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K E Holsinger

Publications and source records attributed to K E Holsinger.

14 recordsLinked to original sources
PubMed2002

S-RNase-mediated gametophytic self-incompatibility is ancestral in eudicots.

The evolutionary relationship between self-incompatibility systems in different families of flowering plants has long been a topic of interest. Physiological differences in the mode of gene action and the enormous sequence differences between genes with different modes of action suggest that many instances of self-incompatibility have arisen independently. In contrast, previous analyses of the S-RNase associated with gametophytic self-incompatibility in the eudicot families (Solanaceae, Scrophulariaceae, and Rosaceae) have suggested that sequences within families form well-supported and distinct lineages. In this study we demonstrate that in fact, S-RNase-mediated gametophytic self-incompatibility evolved only once in the eudicots.

Magnoliopsida↗
PubMed2000

Reproductive systems and evolution in vascular plants.

Differences in the frequency with which offspring are produced asexually, through self-fertilization and through sexual outcrossing, are a predominant influence on the genetic structure of plant populations. Selfers and asexuals have fewer genotypes within populations than outcrossers with similar allele frequencies, and more genetic diversity in selfers and asexuals is a result of differences among populations than in sexual outcrossers. As a result of reduced levels of diversity, selfers and asexuals may be less able to respond adaptively to changing environments, and because genotypes are not mixed across family lineages, their populations may accumulate deleterious mutations more rapidly. Such differences suggest that selfing and asexual lineages may be evolutionarily short-lived and could explain why they often seem to be of recent origin. Nonetheless, the origin and maintenance of different reproductive modes must be linked to individual-level properties of survival and reproduction. Sexual outcrossers suffer from a cost of outcrossing that arises because they do not contribute to selfed or asexual progeny, whereas selfers and asexuals may contribute to outcrossed progeny. Selfing and asexual reproduction also may allow reproduction when circumstances reduce opportunities for a union of gametes produced by different individuals, a phenomenon known as reproductive assurance. Both the cost of outcrossing and reproductive assurance lead to an over-representation of selfers and asexuals in newly formed progeny, and unless sexual outcrossers are more likely to survive and reproduce, they eventually will be displaced from populations in which a selfing or asexual variant arises.

Journal Article↗
PubMed1996

The effect of topology on estimates of among-site rate variation.

Among-site rate variation, as quantified by the gamma-distribution shape parameter, a or alpha, and the ratio of transition rate to transversion rate (Ts/Tv) influence phylogenetic inference. We examine the effect of topology on estimates of these two parameters in 12S rRNA sequences from nine species of mice belonging to the genera Onychomys and Peromyscus by generating 100 random topologies and estimating these parameters using parsimony and maximum-likelihood methods for each of the random topologies. The parsimony-based estimate of Ts/Tv from the well-corroborated topology falls within the distribution of estimates based on random topologies, whereas the maximum-likelihood estimate of Ts/Tv based on the well-corroborated topology lies well outside the distribution of estimates derived from random topologies. The Ts/Tv ratio derived via maximum-likelihood estimation is three times the parsimony-based estimate, suggesting that parsimony-based estimates are severe underestimates even when the correct topology is used. Both parsimony- and likelihood-based estimates of the gamma-distribution shape parameter (alpha) are sensitive to topology because the best estimates based on the well-corroborated topology are well outside the distributions of estimates derived from random topologies for both methods. We show that the reason for topology dependence is the presence of long internal branches in the underlying topology.

Animals↗
PubMed1996

Hierarchical analysis of nucleotide diversity in geographically structured populations.

Existing methods for analyzing nucleotide diversity require investigators to identify relevant hierarchical levels before beginning the analysis. We describe a method that partitions diversity into hierarchical components while allowing any structure present in the data to emerge naturally. We present an unbiased version of NEI's nucleotide diversity statistics and show that our modification has the same properties as WRIGHT's FST. We compare its statistical properties with several other FST estimators, and we describe how to use these statistics to produce a rooted tree of relationships among the sampled populations in which the mean time to coalescence of haplotypes drawn from populations belonging to the same node is smaller than the mean time to coalescence of haplotypes drawn from populations belonging to different nodes. We illustrate the method by applying it to data from a recent survey of restriction site variation in the chloroplast genome of Coreopsis grandiflora.

Chloroplasts↗
PubMed1995

Population structure, fitness surfaces, and linkage in the shifting balance process.

Wright first introduced the idea that random genetic drift and classical mass-action selection might combine in such a way as to allow populations to find the highest peak in complicated adaptive surfaces. His theory assumes large but structured populations, in which mating is spatially local. If gene flow is sufficiently low, and the subpopulations (demes) are small enough, they will be subject to genetic drift. Distant demes drift independently, allowing many independent searches of the adaptive surface to take place. A deme that has shifted to a higher peak can, by emigration, cause the rest of the demes to shift to the higher peak. The probability of this shift depends on the migration rate. Previous studies have concluded that very little migration is necessary to effect the shift in adaptive peaks that characterizes the last phase of Wright's Shifting Balance Process (SBP). Here we present the results of a computer study that investigates the roles of dispersal distance, the degree of epistasis in the fitness surface, and recombination on the shifting balance process. In particular, we measure their effect on the population's mean fitness. We show that over a range of dispersal distances the advantage of the SBP is a monotonically increasing function of the amount of epistasis. Our results show that the extent of dispersal that results in the greatest effect of the SBP in increasing mean fitness depends on the extent of epistasis. Finally, for low levels of epistasis, higher recombination performs better, while for intermediate levels, lower recombination results in a greater advantage of the SBP.

