Biomedical subjects

L Lacey Knowles

Publications and source records attributed to L Lacey Knowles.

8 recordsLinked to original sources

PubMed2006

Inferring phylogeny despite incomplete lineage sorting.

It is now well known that incomplete lineage sorting can cause serious difficulties for phylogenetic inference, but little attention has been paid to methods that attempt to overcome these difficulties by explicitly considering the processes that produce them. Here we explore approaches to phylogenetic inference designed to consider retention and sorting of ancestral polymorphism. We examine how the reconstructability of a species (or population) phylogeny is affected by (a) the number of loci used to estimate the phylogeny and (b) the number of individuals sampled per species. Even in difficult cases with considerable incomplete lineage sorting (times between divergences less than 1 N(e) generations), we found the reconstructed species trees matched the "true" species trees in at least three out of five partitions, as long as a reasonable number of individuals per species were sampled. We also studied the tradeoff between sampling more loci versus more individuals. Although increasing the number of loci gives more accurate trees for a given sampling effort with deeper species trees (e.g., total depth of 10 N(e) generations), sampling more individuals often gives better results than sampling more loci with shallower species trees (e.g., depth = 1 N(e)). Taken together, these results demonstrate that gene sequences retain enough signal to achieve an accurate estimate of phylogeny despite widespread incomplete lineage sorting. Continued improvement in our methods to reconstruct phylogeny near the species level will require a shift to a compound model that considers not only nucleotide or character state substitutions, but also the population genetics processes of lineage sorting. [Coalescence; divergence; population; speciation.].

Evolution, Molecular↗

PubMed2006

Evidence for overdominant selection maintaining X-linked fitness variation in Drosophila melanogaster.

The role of balancing selection in maintaining genetic variation for fitness is largely unresolved. This reflects the inherent difficulty in distinguishing between models of recurrent mutation versus selection, which produce similar patterns of inbreeding depression, as well as the limitations of testing such hypotheses when fitness variation is averaged across the genome. Signatures of X-linked overdominant selection are less likely to be obscured by mutational variation because X-linked mutations are rapidly eliminated by purifying selection in males. Although models maintaining genetic variation for fitness are not necessarily mutually exclusive, a series of predictions for identifying X-linked overdominant selection can be used to separate its contribution from other underlying processes. We consider the role of overdominant selection in maintaining fitness variation in a sample of 12 X chromosomes from a population of Drosophila melanogaster. Substantial variation was observed for male reproductive success and female fecundity, with heterozygous-X genotypes exhibiting the greatest degree of variance, a finding that agrees well with predictions of the overdominance model. The importance of X-linked overdominant selection is discussed along with models of recurrent mutation and sexually antagonistic selection.

Alleles↗

PubMed2005

Intergenomic conflict revealed by patterns of sex-biased gene expression.

Intergenomic conflict can affect the distribution of genes across eukaryotic genomes. Because the phenotypic optima of males and females often differ, the fitness consequences of newly arisen alleles might not be concordant between the sexes and can be sexually antagonistic--genetic variants favored in one sex are deleterious in the other. In this article, we demonstrate that previously unexplained patterns of sex-biased gene expression in Drosophila melanogaster might have evolved by sexual antagonism, and that the majority of sex-biased expression is due to adaptive changes in males, implying that males experience stronger selection than females.

Animals↗

PubMed2005

Importance of genetic drift during Pleistocene divergence as revealed by analyses of genomic variation.

Determining what factors affect the structuring of genetic variation is key to deciphering the relative roles of different evolutionary processes in species differentiation. Such information is especially critical to understanding how the frequent shifts and fragmentation of species distributions during the Pleistocene translates into species differences, and why the effect of such rapid climate change on patterns of species diversity varies among taxa. Studies of mitochondrial DNA (mtDNA) have detected significant population structure in many species, including those directly impacted by the glacial cycles. Yet, understanding the ultimate consequence of such structure, as it relates to how species divergence occurs, requires demonstration that such patterns are also shared with genomic patterns of differentiation. Here we present analyses of amplified fragment length polymorphisms (AFLPs) in the montane grasshopper Melanoplus oregonensis to assess the evolutionary significance of past demographic events and associated drift-induced divergence as inferred from mtDNA. As an inhabitant of the sky islands of the northern Rocky Mountains, this species was subject to repeated and frequent shifts in species distribution in response to the many glacial cycles. Nevertheless, significant genetic structuring of M. oregonensis is evident at two different geographic and temporal scales: recent divergence associated with the recolonization of the montane meadows in individual sky islands, as well as older divergence associated with displacements into regional glacial refugia. The genomic analyses indicate that drift-induced divergence, despite the lack of long-standing geographic barriers, has significantly contributed to species divergence during the Pleistocene. Moreover, the finding that divergence associated with past demographic events involves the repartitioning of ancestral variation without significant reductions of genomic diversity has intriguing implications - namely, the further amplification of drift-induced divergence by selection.

