Evolutionary consequences of DNA mismatch inhibited repair opportunity

Relation between mitochondrial DNA hyperdiversity, mutation rate and mitochondrial genome evolution in Melarhaphe neritoides (Gastropoda: Littorinidae) and other Caenogastropoda

Mitochondrial DNA hyperdiversity is primarily caused by high mutation rates (µ) and has potential implications for mitogenome architecture and evolution. In the hyperdiverse mtDNA of Melarhaphe neritoides (Gastropoda: Littorinidae), high mutational pressure generates unusually large amounts of synonymous variation, which is expected to (1) promote changes in synonymous codon usage, (2) reflect selection at synonymous sites, (3) increase mtDNA recombination and gene rearrangement, and (4) be correlated with high mtDNA substitution rates. The mitogenome of M. neritoides was sequenced, compared to closely related littorinids and put in the phylogenetic context of Caenogastropoda, to assess the influence of mtDNA hyperdiversity and high µ on gene content and gene order. Most mitogenome features are in line with the trend in Mollusca, except for the atypical secondary structure of the methionine transfer RNA lacking the TΨC-loop. Therefore, mtDNA hyperdiversity and high µ in M. neritoides do not seem to affect its mitogenome architecture. Synonymous sites are under positive selection, which adds to the growing evidence of non-neutral evolution at synonymous sites. Under such non-neutrality, substitution rate involves neutral and non-neutral substitutions, and high µ is not necessarily associated with high substitution rate, thus explaining that, unlike high µ, a high substitution rate is associated with gene order rearrangement.

Detecting positive selection in the genome

Population geneticists have long sought to understand the contribution of natural selection to molecular evolution. A variety of approaches have been proposed that use population genetics theory to quantify the rate and strength of positive selection acting in a species’ genome. In this review we discuss methods that use patterns of between-species nucleotide divergence and within-species diversity to estimate positive selection parameters from population genomic data. We also discuss recently proposed methods to detect positive selection from a population’s haplotype structure. The application of these tests has resulted in the detection of pervasive adaptive molecular evolution in multiple species.

Crossing-over in a hypervariable species preferentially occurs in regions of high local similarity

Recombination between double-stranded DNA molecules is a key genetic process which occurs in a wide variety of organisms. Usually, crossing-over (CO) occurs during meiosis between genotypes with 98.0–99.9% sequence identity, because within-population nucleotide diversity only rarely exceeds 2%. However, some species are hypervariable and it is unclear how CO can occur between genotypes with less than 90% sequence identity. Here, we study CO in Schizophyllum commune, a hypervariable cosmopolitan basidiomycete mushroom, a frequently encountered decayer of woody substrates. We crossed two haploid individuals, from the United States and from Russia, and obtained genome sequences for their 17 offspring. The average genetic distance between the parents was 14%, making it possible to study CO at very high resolution. We found reduced levels of linkage disequilibrium between loci flanking the CO sites indicating that they are mostly confined to hotspots of recombination. Furthermore, CO events preferentially occurred in regions under stronger negative selection, in particular within exons that showed reduced levels of nucleotide diversity. Apparently, in hypervariable species CO must avoid regions of higher divergence between the recombining genomes due to limitations imposed by the mismatch repair system, with regions under strong negative selection providing the opportunity for recombination. These patterns are opposite to those observed in a number of less variable species indicating that population genomics of hypervariable species may reveal novel biological phenomena.

Molecular hyperdiversity and evolution in very large populations

The genomic density of sequence polymorphisms critically affects the sensitivity of inferences about ongoing sequence evolution, function and demographic history. Most animal and plant genomes have relatively low densities of polymorphisms, but some species are hyperdiverse with neutral nucleotide heterozygosity exceeding 5%. Eukaryotes with extremely large populations, mimicking bacterial and viral populations, present novel opportunities for studying molecular evolution in sexually reproducing taxa with complex development. In particular, hyperdiverse species can help answer controversial questions about the evolution of genome complexity, the limits of natural selection, modes of adaptation and subtleties of the mutation process. However, such systems have some inherent complications and here we identify topics in need of theoretical developments. Close relatives of the model organisms Caenorhabditis elegans and Drosophila melanogaster provide known examples of hyperdiverse eukaryotes, encouraging functional dissection of resulting molecular evolutionary patterns. We recommend how best to exploit hyperdiverse populations for analysis, for example, in quantifying the impact of noncrossover recombination in genomes and for determining the identity and micro-evolutionary selective pressures on noncoding regulatory elements.

