Patterns of molecular variation and evolution in Drosophila americana and its relatives

Niche evolution and thermal adaptation in the temperate species Drosophila americana

The study of ecological niche evolution is fundamental for understanding how the environment influences species' geographical distributions and their adaptation to divergent environments. Here, we present a study of the ecological niche, demographic history and thermal performance (locomotor activity, developmental time and fertility/viability) of the temperate species Drosophila americana and its two chromosomal forms. Temperature is the environmental factor that contributes most to the species' and chromosomal forms' ecological niches, although precipitation is also important in the model of the southern populations. The past distribution model of the species predicts a drastic reduction in the suitable area for the distribution of the species during the last glacial maximum (LGM), suggesting a strong bottleneck. However, DNA analyses did not detect a bottleneck signature during the LGM. These contrasting results could indicate that D. americana niche preference evolves with environmental change, and thus, there is no evidence to support niche conservatism in this species. Thermal performance experiments show no difference in the locomotor activity across a temperature range of 15 to 38 °C between flies from the north and the south of its distribution. However, we found significant differences in developmental time and fertility/viability between the two chromosomal forms at the model's optimal temperatures for the two forms. However, results do not indicate that they perform better for the traits studied here in their respective optimal niche temperatures. This suggests that behaviour plays an important role in thermoregulation, supporting the capacity of this species to adapt to different climatic conditions across its latitudinal distribution.

Weak selection and protein evolution

The "nearly neutral" theory of molecular evolution proposes that many features of genomes arise from the interaction of three weak evolutionary forces: mutation, genetic drift, and natural selection acting at its limit of efficacy. Such forces generally have little impact on allele frequencies within populations from generation to generation but can have substantial effects on long-term evolution. The evolutionary dynamics of weakly selected mutations are highly sensitive to population size, and near neutrality was initially proposed as an adjustment to the neutral theory to account for general patterns in available protein and DNA variation data. Here, we review the motivation for the nearly neutral theory, discuss the structure of the model and its predictions, and evaluate current empirical support for interactions among weak evolutionary forces in protein evolution. Near neutrality may be a prevalent mode of evolution across a range of functional categories of mutations and taxa. However, multiple evolutionary mechanisms (including adaptive evolution, linked selection, changes in fitness-effect distributions, and weak selection) can often explain the same patterns of genome variation. Strong parameter sensitivity remains a limitation of the nearly neutral model, and we discuss concave fitness functions as a plausible underlying basis for weak selection.

Adaptive evolution and effective population size in wild house mice

Estimates of the proportion of amino acid substitutions that have been fixed by selection (α) vary widely among taxa, ranging from zero in humans to over 50% in Drosophila. This wide range may reflect differences in the efficacy of selection due to differences in the effective population size (N(e)). However, most comparisons have been made among distantly related organisms that differ not only in N(e) but also in many other aspects of their biology. Here, we estimate α in three closely related lineages of house mice that have a similar ecology but differ widely in N(e): Mus musculus musculus (N(e) ∼ 25,000-120,000), M. m. domesticus (N(e) ∼ 58,000-200,000), and M. m. castaneus (N(e) ∼ 200,000-733,000). Mice were genotyped using a high-density single nucleotide polymorphism array, and the proportions of replacement and silent mutations within subspecies were compared with those fixed between each subspecies and an outgroup, Mus spretus. There was significant evidence of positive selection in M. m. castaneus, the lineage with the largest N(e), with α estimated to be approximately 40%. In contrast, estimates of α for M. m. domesticus (α = 13%) and for M. m. musculus (α = 12 %) were much smaller. Interestingly, the higher estimate of α for M. m. castaneus appears to reflect not only more adaptive fixations but also more effective purifying selection. These results support the hypothesis that differences in N(e) contribute to differences among species in the efficacy of selection.

