Genetic Admixture Analysis Research Articles

Genetic structuring and transfer of marine dinoflagellate Cochlodinium polykrikoides in Japanese and Korean coastal waters revealed by microsatellites

To determine the process of population expansion and ascertain the origin of the Sea of Japan population, in a noxious red tide forming dinoflagellate Cochlodinium polykrikoides, 13 samples, isolated from 11 different localities in Japanese and Korean coasts, were analysed using 10 polymorphic microsatellites. Analyses by nonmetric multidimensional scaling plots of pairwise F(ST), global amova, and genetic admixture analysis identified three clusters--the Sea of Japan populations, Yatsushiro Sea (Kumamoto Pref.) populations, and other populations--indicating genetic structuring of the 13 samples into three distinct populations. In the proportion of shared alleles by pairwise individuals (P(SAxy)) analyses between the Sea of Japan and the other samples, P(SAxy) was extremely low compared with that among the Sea of Japan or among other samples, indicating that a large genetic barrier has occurred between the populations. No significant relationship of isolation-by-distance patterns and almost no genetic distance were detected between pairwise samples of the Sea of Japan, although there is a maximal distance of > 600 km between samples. In addition, P(SAxy) data among the samples were extremely high compared with those among other samples, clearly showing that a large-scale transfer from west to east has occurred via the Tushima Warm Current. In the P(SAxy) data of the Seto Inland Sea and Pacific samples, individuals showing relatively high P(SAxy) were concentrated in the three areas of Nagasaki, Harima, and Mie, suggesting that frequent transfer may have occurred by human-assisted dispersal, although Nagasaki and Mie are separated by a distance of approximately 700 km.

Gene flow of Acanthaster planci (L.) in relation to ocean currents revealed by microsatellite analysis

Population outbreaks of the coral-eating starfish, Acanthaster planci, are hypothesized to spread to many localities in the Indo-Pacific Ocean through dispersal of planktonic larvae. To elucidate the gene flow of A. planci across the Indo-Pacific in relation to ocean currents and to test the larval dispersal hypothesis, the genetic structure among 23 samples over the Indo-Pacific was analysed using seven highly polymorphic microsatellite loci. The F-statistics and genetic admixture analysis detected genetically distinct groups in accordance with ocean current systems, that is, the Southeast African group (Kenya and Mayotte), the Northwestern Pacific group (the Philippines and Japan), Palau, the North Central Pacific group (Majuro and Pohnpei), the Great Barrier Reef, Fiji, and French Polynesia, with a large genetic break between the Indian and Pacific Oceans. A pattern of significant isolation by distance was observed among all samples (P = 0.001, r = 0.88, n = 253, Mantel test), indicating restricted gene flow among the samples in accordance with geographical distances. The data also indicated strong gene flow within the Southeast African, Northwestern Pacific, and Great Barrier Reef groups. These results suggest that the western boundary currents have strong influence on gene flow of this species and may trigger secondary outbreaks.

Genetic and morphological evidence for localised interspecific gene flow in Phormium (Hemerocallidaceae)

Gene flow between two species of Phormium, P. tenax and P. cookianum, was investigated by analysis of morphology, AFLP profiles, and chloroplast simple sequence repeats (cpSSRs). We examined 44 wild samples of Phormium, focusing on Okiwi Bay (Marlborough, New Zealand), where the two species grow in close proximity. Two genetic groups corresponding with P. tenax and P. cookianum are evident in analyses of AFLP profiles from Okiwi Bay. The profiles of Okiwi Bay plants were also compared with profiles from three hypothetically pure P. cookianum populations from Marlborough, and a representative sample of P. tenax combined from sites throughout New Zealand. Bayesian analysis of genetic admixture suggests that all of the plants resembling P. tenax and most of the plants resembling P. cookianum sampled from Okiwi Bay are admixed (i.e., of hybrid origin). Neighbour Net and principal component analyses reveal that P. cookianum and P. tenax from Okiwi Bay are genetically intermediate between “pure” populations of the species. Further, all of the Okiwi Bay samples share the same chloroplast haplotype. Analysis of morphological characters comparing a small number of Okiwi Bay P. tenax plants to selected P tenax plants from throughout New Zealand under common garden conditions confirm that the Okiwi Bay population includes plants with unusually small stature and fruit characters approaching P cookianum. These results support a hypothesis of local introgression between P. tenax and P. cookianum.

