The evolutionary origin of Xanthomonadales genomes and the nature of the horizontal gene transfer process

Determining the influence of horizontal gene transfer (HGT) on phylogenomic analyses and the retrieval of a tree of life is relevant for our understanding of microbial genome evolution. It is particularly difficult to differentiate between phylogenetic incongruence due to noise and that resulting from HGT. We have performed a large-scale, detailed evolutionary analysis of the different phylogenetic signals present in the genomes of Xanthomonadales, a group of Proteobacteria. We show that the presence of phylogenetic noise is not an obstacle to infer past and present HGTs during their evolution. The scenario derived from this analysis and other recently published reports reflect the confounding effects on bacterial phylogenomics of past and present HGT. Although transfers between closely related species are difficult to detect in genome-scale phylogenetic analyses, past transfers to the ancestor of extant groups appear as conflicting signals that occasionally might make impossible to determine the evolutionary origin of the whole genome.     

A state-based model of sperm allocation in a group-breeding salamander

We developed a dynamic program of optimal sperm allocation forgroup-breeding species. Using the small-mouthed salamander,Ambystoma texanum, as a model organism, we considered how spermatophoredeposition is affected by sperm reserves, male and female numberin breeding aggregations, and time during the breeding season.Parameters for part of the model were based on field data ofbreeding-pond arrival times for both sexes and on laboratoryspermatophore deposition data. Our model included simulationsof three different seasonal patterns of female arrival rate:decreasing (as in A. texanum), increasing, and uniform. Generalpredictions are (1) Increased male competitor numbers at breedingaggregations should cause a reduction in spermatophore allocation.(2) Increased female numbers at breeding aggregations shouldincrease spermatophore allocation. (3) The effect of currentsperm reserve levels on sperm allocation depends on the seasonaldistribution of the mean number of females per male during thebreeding season: (3a) If relative female availability decreasesover time, males with low sperm reserves should limit allocationearly in the season but should deposit maximal sperm loadslate in the season; (3b) if female availability increases overtime, males with low sperm loads should limit allocation throughoutthe entire breeding season; and (3c) if female availabilityis constant, sperm reserves are predicted to have little effecton spermatophore allocation tactics. We discuss model predictionsin the context of current sperm allocation theory.     

Adaptation to local ultraviolet radiation conditions among neighbouring Daphnia populations

Understanding the historical processes that generated current patterns of phenotypic diversity in nature is particularly challenging in subdivided populations. Populations often exhibit heritable genetic differences that correlate with environmental variables, but the non-independence among neighbouring populations complicates statistical inference of adaptation. To understand the relative influence of adaptive and non-adaptive processes in generating phenotypes requires joint evaluation of genetic and phenotypic divergence in an integrated and statistically appropriate analysis. We investigated phenotypic divergence, population-genetic structure and potential fitness trade-offs in populations of Daphnia melanica inhabiting neighbouring subalpine ponds of widely differing transparency to ultraviolet radiation (UVR). Using a combination of experimental, population-genetic and statistical techniques, we separated the effects of shared population ancestry and environmental variables in predicting phenotypic divergence among populations. We found that native water transparency significantly predicted divergence in phenotypes among populations even after accounting for significant population structure. This result demonstrates that environmental factors such as UVR can at least partially account for phenotypic divergence. However, a lack of evidence for a hypothesized trade-off between UVR tolerance and growth rates in the absence of UVR prevents us from ruling out the possibility that non-adaptive processes are partially responsible for phenotypic differentiation in this system.     

Whither Pst? The approximation of Qst by Pst in evolutionary and conservation biology

Local adaptation through natural selection can be inferred in case the additive genetic divergence in a quantitative trait across populations (Q(st)) exceeds the neutral expectation based on differentiation of neutral alleles across these populations (e.g. F(st)). As such, measuring Q(st) in relation to neutral differentiation presents a first-line investigation applicable in evolutionary biology (selection on functional genes) and conservation biology (identification of locally adapted coding genes). However, many species, especially those in need of conservation actions, are not amenable for the kind of breeding design required to estimate either narrow- or broad-sense Q(st). In such cases, Q(st) has been approximated by the phenotypic divergence in a trait across populations (P(st)). I here argue that the critical aspect for how well P(st) approximates Q(st) depends on the extent that additive genetic effects determine variation between populations relative to within populations. I review how the sensitivity of conclusions regarding local adaptation based on P(st) have been evaluated in the literature and find that many studies make a anticonservative null assumption in estimating P(st) and/or use a nonconservative approach to explore sensitivity of their conclusions. Data from two studies that have provided a second, independent assessment of selection in their system suggest that P(st)-F(st) comparisons should be interpreted very conservatively. I conclude with recommendations for improving the robustness of the inferences drawn from comparing P(st) with neutral differentiation.     

Parallel evolution of larval morphology and habitat in the snail-killing fly genus Tetanocera

In this study, we sequenced one nuclear and three mitochondrial DNA loci to construct a robust estimate of phylogeny for all available species of Tetanocera. Character optimizations suggested that aquatic habitat was the ancestral condition for Tetanocera larvae, and that there were at least three parallel transitions to terrestrial habitat, with one reversal. Maximum likelihood analyses of character state transformations showed significant correlations between habitat transitions and changes in four larval morphological characteristics (cuticular pigmentation and three characters associated with the posterior spiracular disc). We provide evidence that phylogenetic niche conservatism has been responsible for the maintenance of aquatic-associated larval morphological character states, and that concerted convergence and/or gene linkage was responsible for parallel morphological changes that were derived in conjunction with habitat transitions. These habitat-morphology associations were consistent with the action of natural selection in facilitating the morphological changes that occurred during parallel aquatic to terrestrial habitat transitions in Tetanocera.