Migration rates as inferred from the 2002 Russian census

Migration rates in the modern Russian population have been studied on the basis of the results of the 2002 census. The migration rate at the population level corresponding to a city or rural administrative district is m = 0.443. The migration rate for women (m(F) = 0.463) is 11% higher than for men (m(M) = 0.418); the migration rate for urban populations (m(U) = 0.459) is 15% higher than for rural populations (m(R) = 0.398). The geographic variation of migrations has been studied; the geographic distributions of the migration rates for rural, urban, male, and female populations are presented. Comparison of migrations in the rural population of Russia at two temporal cross-sections (1970 and 2002) has shown that the geographic structure of migrations has remained the same in many respects. The ecological factor has remained the main determinant of the migration geography, which is expressed in the relationship of the settled way of life with the forest-steppe and broad-leaved forest landscapes.     

Alu insertion polymorphisms and an assessment of the genetic contribution of Central Asia to Anatolia with respect to the Balkans

In the evolutionary history of modern humans, Anatolia acted as a bridge between the Caucasus, the Near East, and Europe. Because of its geographical location, Anatolia was subject to migrations from multiple different regions throughout time. The last, well-known migration was the movement of Turkic speaking, nomadic groups from Central Asia. They invaded Anatolia and then the language of the region was gradually replaced by the Turkic language. In the present study, insertion frequencies of 10 Alu loci (A25 = 0.07, APO = 0.96, TPA25 = 0.44, ACE = 0.37, B65 = 0.57, PV92 = 0.18, FXIIIB = 0.52, D1 = 0.40, HS4.32 = 0.66, and HS4.69 = 0.30) have been determined in the Anatolian population. Together with the data compiled from other databases, the similarity of the Anatolian population to that of the Balkans and Central Asia has been visualized by multidimensional scaling method. Analysis suggested that, genetically, Anatolia is more closely related with the Balkan populations than to the Central Asian populations. Central Asian contribution to Anatolia with respect to the Balkans was quantified with an admixture analysis. Furthermore, the association between the Central Asian contribution and the language replacement episode was examined by comparative analysis of the Central Asian contribution to Anatolia, Azerbaijan (another Turkic speaking country) and their neighbors. In the present study, the Central Asian contribution to Anatolia was estimated as 13%. This was the lowest value among the populations analyzed. This observation may be explained by Anatolia having the lowest migrant/resident ratio at the time of migrations.     

Geography of genetic processes in populations: gene migrations in Siberia and Far East

A map of gene migration rate m in the indigenous population of Siberia and the Russian Far East was constructed on the basis of data obtained from questionnaires of 1960 to 1990. The mean gene migration rate weighted with respect to the region area and averaged over 3951 grid nodes was m = 0.0083. Weighting with respect to population density yielded a significantly lower rate (m = 0.0053), which reflected a more intense gene exchange in less populous regions of traditional nomadism. The association between gene migration rate m and genetically effective population size Ne was analyzed. The parameter Nem, which characterizes the interpopulation gene diversity, was used to identify regions where this parameter is autoregulated and those where the autoregulatory mechanisms were disrupted. A tree of ethnolinguistic types was constructed. Its analysis did not reveal any association between migration structure and linguistic characteristics, suggesting that the spreading of cultural elements is not necessarily associated with migration. The tree was also used to construct a map of ethnos-forming migration; its major element reflected migration from the Baikal and Altai regions to the ethnic region of modern Yakuts.     

Genetic demography of Ukrainian urban populations in the 1990s: the ethnic composition of the migration flow in the Kharkov population

Marriage records were used to study the dynamics of the migration flow into the population of Kharkov in 1960-1993. The decrease in the migration rate was accompanied by changes in the ethnic composition of the migrants. The entire migration flow from the republics of the Baltic region consisted of Russians and Ukrainians. The increase in the migration flow from Transcaucasia was mainly accounted for by the migration activity of indigenous populations. Most migrants from Moldova, Central Asia, Kazakhstan, and Kyrgyzstan were also representatives of the respective indigenous populations. Malecot's coefficient of isolation by distance (b) decreased from 0.00123 to 0.0081.     

