Biomedical subjects

Kent E Holsinger

Publications and source records attributed to Kent E Holsinger.

9 recordsLinked to original sources

PubMed2006

Differentiation among populations with migration, mutation, and drift: implications for genetic inference.

Populations may become differentiated from one another as a result of genetic drift. The amounts and patterns of differentiation at neutral loci are determined by local population sizes, migration rates among populations, and mutation rates. We provide exact analytical expressions for the mean, variance, and covariance of a stochastic model for hierarchically structured populations subject to migration, mutation, and drift. In addition to the expected correlation in allele frequencies among populations in the same geographic region, we demonstrate that there is a substantial correlation in allele frequencies among regions at the top level of the hierarchy. We propose a hierarchical Bayesian model for inference of Wright's F-statistics in a two-level hierarchy in which we estimate the among-region correlation in allele frequencies by substituting replication across loci for replication across time. We illustrate the approach through an analysis of human microsatellite data, and we show that approaches ignoring the among-region correlation in allele frequencies underestimate the amount of genetic differentiation among major geographic population groups by approximately 30%. Finally, we discuss the implications of these results for the use and interpretation of F-statistics in evolutionary studies.

Animal Migration↗

PubMed2005

Genetic consequences of tropical second-growth forest regeneration.

Secondary forests are more extensive than old-growth forests in many tropical regions, yet the genetic composition of colonizing populations is poorly understood. We analyzed the parentage of a founder population of 130 individuals of the canopy palm Iriartea deltoidea in a 24-year-old second-growth forest in lowland Costa Rica. Among 66 trees in adjacent old-growth forest, only two individuals contributed 56% of the genes in founders. Second-growth trees had lower genetic diversity and larger patches of similar genotypes than old-growth trees. Recovery of genetic diversity of populations in tropical second-growth forests may take many generations and will require continued dispersal from genetically diverse source populations.

Arecaceae↗

PubMed2005

Polytomies and Bayesian phylogenetic inference.

Bayesian phylogenetic analyses are now very popular in systematics and molecular evolution because they allow the use of much more realistic models than currently possible with maximum likelihood methods. There are, however, a growing number of examples in which large Bayesian posterior clade probabilities are associated with very short branch lengths and low values for non-Bayesian measures of support such as nonparametric bootstrapping. For the four-taxon case when the true tree is the star phylogeny, Bayesian analyses become increasingly unpredictable in their preference for one of the three possible resolved tree topologies as data set size increases. This leads to the prediction that hard (or near-hard) polytomies in nature will cause unpredictable behavior in Bayesian analyses, with arbitrary resolutions of the polytomy receiving very high posterior probabilities in some cases. We present a simple solution to this problem involving a reversible-jump Markov chain Monte Carlo (MCMC) algorithm that allows exploration of all of tree space, including unresolved tree topologies with one or more polytomies. The reversible-jump MCMC approach allows prior distributions to place some weight on less-resolved tree topologies, which eliminates misleadingly high posteriors associated with arbitrary resolutions of hard polytomies. Fortunately, assigning some prior probability to polytomous tree topologies does not appear to come with a significant cost in terms of the ability to assess the level of support for edges that do exist in the true tree. Methods are discussed for applying arbitrary prior distributions to tree topologies of varying resolution, and an empirical example showing evidence of polytomies is analyzed and discussed.

Bayes Theorem↗

PubMed2004

Bayesian models for the analysis of genetic structure when populations are correlated.

MOTIVATION: Population allele frequencies are correlated when populations have a shared history or when they exchange genes. Unfortunately, most models for allele frequency and inference about population structure ignore this correlation. Recent analytical results show that among populations, correlations can be very high, which could affect estimates of population genetic structure. In this study, we propose a mixture beta model to characterize the allele frequency distribution among populations. This formulation incorporates the correlation among populations as well as extending the model to data with different clusters of populations. RESULTS: Using simulated data, we show that in general, the mixture model provides a good approximation of the among-population allele frequency distribution and a good estimate of correlation among populations. Results from fitting the mixture model to a dataset of genotypes at 377 autosomal microsatellite loci from human populations indicate high correlation among populations, which may not be appropriate to neglect. Traditional measures of population structure tend to overestimate the amount of genetic differentiation when correlation is neglected. Inference is performed in a Bayesian framework. CONTACT: fur@ohsu.edu.

Bayes Theorem↗

PubMed2004

Natural selection on light response curve parameters in the herbaceous annual, Impatiens capensis.

We tested for genetic variation in light response curves and their acclimation to sun versus shade in recombinant inbred lines (RILs) of the annual species Impatiens capensis derived from a cross between sun and shade populations. We exposed replicates of 49 RILs to experimentally manipulated light levels (open versus shade) in a greenhouse and measured photosynthetic light response curves, height, biomass, and reproduction. Plants were taller in the shade treatment, but we were unable to detect differences between light treatments (i.e., acclimation) in the maximal rate of photosynthesis, the light compensation point, or the quantum efficiency of photosynthesis. Genotypic selection analyses indicated that higher maximal rates of carbon assimilation and higher light compensation points (typical of sun-acclimated light curves) were favored by natural selection in both light treatments. Thus, it appears that the pattern of selection on photosynthetic parameters may not depend on light environment in this species.

