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PubMed1998

Population genetic structure, phylogeography and spawning philopatry in walleye (Stizostedion vitreum) from mitochondrial DNA control region sequences.

Mitochondrial (mt) DNA control region sequences were used to test the genetic and phylogeographic structure of walleye Stizostedion vitreum populations at different geographical scales: among spawning sites, lake basins, lakes, and putative glacial refugia in the Great Lakes region. Sequencing 199 walleye revealed nucleotide substitutions and tandemly repeated sequences that varied in copy number, as well as in sequence composition, in approximately 1200 bp of the mtDNA control region. Variable numbers of copies of an 11-bp tandem repeat showed no geographical patterning and were not used in further analyses. Substitutions in the other areas of the control region yielded 19 haplotypes, revealing phylogeographic structure and significant differences among glacial refugia, lakes, basins and some spawning sites. Differences among spawning populations were consistent with reduced gene flow, philopatry and possible natal homing. Analysis of spawning populations showed consistency of genotypic frequencies among years and between males and females, supporting philopatry in both sexes. The unglaciated plateau in southern Ohio, USA housed a very different haplotype that diverged prior to the Missouri, Mississippi and Atlantic glacial refugia types. Haplotypes from the three refugia colonized the Great Lakes after retreat of the Wisconsin glaciers, and their present distribution reflects the geography of their prior isolation and differential colonization. Populations that became associated with spawning localities appear to have diverged further due to philopatry, resulting in fine-scale phylogeographic structuring.

Animals↗
PubMed1997

Population genetic structure of Ixodes pacificus (Acari:Ixodidae) using allozymes.

Genetic analysis of the population structure of the western blacklegged tick, Ixodes pacificus Cooley & Kohls, was conducted using allozymes. This vector tick transmits the Lyme disease spirochete, Borrelia burgdorferi Johnson, Schmid, Hyde, Steigerwalt & Brenner, in the far-western United States. It ranges from British Columbia to Baja California and disjunct populations are present in Oregon, Nevada, Utah, and Arizona. Host-seeking adult ticks were collected from vegetation across the range of the species and were partially fed on rabbits prior to analysis. Twelve putative loci were resolved using starch gel electrophoresis. One locus, glucose-6-phosphate isomerase, formed an apparent north/south latitudinal cline and showed significant geographic structure. None of the remaining loci exhibited much genetic differentiation. Estimates of gene flow were high relative to other arthropods. Isolation-by-distance analysis suggests a recent and rapid range expansion. We conclude that the overall lack of differentiation is due high rates of gene flow.

Alleles↗
PubMed1998

Population genetics and forensic applications using multiplex PCR (CSF1PO, TPOX, and TH01) loci in the Basque Country.

A population study in a sample of 200 unrelated individuals from the Basque Country (Northern Spain) was carried out using the GenePrint STR Multiplex System. The PCR products were electrophorized on a denaturing polyacrylamide gel and visualized by silver staining. The loci are TH01, TPOX, and CSF1PO. All loci meet Hardy-Weinberg expectations, and independence of alelles at these STR loci was found. A comparison with other population groups appeared to indicate that frequencies are well conserved in Caucasians, but differ from those of other racial groups. We have also calculated Fst as a measure of population subdivision. No appreciable genetic subdivision in the Caucasian populations studied here was found. Some statistical parameters of forensic interest (Pex, PM and PD) were also calculated. No exclusions were found in 100 mother-child and father-child meiosis. To evaluate the applicability of these systems to forensic casework, we studied the minimum quantity of DNA which can be used applying the multiplex methodology, and the minimum quantity that can be typed in a mixed sample. We also examined several samples such as hair roots, semen stains, vaginal swabs, blood stains and temporary teeth, each of these of varying ages.

Alleles↗
PubMed2006

Fundamentals of fungal molecular population genetic analyses.

The last two decades have seen tremendous growth in the development and application of molecular methods in the analyses of fungal species and populations. In this paper, I provide an overview of the molecular techniques and the basic analytical tools used to address various fundamental population and evolutionary genetic questions in fungi. With increasing availability and decreasing cost, DNA sequencing is becoming a mainstream data acquisition method in fungal evolutionary genetic studies. However, other methods, especially those based on the polymerase chain reaction, remain powerful in addressing specific questions for certain groups of taxa. These developments are bringing fungal population and evolutionary genetics into mainstream ecology and evolutionary biology.

