On the genetic uniqueness of the Ami aborigines of Formosa

In the attempt to reconstruct the prehistory of Pacific and Indian Ocean populations, Taiwan's aborigines appear to be of particular interest. Linguistic and archeological evidence indicates that the dispersal of Austronesian speakers throughout the islands of Oceania and Southeast Asia may have originated from Taiwan about 5,000 years ago. The Ami are Taiwan's largest aboriginal group. Here, we report on six polymorphic point mutation loci in Ami individuals and compare allelic frequencies to worldwide populations. In order to examine the genetic characteristics and relationships of the Ami aborigines, we used the allelic frequency data to generate expected heterozygosities, power of discrimination values, maximum likelihood phylogenetic trees, principal component maps, and centroid gene flow plots. These analyses argue for the genetic isolation and uniqueness of the Ami people. Data supportive of limited gene flow and/or small population size, as well as genetic similarities to Native Americans, were observed.     

Ascertaining the role of Taiwan as a source for the Austronesian expansion

Taiwanese aborigines have been deemed the ancestors of Austronesian speakers which are currently distributed throughout two‐thirds of the globe. As such, understanding their genetic distribution and diversity as well as their relationship to mainland Asian groups is important to consolidating the numerous models that have been proposed to explain the dispersal of Austronesian speaking peoples into Oceania. To better understand the role played by the aboriginal Taiwanese in this diaspora, we have analyzed a total of 451 individuals belonging to nine of the tribes currently residing in Taiwan, namely the Ami, Atayal, Bunun, Paiwan, Puyuma, Rukai, Saisiyat, Tsou, and the Yami from Orchid Island off the coast of Taiwan across 15 autosomal short tandem repeat loci. In addition, we have compared the genetic profiles of these tribes to populations from mainland China as well as to collections at key points throughout the Austronesian domain. While our results suggest that Daic populations from Southern China are the likely forefathers of the Taiwanese aborigines, populations within Taiwan show a greater genetic impact on groups at the extremes of the current domain than populations from Indonesia, Mainland, or Southeast Asia lending support to the “Out of Taiwan” hypothesis. We have also observed that specific Taiwanese aboriginal groups (Paiwan, Puyuma, and Saisiyat), and not all tribal populations, have highly influenced genetic distributions of Austronesian populations in the pacific and Madagascar suggesting either an asymmetric migration out of Taiwan or the loss of certain genetic signatures in some of the Taiwanese tribes due to endogamy, isolation, and/or drift. Am J Phys Anthropol 150:551–564, 2013. © 2013 Wiley Periodicals, Inc.     

Genetic variation at 9 autosomal microsatellite loci in Asian and Pacific populations.

Genetic variation at 9 autosomal microsatellite loci (CFS1R, TH01, PLA2A, F13A1, CYP19, LPL, D20S481, D20S473, and D20S604) has been characterized in 16 Asian and Oceanic populations, mostly from mainland and insular Southeast Asia. The neighbor-joining tree and the principal coordinates analysis of the genetic relationships of these populations show a clear separation of Papua New Guinea Highlanders and, to a lesser extent, Malayan aborigines (Orang Asli or Semai) from the rest of the populations. Although the number of markers used in this study appears to be inadequate for clarifying the patterns of genetic relationships among the studied populations, in the principal coordinates analysis a geographic trend is observed in the mainland and insular Southeast Asian populations. Furthermore, in an attempt to contrast the extent of variation between autosomal and Y-chromosome-specific microsatellite loci and to reveal potential differences in the patterns of male and female migrations, we have also compared genetic variation at these 9 autosomal loci with variation observed at 5 Y-chromosome-specific microsatellites in a common set of 14 Asian populations.     

