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PubMed2003

The population genetics of clonal and partially clonal diploids.

The consequences of variable rates of clonal reproduction on the population genetics of neutral markers are explored in diploid organisms within a subdivided population (island model). We use both analytical and stochastic simulation approaches. High rates of clonal reproduction will positively affect heterozygosity. As a consequence, nearly twice as many alleles per locus can be maintained and population differentiation estimated as F(ST) value is strongly decreased in purely clonal populations as compared to purely sexual ones. With increasing clonal reproduction, effective population size first slowly increases and then points toward extreme values when the reproductive system tends toward strict clonality. This reflects the fact that polymorphism is protected within individuals due to fixed heterozygosity. Contrarily, genotypic diversity smoothly decreases with increasing rates of clonal reproduction. Asexual populations thus maintain higher genetic diversity at each single locus but a lower number of different genotypes. Mixed clonal/sexual reproduction is nearly indistinguishable from strict sexual reproduction as long as the proportion of clonal reproduction is not strongly predominant for all quantities investigated, except for genotypic diversities (both at individual loci and over multiple loci).

Alleles↗

PubMed2001

Application of microsatellite markers to population genetics studies of Japanese flounder Paralichthys olivaceus.

We examined population genetic structure by means of microsatellite analysis among 7 Japanese flounder (Paralichthys olivaceus) populations collected from coastal sea areas around Japan. As was expected, all of the 11 microsatellite loci examined were variable in all populations (number of alleles per locus, 15.2-18.2; average of expected heterozygosity, 0.74-0.78). Eleven population pairs in 21 possible pairwise comparisons showed significant genetic heterogeneity associated with allele frequency distributions or fixation index (F(ST)). Modified Cavalli-Sforza chord distance (D(A)) and Nei's standard genetic distance (D(ST)) ranged from 0.051 to 0.090, and from 0.000 to 0.025, respectively. There was evidence that the populations assessed in this study were not drawn from a single panmictic population; however, it appears that Japanese flounder populations around Japan are not well-structured, as an estimate of the fixation index value among the 7 localities was very low (F(ST) = 0.0025).

Journal Article↗

PubMed2004

The role of chemokines in atherosclerosis: recent evidence from experimental models and population genetics.

PURPOSE OF REVIEW: Atherosclerosis is an inflammatory disease process. This review discusses the recent genetic evidence from animal models and human populations that highlight the importance of chemokines in atherosclerosis. RECENT FINDINGS: CC-chemokine/CC-chemokine receptors (CCR), including CCR2/ MCP-1 (monocyte chemoattractant protein-1) and CCR5/RANTES (regulated on activation, normal T-cell expressed and secreted), have been shown in animal knockout and transgenic studies to have significant effects on atherosclerotic lesion size and macrophage recruitment. More recently fractalkine (CX3C1) and its receptor (CX3CR1) have emerged as another important pathway in atherosclerosis. For example, fractalkine is present in human atherosclerotic lesions and is able to stimulate platelet activation and adhesion. CX3CR1 is expressed on human aortic smooth muscle cells and CX3CR1/apolipoprotein E double knockout mice have significantly reduced atherosclerotic lesion size and macrophage recruitment. Human population genetic studies have tried to assess the importance of chemokines in human atherosclerosis. Currently, there is conflicting evidence regarding an association between polymorphisms in CCR2/MCP-1 and CCR5/RANTES and coronary artery disease. There is evidence, however, for an association between the fractalkine receptor polymorphism (CX3CR1-I249) and coronary artery disease in both human population and function studies. SUMMARY: Recent transgenic and gene knockout studies in murine models of atherosclerosis have highlighted the importance of chemokines and their receptors in atherosclerosis. Genetic evidence for a role of chemokines and their receptors in human population studies remains under investigation. Identifying chemokine polymorphisms could help to determine pathways that are important in atherosclerosis disease pathology and that may suggest novel therapeutic targets.

Animals↗

PubMed1986

[Population genetic studies in Ethiopia: distribution of blood group polymorphisms in Amhara/Tigrai ethnic groups].

