种群间的过渡。     

Allozyme Variation and Genetic Relationships among Species of Cimicifuga (Ranunculaceae) from Korea

Allozyme investigation of the five Cimicifuga taxa in Korea was conducted to assess genetic and clonal diversity within populations and genetic divergence among populations and taxa. Levels of allozyme variation maintained in Korean Cimicifuga taxa were comparable to those for most herbaceous perennials. In general, samples excluding copies of the same multilocus genotype maintained higher levels of genetic diversity than the total samples within populations. Copies of homozygous genotypes at several loci resulting from clonal spread lead to decreased levels of genetic diversity within populations, indicating that clonal reproduction found in Cimicifuga affects population genetic structure. In general, more widely distributed species such as C. dahurica and C. japonica harbored higher levels of allozyme diversity than the other taxa examined. Although two varieties of C. heracleifolia are geographically and reproductively isolated, the genetic and clonal structure of var. bifida seems to resemble var. heracleifolia, indicating that the two varieties may have had a similar evolutionary history. However, the allozyme data strongly indicate that the two morphological types (Groups I and II) of C. simplex should be treated as separate species.     

Random amplified polymorphic DNA analysis of Anopheles nuneztovari (Diptera: Culicidae) from Western and northeastern Colombia

Random amplified polymorphic DNA (RAPD) markers were used to analyze 119 DNA samples of three Colombian Anopheles nuneztovari populations to study genetic variation and structure. Genetic diversity, estimated from heterozygosity, averaged 0.34. Genetic flow was greater between the two populations located in Western Colombia (F ST: 0.035; Nm: 6.8) but lower between these two and the northeastern population (F ST: 0.08; Nm: 2.8). According to molecular variance analysis, the genetic distance between populations was significant (phi ST 0.1131, P < 0.001). The variation among individuals within populations (phi ST 0.8869, P < 0.001)was also significant, suggesting a greater degree of population subdivision, not considered in this study. Both the parameters evaluated and the genetic flow suggest that Colombian An. nuneztovari populations are co-specific.