Genetic-demographic study of the Gagauz population of Moldava

The genetic demographic structure of the Gagauz population of Moldova has been described for the first time. Data of interviews and official records have been used to analyze the sex and age structure of the population and marriage relationships, as well as to estimate the effective sizes of the populations of six settlements and selection intensity (according to Crow's formula). The demographic data indicate that social transformations have substantially affected the genetic demographic parameters of the population. The gene exchange rate per generation has been determined (m = 0.0204 in 1972 and m = 0.0309 in 1997). The estimated ratio between the components of Crow's index (I(m) < I(f)) in the Gagauz population is similar to those for the populations of developed countries with traditionally rural lifestyles. The study of marriage relationships of the Gagauz population has shown that Gagauzes are intensely mixing with Moldovans, Bulgarians, Russians, and Ukrainians.     

Genetic Demographic Structure of Rural Populations of Kyrgyzstan

The genetic demographic parameters of rural populations of Kyrgyzstan have been studied. The rural population of Kyrgyzstan has the following demographic characteristics: (1) it is demographically young (the population mean age is 25–28 years); (2) the sex ratio in reproductive age groups is unfavorable; (3) the fertility is high (5.78–7.68 pregnancies and 4.27–5.20 surviving children per woman of postreproductive age; (4) interethnic marriages are rare (1.0–5.9%), whereas consanguineous marriages are frequent (1.4–12%); (5) Crow's indices are relatively low (I _tot = 0.24–0.29, I _m = 0.05–0.13, I _f = 0.14–0.22); and (6) both male and female contributions of different regions of the republic make unequal contributions to the gametic structure of the population, with the gametic structure varying from generation to generation. Demographic parameters vary in rural populations of different geographic regions and with different ethnic compositions.     

Genetic and Demographic Structure of the Yakut Population: Reproduction Indices

Genetic and demographic information for the Yakut population living in the Republic of Sakha (Yakutia) is presented. The mean number of children per woman constituted 4.605. Crow's index (I _tot) and its components (I _m and I _f) were 0.483, 0.104, and 0.343, respectively.     

Comparison of Chuvashes,Maris, and Russians with Respect to Vital Statistics and Crow's Index

Genetic demographic characteristics were calculated for Chuvash and Russian inhabitants of the Republic of Chuvashia. The generation lengths were 27.09 and 26.4 years and the sibship sizes were 2.54 and 1.82 for Chuvashes and Russians, respectively. Crow's indices and their components were as follows: I _m = 0.05, I _f = 0.31, and I _tot = 0.37 for Chuvashes and I _m = 0.03, I _f = 0.43, and I _tot = 0.46 for Russians. The genetic demographic characteristics obtained were compared with those for Highland and Meadow Maris.     

Genetic Demographic Description of the Ust-Aldan Rural Population of Sakha Republic (Yakutia): Ethnic, Sex, and Age Compositions, Vital Statistics, and Surname Structure

Information on the sex, age, and ethnic compositions; reproductive parameters; intensity of natural selection (Crow's indices); and surname diversity of three rural populations (the Byadi, Dyupsya, and Cheriktey villages) of the Ust-Aldan ulus (district) of Sakha Republic (Yakutia) has been analyzed. The rural Yakut population of the Ust-Aldan ulus is demographically young (the mean age 25–31 years) and characterized by low outbreeding, unfavorable sex ratio in both prereproductive and reproductive ages, and high fertility (3.58–5.45 children surviving until the reproductive age per woman that has completed the reproductive period), although the actual reproductively active period is shorter than half its physiological duration. In the structure of index of total selection, the differential-fertility component is considerably greater than the differential-mortality component (I _tot = 0.625, I _m = 0.093, and I _f = 0.487). In the villages studied, some surnames are accumulated (45–65% of the population have five most frequent surnames), which determines the low surname diversity ( = 11.62–25.19) and high random isonymy (I _r= 0.0391–0.0823).     