During 1981-1982 and 1983-1984 a population-genetic study has been performed in the Amhara/Tigrai ethnic groups of Northwestern Ethiopia (Gondar). Blood group frequencies are reported for 6 systems (AB0, MNSs, Rh, P, Kell, Kidd), secretor status, haptoglobin, Gc, Gm/Km, HLA-A and -B as well as for the erythrocytic enzyme polymorphisms AcP, PGM1, ADA, EsD, GPT, AK and GLO I. The results are compared with other reports from East Africa and the Arabian peninsula. The mixed caucasoid-negroid gene pool of the Amhara/Tigrai as well as their relations with Arabia are confirmed.

ABO Blood-Group System↗

PubMed1994

[Application of multilocus enzyme electrophoresis in studies of taxonomy and population genetics of S. typhi in Xinjiang].

Multilocus enzyme electrophoresis (MEE) was employed to study the genotype taxon and population genetics of 154 isolates of S. typhi from Xinjiang in recent 11 years. Seven kinds of enzymes were examined and determined. One hundred and fifty-four strains of S. typhi were classified into 69 electroretic types (ETs) and 10 clones (CLa-CLj). Among those 154 strains 80 epidemic isolates belonged to 21 ETs and 3 clones (CLe, f, j). ET17, 20, 21, 24, 26, 27 were the main ETs (61.30%), and CLf was the dominant clone (95.00%). Seventy-four non-epidemic isolates belonged to 48 ETs and 9 clones (CLa, b, c, d, f, g, h, i, j), no obvious dominant ET was found in them, and the main clone CLh accounted for 43.30%. It demonstrated that both outbreak and sporadic epidemics could be caused by many strains of ETs and clones, but the distribution of the former ETs was more concentrated and the preponderance of clones was more obvious. The analyses on structure of population genetics indicated that all of 7 enzymes were polymorphic. Genetic diversity among the enzyme loci was quite high, with an average of 0.35 per locus (H). The average number of alleles per locus (h) was 6.14. There was no significant difference in h or H between the isolates of different sources (P > 0.05). It was clear that S. typhi of different sources in Xinjiang were originated from the same population. The results also showed that there was a dominant allele in every enzyme locus. Natural selection was the main role in the evolution of S. typhi.

Alleles↗

PubMed2000

Bottlenecks and multiple introductions: population genetics of the vector of avian malaria in Hawaii.

Avian malaria has had a profound impact on the demographics and behaviour of Hawaiian forest birds since its vector, Culex quinquefasciatus the southern house mosquito, was first introduced to Hawaii around 1830. In order to understand the dynamics of the disease in Hawaii and gain insights into the evolution of vector-mediated parasite-host interactions in general we studied the population genetics of Cx. quinquefasciatus in the Hawaiian Islands. We used both microsatellite and mitochondrial loci. Not surprisingly we found that mosquitoes in Midway, a small island in the Western group, are quite distinct from the populations in the main Hawaiian Islands. However, we also found that in general mosquito populations are relatively isolated even among the main islands, in particular between Hawaii (the Big Island) and the remaining Hawaiian Islands. We found evidence of bottlenecks among populations within the Big Island and an excess of alleles in Maui, the site of the original introduction. The mitochondrial diversity was typically low but higher than expected. The current distribution of mitochondrial haplotypes combined with the microsatellite information lead us to conclude that there have been several introductions and to speculate on some processes that may be responsible for the current population genetics of vectors of avian malaria in Hawaii.

Animals↗

PubMed2004

Contrasting population genetic patterns and evolutionary histories among sympatric Sonoran Desert cactophilic Drosophila.

We studied population genetic differentiation in the sympatric Sonoran Desert cactophilic flies Drosophila pachea, D. mettleri and D. nigrospiracula across their continental and peninsular ranges. These flies show marked differences in ecology and behaviour including dispersal distances and host cactus specialization. Examination of a fragment of the mitochondrial cytochrome oxidase subunit I gene (mtCOI) reveals that the Sea of Cortez has constituted an effective dispersal barrier for D. pachea, leading to significant genetic differentiation between the continental and peninsular ranges of this species. No genetic differentiation was detected, however, within its continental and peninsular ranges. In contrast, our mtCOI-based results for D. mettleri and D. nigrospiracula are consistent with a previous allozyme-based study that showed no significant genetic differentiation between continental and peninsular ranges of these two species. For D. mettleri, we also found that the insular population from Santa Catalina Island, California, is genetically differentiated with respect to continental and peninsular localities. We discuss how differences in the genetic structure patterns of D. pachea, D. mettleri and D. nigrospiracula may correspond to differences in their dispersal abilities, host preferences and behaviour.

