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PubMed2003

Population genetic structure of the spotted seal Phoca largha along the Coast of Hokkaido, based on mitochondrial DNA sequences.

Population genetic structure of the spotted seal, Phoca largha, along coastal regions of Hokkaido was investigated, using mitochondrial DNA (mtDNA) sequences. A 571-bp fragment of the mtDNA control region and adjacent threonine and proline transfer RNA genes was sequenced from 66 seals. We categorized all individuals into three groups considering sampling area and season: twenty-four seals from the Sea of Okhotsk in winter, 11 seals from the Sea of Okhotsk coast in fall, and 31 seals from the Sea of Japan coast in winter. From the 66 animals, 57 haplotypes were identified. Compared with the harbor seal sequence, all spotted seals examined shared two deletions in the control region, which distinguished between the two species. Forty-nine haplotypes were represented by a single individual, and haplotypes shared by more than two animals were generally restricted to same sampling-groups. Phylogenetic trees did not indicate clear geographic differences among the three groups. An Analysis of molecular variances (AMOVA) did not showed any significant population genetic structure in Hokkaido spotted seals (Phi(st )= -0.003). Our results showed a high level of diversity but no genetic structure, and did not deny the possibility that seals in the Okhotsk breeding concentration mainly stayed in the fall Okhotsk and also inhabited in the winter Sea of Japan.

Animals↗
PubMed2005

Comparison of Bayesian and maximum-likelihood inference of population genetic parameters.

UNLABELLED: Comparison of the performance and accuracy of different inference methods, such as maximum likelihood (ML) and Bayesian inference, is difficult because the inference methods are implemented in different programs, often written by different authors. Both methods were implemented in the program MIGRATE, that estimates population genetic parameters, such as population sizes and migration rates, using coalescence theory. Both inference methods use the same Markov chain Monte Carlo algorithm and differ from each other in only two aspects: parameter proposal distribution and maximization of the likelihood function. Using simulated datasets, the Bayesian method generally fares better than the ML approach in accuracy and coverage, although for some values the two approaches are equal in performance. MOTIVATION: The Markov chain Monte Carlo-based ML framework can fail on sparse data and can deliver non-conservative support intervals. A Bayesian framework with appropriate prior distribution is able to remedy some of these problems. RESULTS: The program MIGRATE was extended to allow not only for ML(-) maximum likelihood estimation of population genetics parameters but also for using a Bayesian framework. Comparisons between the Bayesian approach and the ML approach are facilitated because both modes estimate the same parameters under the same population model and assumptions.

Bayes Theorem↗
PubMed2002

[DNA polymorphism in population genetics].

In the review, the literature evidence on DNA polymorphism obtained in the last 10-15 years using various molecular-genetic methods is summarized. All main types of DNA variation are considered but attention is focused on those extensively used in population genetics. The areas of using DNA markers are outlined and the limitations of their potential in analyzing genetic processes in populations are discussed. Particular emphasis is placed on the relationship between the earlier developed biochemical genetics based on protein polymorphism analysis and modern molecular population genetics based on DNA polymorphism. The possible role of selection in maintaining DNA variation is considered.

Animals↗
PubMed1983

Inference problems in population genetics: DNA sequences, restriction endonucleases and ascertainment sampling.

A major trend of population genetics theory in the 1970s was the increased emphasis on inductive arguments, based on observed genetic data, rather than on deductive arguments based on theory and models. This occurred in part because the deductive theory had largely fulfilled its role of describing evolution as a genetic process, and in part because of the increasing amounts of data available on the genetic constitution of natural populations. Inference procedures raise difficulties not present in the deductive theory. Often conditional arguments are necessary since the data often must fulfil some condition to be observed. Different inference procedures, having different efficiencies, apply for data from different apparatuses. Care must be taken in deciding what it is that the inference concerns. These problems are illustrated by reference to restriction endonuclease techniques and ascertainment sampling.

Base Sequence↗
PubMed2002

Population genetic structure and male-biased dispersal in the queenless ant Diacamma cyaneiventre.