Dynamics of the genetic demographic structure of the Kursk province population: migration processes

Marriage records from parish books of the second half of the 19th century and marriage records of 1967-1970 and 1993-1995 obtained from registry offices were used to analyze the dynamics of genetically significant parameters of migration and marriage structure with respect to spouses' birthplaces in populations of different hierarchical levels in the Kursk oblast. It was found that, among the persons contracting marriage (both males and females), the proportions of those who were born in the same population and those who were born in any population of the Kursk oblast decreased by about one third and one fifth, respectively, for the 130-year period. In rural and small urban populations, the coefficients of marriage migration in the 19th century were an order of magnitude lower than in the 20th century. The immigration to urban populations was maximum in the late 1960s (m = 0.745 in small towns and m = 0.680 in Kursk), and that to rural populations, in the 1990s (m = 0.344). In both urban and rural populations, the mean distance between the spouses' birthplaces has increased by several times for the period studied. The endogamy level has decreased approximately twofold: from 0.797 to 0.380 in Kursk, from 0.897 to 0.419 in small towns, and from 0.958 to 0.440 in rural districts. The marriage assortativeness with respect to birthplace was maximum in the late 19th century (K = 0.393-0.491) and minimum in the 1960s (K = 0.155-0.246). The increase in genetic diversity of the urban population of the Kursk oblast due to migration has been slowing down since the late 20th century, whereas the outbreeding level is still increasing in rural populations.     

Genetic Demography of Ukrainian Urban Populations in the 1990s: The Ethnic Composition of the Migration Flow in the Kharkov Population

Marriage records were used to study the dynamics of the migration flow into the population of Kharkov in 1960–1993. The decrease in the migration rate was accompanied by changes in the ethnic composition of the migrants. The entire migration flow from the republics of the Baltic region consisted of Russians and Ukrainians. The increase in the migration flow from Transcaucasia was mainly accounted for by the migration activity of indigenous populations. Most migrants from Moldova, Central Asia, Kazakhstan, and Kyrgyzstan were also representatives of the respective indigenous populations. Malecot's coefficient of isolation by distance (b) decreased from 0.00123 to 0.0081.     

Population genetic structure of northern Dolly Varden char Salvelinus malma malma in Asia and North America

The level of genetic differentiation of northern Dolly Varden char Salvelinus malma malma from Asia and North America was evaluated using the data on mtDNA variation (regions ND1/ND2, ND5/ND6, and Cytb/D loop) obtained by means of PCR-RFLP analysis. For S. m. malma, the mean values of haplotype and nucleotide diversity were 0.5261 +/- 0.00388 and 0.001558, respectively. The mean estimate of the population nucleotide divergence constituted 0.055%. It was demonstrated that S. m. malma on the most part of the species range examined (drainages of the Beaufort Sea, Chukotka Sea, Bering Sea, and the Sea of Okhotsk) was characterized by the population genetic structure with the low level of genetic differentiation and divergence. At the same time, populations from the Pacific Ocean Gulf of Alaska demonstrated marked genetic differentiation, supported by the high pairwise phi(ST) values (from 0.4198 to 0.5211) and nucleotide divergence estimates (mean divergence, 0.129%), from Asian and North American populations. Nested analysis of molecular variance (AMOVA) showed that most of the mtDNA variation in S. m. malma fell in the intrapopulation component (72.5%). At the same time, the differences between the populations (21.1%) and between the regions (6.4%) made lower contribution to the total variation.     

