Pedigree reconstruction in wild cichlid fish populations

It is common practice to use microsatellites to detect parents and their offspring in wild and captive populations, in order to reconstruct a pedigree. However, correct inference is often constrained by a number of factors, including the absence of demographic data and ignorance regarding the completeness of parental sampling. Here we present a new Bayesian estimator that simultaneously estimates the pedigree and the size of the unsampled population. The method is robust to genotyping error, and can estimate pedigrees in the absence of demographic data. Using a large-scale microsatellite assay in four wild cichlid fish populations of Lake Tanganyika (1000 individuals in total), we assess the performance of the Bayesian estimator against the most popular assignment program, Cervus. We found small but significant pedigrees in each of the tested populations using the Bayesian procedure, but Cervus had very high type I error rates when the size of the unsampled population was assumed to be lower than what it was. The need of pedigree relationships to infer adaptive processes in natural populations places strong constraints on sampling design and identification of multigenerational pedigrees in natural populations.     

Fenetic analysis of aboriginal and introduced sable (Martes zibellina) populations in Russia

Using standard and mulivariate statistic methods, an epigenetic character--foramina in fossa condyloidei inferior, FFCI--was studied in sable populations. This character was shown to be most frequent in southeastern populations of the species (Primorye and the Baikal region) while its distribution in the remaining part of the range was polyclinal. The expression of FFCI was directly associated with coat color and longitude, and inversely associated with skull size. This trend was broken by some western populations formed in the 1950s by introduction, which exhibited stable morphological differences with adjacent aboriginal sable populations. Most populations of the species exhibit differences in the manifestation of the character. Frequency of the FFCI manifestation can be used as an additional population characteristic, an associative diagnostic character that shows high discriminating capability in detecting phenogenetic relationships of intraspecific groups.     

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.     

Analysis of the Alu insertion polymorphism in urban and rural populations of Siberia]

Polymorphic Alu-repeat loci of human genome are commonly used as effective genetic markers in population and evolution studies. In this work, the data on genetic structure of two Russian populations from Siberia obtained via analysis of five polymorphic Alu repeats are presented. The urban population was characterized by a slightly higher level of genetic diversity compared to the rural population. The value of genetic differentiation coefficient for the populations studied was 0.57%, pointing to the absence of genetic subdivision within the urban and rural populations. Phylogenetic analysis of these populations, together with literature data, shows that, with respect to the markers examined, the gene pool structure of Russian population is similar to that of other Caucasoid populations.     

Preservation of the plant and animal gene pools in Siberia]

The results of the work on preservation of the gene pools performed at the two experimental bases of the Institute of Cytology and Genetics of the Siberian Division of Academy of Sciences of the USSR are summarized. The collections obtained are represented by a number of aboriginal animal breeds (cattle, sheep, foxes, etc.) and plant variables (300 specimens belong to 113 species of 25 families.     

Estimation of Allele Frequencies in Indigenous Populations of Siberia Based on Pedigree Data

Procedure is described to estimate allele frequencies in indigenous populations of Siberia using phenotype data not only for pure-blood representatives of the ethnic groups examined, but also for the descendants of mixed marriages. Implementation of the method requires reconstruction of the pedigree structure for the sample examined. Inclusion of the data on descendants of mixed marriages into the analysis increases the sample information content and decreases variance of the estimates obtained. The advantages of the method are illustrated using an example of Tundra Nentsy, for whom it was shown that variance of estimates at the analysis of the blood groups allele frequencies can be diminished approximately by a factor of 1.5.     

Restriction analysis of N-acetyltransferase 2 gene in Caucasian population of West Siberia

Restriction analysis of the NAT2 gene was carried out in inhabitants of Novosibirsk. Polymorphism of this gene for nine known point mutations was studied in a sample of Novosibirsk residents consisting of 109 healthy Caucasians. The frequencies of these mutations did not significantly differ from the frequencies reported for Caucasian populations of other countries. In 79 patients with lung cancer, a region of the NAT2 gene that includes 29.7% of the coding sequence was analyzed for the new mutations by the RFLP analysis. No new mutations were found in this group.     

Functioning of rare plant populations of Central Siberia

Rare plant species of Central Siberia, included in the regional Red Lists, are considered in the context of their population strategies. The potential possibilities and positions of species populations have been analyzed. The functional approach to the evaluation of rare plants behavior is proposed. The functional typology of rare plants and specific features of their behavior is recommended to be used for the development of measures for their protection.     