Population genetic structure, local adaptation, and conservation genetics of Kandelia obovata

Topographic changes during the Pleistocene glacial/interglacial cycles affected the distribution of coastline mangroves and influenced their population genetic structure. The submergence of the continental shelf off southeast China during the postglacial age caused coastline expansions and resulted in the colonization of mangroves. Here, we performed multilocus genome scans using amplified fragment-length polymorphisms to explore the effects of topography and natural selection in structuring Kandelia obovata populations. Long-term isolation by the Taiwan Strait since the end of the last glacial maximum, which obstructed gene flow, differentiated the Taiwanese and Chinese populations. Founders that colonized from both outlets of the Taiwan Strait were sourced from the northern South China Sea and the Ryukyus, thereby creating a melting pot in the Taiwan Strait. Inner-strait currents played roles as vectors for propagule dispersal among populations. Upon examination of the allele-frequency distributions of outlier loci, most negative outliers reflected the widespread polymorphisms shared by common ancestors. Furthermore, significant differentiation in the genetic components of positive outliers between this and other populations and the negative correlation with geographic distance suggested the presence of geography- or latitude-independent population divergence. Restored populations were compared with their sources and revealed biased sampling of nursery seedlings, which caused within-population substructures and reduced effective population sizes. This study indicated that multiple factors affect the population structure of the mangroves off southeast China.     

Source populations of Quercus glauca in the last glacial age in Taiwan revealed by nuclear microsatellite markers

In this work, we attempted to study genetic differentiation between populations of Quercus glauca in Taiwan using nuclear microsatellite markers to infer the potential refugium in the last glaciation stage. Four microsatellite loci for 20 individuals each in 10 populations of Taiwan were analyzed. We found that Q. glauca has relatively high within-population diversity (H(E) = 0.741) and low population differentiation (F(ST) = 0.042) but shows isolation by distance. The most divergent populations, according to the average F(ST) for individual populations in comparison with every other population, were found in populations Cy, Sa, and Hy in southern Taiwan and Pa in north-central Taiwan. Moreover, populations Cy, Sa, and Pa were recognized as being the source populations for gene recolonization after the last glaciation stage. In addition, the three sites of Wu, Ym, and Cy exhibited the highest gene diversities that coincided with populations with the highest chloroplast DNA variations. This may have resulted from an admixture of colonization routes. In conclusion, observations of the most divergent populations and source populations suggest that southern and probably north-central Taiwan may have potentially been refugia for Q. glauca in the last glaciation. This agrees with the possible refugium in southern Taiwan revealed by a previous study using chloroplast DNA markers.     

Genetic differentiation in the Agave deserti (Agavaceae) complex of the Sonoran desert

The Agave deserti complex, comprising A. deserti, A. cerulata and A. subsimplex, represents a group of species and subspecies with a near allopatric distribution and clear differences in morphology. Genetic differentiation and taxonomic status with respect to spatial distribution of 14 populations of the complex were analyzed in an effort to understand the evolution and speciation process within the genus. Allelic frequencies, levels of genetic variation, expected heterozygosity (H(S)), proportion of polymorphic loci (P), and genetic differentiation (theta and Nei's genetic distance) were estimated using 41 putative RAPD loci. All three species show high levels of genetic variation (H(S)=0.12-0.29, P=63.4-95.1), and low genetic differentiation between populations and species (theta populations=0.14+/-0.02 (SE); G(st)=0.11+/-0.02). Accordingly, gene flow among populations was estimated as high by three different methods (N(m)=2.91-6.14). Nei's genetic distances between the three species were low compared to the values obtained from other Agavaceae, and there was no clear correlation with taxonomic divisions. In a UPGMA analysis, A. subsimplex and A. cerulata formed exclusive monospecific clusters, whereas the A. deserti populations appear in more than one cluster together with other species. The results were consistent with a pattern of genetic isolation by distance.     

Characterization of the Genetic Diversity and Population Structure for the Yellow Cattle in Taiwan Based on Microsatellite Markers