Evolution, Molecular↗
PubMed2000

[Population-genetic structure of Dolly varden (Salvelinus malma Walbaum) from Southeastern Sakhalin and Southern Kuril islands].

The genetic structure of Dolly Varden (Salvelinus malma Walbaum) populations from six rivers of southeastern Sakhalin and six rivers of the Kuril Islands was examined using electrophoretic, analysis of 22 enzyme systems encoded by 45 loci. In all populations, mean heterozygosities (0.044-0.105), mean numbers of alleles per locus (1.15-1.52), and proportions of polymorphic loci (18.2-39.4%) were estimated for all loci that had clear resolution. Highly significant heterogeneity of allele frequencies was detected among populations of both Sakhalin and the Kuril islands. By means of cluster analysis and multidimentional scaling, all populations were divided into the Sakhalin and Kuril groups. Within the groups, no association of genetic similarity with geographic distance between populations was observed. Although the average genetic diversity was similar in these regions, the relative interpopulation diversity was almost three times higher in the Kuril (17.6%) than in the Sakhalin (6.5%) groups. In all, the proportion of genetic diversity between regions (8.4%) was somewhat lower than the proportion of mean interpopulation diversity (11.3%). In small populations isolated from the sea, genetic variation was lower than in nonisolated populations. Allozyme differences between the northern and the southern forms of Dolly Varden are discussed.

Electrophoresis, Polyacrylamide Gel↗
PubMed1969

The rate of molecular evolution considered from the standpoint of population genetics.

The rate of amino acid substitutions in the evolution of homologous proteins is remarkably constant. Furthermore, estimated rates of amino acid substitutions based on comparisons of the alpha hemoglobin chains of various mammals with that of the carp are about the same as those based on comparisons of the carp alpha and mammalian beta or the alpha and beta chains in mammals. These uniformities are regarded as evidence for the hypothesis that a majority of amino acid substitutions that occurred in these proteins are the result of random fixation of selectively neutral or nearly neutral mutations. TWO IMPLICATIONS OF THIS POSSIBILITY ARE DISCUSSED: (a) Random gene frequency drift is playing an important role in determining the genetic structure of biological populations and (b) genes in "living fossils" may be expected to have undergone as many DNA base (and therefore amino acid) substitutions as corresponding genes (proteins) in more rapidly evolving species.

Amino Acid Sequence↗
PubMed1996

Population genetics of coincidental DNA matches.

The DNA profiles of two unrelated individuals can match (complete similarity) by chance alone. When the two individuals are related, the probability of a coincidental match is higher. Here, I deal with the probabilities of coincidental matches for both related and unrelated individuals. The derivation starts from first principles; no prior knowledge is required. The results obtained by the method developed here are compared with some other methods.

Child, Preschool↗
PubMed2005

Population genetic differentiation in taxa of Lotus (Fabaceae: Loteae) endemic to the Gran Canarian pine forest.

A survey of allozyme variation at 17 loci in 14 populations representing four taxonomically problematic Gran Canarian pine forest endemic taxa of Lotus (L. genistoides, L. holosericeus, L. spartioides and some taxonomically uncertain populations collected under the designation Lotus sp.) was conducted to examine their diversification and systematic relationships. All groups exhibited high values of genetic variation, although inbreeding was common within populations. Considerable among-population genetic homogeneity was detected, as inferred from low values of Gst within each of the groups. The high population sizes of these taxa and a lack of evidence for isolation by distance or genetic bottlenecks indicate that diversity has accumulated over a long period of environmental stability. The association of high genetic distances with low linear distances, and the substantial increase in the values of Gst when the taxa considered were merged in different combinations hint at an incipient (yet probably taxonomically insufficient) reproductive isolation. The genetic similarity between L. genistoides, L. holosericeus and L. spartioides, together with the different behaviour of the populations collected under the designation Lotus sp., may have important implications for the restructuring of the taxonomy of this group when the ongoing morphological studies are completed.

Atlantic Islands↗
PubMed2004

Breeding system and demography shape population genetic structure across ecological and climatic zones in the African freshwater snail, Bulinus forskalii (Gastropoda, Pulmonata), intermediate host for schistosomes.

