Recently, a new Chlamydia-related organism, Protochlamydia naegleriophila KNic, was discovered within a Naegleria amoeba. To decipher the mechanisms at play in the modeling of genomes from the Protochlamydia genus, we sequenced de novo the full genome of Pr. naegleriophila combining the advantages of two second-generation sequencing technologies. The assembled complete genome comprises a 2,885,111 bp chromosome and a 145,285 bp megaplasmid. For the first time within the Chlamydiales order, a CRISPR system, the immune system of bacteria, was discovered on the chromosome. It is composed of a small CRISPR locus comprising eight repeats and the associated cas and cse genes of the subtype I-E. A CRISPR locus was also found within Chlamydia sp. Diamant, another Pr. naegleriophila strain whose genome was recently released, suggesting that the CRISPR system was acquired by a common ancestor of these two members of Pr. naegleriophila, after the divergence from Pr. amoebophila. The plasmid encodes an F-type conjugative system similar to that found in the Pam100G genomic island of Pr. amoebophila suggesting an acquisition of this conjugative system before the divergence of both Protochlamydia species and the integration of a putative Pr. amoebophila plasmid into its main chromosome giving rise to the Pam100G genomic island. Overall, this new Pr. naegleriophila genome sequence enables to investigate further the dynamic processes shaping the genomes of Chlamydia-related bacteria.

We evaluated the fraction of variation in HIV-1 set point viral load attributable to viral or human genetic factors by using joint host/pathogen genetic data from 541 HIV infected individuals. We show that viral genetic diversity explains 29% of the variation in viral load while host factors explain 8.4%. Using a joint model including both host and viral effects, we estimate a total of 30% heritability, indicating that most of the host effects are reflected in viral sequence variation.

Over the last decade tremendous progress has been made towards a comparative understanding of gene regulatory evolution. However, we know little about how gene regulation evolves in birds, and how divergent genomes interact in their hybrids. Because of unique features of birds – female heterogamety, a highly conserved karyotype, and the slow evolution of reproductive incompatibilities – an understanding of regulatory evolution in birds is critical to a comprehensive understanding of regulatory evolution and its implications for speciation. Using a novel complement of analyses of replicated RNA-seq libraries, we demonstrate abundant divergence in gene expression between subspecies of zebra finches Taeniopygia guttata. By comparing parental populations and their F1 hybrids, we also show that gene misexpression is relatively rare, a pattern that may partially explain the slow buildup of postzygotic reproductive isolation observed in birds relative to other taxa. Although we expected that the action of genetic drift on the island-dwelling zebra finch subspecies would be manifested in a high rate of trans regulatory divergence, we found that most divergence was in cis regulation, following a pattern commonly observed in other taxa. Thus our study highlights both unique and shared features of avian regulatory evolution.

The stingless bee Tetragonisca angustula Latreille 1811 is one of the most widespread bee species in the Neotropics, distributed from Mexico to Argentina. However, this wide distribution contrasts with the low distance that females travel to build new nests whereas nothing is known about male dispersion. Previous studies of T. angustula were ambiguous concerning its genetic structure and were based only on nuclear markers and on small and/or limited sample size. Here we evaluate the genetic structure of several populations of T. angustula by using mitochondrial DNA and microsatellites. These markers can help us to detect differences in the migratory behavior between males and females. Our results showed that the populations were highly differentiated suggesting that both females and males are low dispersers. Therefore, its continental distribution might consist of several different taxa.

Selective breeding of dogs has resulted in repeated artificial selection on breed-specific morphological phenotypes. A number of quantitative trait loci associated with these phenotypes have been identified in genetic mapping studies. We analyzed the population genomic signatures observed around the causal mutations for 12 of these loci in 25 dog breeds, for which we genotyped 25 individuals in each breed. By measuring the population frequencies of the causal mutations in each breed, we identified those breeds in which specific mutations most likely experienced positive selection. These instances were then used as positive controls for assessing the performance of popular statistics to detect selection from population genomic data. We found that artificial selection during dog domestication has left characteristic signatures in the haplotype and nucleotide polymorphism patterns around selected loci that can be detected in the genotype data from a single population sample. However, the sensitivity and accuracy at which such signatures were detected varied widely between loci, the particular statistic used, and the choice of analysis parameters. We observed examples of both hard and soft selective sweeps and detected strong selective events that removed genetic diversity almost entirely over regions >10 Mbp. Our study demonstrates the power and limitations of selection scans in populations with high levels of linkage disequilibrium due to severe founder effects and recent population bottlenecks.