In recent years, the population size of Taiwan yellow cattle has drastically declined, even become endangered. A preservation project, Taiwan Yellow Cattle Genetic Preservation Project (TYCGPP), was carried out at the Livestock Research Institute (LRI) Hengchun branch (1988–present). An analysis of intra- and inter- population variability was performed to be the first step to preserve this precious genetic resource. In this work, a total number of 140 individuals selected from the five Taiwan yellow cattle populations were analyzed using 12 microsatellite markers (loci). These markers determined the level of genetic variation within and among populations as well as the phylogenetic structure. The total number of alleles detected (122, 10.28 per locus) and the expected heterozygosity (0.712) indicated that these five populations had a high level of genetic variability. Bayesian cluster analysis showed that the most likely number of groups was 2 (K = 2). Genetic differentiation among clusters was moderate (F _ST = 0.095). The result of AMOVA showed that yellow cattle in Taiwan had maintained a high level of within-population genetic differentiation (91%), the remainder being accounted for by differentiation among subpopulations (4%), and by differentiation among regions (5%). The results of STRUCTURE and principal component analysis (PCA) revealed two divergent clusters. The individual unrooted phylogenetic tree showed that some Kinmen yellow cattle in the Hengchun facility (KMHC individuals) were overlapped with Taiwan yellow cattle (TW) and Taiwan yellow cattle Hengchun (HC) populations. Also, they were overlapped with Kinmen × Taiwan (KT) and Kinmen yellow cattle (KM) populations. It is possible that KMHC kept similar phenotypic characteristics and analogous genotypes between TW and KM. A significant inbreeding coefficient (F _IS = 0.185; P < 0.01) was detected, suggesting a medium level of inbreeding for yellow cattle in Taiwan. The hypothesis that yellow cattle in Taiwan were derived from two different clusters was also supported by the phylogenetic tree constructed by the UPGMA, indicating that the yellow cattle in Taiwan and in Kinmen should be treated as two different management units. This result will be applied to maintain a good level of genetic variability and rusticity (stress-resistance) and to avoid further inbreeding for yellow cattle population in Taiwan.     

The phylogeography of Fagus hayatae (Fagaceae): genetic isolation among populations

The beech species Fagus hayatae is an important relict tree species in subtropical China, whose biogeographical patterns may reflect floral responses to climate change in this region during the Quaternary. Previous studies have revealed phylogeography for three of the four Fagus species in China, but study on F. hayatae, the most sparsely distributed of these species, is still lacking. Here, molecular methods based on eight simple sequence repeat (SSR) loci of nuclear DNA (nDNA) and three chloroplast DNA (cpDNA) sequences were applied for analyses of genetic diversity and structure in 375 samples from 14 F. hayatae populations across its whole range. Both nDNA and cpDNA indicated a high level of genetic diversity in this species. Significant fixation indexes and departures from the Hardy–Weinberg equilibrium, with a genetic differentiation parameter of R_st of 0.233, were detected in nDNA SSR loci among populations, especially those on Taiwan Island, indicating strong geographic partitioning. The populations were classified into two clusters, without a prominent signal of isolation‐by‐distance. For the 15 haplotypes detected in the cpDNA sequence fragments, there was a high genetic differentiation parameter (G_st = 0.712) among populations. A high G_st of 0.829 was also detected outside but not within the Sichuan Basin. Consistent with other Fagus species in China, no recent population expansion was detected from tests of neutrality and mismatch distribution analysis. Overall, genetic isolation with limited gene flow was prominent for this species and significant phylogeographic structures existed across its range except for those inside the Sichuan Basin. Our study suggested long‐term geographic isolation in F. hayatae with limited population admixture and the existence of multiple refugia in the mountainous regions of the Sichuan Basin and southeast China during the Quaternary. These results may provide useful information critical for the conservation of F. hayatae and other Chinese beech species.     

A signal for independent coastal and continental histories among North American wolves

Relatively little genetic variation has been uncovered in surveys across North American wolf populations. Pacific Northwest coastal wolves, in particular, have never been analysed. With an emphasis on coastal Alaska wolf populations, variation at 11 microsatellite loci was assessed. Coastal wolf populations were distinctive from continental wolves and high levels of diversity were found within this isolated and relatively small geographical region. Significant genetic structure within southeast Alaska relative to other populations in the Pacific Northwest, and lack of significant correlation between genetic and geographical distances suggest that differentiation of southeast Alaska wolves may be caused by barriers to gene flow, rather than isolation by distance. Morphological research also suggests that coastal wolves differ from continental populations. A series of studies of other mammals in the region also has uncovered distinctive evolutionary histories and high levels of endemism along the Pacific coast. Divergence of these coastal wolves is consistent with the unique phylogeographical history of the biota of this region and re-emphasizes the need for continued exploration of this biota to lay a framework for thoughtful management of southeast Alaska.     

