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PubMed2000

Population genetics of black abalone, Haliotis cracherodii, along the central California coast.

Over the past three decades, the black abalone, Haliotis cracherodii, has experienced precipitous declines in abundance over portions of its range in southern and central California. The potential for recovery of these populations is dependent in part on dispersal processes; that is, can distant populations serve as sources of recruits to locales that no longer harbor H. cracherodii? Here we use population genetic analysis to assess levels of population subdivision and infer recruitment processes. Epipodial tissue samples were obtained from over 400 black abalone from seven geographic sites between Santa Cruz and Santa Barbara counties in central California. Allelic frequencies were determined for each population at three polymorphic enzyme-encoding loci (GPI, AAT-1 and PGM). Significant allelic frequency differentiation among sites was observed at all three loci. Genetic distance was found to be independent of geographic distance over the approximately 300-km sampling range. In addition, a limited number of DNA sequences (total N=51) were obtained for the mitochondrial cytochrome oxidase subunit I gene (COI) from five of the populations. Since the same common COI haplotype dominated each population, this analysis had little statistical power and failed to detect population structure. The observed level of population differentiation at allozyme loci was three-fold higher than that observed in California red abalone, H. rufescens. The species differ in their breeding period and it is suggested that the relatively short, summer breeding season of black abalone limits dispersal because larvae experience reduced variance in oceanographic conditions relative to red abalone that spawn year-round. Based on these results, rates of recolonization and recovery of locally depressed or extirpated black abalone populations are likely to be slow despite harvest restrictions.

Journal Article↗
PubMed2001

A preliminary study of the population genetics of Aedes aegypti (Diptera: Culicidae) from Mexico using microsatellite and AFLP markers.

Dengue fever recently reemerged in the Americas. Because vaccines are still under development, dengue prevention depends entirely on vector control. Since Aedes aegypti (Linnaeus, 1762) is the principal vector of this arbovirus, knowledge of the genetic structure of the insect is therefore required to maintain effective vector control strategies and to estimate levels of gene flow from which movement can be inferred. This preliminary study uses microsatellite and amplified fragment length polymorphism (AFLP) markers, to provide insights into genetic diversity of A. aegypti populations from different districts of two towns, located in the north-west of Mexico, Hermosillo and Guaymas. Although the microsatellites used were found to display limited polymorphism, they allowed discrimination between mosquitoes from the northern and the southern districts of Hermosillo. Using AFLP markers, clustering of individuals from the same town and from the same district was observed. Data from microsatellite and AFLP markers analysis both suggest that reinvasion of A. aegypti probably occurs from Guaymas to Hermosillo.

Aedes↗
PubMed2003

Hierarchical analysis of colony and population genetic structure of the eastern subterranean termite, Reticulitermes flavipes, using two classes of molecular markers.

Termites (Isoptera) comprise a large and important group of eusocial insects, yet, in contrast to the eusocial Hymenoptera (ants, bees, wasps), the breeding systems of termites remain poorly understood. In this study, I inferred the breeding system of the subterranean termite Reticulitermes flavipes based on colony and population genetic structure as determined from microsatellite and mitochondrial DNA markers. Termites were sampled from natural wood debris from three undisturbed, forested sites in central North Carolina. In each site, two transects separated by 1 km were sampled at approximately 15-m intervals. A total of 1272 workers collected from 57 collection points were genotyped at six microsatellite loci, and mitochondrial DNA haplotype was determined for a subset of these individuals using either restriction fragment length polymorphism or sequence variation in the AT-rich region. Colonies appeared to be localized: workers from the 57 collection points represented 56 genetically distinct colonies with only a single colony occupying two collection points located 15 m apart. Genetic analysis of family structure and comparisons of estimates of F-statistics (F(IT), F(IC), F(CT)) and coefficients of relatedness (r) among nestmate workers with results of computer simulations of potential breeding systems suggested that 77% of all colonies were simple families headed by outbred monogamous pairs, whereas the remaining colonies were extended (inbred) families headed by low numbers of neotenics (about two females and one male) who were the direct offspring of the colony founders. There was no detectable isolation by distance among colonies along transects, suggesting that colony reproduction by budding is not common and that dispersal of reproductives during mating flights is not limited over this distance. Higher-level analysis of the microsatellite loci indicated weak but significant differentiation among sites (F(ST) = 0.06), a distance of 16-38 km, and between transects within sites (F(ST) = 0.06), a distance of 1 km. No significant differentiation at either the transect or site level was detected in the mitochondrial DNA sequence data. These results indicate that the study populations of R. flavipes have a breeding system characterized by monogamous pairs of outbred reproductives and relatively low levels of inbreeding because most colonies do not live long enough to produce neotenics, and those colonies that do generate neotenics contain an effectively small number of them.

