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PubMed1999

Genetic structure of typical and atypical populations of Candida albicans from Africa.

Atypical isolates of the pathogenic yeast Candida albicans have been reported with increasing frequency. To investigate the origin of a set of atypical isolates and their relationship to typical isolates, we employed a combination of molecular phylogenetic and population genetic analyses using rDNA sequencing, PCR fingerprinting, and analysis of co-dominant DNA nucleotide polymorphisms to characterize the population structure of one typical and two atypical populations of C. albicans from Angola and Madagascar. The extent of clonality and recombination was assessed in each population. The analyses revealed that the structure of all three populations of C. albicans was predominantly clonal but, as in previous studies, there was also evidence for recombination. Allele frequencies differed significantly between the typical and the atypical populations, suggesting very low levels of gene flow between them. However, allele frequencies were quite similar in the two atypical C. albicans populations, suggesting that they are closely related. Phylogenetic analysis of partial sequences encoding the nuclear 26S rDNA demonstrated that all three populations belong to a single monophyletic group, which includes the type strain of C. albicans.

Africa↗
PubMed2006

Effects of historical climate change, habitat connectivity, and vicariance on genetic structure and diversity across the range of the red tree vole (Phenacomys longicaudus) in the Pacific Northwestern United States.

Phylogeographical analyses conducted in the Pacific Northwestern United States have often revealed concordant patterns of genetic diversity among taxa. These studies demonstrate distinct North/South genetic discontinuities that have been attributed to Pleistocene glaciation. We examined phylogeographical patterns of red tree voles (Phenacomys longicaudus) in western Oregon by analysing mitochondrial control region sequences for 169 individuals from 18 areas across the species' range. Cytochrome b sequences were also analysed from a subset of our samples to confirm the presence of major haplotype groups. Phylogenetic network analyses suggested the presence of two haplotype groups corresponding to northern and southern regions of P. longicaudus' range. Spatial genetic analyses (samova and Genetic Landscape Shapes) of control region sequences demonstrated a primary genetic discontinuity separating northern and southern sampling areas, while a secondary discontinuity separated northern sampling areas into eastern and western groups divided by the Willamette Valley. The North/South discontinuity likely corresponds to a region of secondary contact between lineages rather than an overt barrier. Although the Cordilleran ice sheet (maximum approximately 12,000 years ago) did not move southward to directly affect the region occupied by P. longicaudus, climate change during glaciation fragmented the forest landscape that it inhabits. Signatures of historical fragmentation were reflected by positive associations between latitude and variables such as Tajima's D and patterns associated with location-specific alleles. Genetic distances between southern sampling areas were smaller, suggesting that forest fragmentation was reduced in southern vs. northern regions.

Animals↗
PubMed1992

Beginning or end? Telomere structure, genetics and biology.

The word telomere derives from the Greek word telos meaning 'end', roughly translating as 'the thing at the end' when the end is that of a chromosome. Telomeres belie their apparent simplicity of structure by being involved in a wide range of diverse biological phenomena. Much of our understanding of telomere behaviour comes from studies in lower eukaryotes such as ciliates and yeast, the subject of many recent reviews. Here we concentrate on the mammalian telomere, recent progress in its study, and how recent evidence for an involvement of telomeres in the regulation of gene expression and DNA replication in yeast points to new aspects of mammalian telomere function yet to be explored.

Animals↗
PubMed2006

Genetic structure and evolutionary history of a diploid hybrid pine Pinus densata inferred from the nucleotide variation at seven gene loci.

Although homoploid hybridization is increasingly recognized as an important phenomenon in plant evolution, its evolutionary genetic mechanisms are poorly documented and understood. Pinus densata, a pine native to the Tibetan Plateau, represents a good example of a homoploid hybrid speciation facilitated by adaptation to extreme environment and ecological isolation from the parents. Its ecologically and reproductively stabilized nature offers excellent opportunity for studying genetic processes associated with hybrid speciation. In this study, we investigated the levels and patterns of nucleotide variation in P. densata and its putative parents. Haplotype composition, gene genealogies, and the levels and patterns of nucleotide variation gave further support to the hybrid nature of P. densata. Allelic history, as revealed by our data, suggests the ancient nature of the hybrid preceding elevation of the Tibetan Plateau. We detected more deviations from neutrality in P. densata than in the parental species. Thus, at least some of the evolutionary forces that have shaped the genetic variation in P. densata are likely to be different from those acting upon parental species. We speculate that when populations of P. densata invaded new territories, they had elevated rates of response to selection in order to develop traits that help them to survive and adapt in the new environments.