Genetic Affinities of the Siddis of South India: An Emigrant Population of East Africa

Historical records indicate that the Portuguese brought the African Siddis to Goa, India, as slaves about 500 years ago. Subsequently, the Siddis moved into the interior regions of the state of Karnataka, India, and have remained there ever since. Over time the Siddis have experienced considerable cultural changes because of their proximity to neighboring population groups. To understand the biological consequences of these changes, we studied the Siddis to determine the extent of genetic variation and the contributions from the African, European, and Indian ancestral populations. In the present study we typed the Siddis for 20 polymorphic serological, red cell, and Alu insertion-deletion loci. The overall pattern of phenotype (and genotype) distribution is in accordance with Hardy-Weinberg expectations. Considering the ethnohistorical records and the availability of secondary-source genetic data, we used two data sets in the analysis: one comprising eight serological and red cell enzyme markers with eight population groups and another comprising six Alu insertion-deletion markers with seven tribal groups of South India. The dendrograms generated from these two data sets on the basis of genetic distance analysis between the selected populations of African, European, and Indian descent reveals that the Siddis are closer to the Africans than they are to the South Indian populations. Genetic admixture analysis using a dihybrid model (19 loci) and a trihybrid model (10 loci and 8 loci) shows that the predominant influence comes from the Africans, a lesser contribution from the South Indians, and a slight contribution from the Portuguese. Thus the original composition of the African genes among the Siddis has been diluted to some extent by the contribution from southern Indian population groups. There is no nonrandom association of alleles among a set of 10 genetic marker systems considered in the present study. The demonstration of genetic homogeneity of the Siddis, despite their admixed origin, suggests the utility of this population for genetic and epidemiological studies.

Genetic Affinities of the Siddis of South India: An Emigrant Population of East Africa

Historical records indicate that the Portuguese brought the African Siddis to Goa, India, as slaves about 500 years ago. Subsequently, the Siddis moved into the interior regions of the state of Karnataka, India, and have remained there ever since. Over time the Siddis have experienced considerable cultural changes because of their proximity to neighboring population groups. To understand the biological consequences of these changes, we studied the Siddis to determine the extent of genetic variation and the contributions from the African, European, and Indian ancestral populations. In the present study we typed the Siddis for 20 polymorphic serological, red cell, and Alu insertion-deletion loci. The overall pattern of phenotype (and genotype) distribution is in accordance with Hardy-Weinberg expectations. Considering the ethnohistorical records and the availability of secondary-source genetic data, we used two data sets in the analysis: one comprising eight serological and red cell enzyme markers with eight population groups and another comprising six Alu insertion-deletion markers with seven tribal groups of South India. The dendrograms generated from these two data sets on the basis of genetic distance analysis between the selected populations of African, European, and Indian descent reveals that the Siddis are closer to the Africans than they are to the South Indian populations. Genetic admixture analysis using a dihybrid model (19 loci) and a trihybrid model (10 loci and 8 loci) shows that the predominant influence comes from the Africans, a lesser contribution from the South Indians, and a slight contribution from the Portuguese. Thus the original composition of the African genes among the Siddis has been diluted to some extent by the contribution from southern Indian population groups. There is no nonrandom association of alleles among a set of 10 genetic marker systems considered in the present study. The demonstration of genetic homogeneity of the Siddis, despite their admixed origin, suggests the utility of this population for genetic and epidemiological studies.

Genetic diversity and admixture analysis of Sanfratellano and three other Italian horse breeds assessed by microsatellite markers

Sanfratellano is a native Sicilian horse breed, mainly reared in the north east of the Island, developed in the 19th century from local dams and sires with a restricted introgression of Oriental, African and, more recently, Maremmano stallions. In this study, the genetic relationships and admixture among Sanfratellano, the other two Sicilian autochthonous breeds and Maremmano breed were assessed using a set of microsatellites. The main goals were to infer the impact of Maremmano breed in the current Sanfratellano horse and to provide genetic information useful to improve the selection strategies of the Sanfratellano horse. The whole sample included 384 horses (238 Sanfratellano, 50 Sicilian Oriental Purebred, 30 Sicilian Indigenous and 66 Maremmano), chosen avoiding closely related animals. A total of 111 alleles from 11 microsatellite loci were detected, from four at HTG7 to 15 at ASB2 locus. The mean number of alleles was the lowest in Oriental Purebred (6.7), the highest in Sanfratellano (8.3). All the breeds showed a high level of gene diversity (He) ranging from 0.71 ± 0.04 in Sicilian Oriental Purebred to 0.81 ± 0.02 in Sicilian Indigenous. The genetic differentiation index was low; only about 6% of the diversity was found among breeds. Nei’s standards (DS) and Reynolds’ (DR) genetic distances reproduced the same population ranking. Individual genetic distances and admixture analysis revealed that: (a) nowadays Maremmano breed does not significantly influence the current Sanfratellano breed; (b) within Sanfratellano breed, it is possible to distinguish two well-defined groups with different proportions of Indigenous blood.