Animals↗

PubMed2005

Nonantagonistic interactions between the sexes revealed by the ecological consequences of reproductive traits.

In addition to the obvious role reproductive traits play in mating-system evolution, reproductive characters can also have critical ecological or life history consequences. In this study we examine the ecological consequences of mating for female cactophilic Drosophila to test different hypotheses about the processes driving divergence in reproductive characters. Comparisons between intra- and interpopulation matings suggest that population differences in mating benefits, namely increased desiccation resistance in mated females, is not solely attributable to either a male or female-specific reproductive trait. Instead, the results indicate that increased desiccation resistance is a product of a male-female postmating-prezygotic interactions. The results underscore that postmating-prezygotic interactions can serve as an arena for the evolution of male characters that confer substantial benefits to females, not just costs arising from sexual conflict. Variation in the relative benefits conferred by mating between intra- and interpopulation matings also suggests that the relationship between speciation and divergence in reproductive characters via male-female interaction will be difficult to predict.

Animals↗

PubMed2004

Exploring the consequences of postmating-prezygotic interactions between the sexes.

The role of male-female interactions in the divergence of postmating-prezygotic reproductive traits has recently focused on sexual conflict as the selective force. While an association between mating costs and benefits suggests that antagonistic interactions may be important, a mosaic of processes may actually mediate the evolutionary dynamics of postmating-prezygotic interactions. Our study examines the ecological relevance of mating effects on females. We test this critical but often overlooked assumption in desert Drosophila, where the species' ecology provides a framework for evaluating the evolutionary implications of such mating consequences. We show that mating has a profound impact on an ecologically critical character--desiccation resistance. To explore what selective factors might underlie the observed population differences in mating effects, we test whether trends in the data match predictions based on the species' ecology. While these preliminary data are consistent with the expectation that the mating benefits are positively correlated with environmental conditions, further examination reveals an additional unanticipated association with the reproductive environment. This unexpected association challenges existing assumptions regarding the forces driving divergence of traits involved in mating.

Animals↗

PubMed2002

The mechanisms of morph determination in the amphipod Jassa: implications for the evolution of alternative male phenotypes.

The proximal basis for and the maintenance of alternative male reproductive strategies and tactics are generally not understood in most species, despite the occurrence of male polymorphism across many taxa. In the marine amphipod Jassa marmorata, males differ in morphology as well as behaviour. This dimorphism corresponds to two contrasting reproductive strategies: small sneaker males or 'minors', and large fighter males or 'majors'. This study uses quantitative genetic analyses in conjunction with experimental manipulations to assess the relative importance of genetic versus environmental factors in the determination and maintenance of these alternative mating strategies. Heritability analyses indicated the reproductive phenotypes do not reflect genetic differences between dimorphic males. By contrast, morph determination was significantly affected by diet quality. Majors essentially only developed on high-protein diets. Field studies also identified a strong correlation between seasonal shifts in the relative proportions of morphs and changes in food (i.e. phytoplankton) quantity and composition, corroborating that diet cues the switch between alternative reproductive tactics. Moreover, the comparison of major and minor growth trajectories identified a heterochronic shift in maturation times between morphs, indicating that ecological selective pressures, rather than just sexual selection, may be involved in the maintenance of this conditional strategy.

Amphipoda↗

PubMed2002

Statistical phylogeography.

While studies of phylogeography and speciation in the past have largely focused on the documentation or detection of significant patterns of population genetic structure, the emerging field of statistical phylogeography aims to infer the history and processes underlying that structure, and to provide objective, rather than ad hoc explanations. Methods for parameter estimation are now commonly used to make inferences about demographic past. Although these approaches are well developed statistically, they typically pay little attention to geographical history. In contrast, methods that seek to reconstruct phylogeographic history are able to consider many alternative geographical scenarios, but are primarily nonstatistical, making inferences about particular biological processes without explicit reference to stochastically derived expectations. We advocate the merging of these two traditions so that statistical phylogeographic methods can provide an accurate representation of the past, consider a diverse array of processes, and yet yield a statistical estimate of that history. We discuss various conceptual issues associated with statistical phylogeographic inferences, considering especially the stochasticity of population genetic processes and assessing the confidence of phylogeographic conclusions. To this end, we present some empirical examples that utilize a statistical phylogeographic approach, and then by contrasting results from a coalescent-based approach to those from Templeton's nested cladistic analysis (NCA), we illustrate the importance of assessing error. Because NCA does not assess error in its inferences about historical processes or contemporary gene flow, we performed a small-scale study using simulated data to examine how our conclusions might be affected by such unconsidered errors. NCA did not identify the processes used to simulate the data, confusing among deterministic processes and the stochastic sorting of gene lineages. There is as yet insufficient justification of NCA's ability to accurately infer or distinguish among alternative processes. We close with a discussion of some unresolved problems of current statistical phylogeographic methods to propose areas in need of future development.

Animals↗