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Population genetic structure of two rare tree species (Colubrina oppositifolia and Alphitonia ponderosa, Rhamnaceae) from Hawaiian dry and mesic forests using random amplified polymorphic DNA markers.

Hawaiian dry and mesic forests contain an increasingly rare assemblage of species due to habitat destruction, invasive alien weeds and exotic pests. Two rare Rhamnaceae species in these ecosystems, Colubrina oppositifolia and Alphitonia ponderosa, were examined using random amplified polymorphic DNA (RAPD) markers to determine the genetic structure of the populations and the amount of variation relative to other native Hawaiian species. Relative variation is lower than with other Hawaiian species, although this is probably not a consequence of genetic bottleneck. Larger populations of both species contain the highest levels of genetic diversity and smaller populations generally the least as determined by number of polymorphic loci, estimated heterozygosity, and Shannon's index of genetic diversity. Populations on separate islands were readily discernible for both species as were two populations of C. oppositifolia on Hawai'i island (North and South Kona populations). Substructure among Kaua'i subpopulations of A. ponderosa that were ecologically separated was also evident. Although population diversity is thought to have remained at predisturbance levels, population size continues to decline as recruitment is either absent or does not keep pace with senescence of mature plants. Recovery efforts must focus on control of alien species if these and other endemic dry and mesic forest species are to persist.

Colubrina↗

Population genetics of multigene families that are dispersed into two or more chromosomes.

The evolution of multigene families whose members are dispersed into two or more nonhomologous chromosomes is studied from the standpoint of population genetics. By using a simple model of gene conversion, equilibrium and transient properties of the probability of identity of genes belonging to the family are investigated. Also, the time until fixation of a mutant belonging to a subdivided multigene family is studied by an approximation method. It is shown that dispersion of the family into two or more chromosomes has a relatively minor effect on the extent of identity between genes, unless the conversion rate between genes on nonhomologous chromosomes is extremely low, or unless the number of nonhomologous chromosomes on which gene members are dispersed is large.

Animals↗

Multilocus genotyping of Cryptosporidium parvum Type 2: population genetics and sub-structuring.

Cryptosporidium parvum is an intracellular protozoan parasite that infects the gastrointestinal tract of humans and other mammals. It has significant economic importance as a pathogen of livestock and, as there is no effective treatment or vaccine available, understanding transmission routes and identifying sources of infection is key to preventing future outbreaks and controlling this disease. In this study we have determined the multilocus genotype (MLG) of 240 C. parvum Type 2 (bovine) isolates using a combination of seven micro- and minisatellite markers. These isolates were collected over a period of 19 months and are from three different geographical locations within Scotland and three different host species. The results of this study have enabled us to address questions concerning C. parvum population genetics in relation to host, temporal and geographical sub-structuring. We identified 48 multilocus genotypes within the Type 2 C. parvum isolates and found no evidence to support geographic or temporal sub-structuring of the populations. However host sub-structuring was identified within the human Type 2 population highlighting the potential use of such a typing system in understanding the epidemiology of this parasite in addition to raising interesting questions with regard to its population genetic structure. We also isolated two C. parvum 'monkey type' isolates from two separate human cases indicating that this genotype is not restricted to monkey hosts with the multilocus genotypes of these isolates distinguishing them from all other isolates.

Alleles↗

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↗

Darwinian adaptation, population genetics and the streetcar theory of evolution.

This paper investigates the problem of how to conceive a robust theory of phenotypic adaptation in non-trivial models of evolutionary biology. A particular effort is made to develop a foundation of this theory in the context of n-locus population genetics. Therefore, the evolution of phenotypic traits is considered that are coded for by more than one gene. The potential for epistatic gene interactions is not a priori excluded. Furthermore, emphasis is laid on the intricacies of frequency-dependent selection. It is first discussed how strongly the scope for phenotypic adaptation is restricted by the complex nature of 'reproduction mechanics' in sexually reproducing diploid populations. This discussion shows that one can easily lose the traces of Darwinism in n-locus models of population genetics. In order to retrieve these traces, the outline of a new theory is given that I call 'streetcar theory of evolution'. This theory is based on the same models that geneticists have used in order to demonstrate substantial problems with the 'adaptationist programme'. However, these models are now analyzed differently by including thoughts about the evolutionary removal of genetic constraints. This requires consideration of a sufficiently wide range of potential mutant alleles and careful examination of what to consider as a stable state of the evolutionary process. A particular notion of stability is introduced in order to describe population states that are phenotypically stable against the effects of all mutant alleles that are to be expected in the long-run. Surprisingly, a long-term stable state can be characterized at the phenotypic level as a fitness maximum, a Nash equilibrium or an ESS. The paper presents these mathematical results and discusses - at unusual length for a mathematical journal - their fundamental role in our current understanding of evolution.