Polymorphic chromosomal rearrangements, which can bind together hundreds of genes into single genetic loci with diverse effects, are increasingly associated with local adaptation and speciation. They may also be an important component of genetic variation within populations. We genetically and phenotypically characterized a novel segregating inversion (inv6) in the Iron Mountain (IM) population of Mimulus guttatus (yellow monkeyflower). We first identified a region of recombination suppression in three F2 mapping populations resulting from crosses among IM plants; in each case, the F1 hybrid parent was heterozygous for a homogenous derived haplotype (inv6) across markers spanning over 4.2 Mb of Linkage Group 6. Genotype-phenotype associations in the three F2 populations demonstrated negative inv6 effects on male and female fitness components. In addition, inv6 carriers suffered a ~30% loss of pollen viability in the field. Despite these costs, inv6 exists at moderate and apparently stable frequency (~7%) in the natural population, suggesting counter-balancing fitness benefits that maintain the polymorphism. Across four years of monitoring in the field, inv6 had an overall significant positive effect on the seed production (lifetime female fitness) of carriers. This benefit was particularly strong in harsh years and may be mediated (in part) by strong positive inv6 effects on flower production. These data suggest that opposing fitness effects maintain an intermediate frequency, and as a consequence, inv6 generates inbreeding depression and high genetic variance. We discuss these findings in the context of theory about the genetic basis of inbreeding depression and the role for chromosomal rearrangements in population divergence with gene flow.

Genetic mapping studies of quantitative traits typically focus on detecting loci that contribute additively to trait variation. Genetic interactions are often proposed as a contributing factor to trait variation, but the relative contribution of interactions to trait variation is a subject of debate. Here, we use a very large cross between two yeast strains to accurately estimate the fraction of phenotypic variance due to pairwise QTL-QTL interactions for 20 quantitative traits. We find that this fraction is 9% on average, substantially less than the contribution of additive QTL (43%). Statistically significant QTL-QTL pairs typically have small individual effect sizes, but collectively explain 40% of the pairwise interaction variance. We show that pairwise interaction variance is largely explained by pairs of loci at least one of which has a significant additive effect. These results refine our understanding of the genetic architecture of quantitative traits and help guide future mapping studies.

Standard models of molecular evolution cannot estimate absolute speciation times alone, and require external calibrations to do so. Because fossil calibration methods rely on the unreliable fossil record, most nodes in the tree of life are dated with poor accuracy. However, many major paleogeographical events are dated, and since biogeographic processes depend on paleogeographical conditions, biogeographic dating may be used as an alternative or complementary method to fossil dating. I demonstrate how a time-stratified biogeographic stochastic process may be used to estimate absolute divergence times by conditioning on dated paleogeographical events. Informed by the current paleogeographical literature, I construct an empirical dispersal graph using 25 areas and 26 epochs for the past 540 Ma of Earth’s history. Simulations indicate biogeographic dating performs well so long as paleogeography imposes constraint on biogeographic character evolution. To gauge whether biogeographic dating may have any practical use, I analyze the well-studied turtle clade (Testudines) then assess how well biogeographic dating fares compared to heavily fossil-calibrated dating results as reported in the literature. Fossil-free biogeographic dating estimated the age of the most recent common ancestor of extant turtles to be approximately 201 Ma, which is consistent with fossil-based estimates. Accuracy improves further when including a root node fossil calibration. The described model, paleogeographical dispersal graph, and analysis scripts are available for use with RevBayes.