Gene Conversion Among Paralogs Results in Moderate False Detection of Positive Selection Using Likelihood Methods

Previous studies have shown that recombination between allelic sequences can cause likelihood-based methods for detecting positive selection to produce many false-positive results. In this article, we use simulations to study the impact of nonallelic gene conversion on the specificity of PAML to detect positive selection among gene duplicates. Our results show that, as expected, gene conversion leads to higher rates of false-positive results, although only moderately. These rates increase with the genetic distance between sequences, the length of converted tracts, and when no outgroup sequences are included in the analysis. We also find that branch-site models will incorrectly identify unconverted sequences as the targets of positive selection when their close paralogs are converted. Bayesian prediction of sites undergoing adaptive evolution implemented in PAML is affected by conversion, albeit in a less straightforward way. Our work suggests that particular attention should be devoted to the evolutionary analysis of recent duplicates that may have experienced gene conversion because they may provide false signals of positive selection. Fortunately, these results also imply that those cases most susceptible to false-positive results—i.e., high divergence between paralogs, long conversion tracts—are also the cases where detecting gene conversion is the easiest. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Genetic Architecture and Fitness of Bacterial Interspecies Hybrids

Integration of a conjugative plasmid into a bacterial chromosome can promote the transfer of chromosomal DNA to other bacteria. Intraspecies chromosomal conjugation is believed responsible for creating the global pathogens Klebsiella pneumoniae ST258 and Escherichia coli ST1193. Interspecies conjugation is also possible but little is known about the genetic architecture or fitness of such hybrids. To study this, we generated by conjugation 14 hybrids of E. coli and Salmonella enterica. These species belong to different genera, diverged from a common ancestor >100 Ma, and share a conserved order of orthologous genes with ∼15% nucleotide divergence. Genomic analysis revealed that all but one hybrid had acquired a contiguous segment of donor E. coli DNA, replacing a homologous region of recipient Salmonella chromosome, and ranging in size from ∼100 to >4,000 kb. Recombination joints occurred in sequences with higher-than-average nucleotide identity. Most hybrid strains suffered a large reduction in growth rate, but the magnitude of this cost did not correlate with the length of foreign DNA. Compensatory evolution to ameliorate the cost of low-fitness hybrids pointed towards disruption of complex genetic networks as a cause. Most interestingly, 4 of the 14 hybrids, in which from 45% to 90% of the Salmonella chromosome was replaced with E. coli DNA, showed no significant reduction in growth fitness. These data suggest that the barriers to creating high-fitness interspecies hybrids may be significantly lower than generally appreciated with implications for the creation of novel species.     

Chromosomal stasis in diploids contrasts with genome restructuring in auto- and allopolyploid taxa of Hepatica (Ranunculaceae)

Polyploidization and chromosomal rearrangements are recognized as major forces in plant evolution. Their role is investigated in the disjunctly distributed northern hemisphere Hepatica (Ranunculaceae). Chromosome numbers, karyotype morphology, banding patterns, 5S and 35S rDNA localization in all known species were investigated and interpreted in a phylogenetic context established from nuclear internal transcribed spacer (ITS) and plastid matK sequences. All species had a chromosome base number of x = 7. The karyotype was symmetric and showed little variation among diploids with one locus each of 5S and 35S rDNA, except for interpopulational variation concerning 35S rDNA loci number and localization in H. asiatica. Tetraploids exhibited chromosomal changes, including asymmetry and/or loss of rDNA loci. Nuclear and plastid sequences resulted in incongruent topologies because of the positions of some tetraploid taxa. The diversification of Hepatica occurred not earlier than the Pliocene. Genome restructuring, especially involving 35S rDNA, within a few million yr or less characterizes evolution of both auto- and allopolyploids and of the diploid species H. asiatica, which is the presumptive ancestor of two other diploid species.     

Positive Selection on HIV Accessory Proteins and the Analysis of Molecular Adaptation After Interspecies Transmission

Studies examining positive selection on accessory proteins of HIV are rare, although these proteins play an important role in pathogenesis in vivo. Moreover, despite the biological relevance of analyses of molecular adaptation after viral transmission between species, the issue is still poorly studied. Here we present evidence that accessory proteins are subjected to positive selective forces exclusively in HIV. This scenario suggests that accessory protein genes are under adaptive evolution in HIV clades, while in SIVcpz such a phenomenon could not be detected. As a result, we show that comparative studies are critical to carry out functional investigation of positively selected protein sites, as they might help to achieve a better comprehension of the biology of HIV pathogenesis.     