Animals↗
PubMed1989

A population genetical model for sequence evolution under multiple types of mutation.

DNA sequencing and restriction mapping provide us with information on DNA sequence evolution within populations, from which the phylogenetic relationships among the sequences can be inferred. Mutations such as base substitutions, deletions, insertions and transposable element insertions can be identified in each sequence. Theoretical study of this type of sequence evolution has been initiated recently. In this paper, population genetical models for sequence evolution under multiple types of mutation are developed. Models of infinite population size with neutral mutation, infinite population size with deleterious mutation and finite population size with neutral mutation are considered.

Base Sequence↗
PubMed2005

Fisher's theorems for multivariable, time- and space-dependent systems, with applications in population genetics and chemical kinetics.

We study different physical, chemical, or biological processes involving replication, transformation, and disappearance processes, as well as transport processes, and assume that the time and space dependence of the species densities are known. We derive two types of Fisher equations. The first type relates the average value of the time derivative of the relative time-specific rates of growth of the different species to the variance of the relative, time-specific rates of growth. A second type relates the average value of the gradient or the divergence of the relative, space-specific rates of growth to the space correlation matrix of the relative, space-specific rates of growth. These Fisher equations are exact results, which are independent of the detailed kinetics of the process: they are valid whether the evolution equations are linear or nonlinear, local or nonlocal in space and/or time and can be applied for the study of a large class of physical, chemical, and biological systems described in terms of time- and/or space-dependent density fields. We examine the implications of our generalized Fisher relations in population genetics, biochemistry, and chemical kinetics (reaction-diffusion systems). We show that there is a connection between the enhanced (hydrodynamic) transport of mutations induced by population growth and space-specific rate vectors: the velocity of enhanced transport is proportional to the product of the diffusion coefficient of the species and the space rate vector; this relation is similar to a fluctuation-dissipation relation in statistical mechanics.

Analysis of Variance↗
PubMedDate not supplied

Population genetics of a polyploid: is there hybridization between lineages of Hyla versicolor?

Several studies have demonstrated that polyploid species can form recurrently from their progenitors, but few studies have evaluated gene flow between the resultant polyploid lineages. Here we examine the possibility of hybridization between lineages of the tetraploid common gray treefrog (Hyla versicolor). We utilize a polymerase chain reaction (PCR) cloning approach to estimate the genotypes of tetraploid individuals and measure genetic differentiation between (1) sympatric populations of two lineages and (2) allopatric populations of a single lineage. We find that allele frequencies in sympatric populations of two lineages do not differ, suggesting that frogs of these two lineages hybridize in areas where they co-occur.

Animals↗
PubMed1993

Population genetics of Trypanosoma brucei in central Africa: taxonomic and epidemiological significance.