Selection on codon usage and base composition in Drosophila americana

We have used a polymorphism dataset on introns and coding sequences of X-linked loci in Drosophila americana to estimate the strength of selection on codon usage and/or biased gene conversion (BGC), taking into account a recent population expansion detected by a maximum-likelihood method. Drosophila americana was previously thought to have a stable demographic history, so that this evidence for a recent population expansion means that previous estimates of selection need revision. There was evidence for natural selection or BGC favouring GC over AT variants in introns, which is stronger for GC-rich than GC-poor introns. By comparing introns and coding sequences, we found evidence for selection on codon usage bias, which is much stronger than the forces acting on GC versus AT basepairs in introns.

Weighing the evidence for adaptation at the molecular level

The abundance of genome polymorphism and divergence data has provided unprecedented insight into how mutation, drift and natural selection shape genome evolution. Application of the McDonald-Kreitman (MK) test to such data indicates a pervasive influence of positive selection, particularly in Drosophila species. However, evidence for positive selection in other species ranging from yeast to humans is often weak or absent. Although evidence for positive selection could be obscured in some species, there is also reason to believe that the frequency of adaptive substitutions could be overestimated as a result of epistatic fitness effects or hitchhiking of deleterious mutations. Based on these considerations it is argued that the common assumption of independence among sites must be relaxed before abandoning the neutral theory of molecular evolution.

Estimation of the neutrality index

The McDonald-Kreitman (MK) test is a simple and widely used test of selection in which the numbers of nonsilent and silent substitutions (D(n) and D(s)) are compared with the numbers of nonsilent and silent polymorphisms (P(n) and P(s)). The neutrality index (NI = D(s)P(n)/D(n)P(s)), the odds ratio (OR) of the MK table, measures the direction and degree of departure from neutral evolution. The mean of NI values across genes is often taken to summarize patterns of selection in a species. Here, we show that this leads to statistical bias in both simulated and real data to the extent that species, which show a pattern of adaptive evolution, can apparently be subject to weak purifying selection and vice versa. We show that this bias can be removed by using a variant of the Cochran-Mantel-Haenszel procedure for estimating a weighted average OR. We also show that several point estimators of NI are statistically biased even when cutoff values are employed. We therefore suggest that a new statistic be used to study patterns of selection when data are sparse, the direction of selection: DoS = D(n)/(D(n) + D(s)) - P(n)/(P(n) + P(s)).

Evidence for pervasive adaptive protein evolution in wild mice

The relative contributions of neutral and adaptive substitutions to molecular evolution has been one of the most controversial issues in evolutionary biology for more than 40 years. The analysis of within-species nucleotide polymorphism and between-species divergence data supports a widespread role for adaptive protein evolution in certain taxa. For example, estimates of the proportion of adaptive amino acid substitutions (alpha) are 50% or more in enteric bacteria and Drosophila. In contrast, recent estimates of alpha for hominids have been at most 13%. Here, we estimate alpha for protein sequences of murid rodents based on nucleotide polymorphism data from multiple genes in a population of the house mouse subspecies Mus musculus castaneus, which inhabits the ancestral range of the Mus species complex and nucleotide divergence between M. m. castaneus and M. famulus or the rat. We estimate that 57% of amino acid substitutions in murids have been driven by positive selection. Hominids, therefore, are exceptional in having low apparent levels of adaptive protein evolution. The high frequency of adaptive amino acid substitutions in wild mice is consistent with their large effective population size, leading to effective natural selection at the molecular level. Effective natural selection also manifests itself as a paucity of effectively neutral nonsynonymous mutations in M. m. castaneus compared to humans.

Estimating the rate of adaptive molecular evolution in the presence of slightly deleterious mutations and population size change