Animals↗

Evolution equation of population genetics: relation to the density-matrix theory of quasiparticles with general dispersion laws.

The Waxman-Peck theory of population genetics is discussed in regard of soil bacteria. Each bacterium is understood as a carrier of a phenotypic parameter p. The central objective is the calculation of the probability density with respect to p, Phi(p,t;p(0)), of the carriers living at time t>0, provided that initially at t(0)=0, all bacteria carried the phenotypic parameter p(0)=0. The theory involves two small parameters: the mutation probability mu and a parameter gamma involved in a function w(p) defining the fitness of the bacteria to survive the generation time tau and give birth to an offspring. The mutation from a state p to a state q is defined by a Gaussian with a dispersion sigma(2)(m). The author focuses our attention on a function phi(p,t) which determines uniquely the function Phi(p,t;p(0)) and satisfies a linear equation (Waxman's equation). The Green function of this equation is mathematically identical with the one-particle Bloch density matrix, where mu characterizes the order of magnitude of the potential energy. (In the x representation, the potential energy is proportional to the inverted Gaussian with the dispersion sigma(2)(m)). The author solves Waxman's equation in the standard style of a perturbation theory and discusses how the solution depends on the choice of the fitness function w(p). In a sense, the function c(p)=1-w(p)/w(0) is analogous to the dispersion function E(p) of fictitious quasiparticles. In contrast to Waxman's approximation, where c(p) was taken as a quadratic function, c(p) approximately gammap(2), the author exemplifies the problem with another function, c(p)=gamma[1-exp(-ap(2))], where gamma is small but a may be large. The author shows that the use of this function in the theory of the population genetics is the same as the use of a nonparabolic dispersion law E=E(p) in the density-matrix theory. With a general function c(p), the distribution function Phi(p,t;0) is composed of a delta-function component, N(t)delta(p), and a blurred component. When discussing the limiting transition for t--> infinity, the author shows that his function c(p) implies that N(t)-->N( infinity ) not equal 0 in contrast with the asymptotics N(t)-->0 resulting from the use of Waxman's function c(p) approximately p(2).

Journal Article↗

Differential plague-transmission dynamics determine Yersinia pestis population genetic structure on local, regional, and global scales.

Plague, the disease caused by the bacterium Yersinia pestis, has greatly impacted human civilization. Y. pestis is a successful global pathogen, with active foci on all continents except Australia and Antarctica. Because the Y. pestis genome is highly monomorphic, previous attempts to characterize the population genetic structure within a single focus have been largely unsuccessful. Here we report that highly mutable marker loci allow determination of Y. pestis population genetic structure and tracking of transmission patterns at two spatial scales within a single focus. In addition, we found that in vitro mutation rates for these loci are similar to those observed in vivo, which allowed us to develop a mutation-rate-based model to examine transmission mechanisms. Our model suggests there are two primary components of plague ecology: a rapid expansion phase for population growth and dispersal followed by a slower persistence phase. This pattern seems consistent across local, regional, and even global scales.

Animals↗

Speciation in parasites: a population genetics approach.

Parasite speciation and host-parasite coevolution should be studied at both macroevolutionary and microevolutionary levels. Studies on a macroevolutionary scale provide an essential framework for understanding the origins of parasite lineages and the patterns of diversification. However, because coevolutionary interactions can be highly divergent across time and space, it is important to quantify and compare the phylogeographic variation in both the host and the parasite throughout their geographical range. Furthermore, to evaluate demographic parameters that are relevant to population genetics structure, such as effective population size and parasite transmission, parasite populations must be studied using neutral genetic markers. Previous emphasis on larger-scale studies means that the connection between microevolutionary and macroevolutionary events is poorly explored. In this article, we focus on the spatial fragmentation of parasites and the population genetics processes behind their diversification in an effort to bridge the micro- and macro-scales.