In order to estimate the value of population genetics for both the taxonomy of trypanosomes belonging to the species Trypanosoma brucei and a better understanding of Human African Trypanosomiasis (HAT), we undertook a cellulose acetate electrophoresis isoenzyme study involving 55 stocks isolated from man and animals in Congo, Zaire and Cameroun. Out of the 24 loci surveyed, 15 exhibited variability, which made it possible to delimit 23 zymodemes, divided into 2 groups. The first group equated to the classical subspecies Trypanosoma brucei gambiense, while the second corresponded to the classical subspecies Trypanosoma brucei brucei. These results broadly agree with the current taxonomy, and are corroborated by RFLP analysis of kDNA. Statistical analysis indicates a basically clonal reproduction system of the trypanosomes in the area studied; the zymodemes are equivalent to natural clones (or a family of closely related clones), stable in space and time. Epidemiological hypotheses are proposed according to the geographic distribution of the clones in this area.

Africa, Central↗
PubMed2004

Comparative population genetics of the panicoid grasses: sequence polymorphism, linkage disequilibrium and selection in a diverse sample of sorghum bicolor.

Levels of genetic variation and linkage disequilibrium (LD) are critical factors in association mapping methods as well as in identification of loci that have been targets of selection. Maize, an outcrosser, has a high level of sequence variation and a limited extent of LD. Sorghum, a closely related but largely self-pollinating panicoid grass, is expected to have higher levels of LD. As a first step in estimation of population genetic parameters in sorghum, we surveyed 27 diverse S. bicolor accessions for sequence variation at a total of 29,186 bp in 95 short regions derived from genetically mapped RFLPs located throughout the genome. Consistent with its higher level of inbreeding, the extent of LD is at least severalfold greater in sorghum than in maize. Total sequence variation in sorghum is about fourfold lower than that in maize, while synonymous variation is fivefold lower, suggesting a smaller effective population size in sorghum. Because we surveyed a species-wide sample, the mating system, which primarily affects population-level diversity, may not be primarily responsible for this difference. Comparisons of polymorphism and divergence suggest that both directional and diversifying selection have played important roles in shaping variation in the sorghum genome.

Genes, Plant↗
PubMed2004

Population genetic and phylogenetic evidence for positive selection on regulatory mutations at the factor VII locus in humans.

The abundance of cis-regulatory polymorphisms in humans suggests that many may have been important in human evolution, but evidence for their role is relatively rare. Four common polymorphisms in the 5' promoter region of factor VII (F7), a coagulation factor, have been shown to affect its transcription and protein abundance both in vitro and in vivo. Three of these polymorphisms have low-frequency alleles that decrease expression of F7 and may provide protection against myocardial infarction (heart attacks). The fourth polymorphism has a minor allele that increases the level of transcription. To look for evidence of natural selection on the cis-regulatory variants flanking F7, we genotyped three of the polymorphisms in six Old World populations for which we also have data from a group of putatively neutral SNPs. Our population genetic analysis shows evidence for selection within humans; surprisingly, the strongest evidence is due to a large increase in frequency of the high-expression variant in Singaporean Chinese. Further characterization of a Japanese population shows that at least part of the increase in frequency of the high-expression allele is found in other East Asian populations. In addition, to examine interspecific patterns of selection we sequenced the homologous 5' noncoding region in chimpanzees, bonobos, a gorilla, an orangutan, and a baboon. Analysis of these data reveals an excess of fixed differences within transcription factor binding sites along the human lineage. Our results thus further support the hypothesis that regulatory mutations have been important in human evolution.

Animals↗
PubMed2004

Molecular population genetics of Cucumber mosaic virus in California: evidence for founder effects and reassortment.

The structure and genetic diversity of a California Cucumber mosaic virus (CMV) population was assessed by single-strand conformation polymorphism and nucleotide sequence analyses of genomic regions 2b, CP, MP, and the 3' nontranslated region of RNA3. The California CMV population exhibited low genetic diversity and was composed of one to three predominant haplotypes and a large number of minor haplotypes for specific genomic regions. Extremely low diversity and close evolutionary relationships among isolates in a subpopulation suggested that founder effects might play a role in shaping the genetic structure. Phylogenetic analysis indicated a naturally occurring reassortant between subgroup IA and IB isolates and potential reassortants between subgroup IA isolates, suggesting that genetic exchange by reassortment contributed to the evolution of the California CMV population. Analysis of various population genetics parameters and distribution of synonymous and nonsynonymous mutations revealed that different coding regions and even different parts of coding regions were under different evolutionary constraints, including a short region of the 2b gene for which evidence suggests possible positive selection.