The prevalence of adaptive evolution relative to genetic drift is a central problem in molecular evolution. Methods to estimate the fraction of adaptive nucleotide substitutions (alpha) have been developed, based on the McDonald-Kreitman test, that contrast polymorphism and divergence between selectively and neutrally evolving sites. However, these methods are expected to give downwardly biased estimates of alpha if there are slightly deleterious mutations, because these inflate polymorphism relative to divergence. Here, we estimate alpha by simultaneously estimating the distribution of fitness effects of new mutations at selected sites from the site frequency spectrum and the number of adaptive substitutions. We test the method using simulations. If data meet the assumptions of the analysis model, estimates of alpha show little bias, even when there is little or no recombination. However, population size differences between the divergence and polymorphism phases may cause alpha to be over or underestimated by a predictable factor that depends on the magnitude of the population size change and the shape of the distribution of effects of deleterious mutations. We analyze several data sets of protein-coding genes and noncoding regions from hominids and Drosophila. In Drosophila genes, we estimate that approximately 50% of amino acid substitutions and approximately 20% of substitutions in introns are adaptive. In protein-coding and noncoding data sets of humans, comparison to macaque sequences reveals little evidence for adaptive substitutions. However, the true frequency of adaptive substitutions in human-coding DNA could be as high as 40%, because estimates based on current polymorphism may be strongly downwardly biased by a decrease in the effective population size along the human lineage.

Pervasive natural selection in the Drosophila genome?

Over the past four decades, the predominant view of molecular evolution saw little connection between natural selection and genome evolution, assuming that the functionally constrained fraction of the genome is relatively small and that adaptation is sufficiently infrequent to play little role in shaping patterns of variation within and even between species. Recent evidence from Drosophila, reviewed here, suggests that this view may be invalid. Analyses of genetic variation within and between species reveal that much of the Drosophila genome is under purifying selection, and thus of functional importance, and that a large fraction of coding and noncoding differences between species are adaptive. The findings further indicate that, in Drosophila, adaptations may be both common and strong enough that the fate of neutral mutations depends on their chance linkage to adaptive mutations as much as on the vagaries of genetic drift. The emerging evidence has implications for a wide variety of fields, from conservation genetics to bioinformatics, and presents challenges to modelers and experimentalists alike.

Nucleotide polymorphism and within-gene recombination in Daphnia magna and D. pulex, two cyclical parthenogens

Theory predicts that partially asexual organisms may make the "best of both worlds": for the most part, they avoid the costs of sexual reproduction, while still benefiting from an enhanced efficiency of selection compared to obligately asexual organisms. There is, however, little empirical data on partially asexual organisms to test this prediction. Here we examine patterns of nucleotide diversity at eight nuclear loci in continentwide samples of two species of cyclically parthenogenetic Daphnia to assess the effect of partial asexual reproduction on effective population size and amount of recombination. Both species have high nucleotide diversities and show abundant evidence for recombination, yielding large estimates of effective population sizes (300,000-600,000). This suggests that selection will act efficiently even on mutations with small selection coefficients. Divergence between the two species is less than one-tenth of previous estimates, which were derived using a mitochondrial molecular clock. As the two species investigated are among the most distantly related species of the genus, this suggests that the genus Daphnia may be considerably younger than previously thought. Daphnia has recently received increased attention because it is being developed as a model organism for ecological and evolutionary genomics. Our results confirm the attractiveness of Daphnia as a model organism, because the high nucleotide diversity and low linkage disequilibrium suggest that fine-scale mapping of genes affecting phenotypes through association studies should be feasible.

Reduced effectiveness of selection caused by a lack of recombination

Genetic recombination associated with sexual reproduction is expected to have important consequences for the effectiveness of natural selection. These effects may be evident within genomes, in the form of contrasting patterns of molecular variation and evolution in regions with different levels of recombination. Previous work reveals patterns that are consistent with a benefit of recombination for adaptation at the level of protein sequence: both positive selection for adaptive variants and purifying selection against deleterious ones appear to be compromised in regions of low recombination [1-11]. Here, we re-examine these patterns by using polymorphism and divergence data from the Drosophila dot chromosome, which has a long history of reduced recombination. To avoid confounding selection and demographic effects, we collected these data from a species with an apparently stable demographic history, Drosophila americana. We find that D. americana dot loci show several signatures of ineffective purifying and positive selection, including an increase in the rate of protein evolution, an increase in protein polymorphism, and a reduction in the proportion of amino acid substitutions attributable to positive selection.

Similar rates of protein adaptation in Drosophila miranda and D. melanogaster, two species with different current effective population sizes

BACKGROUND

Adaptive protein evolution is common in several Drosophila species investigated. Some studies point to very weak selection operating on amino-acid mutations, with average selection intensities on the order of Nes approximately in D. melanogaster and D. simulans. Species with lower effective population sizes should undergo less adaptation since they generate fewer mutations and selection is ineffective on a greater proportion of beneficial mutations.