Diploidy↗
PubMed2000

Genetic structure of populations of the red sea urchin, Strongylocentrotus franciscanus.

Population subdivision was evaluated in the red sea urchin, Strongylocentrotus franciscanus, using DNA sequence data from 134 adult individuals collected in 1995 and 1996. On average 22 individuals were sequenced from six geographic locations between Alaska and Baja California (N=134), nearly the full extent of the species range. DNA sequence data was obtained from direct sequencing of a 273 base pair region of the bindin gene, which encodes a sperm fertilization protein. Results indicate that bindin is sufficiently polymorphic to serve as a genetic marker. We identified 14 unique alleles present in the entire range sampled with a maximum of eight alleles at a specific site. Mean pairwise comparison of the 14 unique alleles indicates moderate sequence diversity (p-distance=1.06). Although there is conflicting evidence to suggest that Alaska populations may deviate from the Hardy-Weinberg expectations, analysis of bindin genotype frequencies indicate that it is not possible to reject the null hypothesis of random mating throughout the species range. The results of a chi-square test with pooling conform to Hardy-Weinberg expectations for all populations (P>0.05) except for the Alaska population (P=0.037). Inbreeding coefficients are consistent with this result and suggest that for the bindin locus, there is high gene flow. These results are compared with previously published results of genetic substructuring in sea urchins to examine relationships among population structure, dispersal potential and biogeography.

Journal Article↗
PubMed2003

Population genetic structure of rock ptarmigan Lagopus mutus in Northern and Western Europe.

Alpine species may be losing habitat because of global warming. Setting management priorities for such species is thus urgent and cannot be achieved without data on population structure. We studied the structure of rock ptarmigan (Lagopus mutus) populations in the Pyrenees, Alps and Norway, using six microsatellites. We found that rock ptarmigan in the Pyrenees were genetically impoverished compared with those in the Alps and Norway, and displayed a greater divergence (Pyrenees vs. Alps or Norway: theta(ST) = 0.16, Alps vs. Norway, theta(ST) = 0.04). In the Alps, despite a weak genetic differentiation between localities up to 200 km apart (theta(ST) = 0.011), a significant isolation-by-distance (IBD) effect was detected. When computed for each sex separately this IBD effect was significant for males but not for females, suggesting that males are highly philopatric.

Animals↗
PubMed2000

[Genetic structure of species community of macromycetes of the genus Leccinum Gray (Basidiomycetes, Boletaceae) of the right-bank Poles'ye].

The biochemical gene marking of the macromycete community of the genus Leccinum revealed nine reproductively isolated genetically differentiated forms instead of 2-5 forms traditionally recognized in Poles'ye. From 20 to 85% of the loci studied were found to have genetic distinctions and the degree of genetic variation did not always correlate with the morphological features of the forms identified. The variation of the locus number was found to be an important differentiating factor characteristic for this genus. In the group of L. scabrum s. I., every second locus was duplicated, whereas multiple isozymes were absent in L. aurantiacum s. I. The extremely high level of allozyme variation in macromycetes was found. The equilibrium between the expected and observed genotypes in the fruit body samples was established and discussed. It was the evidence of the fact that a panmictic model can be applied to the mushrooms of this genus, and that each fruit body is an individual organism.

Basidiomycota↗
PubMed1978

[Genetic structure of an isolated group of the native population of northern Sibiria, the Nganasani (Tavgi) of the Taimyr. III. A family analysis of blood groups].

Family analysis of ABO, MNSs, Rhesus, Duffy and Kell (Kp) in 50 families of nganasans is carried out. Segregation deviations are found in those families where the variation among the children is the widest. The proportion of children from unmarried persons is found to be very small, which supports the existence of traditional monogamic breeding structure in nganasans.

Adult↗
PubMed2005

Chromosomal inversion polymorphism leads to extensive genetic structure: a multilocus survey in Drosophila subobscura.

The adaptive character of inversion polymorphism in Drosophila subobscura is well established. The O(ST) and O(3+4) chromosomal arrangements of this species differ by two overlapping inversions that arose independently on O(3) chromosomes. Nucleotide variation in eight gene regions distributed along inversion O(3) was analyzed in 14 O(ST) and 14 O(3+4) lines. Levels of variation within arrangements were quite similar along the inversion. In addition, we detected (i) extensive genetic differentiation between arrangements in all regions, regardless of their distance to the inversion breakpoints; (ii) strong association between nucleotide variants and chromosomal arrangements; and (iii) high levels of linkage disequilibrium in intralocus and also in interlocus comparisons, extending over distances as great as approximately 4 Mb. These results are not consistent with the higher genetic exchange between chromosomal arrangements expected in the central part of an inversion from double-crossover events. Hence, double crossovers were not produced or, alternatively, recombinant chromosomes were eliminated by natural selection to maintain coadapted gene complexes. If the strong genetic differentiation detected along O(3) extends to other inversions, nucleotide variation would be highly structured not only in D. subobscura, but also in the genome of other species with a rich chromosomal polymorphism.