Biosocial covariates of adult male body mass index in Central India

Body mass index (BMI) is the 'measuring rod' of nutritional status. This study investigates the type and extent of correlation between adult male BMI and socioeconomic, cultural and bio-demographical variables using data from 11,496 individuals from 38 districts of Central India. For each individual, stature, body weight and sitting height data were collected, their Cormic index and BMI computed, and averages for each district calculated. Mean BMI was found to be lowest for the population of Tikamgarh (17.90+/-1.91 kg m(-2)) and highest for that of Durg district (19.33+/-2.16 kg m(-2)), whereas the mean BMI for the total population of Central India was 18.67+/-2.18 kg m(-2), which is lower than that of well-to-do individuals in India as a whole. The F ratio indicates that there is inter-district variation in anthropometric characteristics of populations. District-wise biosocial indicators were obtained, namely population density per square kilometre, percentage urban population, percentage of population that is of scheduled caste/tribe, sex ratio, average rural population per PHC/CHC (primary or community health centre), literacy rate, life expectancy, total fertility rate, infant mortality rate, gender development index and human development index. Most of these variables were found to be significantly correlated with each other, but BMI was only significantly correlated with three of them, viz. gender development index (R2=0.211), life expectancy (R2=0.130) and infant mortality rate (R2=0.128). Gender development index and life expectancy were positively correlated with BMI, whereas infant mortality rate was negatively correlated. It is concluded that if BMI increases then life expectancy will also increase. Thus better nutritional status may be a helpful tool for reducing infant mortality rate, which is an indicator of socioeconomic status, health condition, health care and ultimately overall development of a region or population.     

Evolutionary history of Helicobacter pylori sequences reflect past human migrations in Southeast Asia

The human population history in Southeast Asia was shaped by numerous migrations and population expansions. Their reconstruction based on archaeological, linguistic or human genetic data is often hampered by the limited number of informative polymorphisms in classical human genetic markers, such as the hypervariable regions of the mitochondrial DNA. Here, we analyse housekeeping gene sequences of the human stomach bacterium Helicobacter pylori from various countries in Southeast Asia and we provide evidence that H. pylori accompanied at least three ancient human migrations into this area: i) a migration from India introducing hpEurope bacteria into Thailand, Cambodia and Malaysia; ii) a migration of the ancestors of Austro-Asiatic speaking people into Vietnam and Cambodia carrying hspEAsia bacteria; and iii) a migration of the ancestors of the Thai people from Southern China into Thailand carrying H. pylori of population hpAsia2. Moreover, the H. pylori sequences reflect iv) the migrations of Chinese to Thailand and Malaysia within the last 200 years spreading hspEasia strains, and v) migrations of Indians to Malaysia within the last 200 years distributing both hpAsia2 and hpEurope bacteria. The distribution of the bacterial populations seems to strongly influence the incidence of gastric cancer as countries with predominantly hspEAsia isolates exhibit a high incidence of gastric cancer while the incidence is low in countries with a high proportion of hpAsia2 or hpEurope strains. In the future, the host range expansion of hpEurope strains among Asian populations, combined with human motility, may have a significant impact on gastric cancer incidence in Asia.     

High genetic variation in leopards indicates large and long-term stable effective population size

In this paper we employ recently developed statistical and molecular tools to analyse the population history of the Tanzanian leopard (Panthera pardus), a large solitary felid. Because of their solitary lifestyle little is known of their past or present population dynamics. Eighty-one individuals were scored at 18 microsatellite loci. Overall, levels of heterozygosity were high (0.77 +/- 0.03), with a small heterozygote deficiency (0.06 +/- 0.03). Effective population size (Ne) was calculated to be 38 000-48 000. A Ne:N ratio of 0.42 (average from four cat studies) gives a present population size of about 100 000 leopards in Tanzania. Four different bottleneck tests indicated that this population has been large and stable for a minimum of several thousand years. FST values were low and no significant genetic structuring of the population could be detected. This concurs well with the large migration values (Nm) obtained (>3.3 individuals/generation). Our analysis reveals that ecological factors (e.g. disease), which are known to have had major impact on other carnivore populations, are unlikely to have impacted strongly on the population dynamics of Tanzanian leopards. The explanation may be found in their solitary life-style, their often nonconfrontational behaviour toward interspecific competitors, or that any bottlenecks have been of limited size, localized, or too short to have affected genetic variation to any measurable degree. Since the genetic structuring is weak, gene flow is not restricted to within protected areas. Local loss of genetic variation is therefore not of immediate concern.     