RESULTS

Here I study patterns of polymorphism and divergence at 91 X-linked loci in D. miranda, a species with a roughly 5-fold smaller effective population size than D. melanogaster. Surprisingly, I find a similar fraction of amino-acid mutations being driven to fixation by positive selection in D. miranda and D. melanogaster. Genes with higher rates of amino-acid evolution show lower levels of neutral diversity, a pattern predicted by recurrent adaptive protein evolution. I fit a hitchhiking model to patterns of polymorphism in D. miranda and D. melanogaster and estimate an order of magnitude higher selection coefficients for beneficial mutations in D. miranda.

CONCLUSION

This analysis suggests that effective population size may not be a major determinant in rates of protein adaptation. Instead, adaptation may not be mutation-limited, or the distribution of fitness effects for beneficial mutations might differ vastly between different species or populations. Alternative explanation such as biases in estimating the fraction of beneficial mutations or slightly deleterious mutation models are also discussed.

Nucleotide variation, linkage disequilibrium and founder-facilitated speciation in wild populations of the zebra finch (Taeniopygia guttata)

The zebra finch has long been an important model system for the study of vocal learning, vocal production, and behavior. With the imminent sequencing of its genome, the zebra finch is now poised to become a model system for population genetics. Using a panel of 30 noncoding loci, we characterized patterns of polymorphism and divergence among wild zebra finch populations. Continental Australian populations displayed little population structure, exceptionally high levels of nucleotide diversity (pi = 0.010), a rapid decay of linkage disequilibrium (LD), and a high population recombination rate (rho approximately 0.05), all of which suggest an open and fluid genomic background that could facilitate adaptive variation. By contrast, substantial divergence between the Australian and Lesser Sunda Island populations (K(ST) = 0.193), reduced genetic diversity (pi = 0.002), and higher levels of LD in the island population suggest a strong but relatively recent founder event, which may have contributed to speciation between these populations as envisioned under founder-effect speciation models. Consistent with this hypothesis, we find that under a simple quantitative genetic model both drift and selection could have contributed to the observed divergence in six quantitative traits. In both Australian and Lesser Sundas populations, diversity in Z-linked loci was significantly lower than in autosomal loci. Our analysis provides a quantitative framework for studying the role of selection and drift in shaping patterns of molecular evolution in the zebra finch genome.

Molecular evolution of synonymous codon usage in Populus

Background

Evolution of synonymous codon usage is thought to be determined by a balance between mutation, genetic drift and natural selection on translational efficiency. However, natural selection on codon usage is considered to be a weak evolutionary force and selection on codon usage is expected to be strongest in species with large effective population sizes.

Results

I examined the evolution of synonymous codons using EST data from five species of Populus. Data on relative synonymous codon usage in genes with high and low gene expression were used to identify 25 codons from 18 different amino acids that were deemed to be preferred codons across all five species. All five species show significant correlations between codon bias and gene expression, independent of base composition, thus indicating that translational selection has shaped synonymous codon usage. Using a set of 158 orthologous genes I detected an excess of unpreferred to preferred (U → P) mutations in two lineages, P. tremula and P. deltoides. Maximum likelihood estimates of the strength of selection acting on synonymous codons was also significantly greater than zero in P. tremula, with the ML estimate of 4N_es = 0.720.

Conclusion

The data is consistent with weak selection on preferred codons in all five species. There is also evidence suggesting that selection on synonymous codons has increased in P. tremula. Although the reasons for the increase in selection on codon usage in the P. tremula lineage are not clear, one possible explanation is an increase in the effective population size in P. tremula.

Clinal distribution of a chromosomal rearrangement: a precursor to chromosomal speciation?