Albumin — vitamin D-binding protein haplotypes in Asian-Pacific populations

Summary We have determined the various haplotypic combinations between alleles as well as restriction fragment length polymorphisms of two linked genetic markers, albumin and vitamin D-binding protein or group-specific component, in a number of Asian-Pacific populations. Using the partial maximum likelihood method, we constructed a phylogenetic network from the haplotype frequencies to assess relationships among the populations sampled. No systematic linkage disequilibrium was detected between most of the combinations, suggesting a lack of operation of any selection pressure at the two loci. The phylogenetic analysis confirmed the known interrelationships among various populations in the Asian-Pacific region. The Australian aborigines clustered closely with the non-Austronesian-speaking highlanders from Papua New Guinea, as expected. Similarly, the Austronesian-speaking Polynesians, Micronesians, and the Southeast Asians branched off together as a separate group. The position of the Austronesian-speaking Tolais from New Britain with respect to other populations from the Southwest Pacific was anomalous. The Tolais revealed a strong affinity with the Australian aborigines, which is inexplicable. The populations from China formed a tight cluster with other populations from the Asian-Pacific region. Genetic interrelationships of these populations with the white Australians were remote, which is in accordance with the known affinities of various human racial groups.     

Microsatellite markers reveal population structure and low gene flow among collections of Bactrocera cucurbitae (Diptera: Tephritidae) in Asia

The melon fruit fly, Bactrocera cucurbitae (Coquillett) (Diptera: Tephritidae), is widespread agricultural pest, and it is known to have the potential to establish invasive populations in various tropical and subtropical areas. Despite the economic risk associated with a putative stable presence of this fly, the population genetics of this pest have remained relatively unexplored in Asia, the main area for distribution of this pest. The goals for this study were to employ nuclear markers to examine geographic collections for population genetic structure and quantify the extent of gene flow within these Southeast Asian and Chinese populations. To achieve these goals, we used 12 polymorphic microsatellite markers. A low level of genetic diversity was found among collections from China and higher levels were seen in Southeast Asia collections. Three genetically distinct groups, Southeast Asia, southwest China, and southeast China, were recovered by Bayesian model-based clustering methods, the phylogenetic reconstruction and the principal coordinate analysis. The Mantel test clearly shows geographical distance contributed in the genetic structuring of B. cucurbitae's populations. No recent bottlenecks for any of the populations examined. The results of clustering, migration analyses, and Mantel test, strongly suggest that the regional structure observed may be due to geographical factors such as mountains, rivers, and islands. We found a high rate of migration in some sites from the southwest China region (cluster 1) and the southeast China region (cluster 2), suggesting that China-Guangdong-Guangzhou (GZ) may be the center of melon fruit fly in the southeast China region.     

Analysis of five y-Specific microsatellite loci in Asian and Pacific populations

We have analyzed five Y-specific microsatellite loci (DYS388, DYS390, DYS391, DYS394, DYS395) in 17 Asian and Pacific populations representing a broad geographical area and different linguistic families, with an emphasis on populations from mainland and insular Southeast Asia. Analysis of gene diversity indicates that several of the studied populations have experienced substantial genetic isolation, and a reduction in male effective sizes (viz. the Northeast Indian populations Nishi, Adi and the Taiwanese aboriginals). The average values of the F_ST and (_ST statistics indicate a high degree of genetic differentiation among these populations at the five Y-specific markers (F_ST =0.21 and (_ST = 0.33, based on individual loci; F_ST = 0.09 and (_ST = 0.36, based on haplotypes), which conform to the expectation of a fourfold smaller effective size of the Y-linked loci compared with the autosomal loci. Dendrogram and principal coordinates analysis, with few exceptions, show a major separation between mainland and insular populations. Among the mainland populations, the Tibeto-Burman speakers from Northeast India cluster in a well-defined group, supported by high bootstrap values. The Southern Chinese, Northern Thai, So, and Cambodian also are integral to this cluster. The other major cluster is rather heterogeneous and includes, among others, the Austronesian-speaking populations. The Samoans of the Pacific, with a distinctive pattern of allelic distributions, stand as an outlier in the tree and PC representations. Although trends of genetic affinities among ethnically and geographically related populations are evident from the Y-specific microsatellite data, microsatellites are not optimal for deciphering complex migratory patterns of human populations, which could possibly be clarified by using additional and more stable genetic markers. Am J Phys Anthropol 110: 1–16, 1999. © 1999 Wiley-Liss, Inc.     