California↗
PubMed2004

Population genetics of 10 short tandem repeat (STR) loci in a population sample of the ethnic group of Polish Tatars living in the Podlasie area (Northeastern Poland).

Laboratories worldwide are contributing to a large and growing database for different populations. This study provides a 10 STR database for a population sample of Polish Tatars living in the area of Podlasie for the use as a highly discriminatory system of genetic markers in the forensic community. The genotype frequency distributions showed no deviations from the Hardy-Weinberg equilibrium (HWE) except for D3S1358, FGA, D18S51 and D16S539, based on the Fisher Exact Test. Significant differences between the Polish Tatars and the native population of Podlasie were found in loci D3S1358, FGA, D2S1338, D21S11 and D19S433. The combined values of the Matching Probability and of the Power of Exclusion are 1 in 2.83 x 10(-12) and 0.998, respectively.

DNA↗
PubMed1990

Population genetic consequences of the fragile-X syndrome, based on the X-inactivation imprinting model.

We have examined the population genetic consequences of the model of Laird (Genetics 117:587-599, 1987) in which the fragile-X syndrome is caused by "imprinting" of a mutant chromosome. The imprinting event in this model results from a block to reactivation of an inactive X chromosome prior to oogenesis. If it is assumed that males carrying the imprinted chromosome never reproduce, the frequencies of females and males carrying the imprinted chromosome are expected to be equal. When a mutation-selection balance is established, there are expected to be somewhat more than twice as many females carrying the nonimprinted fragile X as carry the imprinted fragile-X chromosome, the excess depending on the fertility of fragile-X females. Nonpenetrant (transmitting) males, i.e., those with the nonimprinted fragile-X chromosome, are expected to be present at about the same frequency as are males with the syndrome. More than one-third of the nonimprinted chromosomes in the population are expected to be newly arisen in each generation. We have considered possible alternatives to the model of a mutation-selection balance. Nonimprinted carrier females would need to have 100% fertility excess to avoid postulating a high mutation rate to account for the very high prevalence of the syndrome.

Dosage Compensation, Genetic↗
PubMed2004

Effect of breeding structure on population genetic parameters in Drosophila.

The breeding structure of populations has been neglected in studies of Drosophila, even though Wright and Dobzhansky's pioneering work on the genetics of natural populations was an attempt to tackle what they regarded as an essential factor in evolution. We compared the breeding structure of sympatric populations of D. melanogaster and D. simulans, two sibling species that are widely used in evolutionary studies. We recorded changes in population density and microsatellite variation patterns for 3 years in a temperate environment of southwestern France. Results were distinctively different in the two species. Maximum population levels in summer and in autumn were similar and fluctuated greatly over years, each species being in turn the most abundant. However, genetic data showed that D. melanogaster made up a continuous breeding population in time and space of practically infinite effective size. D. simulans was fragmented into isolates with a local effective size of between 50 and 350 individuals. A consequence of this was that, while a local sample provided a reliable estimate of regional genetic variability in D. melanogaster, a sample from the same area provided an underestimate of this parameter in D. simulans. In practical terms, this means that variations in breeding structure should be accounted for in sampling schemes and in designing evolutionary genetic models. More generally, this suggests the existence of differential reactions to local environments that might contribute to several genomic differences observed between these species.

Animals↗
PubMed1991

Population genetics of hypervariable loci: analysis of PCR based VNTR polymorphism within a population.