Small effective population size in the long-toed salamander

The effective population sizes (Ne) of six populations of the long-toed salamander (Ambystoma macrodactylum) from Montana and Idaho, USA were estimated from allozyme data from samples collected in 1978, 1996 and 1997 using the temporal allele frequency method. Five of the six estimates ranged from 23 to 207 (mean = 123 +/- 79); one estimate was indistinguishable from infinity. In order to infer the actual Ne of salamander populations, we compared the frequency distribution of our observed Ne estimates with distributions obtained from simulated populations of known Ne. Our observed Ne estimate distribution was consistent with distributions from simulated populations with Ne values of 10, 25, and 50, suggesting an actual Ne for each of the six salamander populations of less than 100. This Ne estimate agrees with most other Ne estimates for amphibians. We conclude by discussing the conservation implications of small Ne values in amphibians in the context of increasing isolation of populations due to habitat fragmentation.     

Ancestry of the Iban is predominantly Southeast Asian: genetic evidence from autosomal, mitochondrial, and Y chromosomes

Humans reached present-day Island Southeast Asia (ISEA) in one of the first major human migrations out of Africa. Population movements in the millennia following this initial settlement are thought to have greatly influenced the genetic makeup of current inhabitants, yet the extent attributed to different events is not clear. Recent studies suggest that south-to-north gene flow largely influenced present-day patterns of genetic variation in Southeast Asian populations and that late Pleistocene and early Holocene migrations from Southeast Asia are responsible for a substantial proportion of ISEA ancestry. Archaeological and linguistic evidence suggests that the ancestors of present-day inhabitants came mainly from north-to-south migrations from Taiwan and throughout ISEA approximately 4,000 years ago. We report a large-scale genetic analysis of human variation in the Iban population from the Malaysian state of Sarawak in northwestern Borneo, located in the center of ISEA. Genome-wide single-nucleotide polymorphism (SNP) markers analyzed here suggest that the Iban exhibit greatest genetic similarity to Indonesian and mainland Southeast Asian populations. The most common non-recombining Y (NRY) and mitochondrial (mt) DNA haplogroups present in the Iban are associated with populations of Southeast Asia. We conclude that migrations from Southeast Asia made a large contribution to Iban ancestry, although evidence of potential gene flow from Taiwan is also seen in uniparentally inherited marker data.     

Long-term temporal changes of genetic composition in brown trout (Salmo trutta L.) populations inhabiting an unstable environment

The genetic structure of brown trout (Salmo trutta) populations inhabiting rivers on the island of Bornholm in the Baltic Sea was studied on a spatial and temporal scale. Low water levels in the rivers during the summer period are assumed to have a significant impact on the persistence of local populations, possibly resulting in a metapopulation structure. Extinctions may, however, also be buffered by a remnant strategy, whereby juveniles escape to river outlets during periods of drought. We compared polymorphism at seven microsatellite DNA loci in contemporary and past samples collected from 1944 to 1997. A principal component analysis, a hierarchical gene diversity analysis and assignment tests showed that the genetic composition of populations was not temporally stable, and that temporal genetic differentiation was much stronger than spatial differentiation. Genetic variability was high and stable over time. Effective population sizes (Ne) and migration rate (m) were estimated using a maximum-likelihood-based implementation of the temporal method. Ne estimates were low (ranging from 8.3 to 22.9) and estimates of m were high (between 0.23 and 0.99), in contrast to other Danish trout populations inhabiting larger and more environmentally stable rivers (Ne between 39.2 and 289.9 and m between 0.01 and 0.09). Thus, the observed spatio-temporal patterns of genetic differentiation can be explained by drift in small persisting populations, where levels of genetic variation are maintained by strong gene flow. However, observations of rivers devoid of trout suggested that population turnover also takes place. We suggest that Bornholm trout represent a metapopulation where the genetic structure primarily reflects strong drift and gene flow, combined with occasional extinction-recolonization events.     

