Genetic structure of the Mon-Khmer speaking groups and their affinity to the neighbouring Tai populations in Northern Thailand

In this study, we used genetic and linguistic data that we collected in Central Asia, to better understand how genetic and linguistic diversity correlates in a contact zone. We assessed the levels of genetic differentiation with mitochondrial, Y-chromosomal and autosomal data from 26 populations (1300 individuals) from the two major linguistic groups in Central Asia: Indo-European and Altaic. We computed the linguistic distance between populations with lexical data from several individuals per population.Our results show that the genetic diversity in the area clearly clusters in two groups explained by the linguistic, one that includes the Indo-Iranian populations and the other one the Turkic populations except for Uzbek populations. Also, for two populations we have detected a shift in language that occurred likely through elite-dominance effect. Furthermore computing linguistic distances based on lexical data (Levenstein distance) we find a strong correlation between genetic distances and linguistic distances but no correlation between genetic and geographical distances.In conclusion, Central Asia is an area where linguistic but not geography correlates with genetic diversity, highlighting the importance of a cultural trait in shaping genetic diversity in our species.

AimThe effects of geographic and environmental variables on patterns of genetic and phenotypic differentiation have been thoroughly studied. Ecological speciation involves reproductive isolation due to divergent natural selection that can result in a positive correlation between genetic divergence and adaptive phenotypic divergence (isolation by adaptation, IBA). If the phenotypic target of selection is unknown or not easily measured, environmental variation can be used as a proxy, expecting positive correlation between genetic and environmental distances, independent of geographic distances (isolation by environment, IBE). The null model is that the amount of gene flow between populations decreases as the geographic distance between them increases, and genetic divergence is due simply to the neutral effects of genetic drift (isolation by distance, IBD). However, since phenotypic differentiation in natural populations may be autocorrelated with geographic distance, it is often difficult to distinguish IBA from the neutral expectation of IBD. In this work, we test hypotheses of IBA, IBE, and IBD in the Red‐crowned Ant tanager (Habia rubica).LocationMesoamerica (Mexico—Central America) and South America.TaxonHabia rubica (Aves: Cardinalidae).MethodsWe compiled genetic data, coloration, and morphometric data from specimens from collections in Mexico and the United States. We used the Multiple Matrix Regression with Randomization (MMRR) approach to evaluate the influence of geographic and environmental distances on genetic and phenotypic differentiation of H. rubica at both phylogroup and population levels.ResultsOur results provide strong evidence that geographic distance is the main driver of genetic variation in H. rubica. We did not find evidence that climate variation is driving population differentiation in this species across a widespread geographic region.Main conclusionsOur data point to geographic isolation as the main factor structuring genetic variation within populations of H. rubica and suggest that climate is not playing a major role in genetic differentiation within this species.

Genetic distances among speakers of the European language families were computed by using gene-frequency data for human blood group antigens, enzymes, and proteins of 26 genetic systems. Each system was represented by a different subset of 3369 localities across Europe. By subjecting the matrix of distances to numerical taxonomic procedures, we obtained a grouping of the language families of Europe by their genetic distances as contrasted with their linguistic relationships. The resulting classification largely reflects geographic propinquity rather than linguistic origins. This is evidence for the primary importance of short-range interdemic gene flow in shaping the modern gene pools of Europe. Yet, some language families--i.e., Basque, Finnic (including Lappish), and Semitic (Maltese)--have distant genetic relationships with their geographic neighbors. These results indicate that European gene pools still reflect the remote origins of some ethnic units subsumed by these major linguistic groups.

Evolution in Health and Disease edited by S.C. Stearns

Nusa Tenggara, including East Timor, located at the crossroad between Island Southeast Asia, Near Oceania, and Australia, are characterized by a complex cultural structure harbouring speakers from two different major linguistic groups of different geographic origins (Austronesian (AN) and non-Austronesian (NAN)). This provides suitable possibilities to study gene-language relationship; however, previous studies from other parts of Nusa Tenggara reported conflicting evidence about gene-language correlation in this region. Aiming to investigate gene-language relationships including sex-mediated aspects in East Timor, we analysed the paternally inherited non-recombining part of the Y chromosome (NRY) and the maternally inherited mitochondrial (mt) DNA in a representative collection of AN- and NAN-speaking groups. Y-SNP (single-nucleotide polymorphism) data were newly generated for 273 samples and combined with previously established Y-STR (short tandem repeat) data of the same samples, and with previously established mtDNA data of 290 different samples with, however, very similar representation of geographic and linguistic coverage of the country. We found NRY and mtDNA haplogroups of previously described putative East/Southeast Asian (E/SEA) and Near Oceanian (NO) origins in both AN and NAN speakers of East Timor, albeit in different proportions, suggesting reciprocal genetic admixture between both linguistic groups for females, but directional admixture for males. Our data underline the dual genetic origin of East Timorese in E/SEA and NO, and highlight that substantial genetic admixture between the two major linguistic groups had occurred, more so via women than men. Our study therefore provides another example where languages and genes do not conform due to sex-biased genetic admixture across major linguistic groups.