Horizontal Transfer of the Photosynthesis Gene Cluster and Operon Rearrangement in Purple Bacteria

A 37-kb photosynthesis gene cluster was sequenced in a photosynthetic bacterium belonging to the beta subclass of purple bacteria (Proteobacteria), Rubrivivax gelatinosus. The cluster contained 12 bacteriochlorophyll biosynthesis genes (bch), 7 carotenoid biosynthesis genes (crt), structural genes for photosynthetic apparatuses (puf and puh), and some other related genes. The gene arrangement was markedly different from those of other purple photosynthetic bacteria, while two superoperonal structures, crtEF-bchCXYZ-puf and bchFNBHLM-lhaA-puhA, were conserved. Molecular phylogenetic analyses of these photosynthesis genes showed that the photosynthesis gene cluster of Rvi. gelatinosus was originated from those of the species belonging to the alpha subclass of purple bacteria. It was concluded that a horizontal transfer of the photosynthesis gene cluster from an ancestral species belonging to the alpha subclass to that of the beta subclass of purple bacteria had occurred and was followed by rearrangements of the operons in this cluster.     

Chromosomal distributions of breakpoints in cancer,infertility, and evolution

We extract 11 genome-wide sets of breakpoint positions from databases on reciprocal translocations, inversions and deletions in neoplasms, reciprocal translocations and inversions in families carrying rearrangements and the human-mouse comparative map, and for each set of positions construct breakpoint distributions for the 44 autosomal arms. We identify and interpret four main types of distribution: (i) a uniform distribution associated both with families carrying translocations or inversions, and with the comparative map, (ii) telomerically skewed distributions of translocations or inversions detected consequent to births with malformations, (iii) medially clustered distributions of translocation and deletion breakpoints in tumor karyotypes, and (iv) bimodal translocation breakpoint distributions for chromosome arms containing telomeric proto-oncogenes.     

Chromosomal diversification of diploid number,heterochromatin and rDNAs in two species of Phanaeus beetles (Scarabaeidae,Scarabaeinae)

The genus Phanaeus is included in the tribe Phanaeini, one of the most diverse tribes within the subfamily Scarabaeinae in terms of chromosomal characteristics. However, so far the species of this genus were not studied with differential cytogenetic techniques, limiting any inference of the probable mechanisms responsible for this diversity. In this work, several techniques were applied with the aim of cytogenetically characterizing two Phanaeus species. The karyotype found for Phanaeus (Notiophanaeus) chalcomelas was 2n = 12, neo-XY, and that of P. (N.) splendidulus was 2n = 20, Xy_p, considered primitive for the family Scarabaeidae. The chromosomes of both species showed a high amount of constitutive heterochromatin (CH), with blocks rich in base pairs GC (CMA₃⁺). Moreover, in P. (N.) chalcomelas the marks revealed by C-banding and fluorochrome staining were different in size, showing CH variability. Sites of 18S ribosomal DNA (rDNA) were identified in one autosomal pair of P. (N.) chalcomelas and in five autosomal pairs of P. (N.) splendidulus. On the other hand, only one autosomal pair exhibited 5S rDNA sequences in these species. The results suggest that the karyotype differentiation of the Phanaeus species studied here involved pericentric inversions and centric fusions, as well as mechanisms related to amplification and dispersion of CH and rDNA sequences.     

Chromosomes tell half of the story: the correlation between karyotype rearrangements and genetic diversity in sedges,a group with holocentric chromosomes

Chromosome rearrangements may affect the rate and patterns of gene flow within species, through reduced fitness of structural heterozygotes or by reducing recombination rates in rearranged areas of the genome. While the effects of chromosome rearrangements on gene flow have been studied in a wide range of organisms with monocentric chromosomes, the effects of rearrangements in holocentric chromosomes—chromosomes in which centromeric activity is distributed along the length of the chromosome—have not. We collected chromosome number and molecular genetic data in Carex scoparia, an eastern North American plant species with holocentric chromosomes and highly variable karyotype (2n = 56–70). There are no deep genetic breaks within C. scoparia that would suggest cryptic species differentiation. However, genetic distance between individuals is positively correlated with chromosome number difference and geographic distance. A positive correlation is also found between chromosome number and genetic distance in the western North American C. pachystachya (2n = 74–81). These findings suggest that geographic distance and the number of karyotype rearrangements separating populations affect the rate of gene flow between those populations. This is the first study to quantify the effects of holocentric chromosome rearrangements on the partitioning of intraspecific genetic variance.     