Genetic structure of three Oryza AA genome species (O. rufipogon, O. nivara and O. sativa) as assessed by SSR analysis on the Vientiane Plain of Laos

Microsatellite (SSR) markers can reveal a high level of polymorphic loci, and are increasingly being used in population genetic structure studies. On the Vientiane plain of Laos all components of the rice crop complex exist, wild annual (O. nivara), wild perennial (O. rufipogon) and weedy relatives of rice as well as rice itself. To understand gene flow in the rice complex, the genetic structures of O. rufipogon (10 populations), O. nivara (10 populations) and O. sativa (24 samples) from across the Vientiane Plain, Laos, were compared. Higher genetic differentiation was detected among O. nivara populations (G ST = 0.77, R ST = 0.71) than O. rufipogon populations (G ST = 0.29, R ST = 0.28), whereas genetic diversity for all populations of these two wild species showed similar values (H T = 0.77 and 0.64 in O. rufipogon and O. nivara, respectively). Based on neighbor-joining tree constructed on the basis of genetic distance (D A), three genetic clusters were detected, corresponding to (1) O. sativa samples, (2) O. nivara populations and (3) O. rufipogon populations. Pairwise tests confirmed the genetic differentiation of the three species. Although none of the wild rice individuals used in this study had any cultivated-specific phenotypic traits, genetic admixture analysis detected more than 10% O. sativa membership in three O. rufipogon and one O. nivara populations, indicating that O. sativa alleles may cryptically persist in natural populations of O. rufipogon and O. nivara on the Vientiane Plain.

Genetic Characterization of the Population of Grande Comore Island (Njazidja) According to Major Blood Groups

The Comorian population is historically considered a blend of influences from African Bantus, Arabs, and possibly Austronesians. In this study we present the first genetic data on the current Comorian population. Serologic analysis of the six major blood group systems (ABO, RH, KEL, FY, JK, and MNS) was performed on 164 individuals from Grande Comore Island (Njazidja). In addition, Duffy genotypes were determined by polymerase chain reaction using allele-specific primers. Our findings establish a high frequency of the Fy(a- b-) phenotype (86%), presenting the same genetic background as in sub-Saharan Africa. Analysis of genetic frequencies, distances, and admixture with other populations indicates that African Bantus made the main contribution to the gene pool (73.2%+/-15.5%). The Arab contribution from the Arabian peninsula was smaller (24.2%+/-7%) and the Indonesian contribution was minor (2.6%+/-9%). The major Bantu contribution was commensurate with the Bantu cultural influence. The contribution from the Arabian peninsula seemed in relation to its permeating religious and linguistic influence. As with the language, the Indonesian contribution to the Comorian gene pool was small. These results are in agreement with historical, sociological, and linguistic data.

Dewclaws in wolves as evidence of admixed ancestry with dogs

Vestigial first toes (dewclaws) on the hind legs are common in large dog (Canis lupus familiaris) breeds but are absent in wild canids, including wolves (Canis lupus). Based on observational criteria, dewclaws in wolves have been generally regarded as a clue of hybridization with dogs, although this was not substantiated by molecular evidence. By means of population assignment and genetic admixture analysis, we investigated individual genotypes of three dewclawed wolves from Tuscany (central Italy, 1993–2001). Based on 18 microsatellite markers, dewclawed wolves were not uniquely assigned to the Italian wolf population but appeared to be second or later generation backcrosses of wolf–dog hybrids. Alleles uniquely shared with dogs, and mitochondrial DNA and Y haplotypes identical to those of Italian wolves, further supported their admixed ancestry. Although patterns of dewclaw inheritance in wolf–dog hybrids and backcrosses have not been ascertained, we conclude that dewclaws in wolves, when present, are a clue of admixed ancestry, probably originating in areas where large dog breeds are involved in cross-matings. Other "atypical" morphological traits (e.g., white nails, atypical color patterns or body proportions, dental anomalies) as well might be reliable clues of admixed ancestry, and they deserve careful monitoring and molecular investigation.

Detecting rare introgression of domestic dog genes into wild wolf ( Canis lupus ) populations by Bayesian admixture analyses of microsatellite variation

Hybridization with free-ranging dogs isthought to threat the genetic integrity ofwolves in Europe, although available mtDNA dataevidenced only sporadic cases of crossbreeding.Here we report results of population assignmentand genetic admixture analyses in 107wild-living Italian wolves, 95 dogs including30 different breeds and feral dogs, andcaptive-reared wolves of unknown or hybridorigins, which were genotyped at 18microsatellites. Two Italian wolves showedunusually dark coats (``black wolves''), and oneshowed a spur in both hindlegs (``fifth fingerwolf''), suggesting hybridization. Italianwolves showed significant deficit ofheterozygotes, positive FIS values anddeviations from Hardy-Weinberg equilibrium.Genetic variability was significantlypartitioned between groups, suggesting thatwolves and dogs represent distinct gene pools.Multivariate ordination of individual genotypesand clustering of inter-individual geneticdistances split wolves and dogs into twodifferent clusters congruent with the priorphenotypic classification, but hybrids andwolves of unknown origin were not identifiedfrom genetic information alone. By contrast, aBayesian admixture analysis assigned all theItalian wolves and dogs to two differentclusters, independent of any prior phenotypicinformation, and simultaneously detected theadmixed gene composition of the hybrids, whichwere assigned to more than one cluster.Captive-reared wolves of unknown origin wereprevalently assigned to the Italian wolfpopulation. Admixture analyses showed that one``black wolf'' had mixed ancestry in the dog genepool and could be a hybrid, while the other twowolves with unusual phenotypes were assigned tothe Italian wolf population.