The Tibeto-Burman (TB) populations are one of the four major linguistic population groups of India. They are considered belonging to different stocks and show wide variation in culture and language; however, their genetic relationship, antiquity and migration history among the regional populations has been little investigated. Molecular genetic studies are expected to clearly show the antiquity and genetic diversity of these populations. This paper seeks to understand the extent and magnitude of genetic affinities and diversities among 14 TB populations (12 Indian and two global groups), investigate the findings based on classical genetic markers and verify the historical accounts of their migration and genetic history based on 12 microsatellite markers. The allele frequency data for 12 STR loci of 13 Asian (Tibeto-Burman) populations were obtained from the literature and the Adi Pasi data was obtained by microsatellite typing of their blood samples. The 12 loci studied are D5S818, FGA, D8S1179, D21S11, D7S820, CSF1PO, D3S1358, THO1, D13S317, vWa, TPOX, D18S51. Three different distance measures, two phylogenetic trees and PCA plot have been employed to understand the genetic relationship of the studied populations. Average heterozygosity values range from 68 to 79% and the average G(ST) value is 4.7%. The dendrogram, based on the D(A) distance, shows the clustering of populations based on their diversities and geographical contiguity; the Mizoram and Arunachal Pradesh populations especially cluster together, populations from Sikkim form a separate subcluster and Manipur populations along with the Garo of West Bengal separate out from the other clusters. The Harpending and Ward regression model shows isolated populations positioned below the regression line and others, who experience external gene flow, placed above the line. The results support folklore migration accounts of their possible antiquity with the Tibetan and southern Chinese populations. Overall, geographic contiguity, punctuated by isolating barriers, is a major influencing factor of genetic affinity among the TB population; contiguous populations within a region show greater genetic relationship than with distant TB populations over a wide geographical area. The results of the microsatellite study also support the history of diverse routes of migration of these populations.

Spread and performance of European earthworms invading North America as indicated by molecular markers and climate chamber experiments

Genetic diversity and the relationship between genetic distance and geographical distance in red jungle fowl and 14 Chinese indigenous chicken breeds were evaluated using 29 microsatellite loci. The number of alleles per locus ranged from 2 to 25 and the average expected heterozygosity and PIC of all loci were 0.6683 and 0.50, respectively. The average number of alleles per locus ranged from 3.41 in Gushi chicken breed to 6.28 in Wannan Three-yellow chicken breed. The overall expected heterozygosity of 15 Chinese chicken breeds was 0.6686 ± 0.0254 and all breeds showed relatively large heterozygosity. The average of genetic differentiation among populations was 16.4% (<I>P</I> < 0.001). Red jungle fowl and Gushi chicken had distant genetic relationship from other breeds, while Huainan Partridge and Tibetan chicken were more closely related with other breeds. The results did not provide enough support for a significant correlation between the genetic and geographical pair-wise distances.

Ma JW, Geng SL, Wang SB, Zhang GL, Fu WD & Shu B (2011). Genetic diversity of the newly invasive weed Flaveria bidentis (Asteraceae) reveals consequences of its rapid range expansion in northern China. Weed Research51, 363–372.SummaryThe South American weed Flaveria bidentis has spread rapidly across northern China since its introduction to the Tianjin area in 2001. To explore its introduction dynamics and mechanism of rapid range expansion in northern China, we examined genetic diversity in 26 populations across the invaded range, using inter‐simple sequence repeat markers. We found relatively high intraspecies genetic diversity (He = 0.279; I = 0.415) and wide‐ranging genetic variation within populations (He = 0.095–0.263; I = 0.160–0.383), with relatively high genetic diversity in both older established populations and some newly established populations. Approximately 78% of genetic variation resides within populations, according to analysis of molecular variance. The unweighted pair group method with arithmetic mean clustered populations into two groups, composed of most populations distributed along the G106 or G107 National Roads. Moreover, a Mantel test showed no significant correlation between geographical and genetic distances. The findings indicate that during F. bidentis invasion, sexual reproduction and multiple introductions have maintained high genetic diversity, while secondary introductions or admixtures of populations have mitigated losses of genetic variation caused by founder events and promoted local adaptation and colonisation. In addition, human‐mediated long‐distance seed dispersal, via National Roads, may have contributed to its weak geographical genetic structure and rapid range expansion in northern China. To prevent further introductions, imports should be monitored at Tianjin (the likely first arrival point). To control established populations, efforts should focus on populations with high genetic diversity, populations along the G106 and G107 National Roads and regions that are climatically similar to its native range.