Using a polymerase chain reaction (PCR) based method, genotypes at two hypervariable loci (3' to the Apo-B-structural gene and at the ApoC-II gene) were determined by size classification of alleles. Genotype data at the Apo-B locus (Apo-B VNTR) were obtained on 240 French Caucasians; the sample size for the ApoC-II VNTR was 162. For 160 individuals two-locus genotype data were available. Applications of some recently developed statistical methods to these data indicate that both of these loci are at Hardy-Weinberg equilibrium (HWE) and there is no indication of allelic associations between these two unlinked loci. In addition, the observed numbers of alleles (12 for the Apo-B and 11 for the ApoC-II VNTR loci) are also consistent with their respective expectations based on the observed heterozygosities (76.9% for the Apo-B and 85.9% for the ApoC-II loci) suggesting genetic homogeneity of this population-based sample. The multimodal distribution of allele sizes observed for both loci indicate that the production of new alleles at such VNTR loci may be caused by more than one molecular mechanism. The utility of such highly polymorphic loci for human genetic research and forensic applications are discussed in the context of these findings.

Alleles↗
PubMed1989

[Population genetics study of the functional asymmetry of the brain in native and migrant population of the north-eastern USSR].

It is shown that ethnic groups of the North-East of the USSR (eskimos, coast and reindeer chukchi, koryaks and evens) differ significantly in phenotype frequencies of hemisphere interrelations, and the extent of differences conforms to non-similarity of the cultural and economic structure of these populations. Significant phenotype frequency dynamics observed in new-coming population, depending on the duration of dwelling under the North conditions, makes the phenotype of "long-livers" of the North more distant from the population of middle latitudes and closer to the aboriginal populations. Such a dynamics of phenotypic structure of new-coming populations is due to selective migration of the population. Great adaptability of the right hemisphere relationship type individuals of aboriginal as well as new-coming population to the North-East conditions is grounded. The role of hemisphere relationship type in adaptation to the environmental conditions is under discussion.

Asian People↗
PubMed2000

Population genetic structure of two ecologically distinct Amazonian spiny rats: separating history and current ecology.

Population history and current demographic and ecological factors determine the amount of genetic variation within and the degree of differentiation among populations. Differences in the life history and ecology of codistributed species may lead to differences in hierarchical population genetic structure. Here, we compare patterns of genetic diversity and structure of two species of spiny rats in the genus Proechimys from the Rio Jurui of western Amazonian Brazil. Based on the ecological and life-history differences between the two species, we make predictions as to how they might differ in patterns of genetic diversity and structure. We use mitochondrial sequence data from the cytochrome b gene to test these predictions. Although both species maintain nearly the same number of mitochondrial haplotypes across the sampled range, they differ in levels of genetic diversity and geographic structure. Patterns of gene flow are also different between the two species with average M-values of nearly three in P. steerei and less than one in P. simonsi. Our initial predictions are largely upheld by the genetic data and where conflicting hypotheses arise, we suggest further studies that may allow us to distinguish among evolutionary scenarios. Separating the effects of history and ongoing demography on patterns of genetic diversity is challenging. Combining genetic analyses with field studies remains essential to disentangling these complex processes.

Animals↗
PubMed1979

Population genetic studies of the Philippine Negritos. II. gm and km allotypes of three population groups.

Serum samples of the three tribal Negrito populations in the Philippine Islands (127 from Zambales, 87 from Bataan, and 93 from Agusan) were tested for Glm(1,2,3 and 17), and G3m(5,6,11,13,14,15,16, and 21), and Km(1). The GMpatterm of the Negritos is characterized by three haplotypes, Gm1,17;21, Gm1,2,17;21, and Gm1,3;5,11,13,14, which is also characteristic of Mongoloid-related populations, especially with high incidence of the latter haplotype. They also have the haplotype, Gm1,17;5,13,14, prevalent in Africa, New Guinea, and northern Australia, suggesting an ancient link between the Negritos and the New Guinean-Australian group. Two unusual samples of G3m(15) positive without G3m(16) observed in Zambales Negritos suggest the presence of Gm1,17;5,11,13,14,15 haplotype in the population. This appears to be unique to Zambales Negritos and the first such samples to be found.

Alleles↗