Natural Fertility in Northeastern Mexico: Genetic Structure by Year of Birth and Birthplace

Background The aims of this population genetics study were 1) to ascertain whether 417 Mexican women with natural fertility (45 years of age, married, not using any family planning methods, residing in the state of Nuevo León) were genetically homogeneous, and 2) to compare the genetic structure of this selected population with the previously reported data of random populations of northeastern Mexico. Methods A sample of 417 women was interviewed and selected in seven medical units of the Mexican Social Security Institute. They were grouped by their year of birth (1896–1925 and 1926–1955) and birthplace [persons whose four grandparents were born in the northeastern states (NE) and outside the northeastern states (Not-NE) of Mexico]. Eight genetic marker systems were analyzed. Results Gene diversity analysis suggests that more than 99.1% of the total gene diversity can be attributed to variation between individuals within the population. Genetic admixture analysis suggests that this selected population, stratified by year of birth and birthplace, have received a predominantly Spanish contribution followed by a lesser Mexican Indian contribution. Conclusions The genetic structure of this selected population was homogeneous and similar to the random populations of northeastern Mexico. This finding corroborates the utility of this selected population for genetic and epidemiological studies.

Genetic variation by birth cohorts in Mexican Americans of Starr County, Texas.

Mexican Americans residing in Starr County, Texas, were grouped by their year of birth (1896-1925, 1926-1955, and 1956-1985) to determine the extent of birth cohort-related genetic variation within this population and the genetic differences, if any, from the Mexican population residing in the Metropolitan Monterrey Area (MMA), Nuevo León, México. Twenty-one genetic markers were analyzed which indicate that the three birth cohort groups are genetically indistinguishable. Gene diversity analysis suggests that more than 99.8% of the total gene diversity can be attributed to variation between individuals within the birth cohort populations and that the subdivision by birth cohort has only a small contribution (0.18%) to the total gene diversity. Genetic admixture analysis indicates a predominant influence from the Spanish, and that the three birth cohort groups were similar in terms of contributions of this ancestral population. The genetic structure of the Mexican American population of Starr County was also similar to the Mexican population from the State of Nuevo León, México. These findings, together with previous results, suggest that the Mexican Americans of Starr County, Texas, classified by gender, birthplace, and age, are not genetically distinguishable and are similar to the Mexican populations of the State of Nuevo León. © 1994 Wiley-Liss, Inc.

Gene diversity and estimation of genetic admixture among Mexican-Americans of Starr County, Texas.

The Mexican-Americans of Starr County, Texas, classified by sex and birthplace, were studied to determine the extent of genetic variation and contributions from ancestral populations such as Spanish, Amerindian and West African. Using 21 genetic marker systems, genetic distance and diversity analyses indicate that subpopulations of Mexican-Americans in Starr County are similar, and that more than 99% of the total gene diversity (HT) can be attributed to individual variation within the population. Genetic admixture analysis shows the predominant influence comes from the Spanish, a lesser contribution from Amerindians and a slight one from the West Africans. The contribution of the ancestral population to various subpopulations of the Mexican-Americans of Starr County is similar. The Mexican-Americans of Starr County are similar to the Mexican population from northeastern Mexico. The history of admixture is apparently old enough to have brought the entire Mexican-American gene pool to Hardy-Weinberg equilibrium. There is no non-random association of alleles among the genetic marker systems considered in the present study, in spite of the fact that this population is of admixed origin. These results, in aggregate, suggest genetic homogeneity of the Mexican-Americans of Starr County, Texas, and point towards the utility of this population for genetic and epidemiological studies.

Uralic genes in Europe

We have analysed data of three European populations speaking non-Indoeuropean languages: Hungarians, Lapps, and Finns. Principal coordinate analysis shows that Lapps are almost exactly intermediate between people located geographically near the Ural mountains and speaking Uralic languages, and central and northern Europeans. Hungarians and Finns are definitely closer to Europeans. An analysis of genetic admixture between Uralic and European ancestors shows that Lapps are slightly more than 50% European, Hungarians are 87% European, and Finns are 90% European. There is basic agreement between these conclusions and historical data on Hungary. Less is known about Finns and very little about Lapps.