A previous phylogeography and genetic diversity study of Chamaedaphne calyculata (Ericaceae) showed that populations over its geographic range were strongly separated into two groups: a Eurasian/NW North American group and a NE North American one corresponding with the disjunct distribution of Sphagnum-dominated peatlands in north-western and central-eastern North America. Here, I have extended the survey and focused on the species’ detailed postglacial origin and the effect of isolation on genetic diversity patterns, particularly within island-like populations at the western periphery of its range in Europe. Using AFLP markers, estimates of genetic diversity within 16 C. calyculata populations in the Eurasian group were low (percentage of polymorphic loci P PL=14.9–24.8 %, Nei’s gene diversity H=0.060–0.119). Genetic diversity patterns within this species did not support the hypothesis that genetic diversity decreases towards the periphery of the range. Bayesian clustering analysis showed that population-level admixture was present in almost all studied 16 populations, suggesting multi-directional gene flow. On the other hand, the majority of assigned individuals (ca. 98 % of individuals) were offspring of the original residents, confirming that C. calyculata populations in the present day acted as discrete genetic units both in its continuous range and at its western periphery, and that gene flow was historic rather than contemporary in Eurasia. There was no correlation between genetic and geographic distance in the Eurasian group (r=0.02, P>0.05, Mantel test) nor at the western periphery (r=0.15, P>0.05, Mantel test). The isolation-by-distance (IBD) scatterplot matched Hutchinson and Templeton’s interpretation (case III), and geographic distance between populations was not a reliable predictor of the degree of genetic differentiation between populations. It is suggested that the lack of IBD might be a result of random genetic drift in rather disconnected populations that have become increasingly fragmented relatively recently. Positive and significant relationships between genetic and geographic distance on a small population scale was the result of biparental inbreeding of C. calyculata and restricted seed rain. Despite sporadic generative reproduction and limited dispersal, the fine-scale genetic structure within populations has been maintained, even though population sizes have been reduced to small fragments in recent years.

Dipteronia is an endemic genus to China and includes only two species, Dipteronia sinensis and D. dyeriana. Based on random amplified polymorphic DNA (RAPD) markers, a comparative study of the genetic diversity and genetic structure of Dipteronia was performed. In total, 128 and 103 loci were detected in 17 D. sinensis populations and 4 D. dyeriana populations, respectively, using 18 random primers. These results showed that the proportions of polymorphic loci for the two species were 92.97% and 81.55%, respectively, indicating that the genetic diversity of D. sinensis was higher than that of D. dyeriana. Analysis, based on similarity coefficients, Shannon diversity index and Nei gene diversity index, also confirmed this result. AMOVA analysis demonstrated that the genetic variation of D. sinensis within and among populations accounted for 56.89% and 43.11% of the total variation, respectively, and that of D. dyeriana was 57.86% and 42.14%, respectively. The Shannon diversity index and Nei gene diversity index showed similar results. The abovementioned characteristics indicated that the genetic diversity levels of these two species were extremely similar and that the interpopulational genetic differentiation within both species was relatively high. Analysis of the genetic distance among populations also supported this conclusion. Low levels of interpopulational gene flow within both species were believed to be among the leading causes for the above-mentioned phenomenon. The correlation analysis between genetic and geographical distances showed the existence of a remarkably significant correlation between the genetic distance and the longitudinal difference among populations of D. sinensis (p < 0.01), while no significant correlation was found between genetic and geographical distances among populations of D. dyeriana. This indicated that genetic distance was correlated with geographical distances on a large scale rather than on a small scale. This result may be related to differences in the selection pressure on species by their habitats with different distribution ranges. We suggest that in situ conservation efforts should focus on establishing more sites to protect the natural populations and their habitats. Ex situ conservation efforts should focus on enhancing the exchange of seeds and seedlings among populations to facilitate gene exchange and recombination, and to help conserve genetic diversity.