In this study we investigated the population genetic structure of the queenless ant Diacamma cyaneiventre. This species, lacking winged queens, is likely to have a restricted female dispersal. We used both mitochondrial and microsatellite markers to assess the consequence of such restricted female dispersal at three geographical scales: within a given locality (< 1 km), between localities within a given region (< 10 km) and between regions (> 36 km). Within a locality, a strong population structure was observed for mitochondrial DNA (mtDNA) whereas weak or nonexistent population genetic structure was observed for the microsatellites (around 5% of the value for mtDNA). Male gene flow was estimated to be about 20-30 times higher than female gene flow at this scale. At a larger spatial scale, very strong genetic differentiation for both markers was observed between localities - even within a single region. Female dispersal is nonexistent at these scales and male dispersal is very restricted, especially between regions. The phylogeographical structure of the mtDNA haplotypes as well as the very low genetic diversity of mtDNA within localities indicate that new sites are colonized by a single migration event from adjacent localities, followed by successive colony fissions. These patterns of genetic variability and differentiation agree with what is theoretically expected when colonization events are kin-structured and when, following colonization, dispersion is mainly performed by males.

Animals↗
PubMed1989

Gustave Malécot and the transition from classical to modern population genetics.

The contributions of Gustave Malécot to theoretical population genetics are described, discussed, and put into perspective relative to earlier and later work. In this context, certain aspects of the theory of inbreeding, the correlation between relatives, the evolution of finite panmictic populations, and (in more depth) spatial variation are reviewed. A brief biographical sketch of Malécot is also presented.

France↗
PubMed2003

Estimating recombination rates from population-genetic data.

Obtaining an accurate measure of how recombination rates vary across the genome has implications for understanding the molecular basis of recombination, its evolutionary significance and the distribution of linkage disequilibrium in natural populations. Although measuring the recombination rate is experimentally challenging, good estimates can be obtained by applying population-genetic methods to DNA sequences taken from natural populations. Statistical methods are now providing insights into the nature and scale of variation in the recombination rate, particularly in humans. Such knowledge will become increasingly important owing to the growing use of population-genetic methods in biomedical research.

Genetics, Population↗
PubMed2004

Founding events influence genetic population structure of sockeye salmon (Oncorhynchus nerka) in Lake Clark, Alaska.

Bottlenecks can have lasting effects on genetic population structure that obscure patterns of contemporary gene flow and drift. Sockeye salmon are vulnerable to bottleneck effects because they are a highly structured species with excellent colonizing abilities and often occupy geologically young habitats. We describe genetic divergence among and genetic variation within spawning populations of sockeye salmon throughout the Lake Clark area of Alaska. Fin tissue was collected from sockeye salmon representing 15 spawning populations of Lake Clark, Six-mile Lake, and Lake Iliamna. Allele frequencies differed significantly at 11 microsatellite loci in 96 of 105 pairwise population comparisons. Pairwise estimates of FST ranged from zero to 0.089. Six-mile Lake and Lake Clark populations have historically been grouped together for management purposes and are geographically proximate. However, Six-mile Lake populations are genetically similar to Lake Iliamna populations and are divergent from Lake Clark populations. The reduced allelic diversity and strong divergence of Lake Clark populations relative to Six-mile Lake and Lake Iliamna populations suggest a bottleneck associated with the colonization of Lake Clark by sockeye salmon. Geographic distance and spawning habitat differences apparently do not contribute to isolation and divergence among populations. However, temporal isolation based on spawning time and founder effects associated with ongoing glacial retreat and colonization of new spawning habitats contribute to the genetic population structure of Lake Clark sockeye salmon. Nonequilibrium conditions and the strong influence of genetic drift caution against using estimates of divergence to estimate gene flow among populations of Lake Clark sockeye salmon.

Alaska↗
PubMed2000

Population genetics of nine STR loci in two populations from Brazil.

The Short Tandem Repeats (STRs) D3S1358, HUMvWA31/A, HUMFIBRA/FGA, D8S 1179, D2S11, D18S51, D5S818, D13S317, and D7S820 were studied in two Brazilian populations (from Amazonia and S. Paulo) using the "AmpF1 STR Profiler Plus PCR Amplification Kit." The nine loci showed a combined discrimination power greater than 0.9999999999 and a chance of exclusion of 0.9999.

Brazil↗
PubMed2005

Population genetics of nine STR loci from Baoan population in NW China.