Geographically structured genetic variants provide an effective means to assess sources of natural selection and mechanisms of adaptation to local environments. Correlated selection pressures along environmental gradients favor subdivision of genomes through chromosomal rearrangement. This study examines populations of Drosophila americana to evaluate selection pressures affecting chromosomal forms distinguished by a centromeric fusion. Analyses of chromosomal polymorphism throughout the Mississippi River Valley in the central United States reveal the presence of a distinct latitudinal cline for the chromosomal rearrangement. The cline has a width of 623 km centered at 35.97 degrees N and displays a characteristic sigmoid shape consistent with a balance between selection and dispersal. Extreme low temperature during January, an indicator of winter severity, was identified as the environmental variable that most accurately predicts arrangement frequency. An intriguing relationship identified between the chromosomal cline and operational sex ratio indicates that these alternative arrangements of the X chromosome may influence sex-specific survival. A hypothesis for the cline is presented wherein variation associated with the alternative chromosome forms influences distinct overwintering strategies. The resulting subdivision within the genome embodies a transitory stage of a speciation process in which locally adapted gene complexes provide a foundation for species formation.

Inferring the evolutionary history of Drosophila americana and Drosophila novamexicana using a multilocus approach and the influence of chromosomal rearrangements in single gene analyses

The evolutionary history of closely related organisms can prove sometimes difficult to infer. Hybridization and incomplete lineage sorting are the main concerns; however, genome rearrangements can also influence the outcome of analyses based on nuclear sequences. In the present study, DNA sequences from 12 nuclear genes, for which the approximate chromosomal locations are known, have been used to estimate the evolutionary history of two forms of Drosophila americana (Drosophila americana americana and Drosophila americana texana) and Drosophila novamexicana (virilis group of species). The phylogenetic analysis of the combined data set resulted in a phylogeny showing reciprocal monophyly for D. novamexicana and D. americana. Single gene analyses, however, resulted in incongruent phylogenies influenced by chromosomal rearrangements. Genetic differentiation estimates indicated a significant differentiation between the two species for all genes. Within D. americana, however, there is no evidence for differentiation between the chromosomal forms except at genes located near the X/4 fusion and Xc inversion breakpoint. Thus, the specific status of D. americana and D. novamexicana is confirmed, but there is no overall evidence for genetic differentiation between D. a. americana and D. a. texana, not supporting a subspecific status. Based on levels of allele and nucleotide diversity found in the strains used, it is proposed that D. americana has had a stable, large population during the recent past while D. novamexicana has speciated from a peripheral southwestern population having had an ancestral small effective population size. The influence of chromosomal rearrangements in single gene analyses is also examined.

Ancestral inference and the study of codon bias evolution: implications for molecular evolutionary analyses of the Drosophila melanogaster subgroup

Reliable inference of ancestral sequences can be critical to identifying both patterns and causes of molecular evolution. Robustness of ancestral inference is often assumed among closely related species, but tests of this assumption have been limited. Here, we examine the performance of inference methods for data simulated under scenarios of codon bias evolution within the Drosophila melanogaster subgroup. Genome sequence data for multiple, closely related species within this subgroup make it an important system for studying molecular evolutionary genetics. The effects of asymmetric and lineage-specific substitution rates (i.e., varying levels of codon usage bias and departures from equilibrium) on the reliability of ancestral codon usage was investigated. Maximum parsimony inference, which has been widely employed in analyses of Drosophila codon bias evolution, was compared to an approach that attempts to account for uncertainty in ancestral inference by weighting ancestral reconstructions by their posterior probabilities. The latter approach employs maximum likelihood estimation of rate and base composition parameters. For equilibrium and most non-equilibrium scenarios that were investigated, the probabilistic method appears to generate reliable ancestral codon bias inferences for molecular evolutionary studies within the D. melanogaster subgroup. These reconstructions are more reliable than parsimony inference, especially when codon usage is strongly skewed. However, inference biases are considerable for both methods under particular departures from stationarity (i.e., when adaptive evolution is prevalent). Reliability of inference can be sensitive to branch lengths, asymmetry in substitution rates, and the locations and nature of lineage-specific processes within a gene tree. Inference reliability, even among closely related species, can be strongly affected by (potentially unknown) patterns of molecular evolution in lineages ancestral to those of interest.