Dynamics of the Genetic Demographic Structure of the Kursk Oblast 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.     

An AFLP-based survey of genetic diversity and relationships of major farmed cultivars and geographically isolated wild populations of <Emphasis Type="Italic">Saccharina japonica</Emphasis> (Phaeophyta) along the northwest coasts of the Pacific

The genetic diversity and relationships of six representative cultivars and six geographically isolated wild populations of Saccharina japonica along the northwest coasts of the Pacific Ocean were investigated using AFLP markers. A total of 547 bands were generated across all samples by ten primer combinations. At the cultivar or population level, the percentage of polymorphic loci (P), gene diversity (H), and Shannon’s information index (I) was highest in Dalian population (P 59.05%; H 0.2057; I 0.3062) and lowest in Lianjiang cultivar (P 9.87%; H 0.0331; I 0.0497). At the species level, P, H, and I were 85.01%, 0.1948, and 0.3096, respectively. Unique bands were detected in all the six wild populations, with Dalian being the most. In comparison, only Yanza cultivar possessed one unique band. The G _ST value was 0.6226 and the gene flow (N _m ) was 0.1515, indicating strong genetic differentiation among cultivars and populations. Two UMPGA dendrograms were constructed based on the Dice similarity coefficients among individuals and on genetic distances among cultivars and populations, which generally revealed three major clades corresponding to three countries. Analysis of molecular variance revealed that a larger proportion (60.21%) of the total genetic variation was attributable to differences among cultivars and populations. The Mantel test suggested that genetic differentiation was positively correlated with geographic distance (r = 0.7962, P = 0.011) in the six wild populations, agreeing with the isolation by distance model. On the whole, low to moderate genetic diversity within cultivars and populations (except Dalian population) and high genetic differentiation among cultivars and populations were detected.     

The population structure of rural settlements of Sakha Republic (Yakutia): ethnic, sex, and age composition and vital statistics

The genetic demographic structure of 12 rural populations from eight uluses of Sakha Republic (Yakutia) has been analyzed. The ethnic, sex, and age composition of the population and the reproductive parameters of women that have completed and have not completed the reproductive period are reported. Crow's indices have been estimated in representatives of three indigenous ethnic groups (Yakuts, Evens, and Evenks).     

A Study of Conservation Genetics in Cupressus chengiana,an Endangered Endemic of China,Using ISSR Markers

ISSR markers were used to analyze the genetic diversity and genetic structure of eight natural populations of Cupressus chengiana in China. ISSR analysis using 10 primers was carried out on 92 different samples. At the species level, 136 polymorphic loci were detected. The percentage of polymorphic bands (PPB) was 99%. Genetic diversity (H _e) was 0.3120, effective number of alleles (A _e) was 1.5236, and Shannon’s information index (I) was 0.4740. At the population level, PPB = 48%, A _e=1.2774, H _e=0.1631, and I=0.2452. Genetic differentiation (G _st) detected by Nei’s genetic diversity analysis suggested 48% occurred among populations. The partitioning of molecular variance by AMOVA analysis indicated significant genetic differentiation within populations (54%) and among populations (46%; P < 0.0003). The average number of individuals exchanged between populations per generation (N _m ) was 0.5436. Samples from the same population clustered in the same population-specific cluster, and two groups of Sichuan and Gansu populations were distinguishable. A significantly positive correlation between genetic and geographic distance was detected (r=0.6701). Human impacts were considered one of the main factors to cause the rarity of C. chengiana, and conservation strategies are suggested based on the genetic characters and field investigation, e.g., protection of wild populations, reestablishment of germplasm bank, and reintroduction of more genetic diversity.     