Non-equilibrium gene frequency divergence: persistent founder effects in natural populations

The estimation of gene flow using gene frequency divergence information has become increasingly popular because of the difficulty involved in the direct determination of gene flow among populations. The present study examined allozyme gene frequencies in populations of eighteen aquatic invertebrate taxa at two sites in northern Canada. Gene frequencies at polymorpic loci were significantly different among 8–31 localized populations of all species at Igloolik and among 10–36 populations at Churchill confirming the generality of gene pool fragmentation in pond-dwelling organisms. Measures of gene flow estimated from gene frequency divergence, which assume that gene frequency distributions are at equilibrium, were inconsistent with the probable dispersal capacities of taxa. This provoked an examination of historical events as alternative explanations. Both theory and computer simulations demonstrated that when populations grow rapidly in size after founding from few individuals, the gene frequency divergence established during colonization is resistant to decay by gene exchange. Our work suggests that gene frequency distributions are often not in equilibrium and that caution should be employed in attempts to infer gene flow from them in natural populations.     

Pedigree analysis of plasmid segregation in yeast

We have used pedigree analysis to investigate the mitotic segregation of circular and linear DNA plasmids in Saccharomyces cerevisae. Circular ARS plasmids, which bear putative chromosomal replication origins, have a high segregation frequency and a strong bias to segregate to the mother cell at mitosis. The segregation bias explains how the fraction of plasmid-bearing cells can be small despite the high average copy number of circular ARS plasmids. Linear ARS plasmids do not show strong segregation bias, nor does the 2 mu ori-containing plasmid YEp 13, when it is present in strains containing intact 2 mu circles. In the absence of endogenous 2 mu circles, YEp 13 behaves like an ARS plasmid, showing a strong maternal segregation bias. The presence of a centromere on circular ARS plasmids eliminates segregation bias. We discuss a model for plasmid segregation, which explains these findings and the possible biological significance of mother-daughter segregation bias.     

Tooth wear in Australian aboriginal populations from the River Murray Valley

The study of tooth wear among prehistoric and recent populations has frequently been concerned with the rate and pattern of wear over the dental arches. In this report we considered the question of tooth wear variation among collections of Australian Aboriginal crania recovered from several sites along the Murray River in Southeastern Australia. These crania represent the remains of relatively recent populations from about 2,000 years ago until the early 19th century. The degree of tooth wear for each dental arch was recorded by an established method of determining the ratio of exposed dentin. The pattern or distribution of wear over each arch was summarized by principal component analysis. The mean wear degree and pattern were compared among four geographical grouping of crania separated by up to 700 miles of river frontage. Our results showed, as expected, a significant difference between the well-defined population at the Lower Murray site (Swanport) and the three upriver groups. However, there were significant differences among these three collections as well. Sexual dimorphism was noted but was only significant in the Lower Murray group; the mean wear was greater and also more variable among the males. At the second of the Middle Murray sites the pattern of wear was different and the degree of wear was significantly less than in the other groups. A possible explanation for this diversity may be environmental and subsistence base differences. The evidence from the Lower Murray supports this possibility, but the differences among the other three groups are not as clearly established. However, our results do suggest that the Murray Black collection, from which these crania were obtained, may not be as homogeneous a group as previously believed.     

Mitochondrial DNA polymorphism in populations of aboriginal residents of the Far East

An analysis of mtDNA polymorphism in eight populations of aboriginal residents (N = 519) of the Far East has been performed. The majority of haplogroups revealed in the examined groups were of East Eurasian origin. Haplogroup D was revealed in seven populations and its frequency varied from 2.8% in Koryaks to 28.3% and 28.9% in Nanaians and Evenks, respectively. Chukchi and Koryak populations, which belong to the same language family, exhibited haplogroup G, which has the same motive and indicates the genetic kinship of both populations. The presence of East Eurasian haplogroups A and D with a strong predominance of haplogroup A in Chukchi indicates the closer relationship of this population both with Asian and Canadian Eskimos and northern Atapasks on the other side of Bering Strait. The high level of genetic variability was revealed in populations belonging to the Tungus-Manjur group. The high frequency of east Eurasian haplogroups in Nanaians could result from close historical associations with Siberian Evenks.     