Animals↗

Population genetic analysis of the genes APOE, APOB(3'VNTR) and ACE in some black and Amerindian communities from Colombia.

A population genetic study was carried out with the APOE, APOB and ACE loci in 17 Colombian human populations. Ten of them were Amerindian communities coming from the northeastern part of Colombia, Pacific region, Eastern Plains and Amazonia. Six were black populations from Providence Island, Caribbean and Pacific coasts. Finally, the Mestizo population of Bogota was studied as well. The APOE and ACE loci were in Hardy-Weinberg equilibrium, whereas the APOB locus was not studied in all populations. The genetic heterogeneity was substantially greater among the Amerindian populations (G(ST) = 0.059) than in the Afrocolombian populations (G(ST) = 0.009). Also the gene flow population pair estimates were so much higher among the Afrocolombian populations (Nm = 49.08 +/- 43.07) than among Amerindian populations (Nm = 9.66 +/- 18.04). Different phylogenetic and multivariant analyses showed that the Amerindian populations analyzed were clustered in three different arrays: one constituted by the Colombian northeastern and Pacific populations, the second one by the two Amazon populations (Coreguaje and Nukak) and the last one by the Yuco (the unique Caribbe-speaking population among those studied). The latter population was highly divergent from a genetic point of view from the remainder Amerindian populations studied. By using the Mantel test, the existence of a positive and significant correlation between the genetic and geographical distances found among Amerindian populations was demonstrated. This fact was not observed among the Afrocolombian populations. Nevertheless, an isolation-by-distance Slatkin analysis test did not show a significant clear structure of this special pattern among the Indian tribes studied.

Alleles↗

Population genetics, history, and health patterns in native americans.

Over the past two decades, detailed studies of mitochondrial DNA and the Y chromosome have increased our understanding of the history and population genetics of Native American populations. Variation in autosomal DNA has also been investigated, but to a more limited extent. A low level of genetic diversity in Native American populations is a robust finding from all lines of evidence. In contrast to the previous multiple migration scenarios for the Pleistocene peopling of the Americas, it now seems that a single migration satisfactorily explains the genetic data. Native Americans show greater genetic similarity to populations in east central Asia than they do to the current easternmost Siberian populations. Recent studies on the Y chromosome indicate a date of entry (about 17,000 years ago) into the Americas roughly consistent with the archaeological record. Native Americans experienced two episodes of reduced population size: one with the peopling of the Americas and the other with European contact. The former is the more important determinant for the number of gene lineages and founding haplotypes seen in populations. It may also be an important determinant of the genetic variation underlying common complex diseases, and especially diabetes. The tribal structure of contemporary Native American populations is relevant to the distribution of rare Mendelian disorders because most tribes constitute relatively small, semi-independent gene pools. This leads us to expect that the allelic spectrum for Mendelian diseases will be simple within individual tribes but complex for Native Americans as a whole.

Genetics, Population↗

Population genetic evidence for rapid changes in intraspecific diversity and allelic cycling of a specialist defense gene in Zea.

Two patterns of plant defense gene evolution are emerging from molecular population genetic surveys. One is that specialist defenses experience stronger selection than generalist defenses. The second is that specialist defenses are more likely to be subject to balancing selection, i.e., evolve in a manner consistent with balanced-polymorphism or trench-warfare models of host-parasite coevolution. Because most of the data of specialist defenses come from Arabidopsis thaliana, we examined the genetic diversity and evolutionary history of three defense genes in two outcrossing species, the autotetraploid Zea perennis and its most closely related extant relative the diploid Z. diploperennis. Intraspecific diversity at two generalist defenses, the protease inhibitors wip1 and mpi, were consistent with a neutral model. Like previously studied genes in these taxa, wip1 and mpi harbored similar levels of diversity in Z. diploperennis and Z. perennis. In contrast, the specialist defense hm2 showed strong although distinctly different departures from a neutral model in the two species. Z. diploperennis appears to have experienced a strong and recent selective sweep. Using a rejection-sampling coalescent method, we estimate the strength of selection on Z. diploperennis hm2 to be approximately 3.0%, which is approximately equal to the strength of selection on tb1 during maize domestication. Z. perennis hm2 harbors three highly diverged alleles, two of which are found at high frequency. The distinctly different patterns of diversity may be due to differences in the phase of host-parasite coevolutionary cycles, although higher hm2 diversity in Z. perennis may also reflect reduced efficacy of selection in the autotetraploid relative to its diploid relative.