Chromosomal evolution in Malagasy lemurs: X. chromosomal banding studies of Propithecus diadema edwardsi and Indri indri and phylogenic relationships between all the species of the Indriidae

The R-banded karyotypes of two Indriidae, Propithecus diadema and Indri indri, are described and compared with each other and with those of the other species of this family, previously reported, Avahi laniger and Propithecus verreauxi. These comparisons show that 30 chromosomal rearrangements, including 21 Robertsonian translocations and eight pericentric inversions, differentiate these karyotypes. A phylogenic diagram is proposed, showing the early separation of Avahi and the relatively late divergence of the three other species. A populational evolution has occurred between the three other species, but Indri is clearly separated from the two other species by at least five complex rearrangements, although it shares four Robertsonian translocations with P. verreauxi but not P. diadema.     

Molecular Evolution and Positive Selection of the Symbiotic Gene NORK in Medicago truncatula

Understanding the selective constraints of partner specificity in mutually beneficial symbiosis is a significant, yet largely unexplored, prospect of evolutionary biology. These selective constraints can be explored through the study of nucleotide polymorphism at loci controlling specificity. The membrane-anchored receptor NORK (nodulation receptor kinase) of the legume Medicago truncatula controls early steps of root infection by two symbiotic microorganisms: nitrogen-fixing bacteria (rhizobia) and endomycorrhizal fungi (Glomales). We analyzed the diversity of the gene NORK by sequencing 4 kilobases in 28 inbred lines sampled from natural populations. We detected 33 polymorphic sites with only one nonsynonymous change. Analysis based on Tajima’s D and Fay and Wu’s H summary statistics revealed no departure from the neutral model. We analyzed divergence using sequences from the closely related species M. coerulea. The McDonald-Kreitman test indicated a significant excess of nonsynonymous changes contributing to this divergence. Furthermore, maximum-likelihood analysis of a molecular phylogeny of a few legume species indicated that a number of amino acid sites, likely located in the receptor domain of the protein, evolved under the regime of positive selection. Further research should focus on the rate and direction of molecular coevolution between microorganisms’ signaling molecules and legumes’ receptors. [Reviewing Editor: Dr. Deborah Charlesworth] Sequence data were deposited in the GenBank database under accession nos. AY676428 to AY676457 and AJ884582.     

Positive Selection and Horizontal Gene Transfer in the Genome of a Male-Killing Wolbachia

Wolbachia are a genus of widespread bacterial endosymbionts in which some strains can hijack or manipulate arthropod host reproduction. Male killing is one such manipulation in which these maternally transmitted bacteria benefit surviving daughters in part by removing competition with the sons for scarce resources. Despite previous findings of interesting genome features of microbial sex ratio distorters, the population genomics of male-killers remain largely uncharacterized. Here, we uncover several unique features of the genome and population genomics of four Arizonan populations of a male-killing Wolbachia strain, wInn, that infects mushroom-feeding Drosophila innubila. We first compared the wInn genome with other closely related Wolbachia genomes of Drosophila hosts in terms of genome content and confirm that the wInn genome is largely similar in overall gene content to the wMel strain infecting D. melanogaster. However, it also contains many unique genes and repetitive genetic elements that indicate lateral gene transfers between wInn and non-Drosophila eukaryotes. We also find that, in line with literature precedent, genes in the Wolbachia prophage and Octomom regions are under positive selection. Of all the genes under positive selection, many also show evidence of recent horizontal transfer among Wolbachia symbiont genomes. These dynamics of selection and horizontal gene transfer across the genomes of several Wolbachia strains and diverse host species may be important underlying factors in Wolbachia’s success as a male-killer of divergent host species.     