Wild genetic diversity preservation in a small-sized first generation breeding population of <Emphasis Type="Italic">Allanblackia floribunda</Emphasis> (Clusiaceae)

Founder group size is of prime importance in tree breeding programs. We determined whether sampling 20-plus trees for breeding in Allanblackia floribunda, a tropical forest tree species that has been recently enrolled in tree improvement program for fruit and seed production, would affect neutral genetic diversity and inbreeding level in both breeding and production populations. Using eight informative microsatellite loci, we: (a) assessed the nuclear genetic diversity of ten natural populations, and of the breeding population in the humid forest zone of Cameroon; (b) investigated temporal effective-size fluctuations in A. floribunda natural populations, with a view to identifying the role of past demographic events in the genetic structure of the studied species; and (c) tested the hypothesis that genetic diversity in a founder group of 20 individuals is not different from that existing in the wild. The eight loci were variable. High levels of genetic diversity (A = 4.96; H _E = 0.59) and moderate differentiation (R _ST = 0.061) were found within and among populations in wild stands. High genetic distances existed between populations ( \textaverage chord distance = 0.\text2769 ±0.00\text554 ) \left( {{\text{average chord distance}} = 0.{\text{2769}} \pm 0.00{\text{554}}} \right) . Eight of the ten surveyed populations showed signs of deviation from mutation-drift equilibrium, suggesting Pleistocene population bottlenecks and fluctuations in effective population size. Mantel tests did not reveal any relationships between genetic and geographic distances. A neighbor-joining dendrogram showed a population structure that could be explained by historical factors. The hypothesis tested has been accepted. However, a slight increase in inbreeding was observed in the breeding population.     

Genetic diversity within a declining natural population of Ferocactus histrix (DC) Lindsay

Ferocactus histrix is a barrel cactus that is widespread in Mexico. A population located in Llanos de Ojuelos, a semiarid zone representative of many disturbed regions in north‐central Mexico, was studied. Over a period of 10 years (1997 to 2007), the average number of individuals decreased from 21.95 to 3.53 plants per 300 m². A change in population size structure was also registered over this period of time. In 2008, a plot selected on the basis of plant abundance was established within the population and a genetic analysis was conducted with ISTR and ISSR markers. This analysis revealed low levels of genetic diversity (expected heterozygosity (H_E) = 0.073, Shannon index (I) = 0.113 and H_E = 0.178, I = 0.271, respectively) compared with those of most studied cacti species. The genetic diversity between the different life stages was also evaluated, and a gradual decrease in levels of genetic variation was observed from adults to juveniles and seedlings (H_E = 0.130, I = 0.192 to H_E = 0.103, I = 0.157). These differences, however, were not significant. Loci fixation and a decrease in the frequency of rare alleles were observed in seedling and juvenile classes. The decline in genetic variation may be associated with recent bottlenecks experienced by the population of F. histrix. If the sizes of local populations of F. histrix continue to decrease, genetic variation will be gradually lost, and the risk of extinction will increase.     

Spatial and temporal patterns of neutral and adaptive genetic variation in the endangered African wild dog (Lycaon pictus)

Deciphering patterns of genetic variation within a species is essential for understanding population structure, local adaptation and differences in diversity between populations. Whilst neutrally evolving genetic markers can be used to elucidate demographic processes and genetic structure, they are not subject to selection and therefore are not informative about patterns of adaptive variation. As such, assessments of pertinent adaptive loci, such as the immunity genes of the major histocompatibility complex (MHC), are increasingly being incorporated into genetic studies. In this study, we combined neutral (microsatellite, mtDNA) and adaptive (MHC class II DLA‐DRB1 locus) markers to elucidate the factors influencing patterns of genetic variation in the African wild dog (Lycaon pictus); an endangered canid that has suffered extensive declines in distribution and abundance. Our genetic analyses found all extant wild dog populations to be relatively small (N_e < 30). Furthermore, through coalescent modelling, we detected a genetic signature of a recent and substantial demographic decline, which correlates with human expansion, but contrasts with findings in some other African mammals. We found strong structuring of wild dog populations, indicating the negative influence of extensive habitat fragmentation and loss of gene flow between habitat patches. Across populations, we found that the spatial and temporal structure of microsatellite diversity and MHC diversity were correlated and strongly influenced by demographic stability and population size, indicating the effects of genetic drift in these small populations. Despite this correlation, we detected signatures of selection at the MHC, implying that selection has not been completely overwhelmed by genetic drift.     