Austroasiatic (AA) speakers constitute around 4% of the population of Thailand, while the majority (89.4%) speak Kra-Dai (KD) languages. Previous forensic and population genetic studies in various Thai populations have employed a limited number of short tandem repeats (STRs). This study aims to expand the investigation of the genetic makeup of AA populations in Thailand and their relationship to KD populations using a larger number of autosomal STRs with the VeriFiler™ Plus PCR Amplification Kit. We generated 593 new genotypes from AA-speaking groups and combined them with previously reported data from AA and KD groups. A total of 1,129 genotypes across 23 STR loci were used to construct the largest allelic frequency profile for Thai and Lao populations. However, several loci deviated from Hardy-Weinberg equilibrium, likely due to the reduced genetic diversity in some highland populations, which should be considered in forensic investigations. Beyond forensic applications, our findings reveal genetic differences between AA-speaking groups in Northern and Northeastern Thailand. The AA groups from Northeastern Thailand exhibit greater genetic homogeneity and diversity, likely due to population interactions. In contrast, reduced diversity and increased heterogeneity in AA groups from Northern Thailand are possibly driven by genetic drift and cultural and geographic isolation. In conclusion, we emphasize the usefulness of increasing the number of autosomal STRs in forensic and anthropological genetic studies. Additional Y-STR and X-STR data from various AA-speaking groups in Thailand would further enhance and strengthen forensic STR databases in the region.

Migration is a microevolutionary process that shapes cultural, societal, and genetic diversity in human populations. While previous genetic studies have examined the effects of migrations in several key areas of the world, there is a paucity of such studies in the upper Greater Mekong Subregion (GMS). The upper GMS, encompassing northern Thailand, Laos, Myanmar, and southern China, has been a major corridor for human migration and interaction between East and Southeast Asian populations for thousands of years. We generated new genome-wide data for Tai-Kadai (TK)-speaking ethnic groups, namely Lue and Yong, from northern Thailand and integrated them with data from the upper GMS and across Asia. Our results highlight the genetic diversity among ethnic groups in the GMS, particularly the genetic continuity of TK migration from southern China to northern Thailand. The TK speakers in Thailand predominantly exhibit multiple ancestries from East Asia and Southeast Asia, with regional differentiations. The TK groups in northern Thailand primarily derive their genetic contributions from Dai-related communities, while northeastern Thai populations show a higher proportion of Lao-related ancestry. Those in central and southern Thailand display additional ancestries from other groups, such as Austroasiatic and South Asian populations. The genetic history of TK-speaking Lue populations illustrates the role of TK migration, founder effects, and historical resettlements in shaping genetic diversity. Overall, analyses of genome-wide data reveal that the genetic background of TK speakers in Thailand is predominantly of East Asian origin, with additional contribution from Southeast Asian populations. This pattern supports the idea of sustained migration from southern China into Thailand, particularly concentrated in the northern part. Our findings reinforce the historical continuity of TK movements across the upper GMS and provide new insights into the genetic and cultural transformations that have shaped present-day Thai populations.

Eremopyrum (Triticeae, Poaceae) is a small annual genus of forage importance in dry habitats of Asia. One of its species, E. bonaepartis, has a complicated taxonomic history. Some authors distinguished a separate species as E. confusum while others merged the latter to E. bonaepartis. In this study, we examined the genetic structure and diversity of the E. bonaepartis complex species in Iran using Inter Simple Sequence Repeats (ISSR) markers to determine the E. confusum situation and to assign genotypes to gene pools. Ten ISSR markers were used to evaluate the genetic diversity of 18 populations of the taxa studied. We estimated genetic parameters, genetic distance, gene flow, and genetic variation at both inter- and intra-population levels. AMOVA and structure analyses revealed high genetic diversity (77%) within taxa. Mantel test showed a significant correlation between genetic and geographical distance. A high level of gene flow among the taxa studied was observed. We concluded that there is no clear disjunction between taxa studied and observed admixture in the genetic structure. So we can conclude that E. confusum should not be considered separate from E. bonaepartis.

Ethological reproductive isolation and genetic divergence across 26 protein loci were measured among populations of the salamander Desmognathus ochrophaeus in the southern Appalachian Mountains. Levels of ethological isolation varied from none to complete and were statistically significant for all but two pairings between populations inhabiting different mountain ranges. When geographic and genetic distances were treated as independent variables in multiple correlation analyses, they accounted for about half the variance in levels of ethological isolation. When genetic distance is held constant, the remaining relationship between ethological isolation and geographic distance is still statistically significant. When geographic distance is held constant, the remaining relationship between genetic distance and levels of ethological isolation is nonsignificant, as is the relationship between geographic distance and genetic distance when ethological isolation is held constant. Ethological isolation and genetic divergence evidently both reflect the gradual divergence of allopatric populations, but genetic distance is a poor predictor of ethological isolation in these salamanders.