Allele frequencies for the nine short tandem repeat (STR) loci (D3S1358, FGA, TH01, D7S820, VWA, CSF1PO, D5S818, D13S317, TPOX) were determined in a sample of 120 unrelated individuals of the Baoan ethnic group living in northwest China. The values of observed heterozygosity (H), discrimination power (DP), a priori chance of exclusion (CE) and polymorphism information content (PIC) were calculated. All loci were in accordance with Hardy-Weinberg equilibrium (P=0.05). The obtained frequency distributions were compared with other previously reported population data.

China↗
PubMed1982

Genetic population structure in polygynous formica ants.

Genetic population structures, both mating and interaction structures, were investigated in three polygynous Formica ants by examining how genotype frequencies are distributed among the nests in their populations. The study is based on electrophoretically analysed enzyme polymorphisms. The patterns of genotypic variation among single-nest workers suggest that polygyny is functional in all the three species. The observed genotype frequencies indicate outbreeding within the study areas, and no spatial microdifferentiation in gene frequencies is detected. The coexistent gynes in nests of both F. transkaucasica and F. polyctena are genetically related to each other, and the same holds for worker nest mates. These results support the hypothesis that polygyny is favoured by kin selection. The lack of genetic relatedness among gyne nest mates in the highly polygynous F. aquilonia suggests that additional factors, such as mutualism or parental parasitism, are probably involved in the evolution of polygyny.

Animals↗
PubMed1998

The significance of relatedness and gene flow on population genetic structure in the®subsocial spider Eresus cinnaberinus (Araneae: Eresidae)

Interdemic selection, inbreeding and highly structured populations have been invoked to explain the evolution of cooperative social behaviour in the otherwise solitary and cannibalistic spiders. The family Eresidae consists of species ranging from solitary and intermediate subsocial to species exhibiting fully cooperative social behaviour. In this study we, in a hierarchical analysis, investigated relatedness of putative family clusters, inbreeding and population genetic structure of the subsocial spider Eresus cinnaberinus. Five hierarchical levels of investigation ranging from large scale genetic structure (distances of 250 and 50 km level 1 and 2) over microgeographic structure (20 km2 and 4 km2, level 3 and 4) to a single hill transect of 200 m (level 5) were performed. The purpose of level 5 was two-fold: (1) to investigate the relatedness of putative family groups, and (2) to evaluate the influence of both family living and sampling design on higher level estimates. Relatedness estimates of putative family groups showed an average relatedness of R=0.26. There was no indication of inbreeding. In contrast to social spiders, genetic variation was abundant, Heapproximately0.10. The population genetic structure was intermediate between social and asocial spiders. Genetic variance increased continually across hierarchical levels. Family structured neighbourhoods biased differentiation estimates among level 5 samples (FST=0.04) and level 3 and 4 samples (0.07 0, was caused by disjunct sampling from separate neighbourhoods. Larger scale samples were highly differentiated 0.12<FST<0.26, depending on level and sampling design. Due to a distance effect family living did not influence estimates of the higher level 1. Although the dispersing sex among social spiders and the subsocial E. cinnebarinus differ, females versus males, female behaviour of both sociality classes lead to high genetic variance.Copyright 1998 The Linnean Society of London

Journal Article↗
PubMed2004

[Population genetic structure of Pelophylax nigromaculata in Chinese mainland based on mtDNA control region sequences].

Molecular genetic data were used to investigate population genetic structure and differentiation of Pelophylax nigromaculata (Anura: Ranidae). Frogs were collected from 12 localities across Chinese mainland. Sample sizes of up to 10 frogs per population were assayed for mitochondrial control region sequence variation. The aligned 685 bp of the 5'CR include 111 variable sites. Sixty-seven haplotypes were defined. Most of the haplotypes are unique to local populations, only 7 of the 67 are shared among a few local populations. The overall species haplotype diversity is quite high (h = 0.98 +/- 0.005), and the nucleotide diversity is also high (pi = 0.0303 +/- 0.0029). This is corresponding to huge population size and extensive distribution of Pelophylax nigromaculata throughout Palaearctic and Oriental Regions. Phylogenetic tree of mtDNA control region haplotypes based on maximum parsimony algorithm and reconstructed phylogenetic relationships among the local populations based on neighbor joining algorithm all suggest that the haplotypes of Jiling and Liaoning populations in northeastern China have a sister relationship with 10 local populations in northern, central, southern and southwestern China. The analysis of molecular variance (AMOVA), the pairwise FST values and nucleotide divergence all support significant population subdivision between the Jilin-Liaoning group and multi-population group. The most possible cause of the significant genetic subdivision between the two groups might be referred to the effect of Quaternary glaciation. The possible reasons for the lack of obvious geographic structure on the whole in the multi-population group and the genetic differentiation in some local populations of the multi-population group were also discussed.