粗山羊草种质遗传多样性及群体结构的ISSR分析

粗山羊草分布范围广,遗传变异丰富,被认为是改良普通小麦的重要基因源。为深入了解不同来源粗山羊草种质的遗传多样性和群体结构,该研究利用ISSR分子标记对56份粗山羊草种质进行了遗传多样性和群体结构分析。结果表明:(1)16个ISSR引物共检测170条多态性位点,每个ISSR引物多态性位点为3～18条,平均为10.63条; 多态性信息(PIC)变异范围为0.17～0.85,平均为0.67。(2)粗山羊草4个群体的遗传多样性比较显示,中亚粗山羊草的群体遗传多样性水平最高(H_e=0.225 4,I=0.355 7),群体间的基因流较低(N_m=1.638 6)。(3)聚类结果在遗传相似系数约0.67处,来源于塔吉克斯坦6份和土库曼斯坦2份粗山羊草种质材料聚成一类(Group 2); 其他48份种质材料形成一大类(Group 1),其中Group 1可进一步分成3个Sub亚类,呈现出来源相同的粗山羊草种质材料倾向聚在一起。(4)群体结构分析将56份粗山羊草种质分为5个群体,其中,来源于西亚伊朗V群体种质材料遗传背景比较一致,混杂程度相对较低; 进一步分析各群体Q值,发现IV群体种质材料亲缘关系的来源相对复杂,遗传多样最为丰富。该研究结果可为粗山羊草种质亲缘关系解析、种质多样性保护提供重要参考依据,为其科学利用以及进化研究奠定基础。     

Is population genetic structure of vascular plants shaped more by ecological or geographic factors? A study case on the Mediterranean endemic Centaurea filiformis (Asteraceae)

• All known populations of the Sardinian endemic Centaurea filiformis Viv. (Asteraceae) were studied in order to understand the impact of both geographic and ecological factors on the genetic structuring of this species.
• Fourteen populations and 234 individuals were sampled. The demographic structure of the populations and the reproductive ecology were estimated in 28 plots. Population genetic analyses were based on SSR markers. Genetic structure was investigated by spatial Bayesian methods.
• Average densities of 0.51 individuals m^?2 were detected, with a prevalence of adults. Ten species of pollinators were identified; C. filiformis ability to self‐pollinate and myrmecochory were demonstrated experimentally. The populations displayed an average heterozygosity value of H _e = 0.576 and high genetic differentiation (overall F _ST = 0.218). Bayesian analysis suggests that five is the most probable number of gene pools of origin. A strong correlation between geographic distances and genetic distances among populations was highlighted.
• The demographic population structure of C. filiformis is dominated by adults, suggesting that it is a stable‐regressive or senile species, investing more in local persistence than colonisation ability. Despite the scattered distribution, the populations studied do not present evidence of genetic erosion. The analysis of genetic differentiation reveals very high differentiation levels among populations, thus indicating that effective barriers exist against gene flow. A general conclusion is that population distribution results in a clear genetic structure for the populations studied, and that geography and not ecology is shaping the present distribution of this species.