Animals↗

PubMed1993

Microsatellites and their application to population genetic studies.

Microsatellites may soon become the markers of choice for molecular population genetic studies. However, our knowledge of these simple repetitive sequences and how they evolve in natural populations is far from complete. We highlight some recent results of population studies and advances in our ability to interpret some of the allele frequency distributions that we are beginning to observe.

Alleles↗

PubMed2001

Population genetic structure of the western mosquitofish, Gambusia affinis, in a highly channelized portion of the San Antonio River in San Antonio, TX.

Population genetic assessments were performed on populations of the mosquitofish, Gambusia affinis, sampled at seven sites along a 10 km reach of the upper San Antonio River in San Antonio, TX. Mosquitofish populations were sampled from the downtown area, known as the "Riverwalk", where the river is concrete lined, deeply pooled, and receives heavy tour boat traffic. Populations were also sampled from sites upstream and downstream from the Riverwalk. Allozyme electrophoresis was performed on approximately 50 individuals from each site. Five of 12 loci surveyed were polymorphic (95% criterion). Exact tests over all loci for all populations indicated that allele frequencies differed significantly among sites. Allele frequencies of the upstream population were significantly different from the Riverwalk populations. Differences resulted primarily from significant decreases in frequencies of rare alleles at MDH-2* and two GPI* loci in the downtown area. Mean dissolved oxygen measurements were also significantly lower at Riverwalk sites. These results suggest that selective forces such as non-point source runoff or low dissolved oxygen, perhaps in combination with limited migration due to numerous dams, have reduced genetic diversity of populations in the downtown area.

Animals↗

PubMed2006

The molecular population genetics of shoot development in Arabidopsis thaliana.

Studies in Arabidopsis thaliana have provided us with a wealth of information about the genetic pathways that regulate plant morphogenesis. This developmental genetic treasure trove represents a fantastic resource for researchers interested in the microevolution of development. Several laboratories have begun using molecular population genetic analyses to investigate the evolutionary forces that act upon loci that regulate shoot morphogenesis. Much of this work has focused on coding sequence variation in transcription factors; however, recent studies have explored sequence variation in other types of proteins and in promoter regions. Several genes that regulate shoot development contain signatures of selective sweeps associated with positive selection or harbor putative balanced polymorphisms in coding and noncoding sequences. Other regulatory genes appear to be evolving neutrally, but have accumulated potentially deleterious replacement polymorphisms.

Arabidopsis↗

PubMed2006

Population genetic models of male and mutual mate choice.

Examples of male mate choice are becoming increasingly common, even in polygynous species. We create a series of population genetic models to examine the evolutionary equilibria and dynamics resulting from male mate choice during polygyny, alone and in the context of mutual mate choice by both sexes. We find that unless males with a preference are able to increase their overall courtship output, male preference will be lost. This loss can be counteracted if males choose females not based on arbitrary traits, but based on a trait that indicates high fertility or viability. We also conclude that if male and female preferences and traits are all controlled by different loci, the male and female mate choice systems are decoupled; the presence of a male preference then has no influence on the equilibria or dynamics of female mate choice. If male and female traits are coupled by pleiotropy, it becomes possible for a male preference to be maintained, regardless of whether preferences between the sexes are pleiotropic or controlled by separate loci.

Animals↗

PubMed1992

[Contribution of A.S. Serebrovskiĭ to population genetics].

The article commemorates Professor Alexander Sergeevich Serebrovsky (1892-1948), a prominent Russian geneticist, the founder of the Department of Genetics of Moscow University. A thorough analysis of his publications written in the 20s and 30s demonstrates that A.S. Serebrovsky: 1) developed the principles of such original fields of population genetics as gene geography and the theory of gene pools; 2) specified the significance of random genetic drift for neutral evolution in small populations; 3) showed that subdivision of an isolated population is essential for long-term conservation of its genetic composition. A.S. Serebrovsky's contribution into population genetics is viewed as an achievement of the Russian scientific school, always distinguished by historic and geographical approach to natural phenomena and processes.

Genetics, Population↗

PubMed2005

Population genetics of Y-chromosome STRs in a population sample of the Lithuanian minority residing in the northeastern Poland.