Acclimatization↗

PubMed2004

Bayesian approaches for the analysis of population genetic structure: an example from Platanthera leucophaea (Orchidaceae).

We describe four extensions to existing Bayesian methods for the analysis of genetic structure in populations: (i) use of beta distributions to approximate the posterior distribution of f and theta(B); (ii) use of an entropy statistic to describe the amount of information about a parameter derived from the data; (iii) use of the Deviance Information Criterion (DIC) as a model choice criterion for determining whether there is evidence for inbreeding within populations or genetic differentiation among populations; and (iv) use of samples from the posterior distributions for f and theta(B) derived from different data sets to determine whether the estimates are consistent with one another. We illustrate each of these extensions by applying them to data derived from previous allozyme and random amplified polymorphic DNA surveys of an endangered orchid, Platanthera leucophaea, and we conclude that differences in theta(B) from the two data sets may represent differences in the underlying mutational processes.

Bayes Theorem↗

PubMed2003

Exact moment calculations for genetic models with migration, mutation, and drift.

Using properties of moment stationarity we develop exact expressions for the mean and covariance of allele frequencies at a single locus for a set of populations subject to drift, mutation, and migration. Some general results can be obtained even for arbitrary mutation and migration matrices, for example: (1) Under quite general conditions, the mean vector depends only on mutation rates, not on migration rates or the number of populations. (2) Allele frequencies covary among all pairs of populations connected by migration. As a result, the drift, mutation, migration process is not ergodic when any finite number of populations is exchanging genes. In addition, we provide closed-form expressions for the mean and covariance of allele frequencies in Wright's finite-island model of migration under several simple models of mutation, and we show that the correlation in allele frequencies among populations can be very large for realistic rates of mutation unless an enormous number of populations are exchanging genes. As a result, the traditional diffusion approximation provides a poor approximation of the stationary distribution of allele frequencies among populations. Finally, we discuss some implications of our results for measures of population structure based on Wright's F-statistics.

Gene Frequency↗

PubMed2002

A Bayesian approach to inferring population structure from dominant markers.

Molecular markers derived from polymerase chain reaction (PCR) amplification of genomic DNA are an important part of the toolkit of evolutionary geneticists. Random amplified polymorphic DNA markers (RAPDs), amplified fragment length polymorphisms (AFLPs) and intersimple sequence repeat (ISSR) polymorphisms allow analysis of species for which previous DNA sequence information is lacking, but dominance makes it impossible to apply standard techniques to calculate F-statistics. We describe a Bayesian method that allows direct estimates of FST from dominant markers. In contrast to existing alternatives, we do not assume previous knowledge of the degree of within-population inbreeding. In particular, we do not assume that genotypes within populations are in Hardy-Weinberg proportions. Our estimate of FST incorporates uncertainty about the magnitude of within-population inbreeding. Simulations show that samples from even a relatively small number of loci and populations produce reliable estimates of FST. Moreover, some information about the degree of within-population inbreeding (FIS) is available from data sets with a large number of loci and populations. We illustrate the method with a reanalysis of RAPD data from 14 populations of a North American orchid, Platanthera leucophaea.

Bayes Theorem↗

PubMed2002

The inheritance of mating songs in two cryptic, sibling lacewing species (Neuroptera: Chrysopidae: Chrysoperla).

Speciation often involves incremental responses to natural selection and results in large scale genomic changes, but it may also occur abruptly and with little genetic imprint, as seen in some complexes of cryptic species. Recent attention has focused on sexual selection in rapid speciation, because it can disrupt premating signals that mediate reproductive isolation. Some models require that environmental adaptation assist sexual selection during speciation, while others show that populations can diverge through mate choice alone. We propose that speciation involving environmental adaptation in premating signals is likely to have a polygenic basis, while speciation due to arbitrary changes in premating signals could be accompanied by changes at just a few loci. The sibling species Chrysoperla plorabunda and Chrysoperla johnsoni belong to a large complex of cryptic species of green lacewings, and meet all criteria for speciation via sexual selection. We perform a genetic analysis of line crosses between them, focusing on their substrate-borne premating songs. Measurements of seven song features and their principal components are compared among parentals, F1 and F2 hybrids, and backcrosses. The distributions of phenotypes are consistent with a model of more than one, but not many, genes. Sex linkage and/or maternal effects are negligible. C. plorabunda is dominant for most traits affecting mate choice. Bayesian analyses of segregation variance show significant additive and epistatic effects on line means. A Bayesian Castle-Wright estimate suggests that relatively few effective factors are responsible for variation in volley period (x = two factors), number of volleys per song (x = 1), and PC-1 (x = 4). Our results are consistent with simple genetic architecture of songs, supporting a role for major genes in premating isolation and strengthening the notion that mate choice alone, without significant environmental adaptation, has been responsible for generating new lacewing species.

Acoustic Stimulation↗