Genetic variability of dromedary camel populations based on microsatellite markers

Understanding existing levels of genetic variability of camel populations is capital for conservation activities. This study aims to provide information on the genetic diversity of four dromedary populations, including Guerzni, Harcha, Khouari and Marmouri. Blood samples from 227 individuals belonging to the aforementioned populations were obtained and genotyped by 16 microsatellite markers. A total of 215 alleles were observed, with the mean number of alleles per locus being 13.4 ± 6.26. All loci were polymorphic in the studied populations. The average expected heterozygosity varied from a maximum of 0.748 ± 0.122 in Guerzni population to a minimum of 0.702 ± 0.128 in Harcha population; Guerzni population showed the highest value of observed heterozygosity (0.699 ± 0.088), whereas Harcha population the lowest (0.646 ± 0.130). Mean estimates of F-statistics obtained over loci were F_IS = 0.0726, F_IT = 0.0876 and F_ST = 0.0162. The lowest genetic distance was obtained between Guerzni and Khouari (0.023), and the highest genetic distance between Harcha and Marmouri (0.251). The neighbour-joining phylogenetic tree showed two groups of populations indicating a cluster of Guerzni, Khouari and Marmouri, and a clear isolation of Harcha. The genetic distances, the factorial correspondence analysis, the analysis of genetic structure and the phylogenetic tree between populations revealed significant differences between Harcha and other populations, and a high similarity between Guerzni, Khouari and Marmouri. It is concluded from this study that the camel genetic resources studied are well diversified. However, the herd management, especially the random selection of breeding animals, can increase the level of genetic mixing between different populations, mainly among Guerzni, Khouari and Marmouri, that live in the same habitat and grazing area.     

中国内蒙古鄂伦春族线粒体DNA高变区Ⅰ和高变区Ⅱ遗传多态性

收集50份鄂伦春族无关人群外周血样本, 用ABI PRISM377测序仪对其mtDNA HVRⅠ和HVRⅡ进行测序, 计算多态性位点数、单倍型数目、单倍型频率、平均核苷酸差异数目等多态性指标; 结合已发表的其他民族mtDNA遗传资料, 根据Nei法计算鄂伦春族与各群体之间的遗传距离, 进行聚类分析, 绘制系统发生树。鄂伦春族群体mtDNA两个高变区与CRS序列比对, 分别发现52和24个多态性位点, 分别界定了38和27种单倍型, 单倍型多态性分别为0.964±0.018和0.929±0.019; 平均核苷酸差异分别为7.379和2.408; 用HVRⅠ序列多态性数据计算Fst和dA两种遗传距离, 相关系数r为0.993(P<0.01); 基于HVRⅠ序列的系统树显示鄂伦春族与中国台湾、南方汉族和中国香港人群遗传距离较近, 与北方汉族、蒙古族及其国外人群遗传距离相对较远。我国鄂伦春族人群mtDNA具有相对独特的遗传特征, 其遗传多态性和个体识别力较高, 可用于民族起源、迁徙、法医学个体识别等领域研究。     