     

Inferring demographic processes from the genetic structure of a metapopulation of <Emphasis Type="Italic">Boltonia decurrens</Emphasis>(Asteraceae)

Boltonia decurrens(Asteraceae), a federally listed, threatened floodplain species, requires regular flooding for suitable habitat and seed dispersal. Flood suppression and habitat destruction have resulted in fewer than 25 populations remaining throughout its 400 km range. Because individual populations are widely interspaced (>10 km) and subject to frequent extinction and colonization, seed dispersal along the river, not pollen flow, is likely the primary determinant of population genetic structure. We used neutral genetic markers (isozymes) assayed for fourteen populations to determine which demographic processes contribute to the genetic structure of B. decurrens. Significant genetic differentiation was detected among populations (F _ST=0.098, P< 0.05) but not among regions (F _RT=0.013, P> 0.05), suggesting that long-distance dispersal events occur and involve seed from a small number of populations. Correspondingly, we found no evidence of isolation by distance, and admixture analyses indicate that colonization events involve seed from 3 to 5 source populations. Individual populations exhibited high levels of fixation (mean F _IS=0.192, P< 0.05), yet mean population outcrossing rates were high (t _m=0.87–0.95) and spatial autocorrelation analyses revealed no fine-scale within population structure, indicating that inbreeding alone cannot explain the observed fixation. Rather, genetic bottlenecks, detected for 12 of 14 populations, and admixture at population founding may be important sources of fixation. These observations are consistent with a metapopulation model and confirm the importance of regular flooding events, capable of producing suitable habitat and dispersing seed long distances, to the long-term persistence of B. decurrens.     

Demographic bottlenecks and low gene flow in remnant populations of the critically endangered <Emphasis Type="Italic">Berchemiella wilsonii</Emphasis> var<Emphasis Type="Italic">. pubipetiolata</Emphasis> (Rhamnaceae) inferred from microsatellite markers

Berchemiella wilsonii var. pubipetiolata (Rhamnaceae) is an endangered plant with only four remnant populations in eastern China. Population genetic information is essential for understanding population history and formulating conservation strategies for this species. Thirteen microsatellite loci were used to investigate genetic variation and population structure of the four remnant populations. Moderate levels of expected heterozygosity (H _E = 0.466–0.543) and low allelic diversity (A = 3.1–3.6 and A _R = 2.2–2.4, respectively) were observed within populations. Bottleneck tests found three out of four populations to deviate from mutation-drift equilibrium under the two-phase model (TPM), suggesting a recent population decline, which is congruent with known demographic history. The evolutionary history of the species seems dominated by genetic drift rather than gene flow. Low historical gene flow was inferred from several different approaches and N _m ranged from 0.582 by the private allele method to 0.783 by the coalescent method. Contemporary gene flow was also found to be even lower for only one first generation migrant was detected with individual-based assignment analysis. Restricted pollen and seed dispersal as well as a recent decline in population size associated with habitat fragmentation may have contributed to low levels of historical and contemporary gene flow, and resulted in a high genetic differentiation. Under this scenario, Berchemiella wilsonii var. pubipetiolata populations are expected to display more pronounced population genetic structure in the future as a result of increased inbreeding and genetic drift.     

Population genetic structure of wild-growing ginseng (<Emphasis Type="Italic">Planax ginseng</Emphasis> C.A. Meyer) assessed using AFLP markers

Genetic variability in ten populations of wild-growing ginseng was assessed using AFLP markers with the application of fragment analysis on a genetic analyzer. The variation indices were high in the populations (P = 55.68%, H _S = 0.1891) and for the species (P = 99.65%; H _S = 0.2857). Considerable and statistically significant population differentiation was demonstrated (θ_B = 0.363; Bayesian approach, “full model”; F _ST = 0.36, AMOVA). The results of AMOVA and Bayesian analysis indicate that 64.46% of variability is found within the populations. Mantel test showed no correlation between the genetic and geographic distances among the populations (r = −0.174; p = 0.817). Hierarchical AMOVA and analysis of genetic relationships based on Euclidean distances (NJ, PCoA, and MST) identified two divergent population groups of ginseng. Low gene flow between these groups (N _m = 0.4) suggests their demographic independence. In accordance to the concept of evolutionary significant units (ESU), these population groups, in terms of the strategy and tactics for conservation and management of natural resources, should be treated as management units (MUs). The MS tree topology suggests recolonization of southern Sikhote-Alin by ginseng along two directions, from south and west.     