Introgression of nuclear and mitochondrial DNA markers of Mus musculus musculus to aboriginal populations of wild mice from Central Asia (M. m. wagneri) and South Siberia (M. m. gansuensis)

Variability of the nucleotide sequences of the second intron of the b1-chain of hemoglobin (Hbb-b1) and complete control region of mitochondrial DNA (D-loop) was studied in aboriginal and synanthropic populations of M. m. wagneri from Central Asia and M. m. gansuensis from South Siberia. A difference in the frequency of the Hbb^w1 hemoglobin variant for natural and urban populations of mice was shown. All mice from natural habitats of studied areas have musculus type of mtDNA. Apparently, the substitution of taxon-specific mitochondrial haplotypes of wagneri, and gansuensis might occur due to the absorbing hybridization with nominate subspecies musculus, which is consistent with the results on nuclear DNA (Hbb-b1 gene) obtained in this work. Two differentiated haplogroups among aboriginal subspecies wagneri (d = 0.01), one of which included house mice from Turkmenistan, were discovered for the first time. This may indicate mtDNA introgression from synanthropic forms of Turkmenistan into natural populations of Kazakhstan mice. The type of mtDNA typical for the castaneus subspecies was detected in two individuals from the natural habitat of Kazakhstan and Turkmenistan; it had not been encountered in Central Asia before. It has been suggested that the gene flow of nuclear and mitochondrial genomes in microevolution processes in M. musculus is directed from the synanthropic forms towards wild populations.     

Effective population sizes and temporal stability of genetic structure in Rana pipiens, the northern leopard frog

Although studies of population genetic structure are very common, whether genetic structure is stable over time has been assessed for very few taxa. The question of stability over time is particularly interesting for frogs because it is not clear to what extent frogs exist in dynamic metapopulations with frequent extinction and recolonization, or in stable patches at equilibrium between drift and gene flow. In this study we collected tissue samples from the same five populations of leopard frogs, Rana pipiens, over a 22-30 year time interval (11-15 generations). Genetic structure among the populations was very stable, suggesting that these populations were not undergoing frequent extinction and colonization. We also estimated the effective size of each population from the change in allele frequencies over time. There exist few estimates of effective size for frog populations, but the data available suggest that ranid frogs may have much larger ratios of effective size (Ne) to census size (Nc) than toads (bufonidae). Our results indicate that R. pipiens populations have effective sizes on the order of hundreds to at most a few thousand frogs, and Ne/Nc ratios in the range of 0.1-1.0. These estimates of Ne/Nc are consistent with those estimated for other Rana species. Finally, we compared the results of three temporal methods for estimating Ne. Moment and pseudolikelihood methods that assume a closed population gave the most similar point estimates, although the moment estimates were consistently two to four times larger. Wang and Whitlock's new method that jointly estimates Ne and the rate of immigration into a population (m) gave much smaller estimates of Ne and implausibly large estimates of m. This method requires knowing allele frequencies in the source of immigrants, but was thought to be insensitive to inexact estimates. In our case the method may have failed because we did not know the true source of immigrants for each population. The method may be more sensitive to choice of source frequencies than was previously appreciated, and so should be used with caution if the most likely source of immigrants cannot be identified clearly.     

The population genomic landscape of human genetic structure,admixture history and local adaptation in Peninsular Malaysia

Peninsular Malaysia is a strategic region which might have played an important role in the initial peopling and subsequent human migrations in Asia. However, the genetic diversity and history of human populations—especially indigenous populations—inhabiting this area remain poorly understood. Here, we conducted a genome-wide study using over 900,000 single nucleotide polymorphisms (SNPs) in four major Malaysian ethnic groups (MEGs; Malay, Proto-Malay, Senoi and Negrito), and made comparisons of 17 world-wide populations. Our data revealed that Peninsular Malaysia has greater genetic diversity corresponding to its role as a contact zone of both early and recent human migrations in Asia. However, each single Orang Asli (indigenous) group was less diverse with a smaller effective population size (N _e) than a European or an East Asian population, indicating a substantial isolation of some duration for these groups. All four MEGs were genetically more similar to Asian populations than to other continental groups, and the divergence time between MEGs and East Asian populations (12,000—6,000 years ago) was also much shorter than that between East Asians and Europeans. Thus, Malaysian Orang Asli groups, despite their significantly different features, may share a common origin with the other Asian groups. Nevertheless, we identified traces of recent gene flow from non-Asians to MEGs. Finally, natural selection signatures were detected in a batch of genes associated with immune response, human height, skin pigmentation, hair and facial morphology and blood pressure in MEGs. Notable examples include SYN3 which is associated with human height in all Orang Asli groups, a height-related gene (PNPT1) and two blood pressure-related genes (CDH13 and PAX5) in Negritos. We conclude that a long isolation period, subsequent gene flow and local adaptations have jointly shaped the genetic architectures of MEGs, and this study provides insight into the peopling and human migration history in Southeast Asia.     