The role of breeding system and population bottlenecks in shaping the distribution of neutral genetic variation among populations inhabiting patchily distributed, ephemeral water bodies was examined for the hermaphroditic freshwater snail Bulinus forskalii, intermediate host for the medically important trematode Schistosoma guineensis. Levels of genetic variation at 11 microsatellite loci were assessed for 600 individuals sampled from 19 populations that span three ecological and climatic zones (ecozones) in Cameroon, West Africa. Significant heterozygote deficiencies and linkage disequilibria indicated very high selfing rates in these populations. Despite this and the large genetic differentiation detected between populations, high levels of genetic variation were harboured within these populations. The high level of gene flow inferred from assignment tests may be responsible for this pattern. Indeed, metapopulation dynamics, including high levels of gene flow as well as extinction/contraction and recolonization events, are invoked to account for the observed population structuring, which was not a consequence of isolation-by-distance. Because B. forskalii populations inhabiting the northern, Sahelian area are subject to more pronounced annual cycles of drought and flood than the southern equatorial ones, they were expected to be subject to population bottlenecks of increased frequency and severity and, therefore, show reduced genetic variability and elevated population differentiation. Contrary to predictions, the populations inhabiting the most northerly ecozone exhibited higher genetic diversity and lower genetic differentiation than those in the most southerly one, suggesting that elevated gene flow in this region is counteracting genetic drift.

Africa↗
PubMed1999

Population genetic studies on nine tetrameric short tandem repeat loci using fluorescence dye-labeled primers and capillary electrophoresis in the Austrian population.

The short tandem repeats (STR) D3S1358, VWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317, D7S820 and a locus allowing sex discrimination (amelogenin) can be coamplified by the polymerase chain reaction using a commercially available kit, and subsequently typed using capillary electrophoresis. To establish databases for these loci for Austrian Caucasians, 115 unrelated persons were typed. All loci were in Hardy-Weinberg equilibrium. The combined mean paternity exclusion chance (MEC) was 0.999891 and the combined discriminating power (DP) was 3.08 x 10(-11). The allelic distributions showed no differences to those found for other Caucasian populations. Our data differed significantly from an Afro-American population at 5 loci and from a Chinese population at 4 loci. Linkage disequilibrium between any of the coamplified loci was not evident. Thus the combination of multiplex PCR and capillary electrophoresis can save time and yield excellent results for paternity testing and stain analysis.

Austria↗
PubMed1996

Populations genetic analysis of nuclear and mitochondrial loci in skin biopsies collected from central and northeastern North Atlantic humpback whales (Megaptera novaeangliae): population identity and migratory destinations.

It has been speculated that humpback whales, Megaptera novaeangliae, from the northeastern North Atlantic breed in tropical waters off the coast of West Africa and therefore that they represent a separate breeding population from that which winters in the West Indies. We determined the genotype at six microsatellite loci as well as the sequence of the first 288 nucleotides in the mitochondrial control region of 133 skin biopsies collected from humpback whales in the central North Atlantic (Iceland and Jan Mayen) and the northeastern North Atlantic (Bear Island and the northern coast of Norway). We detected no significant deviations from Hardy-Weinberg proportions nor any differences in genotype frequencies between localities at the nuclear loci. However, the mitochondrial analyses revealed two distinct matrilineal aggregations: the central and the northeastern North Atlantic. Our findings were not compatible with the idea of a separate eastern North Atlantic breeding ground unless one has been established recently. The proposed alternative hypothesis of a common North Atlantic panmictic population (wintering primarily in the West Indies) in which individual whales display maternally directed site-fidelity to specific feeding grounds was supported by re-sightings of two northeastern North Atlantic humpback whales in the West Indies.

Animals↗
PubMed2004

Historicity and the population genetics of Drosophila melanogaster and D. simulans.

We summarize data showing that there is population structure in African populations of Drosophila from the melanogaster-simulans complex. In D. melanogaster, population structuring is found at individual loci, but is obscured by population structuring for large inversions that simultaneously affect several loci. In D. simulans, molecular polymorphism at the X-linked vermilion locus suggests that different groups of populations have been geographically isolated for some time. Invading populations are probably derived from different areas in Africa. European populations originate from an east African population that was probably not at a demographic equilibrium. The origin of the Antilles population is apparently different and is as yet unknown. In south-western France, populations from these two species undergo different population structuring at the scale of a few kilometres: D. melanogaster makes up a large panmictic population, whereas D. simulans forms a metapopulation that is divided into smaller demes.

Africa↗
PubMed1987

Population genetic study in ten endogamous groups of West Bengal, India.