Haplotype and allele frequencies for the 12 Y-STRs were determined in a population sample of 124 unrelated males--members of the Lithuanian minority residing in the northeastern Poland. Three of the haplotypes were encountered in duplicate, while 118 haplotypes were unique. The overall gene diversity was 0.9952. Analysis of molecular variance revealed that the Lithuanian minority can be distinguished from the autochthonous Poles, although these two populations are very close to each other. This database study provides an essential precondition for applying Y-chromosomal STRs estimates in forensic identification of male DNA and tracing of paternal lineages.

Chromosomes, Human, Y↗

PubMed2006

Population genetic data of 15 STR loci in Han population of Henan province (central China).

Allele frequencies of the 15 STR loci were determined in 208 unrelated individuals from Han population living in Henan, China (central China). All loci except D5S818 were found no deviation from Hardy-Weinberg equilibrium. The combined power of discrimination (PD) and the combined chance of exclusion (CE) for the 15 studied loci were >0.9999999 and 0.999996119, respectively. Our data were statistically compared with the previously reported data from other Chinese population groups, and significant difference was found between central Han Chinese (n=208) and eastern Chinese (n=100) at vWA, or between central Han Chinese (n=208) and southeast Chinese (n=122) at D13S317.

Alleles↗

PubMed2005

A practical guide to mitochondrial DNA error prevention in clinical, forensic, and population genetics.

Several suggestions have been made for avoiding errors in mitochondrial DNA (mtDNA) sequencing and documentation. Unfortunately, the current clinical, forensic, and population genetic literature on mtDNA still delivers a large number of studies with flawed sequence data, which, in extreme cases, damage the whole message of a study. The phylogenetic approach has been shown to be useful for pinpointing most of the errors. However, many geneticists, especially in the forensic and medical fields, are not familiar with either effective search strategies or the evolutionary terminology. We here provide a manual that should help prevent errors at any stage by re-examining data fresh from the sequencer in the light of previously published data. A fictitious case study of a European mtDNA data set (albeit composed from the literature) then demonstrates the steps one has to go through in order to assess the quality of sequencing and documentation.

DNA, Mitochondrial↗

PubMed2004

Population genetic analysis of ascertained SNP data.

The large single nucleotide polymorphism (SNP) typing projects have provided an invaluable data resource for human population geneticists. Almost all of the available SNP loci, however, have been identified through a SNP discovery protocol that will influence the allelic distributions in the sampled loci. Standard methods for population genetic analysis based on the available SNP data will, therefore, be biased. This paper discusses the effect of this ascertainment bias on allelic distributions and on methods for quantifying linkage disequilibrium and estimating demographic parameters. Several recently developed methods for correcting for the ascertainment bias will also be discussed.

Bias↗

PubMed2004

Population genetics of Y-chromosome STRs in a population of Podlasie, Northeastern Poland.

Haplotype and allele frequencies for the 12 Y-STRs were determined in a population sample of 186 Polish males. Five of the haplotypes were encountered in duplicate, while 176 haplotypes were unique. The overall gene diversity was 0.9973. This database study provides an essential precondition for applying Y-chromosomal STRs estimates in forensic identification of male DNA and tracing of paternal lineages.

Chromosomes, Human, Y↗

PubMed2005

Genetic population structure of fishes: implications for coastal zone management.

The pattern for distribution of genetic variation within and between populations is referred to as the genetic population structure of the species. To avoid depletion of genetic resources sustainable management should be based on knowledge of this structure. We discuss key aspects of genetic population structure in the context of identifying biological units for fisheries management, suggesting three basic types of structuring: distinct populations; continuous change; and no differentiation. The type of structure determines how units for genetically sustainable management are to be identified. We also review what is currently known regarding the genetic population structure of fishes exploited in the Swedish part of the Baltic Sea, and conclude that sufficient genetic information is lacking for most of the species. This is a serious problem, particularly considering that populations of several commercially exploited fishes are declining and some exhibit recruitment problems. For six species, Atlantic herring, Atlantic salmon, brown trout, European eel, turbot, and pike, sufficient genetic data are available to provide at least basic information on genetic structure and genetic units for biologically sustainable use. Current management practices do not sufficiently consider these data.

Animals↗