Alleles↗

Population genetic structure and the effect of founder events on the genetic variability of moose, Alces alces, in Canada.

Moose, Alces alces, occur naturally throughout most of Canada but successful introductions of known numbers of animals have been made to the islands of Newfoundland and Cape Breton. Five microsatellite loci were used to investigate the population genetic structure and any change in genetic variability due to founder events of moose in Canada. Comparisons of allele frequencies for moose from 11 regions of the country suggested that there are at least seven genetically distinct populations (P < 0.05) in North America, namely Alberta, eastern Ontario, New Brunswick, Cape Breton, Labrador, western Newfoundland, and the Avalon Peninsula of Newfoundland. The average population heterozygosity was approximately 33% (range from 22 to 41%). UPGMA analysis of Nei's genetic distances produced phenograms similar to what would be expected when geographical location and population history are considered. The loss of heterozygosity due to a single founder event (n = 3; two introductions and a natural colonization) ranged from 14 to 30%, and the cumulative loss of heterozygosity due to two successive founder events (an introduction followed by a natural colonization) was 46%. In these examples loss of genetic variability has not been associated with any known phenotypic deviances, suggesting that populations may be established from a small number of founders. However, the viability of these founded populations over evolutionary timescales cannot be determined and is highly dependent upon chance.

Alleles↗

Influence of volcanic activity on the population genetic structure of Hawaiian Tetragnatha spiders: fragmentation, rapid population growth and the potential for accelerated evolution.

Volcanic activity on the island of Hawaii results in a cyclical pattern of habitat destruction and fragmentation by lava, followed by habitat regeneration on newly formed substrates. While this pattern has been hypothesized to promote the diversification of Hawaiian lineages, there have been few attempts to link geological processes to measurable changes in population structure. We investigated the genetic structure of three species of Hawaiian spiders in forests fragmented by a 150-year-old lava flow on Mauna Loa Volcano, island of Hawaii: Tetragnatha quasimodo (forest and lava flow generalist), T. anuenue and T. brevignatha (forest specialists). To estimate fragmentation effects on population subdivision in each species, we examined variation in mitochondrial and nuclear genomes (DNA sequences and allozymes, respectively). Population subdivision was higher for forest specialists than for the generalist in fragments separated by lava. Patterns of mtDNA sequence evolution also revealed that forest specialists have undergone rapid expansion, while the generalist has experienced more gradual population growth. Results confirm that patterns of neutral genetic variation reflect patterns of volcanic activity in some Tetragnatha species. Our study further suggests that population subdivision and expansion can occur across small spatial and temporal scales, which may facilitate the rapid spread of new character states, leading to speciation as hypothesized by H. L. Carson 30 years ago.

Animals↗

GAsDock: a new approach for rapid flexible docking based on an improved multi-population genetic algorithm.

Based on an improved multi-population genetic algorithm, a new fast flexible docking program, GAsDock, was developed. The docking accuracy, screening efficiency, and docking speed of GAsDock were evaluated by the docking results of thymidine kinase (TK) and HIV-1 reverse transcriptase (RT) enzyme with 10 available inhibitors of each protein and 990 randomly selected ligands. Nine of the ten known inhibitors of TK were accurately docked into the protein active site, the root-mean-square deviation (RMSD) values between the docking and X-ray crystal structures are less than 1.7A; binding poses (conformation and orientation) of 9 of the 10 known inhibitors of RT were reproduced by GAsDock with RMSD values less than 2.0A. The docking time is approximately in proportion to the number of rotatable bonds of ligands; GAsDock can finish a docking simulation within 60s for a ligand with no more than 20 rotatable bonds. Results indicate that GAsDock is an accurate and remarkably faster docking program in comparison with other docking programs, which is applausive in the application of virtual screening.