Adaptation of the fungal parasite Zygorhizidium planktonicum during 200 generations of growth on homogeneous and heterogeneous populations of its host, the diatom Asterionella formosa

We followed adaptation of the chytrid parasite Zygorhizidium planktonicum during 200 generations of growth on its host, the freshwater diatom Asterionella formosa, in a serial passage experiment. Evolution of parasite fitness was assessed both on a homogenous and heterogeneous host population, consisting of respectively a single new and ten different new host strains. These 10 host strains were genetically different and also varied in their initial susceptibility to the parasite. Parasite fitness increased significantly and rapidly on the new, genetically homogenous host population, but remained unaltered during 200 generations of growth on the heterogeneous host population. Enhanced parasite fitness was the result of faster and more efficient transmission, resulting in higher values of R0 (number of secondary infections). Consequently, parasites that evolved within the uniclonal host population infected significantly more of these hosts than did their ancestors. We thus provide experimental evidence for the widely held view that host genetic diversity restricts evolution of parasites and moderates their harmful effects. Genetically uniform host populations are not only at increased risk from fungal epidemics because they all share the same susceptibility, but also because new parasite strains are able to adapt quickly to new host environments and to improve their fitness.     

Fast Evolution of Interleukin-2 in Mammals and Positive Selection in Ruminants

Interleukin-2 (IL-2) is a cytokine involved in induction and regulation of the immune response in mammals. There have been numerous reports about the search for IL-2 in species other than mammals, and recently an IL-2-like gene has been isolated in chicken. Using PCR, we searched for IL-2 gene sequences in a wide variety of mammals, including marsupials and monotremes, as well as in birds. Although we can readily amplify IL-2 gene fragments in placental mammals, no amplification was obtained in other species. This is best explained by very high substitution rates. This suggest that strategies to isolate IL-2 homologous genes outside mammals should involve functional assays, as for the chicken gene, and not hybridization-based techniques. Nonsynonymous substitution rates are especially high in ruminants, due to positive selection acting on regions important in term of structure-function. We suggest that, although globally similar, the immune response of various mammals is not identical, mainly at the level of cytokine-mediated regulations. Received: 27 July 1999 / Accepted: 15 April 2000     

Evolution of X-Degenerate Y Chromosome Genes in Greater Apes: Conservation of Gene Content in Human and Gorilla,But Not Chimpanzee

Compared with the X chromosome, the mammalian Y chromosome is considerably diminished in size and has lost most of its ancestral genes during evolution. Interestingly, for the X-degenerate region on the Y chromosome, human has retained all 16 genes, while chimpanzee has lost 4 of the 16 genes since the divergence of the two species. To uncover the evolutionary forces governing ape Y chromosome degeneration, we determined the complete sequences of the coding exons and splice sites for 16 gorilla Y chromosome genes of the X-degenerate region. We discovered that all studied reading frames and splice sites were intact, and thus, this genomic region experienced no gene loss in the gorilla lineage. Higher nucleotide divergence was observed in the chimpanzee than the human lineage, particularly for genes with disruptive mutations, suggesting a lack of functional constraints for these genes in chimpanzee. Surprisingly, our results indicate that the human and gorilla orthologues of the genes disrupted in chimpanzee evolve under relaxed functional constraints and might not be essential. Taking mating patterns and effective population sizes of ape species into account, we conclude that genetic hitchhiking associated with positive selection due to sperm competition might explain the rapid decline in the Y chromosome gene number in chimpanzee. As we found no evidence of positive selection acting on the X-degenerate genes, such selection likely targets other genes on the chimpanzee Y chromosome. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

'Anti-bee' and 'pro-bird' changes during the evolution of hummingbird pollination in Penstemon flowers

Floral phenotypes may be as much the result of selection for avoidance of some animal visitors as selection for improving the interaction with better pollinators. When specializing on hummingbird-pollination, Penstemon flowers may have evolved to improve the morphological fit between bird and flower, or to exclude less-efficient bees, or both. We hypothesized how such selection might work on four floral characters that affect the mechanics of pollen transfer: anther/stigma exsertion, presence of a lower corolla lip, width of the corolla tube, and angle of flower inclination. We surgically modified bee-pollinated P. strictus flowers changing one trait at a time to make them resemble hummingbird-pollinated P. barbatus flowers, and measured pollen transfer by bumblebees and hummingbirds. Results suggest that, apart from 'pro-bird' adaptations, specific 'anti-bee' adaptations have been important in shaping hummingbird-flowers. Moreover, some trait changes may have been selected for only if changing in concert with other traits.     