Differentiation of four Indian aboriginal cattle populations revealed by STR markers

Cattle are the most important livestock in India and play a pivotal role in agrarian economy. There are 34 recognized breeds of cattle and number of unexplored lesser known populations. The present study is a contribution towards determining genetic variation and understanding the relationship among four lesser known populations. A total of 194 unrelated DNA samples from three cattle populations of Orissa (Binjharpuri, Ghumsuri, Motu) and Hill cattle of Kumaun (Kumauni) were collected from respective breeding tracts. Genotyping was done with 23 bovine microsatellite markers as suggested by International Society for Animal Genetics (ISAG) and FAO (DAD-IS) on automated sequencer. The average observed heterozygosity in the four populations lie within the narrow range of 0.623 +/- 0.04 in Binjharpuri to 0.664 +/- 0.03 in Kumauni. Mean estimates of observed and expected heterozygosity over all loci and breeds were 0.651 +/- 0.02 and 0.720 +/- 0.01, respectively. In the overall population, the homozygote excess (F(IT)) of 0.132 +/- 0.03, was partly due to the genetic differentiation among breeds (F(ST) = 0.044 +/- 0.01) and, to a larger extent, to a significant homozygote excess within breeds (F(IS) = 0.094 +/- 0.03). The phylogenetic reconstruction from a UPGMA clustering based on Nei's Standard genetic distance yielded a tree with Binjharpuri and Ghumsuri on a single node and Motu and Kumauni on separate nodes. The most probable clustering detected by STRUCTURE in population was three. Binjharpuri and Ghumsuri animals were assigned to one cluster with high proportion of membership.     

Principal axis analysis of gene frequency data

When a set of populations are compared in respect of gene frequencies, and the chi-square test of heterogeneity is found to be significant, it is pertinent to find out whether the heterogeneity can be explained by a few linear combinations of the gene frequencies, and the total heterogeneity chi-square value can be partitioned as the sum of heterogeneity chi-square values contributed by the linear combinations. The present report describes such a method, and the linear combination that explains the maximum heterogeneity is called the principal axis. An application of this method is presented to find clusters of 31 Mongoloid tribal populations of eastern India using ABO gene frequency data.     

Method of sedimentational-electrophoretic analysis of cell populations]

The described method of analysis of cell populations' heterogeneity involves two parameters simultaneously: the sedimentation velocity and the electrophoretic mobility of cells. The method is based on the photographic registrarion of resulting traces of cell velocity in the fields of gravition and electricity with consequence of the elements of these traces on the photographs. The experimental data on the distribution of these parameters in the ascitic tumor cell population are given.     

Differentiation of four indian aboriginal cattle populations revealed by SIR markers

Cattle are the most important livestock in India and play a pivotal role in agrarian economy. There are 34 recognized breeds of cattle and number of unexplored lesser known populations. The present study is a contribution towards determining genetic Variation and understanding the relationship among four lesser known populations. A total of 194 unrelated DNA samples from three cattle populations of Orissa (Binjharpuri, Ghumsuri, Motu) and Hill cattle of Kumaun (Kumauni) were collected from respective breeding tracts. Genotyping was done with 23 bovine microsatellite markers as suggested by International Society for Animal Genetics (ISAG) and FAO (DAD-IS) on automated sequencer. The average observed heterozygosity in the four populations lie within the narrow range of 0.623 ± 0.04 in Binjharpuri to 0.664 ± 0.03 in Kumauni. Mean estimates of observed and expected heterozygosity over all loci and breeds were 0.651 ± 0.02 and 0.720 ± 0.01, respectively. In the overall population, the homozygote excess (F _IT) of 0.132 ± 0.03, was partly due to the genetic differentiation among breeds (F _ST = 0.044 ± 0.01) and, to a larger extent, to a significant homozygote excess within breeds (F _IS = 0.094 ± 0.03). The phylogenetic reconstruction from a UPGMA clustering based on Nei??s Standard genetic distance yielded a tree with Binjharpuri and Ghumsuri on a single node and Motu and Kumauni on separate nodes. The most probable clustering detected by STRUCTURE in population was three. Binjharpuri and Ghumsuri animals were assigned to one cluster with high proportion of membership.