Algorithms↗

Influence of landscape on the population genetic structure of the alpine butterfly parnassius smintheus (Papilionidae)

Four microsatellite DNA markers were developed which were used to examine the relationship between landscape and population genetic structure among a set of populations of the butterfly Parnassius smintheus located in the foothills of the Canadian Rockies. Detailed information on the dispersal of adult butterflies among this same set of populations was available. Simple and partial Mantel tests were used to examine the relationships between genetic distances, predicted rates of dispersal, and a number of landscape variables, all measured pairwise for 17 sample sites. Nei's standard genetic distance was negatively correlated with predicted dispersal. We observed a significant pattern of isolation by distance at a very small spatial scale. The distance between sites that was through forest was a stronger predictor of genetic distance than the distance through open meadow, indicating a significant effect of landscape on population genetic structure beyond that of simple isolation by distance. Our results suggest that rises in the tree-line in alpine areas, caused by global warming, will lead to reduced gene flow among populations of P. smintheus.

Journal Article↗

A genomic population genetics analysis of the pathogenic enterocyte effacement island in Escherichia coli: the search for the unit of selection.

Comparative genomic analysis is a powerful tool for understanding the history and organization of complete genomes. The mathematical tools of population genetics combined with genomic analysis provide a powerful approach to dissect heterogeneities in genome evolution. This study presents a hierarchical analysis of the enterocyte and effacement island (35 kb), which is found in the enteropathogenic and enterohemorrhagic strains in Escherichia coli and in Citrobacter rodentium. The locus of enterocyte and effacement in E. coli is considered to be a clonal unit inside a clonal organism and is expected to evolve as a single unit. This analysis examines the clonal assumption by determining genetic diversity, GC content, and the substitution rates at the different functional levels of (i) the complete pathogenic island, (ii) the five operons in which the island is organized, and (iii) for each of the individual 41 genes that comprise the locus. We find that there is a conserved region that is composed of genes that belong to the type III secretion system and that may be products of horizontal transfer. A more diverse region is composed of genes for secreted proteins and genes that we infer to be original components of the E. coli genome. This genetic mosaic seems to be differentially affected by selection and mutation. Our results suggest that recombination and selection may be breaking this structure so that different elements are, at best, weakly coupled in their evolution. These observations suggest that the units of selection are not the complete island, but rather, much smaller units that comprise the island.

Codon↗

Population genetics and dynamics of Plasmodium falciparum: an ecological view.

Molecular characterization of the Plasmodium falciparum genome has led to identification of polymorphic loci and the mechanisms generating genetic diversity in this parasite. This information has resulted in the development of molecular methods to type parasite diversity in the field. Consequently, we are now in a position to describe the population genetics and dynamics of P. falciparum. The limited number of field studies that have been conducted to date have revealed an extraordinary degree of genetic diversity in natural parasite populations. Heterozygous recombination which occurs during meiosis appears to be one mechanism for generating genetic diversity. The rate at which such recombination occurs in natural parasite populations defines the genetic structure of the parasite population and can influence the ability of the parasite to respond to selection pressure. The high frequency of single genotype infections and the female-biased gametocyte sex ratios found in hyperendemic malaria areas suggest that self-fertilization occurs frequently. Population-wide surveys of allele frequencies in endemic areas have, however, shown no evidence of linkage disequilibrium and are consistent with a panmictic population structure. We argue that these studies have only sampled symptomatic infections, within which rare or recombinant genotypes may be disproportionately represented. They also take no account of the spatial structure of P. falciparum populations. Systematic investigations of the amount of heterozygosity in small areas as part of population-wide surveys are required to define the genetic structure of P. falciparum populations. Population dynamic studies which consider genetic heterogeneity of P. falciparum have shown fluctuations of different serotypes in space and time. The host immune response appears to play an important role in generating these dynamics. Integrated field and laboratory studies, which consider the interaction between population genetics and dynamics, will be necessary to describe the population biology of P. falciparum.

Animals↗

Population genetics of three VNTR polymorphisms in two different Spanish populations.

Two different Spanish populations, one from Galicia (NW Spain) and the other from the rest of Spain, have been analyzed at three different hypervariable loci (YNH24, MS43a and MS31) using the EDNAP electrophoretic protocol and HinfI as restriction enzyme. Although the "rest of Spain" population is a clearly stratified population using classical blood groups, no evidence of stratification for these loci has been found and the differences to the Galician population were not significant, which suggests that a common Spanish population data-base could be possible. A semiparametric model is proposed for estimating frequencies, using the smoothed cross-validation of Hall et al. (1992) to calculate the size of the window utilized.

Alleles↗