Linkage Disequilibrium Patterns Across a Recombination Gradient in African Drosophila melanogaster

Previous multilocus surveys of nucleotide polymorphism have documented a genome-wide excess of intralocus linkage disequilibrium (LD) in Drosophila melanogaster and D. simulans relative to expectations based on estimated mutation and recombination rates and observed levels of diversity. These studies examined patterns of variation from predominantly non-African populations that are thought to have recently expanded their ranges from central Africa. Here, we analyze polymorphism data from a Zimbabwean population of D. melanogaster, which is likely to be closer to the standard population model assumptions of a large population with constant size. Unlike previous studies, we find that levels of LD are roughly compatible with expectations based on estimated rates of crossing over. Further, a detailed examination of genes in different recombination environments suggests that markers near the telomere of the X chromosome show considerably less linkage disequilibrium than predicted by rates of crossing over, suggesting appreciable levels of exchange due to gene conversion. Assuming that these populations are near mutation-drift equilibrium, our results are most consistent with a model that posits heterogeneity in levels of exchange due to gene conversion across the X chromosome, with gene conversion being a minor determinant of LD levels in regions of high crossing over. Alternatively, if levels of exchange due to gene conversion are not negligible in regions of high crossing over, our results suggest a marked departure from mutation-drift equilibrium (i.e., toward an excess of LD) in this Zimbabwean population. Our results also have implications for the dynamics of weakly selected mutations in regions of reduced crossing over.

Linkage disequilibria and the site frequency spectra in the su(s) and su(w(a)) regions of the Drosophila melanogaster X chromosome

Over the last decade, surveys of DNA sequence variation in natural populations of several Drosophila species and other taxa have established that polymorphism is reduced in genomic regions characterized by low rates of crossing over per physical length. Parallel studies have also established that divergence between species is not reduced in these same genomic regions, thus eliminating explanations that rely on a correlation between the rates of mutation and crossing over. Several theoretical models (directional hitchhiking, background selection, and random environment) have been proposed as population genetic explanations. In this study samples from an African population (n = 50) and a European population (n = 51) were surveyed at the su(s) (1955 bp) and su(w(a)) (3213 bp) loci for DNA sequence polymorphism, utilizing a stratified SSCP/DNA sequencing protocol. These loci are located near the telomere of the X chromosome, in a region of reduced crossing over per physical length, and exhibit a significant reduction in DNA sequence polymorphism. Unlike most previously surveyed, these loci reveal substantial skews toward rare site frequencies, consistent with the predictions of directional hitchhiking and random environment models and inconsistent with the general predictions of the background selection model (or neutral theory). No evidence for excess geographic differentiation at these loci is observed. Although linkage disequilibrium is observed between closely linked sites within these loci, many recombination events in the genealogy of the sampled alleles can be inferred and the genomic scale of linkage disequilibrium, measured in base pairs between sites, is the same as that observed for loci in regions of normal crossing over. We conclude that gene conversion must be high in these regions of low crossing over.

Mitochondrial DNA polymorphism and heteroplasmy in populations of the three species of Tropidurus of the nanuzae group (Squamata, Tropiduridae)

The nanuzae group of lizards includes three species, Tropidurus nanuzae, T. divaricatus and T. amathites. The first species is found along Serra do Espinhaço, in eastern Brazil, and the other two in the northern region of the Brazilian State of Bahia, in continental dunes on both margins of the São Francisco River. Restriction fragment length polymorphisms (RFLP) of the mtDNA in these species were detected in 53 restriction sites. Site and fragment length polymorphisms were characterized, and cases of heteroplasmy involving length variation were observed. In T. divaricatus, these variations involved changes of 50-200 bp, probably in the control region of the molecule. In T. amathites, variation was apparently due to duplication/deletion of a 400-bp segment. Fragment length mutation rate varied among the species, being smaller in T. amathites than in T. divaricatus. Relatively low nucleotide diversity values were detected in these populations, the smallest being found in T. nanuzae. The most polymorphic population was T. divaricatus from Alagoado, followed by that of the same species from Ibiraba, suggesting both probable recovery of mtDNA genetic diversity after putative reductions in population size, and recent population expansion.

Geographic analysis of nucleotide diversity and song sparrow (Aves: Emberizidae) population history

Mitochondrial DNA (mtDNA) control-region (CR) sequences were analysed to address three questions regarding the evolution of geographical variation in song sparrows. (i) Are mtDNA sequences more informative about phylogenetic relationships and population history than previously published restriction fragment (RFLP) data? (ii) Are song sparrow CR sequences evolving in a selectively neutral manner? (iii) What do the haplotype cladogram and geographical pattern of nucleotide diversity (pi) suggest about the recent evolutionary history of song sparrow populations? Results from phylogenetic analyses of CR sequences corroborate RFLP results and reveal instances in which haplotypes do not group by locality. Neutrality tests (Tajima 1989a) suggest that song sparrow mtDNA is evolving in a selectively neutral manner, although exceptions are noted. A novel geographical pattern of pi suggests a model of song sparrow population history involving multiple Pleistocene refugia and colonization of some formerly glaciated regions from multiple sources. Moreover, application of coalescence theory to the haplotype cladogram suggests that two different haplotypes (48NF and 151HA) may have predominated in different parts of the song sparrow's range. This model provides insight into the current distribution of song sparrow mtDNA haplotypes and may explain the discordance between evolutionary history inferred from mtDNA and morphology in this species.