Animals↗
PubMed2002

Cross-species microsatellite markers for elucidating population genetic structure in Arabidopsis and Arabis (Brassicaeae).

Species closely related to model organisms present the opportunity to efficiently apply molecular and functional tools developed by a large research community to taxa with different ecological and evolutionary histories. We complied 42 microsatellite loci that amplify under common conditions in four closely related Arabidopsis: A. thaliana; A. halleri; A. lyrata ssp. lyrata; and A. lyrata ssp. petraea, as well as in one more distantly related crucifer; Arabis drummondii. Variation at these loci is amenable to a diversity of applications including population genetics, phylogeographical analyses, mapping of inter and intraspecific crosses, and recombination mapping. Our analysis of microsatellite variation illustrates significant differences in population genetic parameters among three Arabidopsis species. A population of A. thaliana, an inbreeding annual plant associated with disturbed habitats, was highly monomorphic (P = 8% percent polymorphic loci) and only 0.2% heterozygous for 648 locus-by-individual combinations. A population of the self-incompatible perennial herb, A. halleri, was more genetically variable (P = 71%) and had an excess of heterozygosity that may reflect a recent population bottleneck associated with human-mediated founder events. A population of the self-incompatible perennial herb, A. lyrata ssp. petraea, was even more genetically variable (P = 86%) and appeared to be at mutation-drift equilibrium. Population structure estimated from neutrally evolving loci provides an empirical expectation against which hypotheses of adaptive evolution at functional loci can be tested.

Arabidopsis↗
PubMed2002

Genetic structure of human populations.

We studied human population structure using genotypes at 377 autosomal microsatellite loci in 1056 individuals from 52 populations. Within-population differences among individuals account for 93 to 95% of genetic variation; differences among major groups constitute only 3 to 5%. Nevertheless, without using prior information about the origins of individuals, we identified six main genetic clusters, five of which correspond to major geographic regions, and subclusters that often correspond to individual populations. General agreement of genetic and predefined populations suggests that self-reported ancestry can facilitate assessments of epidemiological risks but does not obviate the need to use genetic information in genetic association studies.

Africa South of the Sahara↗
PubMed1994

Genetic structure of a population with social structure and migration.

Long-tailed macaques (Macaca fascicularis) live in social groups consisting of resident adult females and their offspring, and immigrant males. Subadult males leave their birth group, and might establish themselves as reproducing males in another group. Females do not leave their birth group. Such a social pattern might have consequences for the genetic differentiation between groups and the genetic relationships within groups. In a field study of long-tailed macaques (Macaca fascicularis) in Ketambe, Sumatra, Indonesia, blood samples were taken from individuals in seven adjacent social groups. Electrophoretic analysis showed 17 blood proteins and enzymes to be polymorphic, allowing the computation of heterozygosities and of the F-statistics. Of the F-statistics, F(IS) indicates the deviation from Hardy-Weinberg equilibrium averaged over local populations, FST indicates the differentiation in allele frequency between local populations, and F(IT) indicates the deviation from Hardy-Weinberg equilibrium over the total population. In a computer simulation of the population of long-tailed macaques using many loci with many neutral alleles, F(IS) and FST values proved to be characteristic for a certain demography and life history of the population, and proved not to depend upon the number of alleles or level of heterozygosity. FST values found in the simulation were compatible to those found in the field; in the simulation, values for F(IS) and F(IT) were consistently negative. The explanation for the negative F(IS) appears to be that genetic drift causes differentiation in allele frequencies between groups, and that due to this differentiation, allele frequencies differ between resident females and immigrant males, leading to offspring with an excess of heterozygotes (negative F(IS)) relative to the expectation based upon the overall allele frequency. The excess of heterozygotes might imply that slightly deleterious alleles are protected from selection. A population with a social structure and differential migration of the sexes is liable to accumulate deleterious recessives and, as a consequence, to be very sensitive to inbreeding on disruption of the social structure, as for instance in zoos.

Animals↗