中国西南地区重要木本油料植物扁核木的遗传结构及成因

扁核木(Prinsepia utilis)为中国西南地区温带森林重要的木本油料植物, 但对其野生资源种群遗传结构及成因的了解严重不足。我们采用核微卫星分子标记, 对32个扁核木自然种群共377个个体的群体演化历史进行了探讨, 并评估其遗传资源。研究发现扁核木种群自西向东可划分4个遗传群组, 即喜马拉雅、横断山以及云贵高原西部和东部群组。其中, 最大的遗传分化存在于喜马拉雅和其他区域种群间。与喜马拉雅和云贵高原东部群组相比, 横断山和云贵高原西部群组混合了其他群组的遗传成分。种群动态历史分析显示中部2个群组在喜马拉雅和云贵高原东部群组形成后形成, 不同群组间的分化均发生在更新世晚期。地理隔离和环境隔离分析表明扁核木种群间的遗传分化主要由环境差异导致。环境差异分析显示不同群组间的气候存在不同程度的差异, 其中喜马拉雅和云贵高原东部群组与中部2个群组间的差异显著。此外, 结合该物种不同时期的生态位模拟数据, 我们认为喜马拉雅和云贵高原地区的遗传资源在未来需要优先保护。     

Forest cover mediates genetic connectivity of northwestern cougars

Population structure, connectivity, and dispersal success of individuals can be challenging to demonstrate for solitary carnivores with low population densities. Though the cougar (Puma concolor) is widely distributed throughout North America and is capable of dispersing long distances, populations can be geographically structured and genetic isolation has been documented in some small populations. We described genetic structure and explored the relationship between landscape resistance and genetic variation in cougars in Washington and southern British Columbia using allele frequencies of 17 microsatellite loci for felids. We evaluated population structure of cougars using the Geneland clustering algorithm and spatial principal components analysis. We then used Circuitscape to estimate the landscape resistance between pairs of individuals based on rescaled GIS layers for forest canopy cover, elevation, human population density and highways. We quantified the effect of landscape resistance on genetic distance using multiple regression on distance matrices and boosted regression tree analysis. Cluster analysis identified four populations in the study area. Multiple regression on distance matrices and boosted regression tree models indicated that only forest canopy cover and geographic distance between individuals had an effect on genetic distance. The boundaries between genetic clusters largely corresponded with breaks in forest cover, showing agreement between population structure and genetic gradient analyses. Our data indicate that forest cover promotes gene flow for cougars in the Pacific Northwest, which provides insight managers can use to preserve or enhance genetic connectivity.     

GENETIC DIVERSITY AND POPULATION STRUCTURE IN CAMELLIA JAPONICA L. (THEACEAE)

Camellia japonica is a widespread and morphologically diverse tree native to parts of Japan and adjacent islands. Starch gel electrophoresis was used to score allelic variation at 20 loci in seeds collected from 60 populations distributed throughout the species range. In comparison with other plant species, the level of genetic diversity within C. japonica populations is very high: 66.2% of loci were polymorphic on average per population, with a mean number of 2.16 alleles per locus; the mean observed and panmictic heterozygosities were 0.230 and 0.265, respectively. Genotypic proportions at most loci in most populations fit Hardy-Weinberg expectations. However, small heterozygote deficiencies were commonly observed (mean population fixation index = 0.129). It is suggested that the most likely cause of the observed deficiencies is population subdivision into genetically divergent subpopulations. The overall level of population differentiation is greater than is typically observed in out-breeders: The mean genetic distance and identity (Nei's D and I) between pairs of populations were 0.073 and 0.930, respectively, and Wright's Fst was 0.144. Differences among populations appeared to be manifested as variation in gene frequencies at many loci rather than variation in allelic composition per se. However, the patterns of variation were not random. Reciprocal clinal variation of gene frequencies was observed for allele pairs at six loci. In addition, principal components analysis revealed that populations tended to genetically cluster into four regions representing the geographic areas Kyushu, Shikoku, western Honshu, and eastern Honshu. There was a significant relationship between genetic and geographic distance (r = 0.61; P < 0.01). Analysis of variance on allozyme frequencies showed that there was approximately four times as much differentiation among populations within regions, as among regions. It is likely that the observed patterns of population relationships result from the balance between genetic drift in small subpopulations and gene flow between them.     