Adaptation, Biological↗
PubMed1995

Among-site rate variation and phylogenetic analysis of 12S rRNA in sigmodontine rodents.

We analyze sequences from two mitochondrial genes, cytochrome b (cyt b) and 12S rRNA (12S), for a group of sigmodontine rodents among which phylogenetic relationships are well understood based on concordance of morphological, chromosomal, allozyme, and other DNA data sets. Because these two genes are physically linked on the nonrecombining mitochondrial genome, they necessarily share the same history. Phylogenetic analysis of the cyt b gene recovers the well-corroborated relationships, generally with strong support. None of the methods that we employed, including variously weighted parsimony, neighbor joining on both single-rate and gamma-corrected distances, and maximum likelihood, were able to recover these relationships for the 12S gene. Parsimony analyses of the 12S data resulted in a relatively strongly supported placement of Peromyscus eremicus that conflicts with that suggested by cyt b and all other data. There is extreme among-site rate variation in the 12S sequences and moderate levels in the cyt b sequences. This highly skewed distribution of rates in the 12S gene makes phylogenetic analyses of these sequences particularly susceptible to the misleading effects of nonindependence and other nonrandom noise, suggesting that phylogenetic analyses of data sets that contain a great deal of among-site rate variation be interpreted with caution.

Animals↗
PubMed1986

Selection for increased mutation rates with fertility differences between matings.

Previous studies of mutation modification have considered models in which selection is a result of viability differences that are sex symmetric. The results of a numerical study of a model in which selection is a result of fertility differences between mated pairs demonstrate that the type of selection to which a population is subject can have a significant impact on the evolution of various parameters of the genetic system. When the fertility of matings between individuals with different genotypes exceeds the fertility of at least some of the matings between individuals with the same genotype, selection may favor increased rates of mutation, in contrast to the results from all existing constant viability models with random mating and infinite population size. Increased mutation rates are most frequently favored when forward and back mutation occur at approximately equal rates and when the modifying locus is loosely linked to the selected locus. We present one example in which selection favors increased rates of mutation even though the selection scheme is reducible to one of differential viability between the sexes.

Alleles↗
PubMed1985

Selection in complex genetic systems. VI. Equilibrium properties of two locus selection models with partial selfing.

The results of a combined analytical and numerical study of two locus selection models with partial selfing indicate that several commonly held opinions about the effects of partial self-fertilization do not hold in general. For example, the heterozygosity of a population may actually increase as the selfing rate is increased. Similarly, selection strong enough to guarantee a two locus polymorphism with complete selfing does not necessarily guarantee a two locus polymorphism with intermediate amounts of self-fertilization. The results presented here and a brief review of previously existing results indicate that the predictions of population genetic models based on the assumption of random mating will not be greatly altered by a small amount of self-fertilization, unless the loci involved are tightly linked. On the other hand, the results presented indicate that a very small amount of outcrossing may lead to marked differences from the expectation based on complete self-fertilization.

Biometry↗
PubMed1983

Modifiers of mutation rate: Evolutionary optimum with complete selfing.

It often has been assumed that, for infinite random mating populations in a constant environment, natural selection will favor genotypes at a neutral modifier locus that minimize the mutation rate. Mathematical modeling of this process confirms this assertion, independent of the selection regime. The same model under conditions of complete selfing can produce, under certain nondegenerate overdominance conditions, an optimum mutation rate below which increased mutation is favored and above which decreased mutation is favored. This occurs with unidirectional mutation models and a class of reversible mutation models with fitness overdominance. This is the first time that such a modifier optimum has been produced analytically for an infinite population in a constant environment.

Journal Article↗
PubMed1983

Linkage modification with mixed random mating and selfing: a numerical study.

Although recombination cannot increase under conditions of random mating or complete selfing in regimes of constant selection, with mixed random mating and selfing, selection for increased recombination can occur. For some fitness regimes there may be selection for reduced recombination with both low and high degrees of selfing but selection for increased recombination with moderate degrees of selfing. With some fitness regimes there is a historical effect: depending on which equilibrium a population starts from, there may be selection for either increased or decreased recombination. In other cases the direction of selection may be determined by the present state of individuals within the population. If recombination is already fairly limited, there may be selection for further reduction. If recombination is already fairly frequent, there may be selection for increased recombination. For certain symmetric viability systems there may be an intermediate value of the recombination fraction between 0 and 0.5 toward which the population will evolve. Although it is not yet possible to classify precisely those fitness matrices that can exhibit selection for increased recombination, it does appear that selection for increased recombination can occur only if at least two of the double homozygotes are less fit than would be expected on the basis of a comparison of the fitnesses of the single and double heterozygotes on an additive scale.

Alleles↗