Animals↗
PubMed2006

Population genetic structure of Anopheles maculatus in Thailand.

Anopheles (Cellia) maculatus Theobald is a major malaria vector in southern Thailand and peninsular Malaysia, and previous population genetic studies suggested that mountain ranges act as barriers to gene flow. In this study, we examine the genetic variance among 12 collections of natural populations in southern Thailand by analyzing 7 microsatellite loci. Based on analysis of molecular variance (AMOVA), three geographic populations of An. maculatus are suggested. The southern population exists in western Thailand north of 12 degrees north latitude. Mosquitoes to the south fall into two genetic populations: 1) the middle southern collections located on the west side of the Phuket mountain range between 8 degrees and 10 degrees north latitude, and 2) the southern collections located on the east of the Phuket mountain range located between approximately 6.5 degrees and 11.5 degrees north latitude. AMOVA revealed significant genetic differentiation between northern and middle southern and southern populations. The middle southern population was moderately differentiated from the southern population. Furthermore, gene flow was restricted between proximal collections located on different sides of the Phuket mountain range. Collections separated by 50 km exhibited restriction of gene flow when separated by geographic barriers, whereas greater gene flow was evident among collections 650 km apart but without geographic barriers.

Animals↗
PubMed2004

Population genetics of autocidal control and strain replacement.

The concept that an insect species' genome could be altered in a manner that would result in the control of that species (i.e., autocidal control) or in the replacement of a pestiferous strain of the species with a more benign genotype was first proposed in the mid-twentieth century. A major research effort in population genetics and ecology followed and led to the development of a set of classical genetic control approaches that included use of sterile males, conditional lethal genes, translocations, compound chromosomes, and microbe-mediated infertility. Although there have been a number of major successes in application of classical genetic control, research in this area has declined in the past 20 years for technical and societal reasons. Recent advances in molecular biology and transgenesis research have renewed interest in genetically based control methods because these advances may remove some major technical problems that have constrained effective genetic manipulation of pest species. Population genetic analyses suggest that transgenic manipulations may enable development of strains that would be 10 to over 100 times more efficient than strains developed by classical methods. Some of the proposed molecular approaches to genetic control involve modifications of classical approaches such as conditional lethality, whereas others are novel. Experience from the classical era of genetic control research indicates that the population structure and population dynamics of the target population will determine which, if any, genetic control approaches would be appropriate for addressing a specific problem. As such, there continues to be a need for ongoing communication between scientists who are developing strains and those who study the native pest populations.

Animals↗
PubMed2002

Population genetics and sociobiology: conflicting views of evolution.

This article explores the tension between the population genetics and sociobiological approaches to the study of evolution. Whereas population geneticists, like Stanford's Marc Feldman, insist that the genetic complexities of organisms cannot be overlooked, sociobiologists (many of whom now prefer to call themselves "behavioral ecologists") rely on optimization models that are based on the simplest possible genetics.These optimization approaches have their roots in the classical result known as the fundamental theorem of natural selection, formulated by R. A. Fisher in 1930. From the start there was great uncertainty over the proper interpretation of Fisher's theorem, which became confused with Sewall Wright's immensely influential adaptive landscape concept. In the 1960s, a new generation of mathematical biologists proved that Fisher's theorem did not hold when fitness depended on more than one locus. Similar reasoning was used to attack W. D. Hamilton's inclusive fitness theory. A new theory, known as the theory of long-term evolution, attempts to reconcile the rigorous population genetics approach with the long-standing sociobiological view that natural selection acts to increase the fitness of organisms.

Biological Evolution↗