An electrophoretic investigation of populations of Atherina boyeri Risso, 1810 and A. presbyter Cuvier, 1829 (Teleostei: Atherinidae): genetic evidence in support of the two species

The data obtained using electrophoresis strongly support the specific status of Atherina boyeri Risso, 1810 and A. presbyfer Cuvier, 1829, and thuscontradict the recently proposedsynonymyof the two species. Four populations of A. boyeri and six populations of A. presbyter were assayed for 11 enzymes and general protein using muscle and liver extracts. Eight of the 11 enzymes were shown to be polymorphic at the 95% level. Sixteen loci, encoding 40 putative alleles were consistently resolved in all 10 populations.
The two species were fixed for different alleles at the EST-3 locus. At the G3PDH locus. with the exception of two heterozygotes, all individuals of each species were also homozygous for different alleles. At the PGM locus the common allele was unique to each species.
The mean Nei's genetic distance ( ), over all loci, calculated between populations of A. boyeri (= 0.10 ± 0.06); between populations of A. presbyter ( = 0.02 0.02) and between populations of A. boyeri and A. presbyter ( = 0.42 0.09) indicated the separateness of the two species.
UPGMA cluster analysis based on genetic distances produced a dendrogram whose principal dichotomy resulted in the formation of two clusters. The ordination of populations in the UPGMA cluster analysis strongly reflected the geographic distribution of populations in both species.     

Empirical tests of the reliability of phylogenetic trees constructed with microsatellite DNA

Microsatellite DNA loci or short tandem repeats (STRs) are abundant in eukaryotic genomes and are often used for constructing phylogenetic trees of closely related populations or species. These phylogenetic trees are usually constructed by using some genetic distance measure based on allele frequency data, and there are many distance measures that have been proposed for this purpose. In the past the efficiencies of these distance measures in constructing phylogenetic trees have been studied mathematically or by computer simulations. Recently, however, allele frequencies of 783 STR loci have been compiled from various human populations. We have therefore used these empirical data to investigate the relative efficiencies of different distance measures in constructing phylogenetic trees. The results showed that (1) the probability of obtaining the correct branching pattern of a tree (PC) is generally highest for DA distance; (2) FST*, standard genetic distance (DS), and FST/(1-FST) give similar PC-values, FST* being slightly better than the other two; and (3) (deltamu)2 shows PC-values much lower than the other distance measures. To have reasonably high PC-values for trees similar to ours, at least 30 loci with a minimum of 15 individuals are required when DA distance is used.     

Accuracy of estimated phylogenetic trees from molecular data

The accuracies and efficiencies of three different methods of making phylogenetic trees from gene frequency data were examined by using computer simulation. The methods examined are UPGMA, Farris' (1972) method, and Tateno et al.'s (1982) modified Farris method. In the computer simulation eight species (or populations) were assumed to evolve according to a given model tree, and the evolutionary changes of allele frequencies were followed by using the infinite-allele model. At the end of the simulated evolution five genetic distance measures (Nei's standard and minimum distances, Rogers' distance, Cavalli-Sforza's f theta, and the modified Cavalli-Sforza distance) were computed for all pairs of species, and the distance matrix obtained for each distance measure was used for reconstructing a phylogenetic tree. The phylogenetic tree obtained was then compared with the model tree. The results obtained indicate that in all tree-making methods examined the accuracies of both the topology and branch lengths of a reconstructed tree (rooted tree) are very low when the number of loci used is less than 20 but gradually increase with increasing number of loci. When the expected number of gene substitutions (M) for the shortest branch is 0.1 or more per locus and 30 or more loci are used, the topological error as measured by the distortion index (dT) is not great, but the probability of obtaining the correct topology (P) is less than 0.5 even with 60 loci. When M is as small as 0.004, P is substantially lower. In obtaining a good topology (small dT and high P) UPGMA and the modified Farris method generally show a better performance than the Farris method. The poor performance of the Farris method is observed even when Rogers' distance which obeys the triangle inequality is used. The main reason for this seems to be that the Farris method often gives overestimates of branch lengths. For estimating the expected branch lengths of the true tree UPGMA shows the best performance. For this purpose Nei's standard distance gives a better result than the others because of its linear relationship with the number of gene substitutions. Rogers' or Cavalli-Sforza's distance gives a phylogenetic tree in which the parts near the root are condensed and the other parts are elongated. It is recommended that more than 30 loci, including both polymorphic and monomorphic loci, be used for making phylogenetic trees. The conclusions from this study seem to apply also to data on nucleotide differences obtained by the restriction enzyme techniques.