Gene Conversion Drives Within Genic Sequences: Concerted Evolution of Ribosomal RNA Genes in Bacteria and Archaea

Multiple copies of a given ribosomal RNA gene family undergo concerted evolution such that sequences of all gene copies are virtually identical within a species although they diverge normally between species. In eukaryotes, gene conversion and unequal crossing over are the proposed mechanisms for concerted evolution of tandemly repeated sequences, whereas dispersed genes are homogenized by gene conversion. However, the homogenization mechanisms for multiple-copy, normally dispersed, prokaryotic rRNA genes are not well understood. Here we compared the sequences of multiple paralogous rRNA genes within a genome in 12 prokaryotic organisms that have multiple copies of the rRNA genes. Within a genome, putative sequence conversion tracts were found throughout the entire length of each individual rRNA genes and their immediate flanks. Individual conversion events convert only a short sequence tract, and the conversion partners can be any paralogous genes within the genome. Interestingly, the genic sequences undergo much slower divergence than their flanking sequences. Moreover, genomic context and operon organization do not affect rRNA gene homogenization. Thus, gene conversion underlies concerted evolution of bacterial rRNA genes, which normally occurs within genic sequences, and homogenization of flanking regions may result from co-conversion with the genic sequence. Received: 31 March 2000 / Accepted: 15 June 2000     

Selection in a fluctuating environment and the evolution of sexual dimorphism in the seed beetle Callosobruchus maculatus

Temperature changes in the environment, which realistically include environmental fluctuations, can create both plastic and evolutionary responses of traits. Sexes might differ in either or both of these responses for homologous traits, which in turn has consequences for sexual dimorphism and its evolution. Here, we investigate both immediate changes in and the evolution of sexual dimorphism in response to a changing environment (with and without fluctuations) using the seed beetle Callosobruchus maculatus. We investigate sex differences in plasticity and also the genetic architecture of body mass and developmental time dimorphism to test two existing hypotheses on sex differences in plasticity (adaptive canalization hypothesis and condition dependence hypothesis). We found a decreased sexual size dimorphism in higher temperature and that females responded more plastically than males, supporting the condition dependence hypothesis. However, selection in a fluctuating environment altered sex-specific patterns of genetic and environmental variation, indicating support for the adaptive canalization hypothesis. Genetic correlations between sexes (r(MF) ) were affected by fluctuating selection, suggesting facilitated independent evolution of the sexes. Thus, the selective past of a population is highly important for the understanding of the evolutionary dynamics of sexual dimorphism.     

The devil in the details of life-history evolution: Instability and reversal of genetic correlations during selection on<Emphasis Type="Italic">Drosophila</Emphasis> development

The evolutionary relationships between three major components of Darwinian fitness, development rate, growth rate and preadult survival, were estimated using a comparison of 55 distinct populations ofDrosophila melanogaster variously selected for age-specific fertility, environmental-stress tolerance and accelerated development. Development rate displayed a strong net negative evolutionary correlation with weight at eclosion across all selection treatments, consistent with the existence of a size-versus-time tradeoff between these characters. However, within the data set, the magnitude of the evolutionary correlation depended upon the particular selection treatments contrasted. A previously proposed tradeoff between preadult viability and growth rate was apparent only under weak selection for juvenile fitness components. Direct selection for rapid development led to sharp reductions in both growth rates and viability. These data add to the mounting results from experimental evolution that illustrate the sensitivity of evolutionary correlations to (i) genotype-by-environment (G X E) interaction, (ii) complex functional-trait interactions, and (iii) character definition. Instability, disappearance and reversal of patterns of genetic covariation often occur over short evolutionary time frames and as the direct product of selection, rather than some stochastic process. We suggest that the functional architecture of fitness is a rapidly evolving matrix with reticulate properties, a matrix that we understand only poorly.     

Historical and contingent factors affect re-evolution of a complex feature lost during mass extinction in communities of digital organisms

Re-evolution of complex biological features following the extinction of taxa bearing them remains one of evolution's most interesting phenomena, but is not amenable to study in fossil taxa. We used communities of digital organisms (computer programs that self-replicate, mutate and evolve), subjected to periods of low resource availability, to study the evolution, loss and re-evolution of a complex computational trait, the function EQU (bit-wise logical equals). We focused our analysis on cases where the pre-extinction EQU clade had surviving descendents at the end of the extinction episode. To see if these clades retained the capacity to re-evolve EQU, we seeded one set of multiple subreplicate 'replay' populations using the most abundant survivor of the pre-extinction EQU clade, and another set with the actual end-extinction ancestor of the organism in which EQU re-evolved following the extinction episode. Our results demonstrate that stochastic, historical, genomic and ecological factors can lead to constraints on further adaptation, and facilitate or hinder re-evolution of a complex feature.