Trapped within the city: integrating demography,time since isolation and population‐specific traits to assess the genetic effects of urbanization

Urbanization is a severe form of habitat fragmentation that can cause many species to be locally extirpated and many others to become trapped and isolated within an urban matrix. The role of drift in reducing genetic diversity and increasing genetic differentiation is well recognized in urban populations. However, explicit incorporation and analysis of the demographic and temporal factors promoting drift in urban environments are poorly studied. Here, we genotyped 15 microsatellites in 320 fire salamanders from the historical city of Oviedo (Est. 8th century) to assess the effects of time since isolation, demographic history (historical effective population size; N_e) and patch size on genetic diversity, population structure and contemporary N_e. Our results indicate that urban populations of fire salamanders are highly differentiated, most likely due to the recent N_e declines, as calculated in coalescence analyses, concomitant with the urban development of Oviedo. However, urbanization only caused a small loss of genetic diversity. Regression modelling showed that patch size was positively associated with contemporary N_e, while we found only moderate support for the effects of demographic history when excluding populations with unresolved history. This highlights the interplay between different factors in determining current genetic diversity and structure. Overall, the results of our study on urban populations of fire salamanders provide some of the very first insights into the mechanisms affecting changes in genetic diversity and population differentiation via drift in urban environments, a crucial subject in a world where increasing urbanization is forecasted.     

Habent Fata Sua: The Rise and Fall of Garden Plants

Background: Rare cactus in the Americas and other species worldwide are threatened species because of their high level of habitat specialisation, narrow distribution range and continuing population decline.

Aims: To identify management units (MUs) based on genetic variability and demographic structure in order to propose assertive conservation actions for Mammillaria crucigera and to provide a model case study for other species that are under similar threats.

Methods: We genotyped through eight microsatellite loci in 171 individuals and described demographic structures in six populations of this cactus based on plots of 1 m².

Results: Across populations with a mean density of 2.6 m^?2 and a total of ~500 individuals counted, 30% of the individuals were reproductive (diameter >2 cm). The total heterozygosity was low (H_O = 0.54), but the inbreeding coefficient (F_IS = 0.29) and the allele diversity (N_A = 20) were high. Four genetic groups were distinguished, although considering the demographic structure, we propose three MUs.

Conclusions: It is critical to maintain the genetic connectivity within and among MUs, which can only be achieved through cooperation between government authorities and local habitants to halt the degradation and further destruction of the remnant populations. Searching MUs allows the identification of critical areas for conservation issues for all species whose extant populations are in a fragmented landscape.     

Development of genetic diversity,differentiation and structure over 500 years in four ponderosa pine populations

Population history plays an important role in shaping contemporary levels of genetic variation and geographic structure. This is especially true in small, isolated range‐margin populations, where effects of inbreeding, genetic drift and gene flow may be more pronounced than in large continuous populations. Effects of landscape fragmentation and isolation distance may have implications for persistence of range‐margin populations if they are demographic sinks. We studied four small, disjunct populations of ponderosa pine over a 500‐year period. We coupled demographic data obtained through dendroecological methods with microsatellite data to discern how and when contemporary levels of allelic diversity, among and within‐population levels of differentiation, and geographic structure, arose. Alleles accumulated rapidly following initial colonization, demonstrating proportionally high levels of gene flow into the populations. At population sizes of approximately 100 individuals, allele accumulation saturated. Levels of genetic differentiation among populations (F_ST and Jost's D_est) and diversity within populations (F_IS) remained stable through time. There was no evidence of geographic genetic structure at any time in the populations' history. Proportionally, high gene flow in the early stages of population growth resulted in rapid accumulation of alleles and quickly created relatively homogenous genetic patterns among populations. Our study demonstrates that contemporary levels of genetic diversity were formed quickly and early in population development. How contemporary genetic diversity accumulates over time is a key facet of understanding population growth and development. This is especially relevant given the extent and speed at which species ranges are predicted to shift in the coming century.