Ten endogamous population groups of West Bengal (India)--Rabhas, Garos, Mechs, Rajbanshis, Jalia Kaibartas, Bagdis, Lodhas, Mundas, Brahmins, Vaidyas--have been typed for twelve polymorphic systems: ABO, Gm, Km, Hp, Cp, Tf, Alb, Hb, aP, EsD, AK and PGM1. The results are compared with those obtained on other Indian populations. Serological and anthropometric data, which have been included into population comparisons, reveal a considerable genetic variability of the groups under study. This variability is obviously connected with the population history of West Bengal.

Blood Group Antigens↗
PubMedDate not supplied

[The population genetics of nodule bacteria].

The data are reviewed on the population structure and evolutionary dynamics of the nodule bacteria (rhizobia) which are among the most intensively studied microorganisms. High level of the population polymorphism was demonstrated for the rhizobia populations using the enzyme electrophoresis (MLEE profiles). The average value of Nei's coefficient of heterogeneity (H = 1 - sigma pi2 [n/(n - 1)]) were: 0.590 for rhizobia (Rhizobium, Bradyrhizobium), 0.368 for enterobacteria (Escherichia, Salmonella, Shigella) and 0.452 for pathogenic bacteria (Bordetella, Borrelia, Erysipelothrix, Haemophilus, Helicobacter, Listeria, Mycobacterium, Neisseria, Staphylococcus) populations. In spite of being devoid of the effective systems for the gene conjugative transfer, many rhizobia populations possess an essentially panmictic structure. However, the enterobacteria populations in which the gene transfer may be facilitated due to the conjugative F- and R-factors, usually display the clonal population structure. The legume host plant is proved to be a key factor that determines the high levels of polymorphism and of panmixis as well as high evolutionary rates of the symbiotic bacteria populations. The host may ensure: a) an increase in mutation and gene transfer frequencies; b) stimulation of the competitive (selective) processes in both symbiotic and free-living rhizobia populations. A "cyclic" model of the rhizobia microevolution is presented which allows to assess the inputs the interstrain competition for the saprophytic growth and for the host nodulation into evolution of a plant-associated rhizobia population. The nodulation competitiveness in the rhizobia populations is responsible for the frequency-dependent selection of the rare genotypes which may arise in the soil bacterial communities as a result of the transfer of symbiotic (sym) genes from virulent rhizobia strains to either avirulent rhizobia or to the other (saprophytic, phytopathogenic) bacteria. Therefore, the nodulation competitiveness may ensure: a) panmictic structure of the natural rhizobia populations; b) high taxonomic diversity of rhizobia which was apparently caused by a broad sym gene expansion in the soil bacterial communities. The kin selection models are presented which explain evolution of the "altruistic" (essential for the host plant, but not for the bacteria themselves) symbiotic traits (e.g., the ability for symbiotic nitrogen fixation and for differentiation into non-viable bacteroids) in the rhizobia populations. These models are based on preferential multiplication of the nitrogen-fixing clones either in planta (due to an elevated supply of the nitrogen-fixing nodules with photosynthates) or ex planta (due to a release of the rhizopines from the nitrogen-fixing nodules). Speaking generally, interactions with the host plants provide a range of mechanisms increasing a genetic heterogeneity and an evolutionary potential in the associated rhizobia populations.

Altruism↗
PubMed1977

Genes and people in the Caspian Littoral: a population genetic study in Northern Iran.

Data for the distribution of alleles controlling two blood group systems and secretor status, for hemoglobin types, five serum protein groups and 15 red cell enzyme systems has been obtained. Eleven of the systems showed polymorphic variation and these systems have been used to calculate genetic distances using Morton's Kinship measure. No systematic relationship between genetic distance and geographic location of linguistic affiliation is apparent. There is, however, an apparent cline of decreasing frequency of PGDc from east to west and also significant differences in the frequency of G6PD deficiency corresponding to variation in the ecology of the region. Genetic distance comparisons with other selected populations reveal that the Turkic and Turkoman speaking peoples in the Caspian area cluster with the Kurds, Greeks and Iranis. The Persian speakers are genetically remote from these populations; they are, however, close to the Parsis who migrated from Iran to India at the end of the Seventh Century A.D. Several unusual genetic variants were detected, including a novel MDH phenotype, a superoxide dismutase phenotype identical with the Scandinavian type, and rare forms of LDH, PGM locus 2, ceruloplasmin, diaphorase, peptidases and PHI.

Acid Phosphatase↗