Chromosomal distribution of the 412 retrotransposon in natural populations of Drosophila simulans

The insertion site localization of the 412 retrotransposable element was analysed by in situ hybridization to the polytene chromosomes of 57 individual genomes from 25 natural populations of Drosophila simulans. The 412 insertion sites along the chromosomes show a tendency to aggregate in the distal and proximal ends of the 2R arm, and in several local regions along the 3R arm. The distribution of the 412 insertion sites, weighted by DNA content, along the chromosome arms reveals an overall tendency for the site number to increase from the middle of the arm to the base and tip, with a decrease at the tips, especially pronounced for the X chromosome. Such a distribution differs slightly from that of D. melanogaster, which globally shows an increase of the 412 site number from base to tip of the chromosome arms, indicating differing behaviour of the 412 element in the two species. These results are discussed in connection with the recombination rate along the chromosome arms.

Molecular evolution of angiosperm mitochondrial introns and exons

Numbers of substitutions per site for 15 protein-coding genes and six introns of the plant mitochondria were estimated to compare modes and tempos of evolution between exons and introns, and numbers of insertions-deletions per site also were investigated in introns. Intra-gene homogeneity of numbers of substitutions per site was assessed further among different taxa and between mitochondrial and nuclear paralogs translocated from the mitochondrial genome. Gene-to-gene differences in numbers of substitutions per site were found to be higher for nonsynonymous than synonymous sites, and this could be due to differential selection if mutation rate is assumed constant for the genome. Some mitochondrial genes have evolved as fast as chloroplast genes, thus faster than previously thought. For coxI, relative rate tests showed that woody taxa evolved slower than annuals at synonymous sites. Generation time, population size, and speciation rate are likely factors involved in this rate heterogeneity. Introns were less constrained than their adjacent exons for both overall numbers of substitutions per site and indels, but, on average, overall numbers of substitutions per site for introns were similar to numbers of synonymous substitutions per site for exons. Correlations were generally high between numbers of substitutions and numbers of indels per site for the same intron. Mitochondrial genes transferred to the nucleus had an accelerated rate of substitution per site, which was most significant at synonymous sites. These differences between paralogs in two different genomes are likely the result of different mutation rates.

Chromosomal distribution and population dynamics of the 412 retrotransposon in a natural population of Drosophila melanogaster

The localization of the insertion sites of the 412 retrotransposable element was analysed by in situ hybridization to the polytene chromosomes of the genomes of males from a natural population of Drosophila melanogaster. Non-parametric statistical tests do not reveal any particular distribution of the insertion sites over the chromosomes, suggesting an apparently random distribution of the 412 element. Aggregation and dispersion tests were highly significant with data of copy number (when all genomes are pooled, many copies may be at a given site), suggesting the existence of sites with high insertion frequency. Comparison with other data from the literature confirms the tendency for a low proportion of insertions on the X chromosome in comparison with the autosomes, a result in agreement with selection acting against the detrimental effect of the 412 element insertions.

Population dynamics of the copia, mdg1, mdg3, gypsy, and P transposable elements in a natural population of Drosophila melanogaster

The insertion site polymorphism of the copia, mdg1, mdg3, gypsy, and P transposable elements was analysed by in situ hybridization to the polytene chromosomes in genomes of males from a natural population of Drosophila melanogaster. Parameters of various theoretical models of the population biology of transposable elements were estimated from our data, and different hypotheses explaining TE copy number containment were tested. The copia, mdg1 and gypsy elements show evidence for a deficiency of insertions on the X chromosomes, a result consistent with selection against the mutational effects of insertions. On the contrary, mdg3 and P copy numbers fit a neutral model with a balance between regulated transposition and excisions. There is no strong evidence of a systematic accumulation of elements in the distal and proximal regions of the chromosomes where crossing over and ectopic exchanges are reduced. For all chromosome arms but 3L, however, the TE site density increases from the proximal to the distal parts of the chromosomes (the centromeric regions were excluded in this analysis) with sometimes a sharp decrease in density at the extreme tip, following in part the exchange coefficient. The way the copy number of TEs is contained in genomes depends thus on the element considered, and on various forces acting simultaneously, indicating that models of TE dynamics should include details of each element.