On the origins,rapid expansion and genetic diversity of native Americans from hunting‐gatherers to agriculturalists

Given the importance of Y‐chromosome haplogroup Q to better understand the source populations of contemporary Native Americans, we studied 8 biallelic and 17 microsatellite polymorphisms on the background of 128 Q Y‐chromosomes from geographically targeted populations. The populations examined in this study include three from the Tuva Republic in Central Asia (Bai‐Tai, Kungurtug, and Toora‐Hem, n = 146), two from the northeastern tip of Siberia (New Chaplino and Chukchi, n = 32), and two from Mesoamerica (Mayans from Yucatan, Mexico n = 72, and Mayans from the Guatemalan Highlands, n = 43). We also see evidence of a dramatic Mesoamerican post‐migration population growth in the ubiquitous and diverse Y‐STR profiles of the Mayan and other Mesoamerican populations. In the case of the Mayans, this demographic growth was most likely fueled by the agricultural‐ and trade‐based subsistence adopted during the Pre‐Classic, Classic and Post‐Classic periods of their empire. The limited diversity levels observed in the Altaian and Tuvinian regions of Central Asia, the lowest of all populations examined, may be the consequence of bottleneck events fostered by the spatial isolation and low effective population size characteristic of a nomadic lifestyle. Furthermore, our data illustrate how a sociocultural characteristic such as mode of subsistence may be of impact on the genetic structure of populations. We analyzed our genetic data using Multidimensional Scaling Analysis of populations, Principal Component Analysis of individuals, Median‐joining networks of M242, M346, L54, and M3 individuals, age estimations based on microsatellite variation utilizing genealogical and evolutionary mutation rates/generation times and estimation of Y‐ STR average gene diversity indices. Am J Phys Anthropol, 2013. © 2013 Wiley Periodicals, Inc.     

A genetic metapopulation model for reef fishes in oceanic islands: the case of the surgeonfish,Acanthurus triostegus

Allozyme data on a surgeonfish, Acanthurus triostegus, were analysed from 10 islands in French Polynesia. We compared estimates of gene flow according to the hypothesis of an equilibrium between genetic drift and migration, and estimated genetic divergence times assuming complete genetic isolation without gene flow since foundation. The significant correlation between genetic divergence and geographic distance, at the within-archipelago level (r = 0.709, P = 0.024) indicates exchange of individuals mainly between neighbouring populations. The correlation was, however, not significant at the among-archipelagoes level (r = 0.325, P = 0.330), suggesting that long distance migrations are more sporadic. This addresses the problem of scale in population biology. According to the spatial scale of analysis, results can change from an island model, with no relation between genetic differentiation and geographical distances between archipelagos, to an isolation-by-distance model within an archipelago. These factors lead us to propose a “patchy population” model, in which all patches are occupied and reproductively active, though with few successful migrations between neighbouring populations. This model describes a subdivided population that is stable through time, with an amount of gene flow small enough to allow significant local differentiation in neutral gene frequency, but high enough to prevent differential fixation in the long term, and therefore preserving the genetic cohesion of the species.     

Y-chromosome evidence of southern origin of the East Asian-specific haplogroup O3-M122

The prehistoric peopling of East Asia by modern humans remains controversial with respect to early population migrations. Here, we present a systematic sampling and genetic screening of an East Asian-specific Y-chromosome haplogroup (O3-M122) in 2,332 individuals from diverse East Asian populations. Our results indicate that the O3-M122 lineage is dominant in East Asian populations, with an average frequency of 44.3%. The microsatellite data show that the O3-M122 haplotypes in southern East Asia are more diverse than those in northern East Asia, suggesting a southern origin of the O3-M122 mutation. It was estimated that the early northward migration of the O3-M122 lineages in East Asia occurred approximately 25,000-30,000 years ago, consistent with the fossil records of modern humans in East Asia.