Contribution of symbiotic microbiota to adaptation of <Emphasis Type="Italic">Drosophila melanogaster</Emphasis> to an unfavorable growth medium

The contribution of symbiotic microbiota to the adaptation of Drosophila melanogaster to fodder with an increased content of NaCl has been analyzed. The reproduction efficiency and the development rate of D. melanogaster on the saline fodder medium, on which a homogenate of flies from laboratory salt-adapted lines and from control lines not adapted to the salt were inoculated, were compared. It was established that inoculating with homogenized salt-adapted flies significantly increased the efficiency of use of salty fodders by flies in comparison with the control flies homogenate, which is manifested in the increased number of offspring produced by a pair of parents over a fixed time, and also in faster larval development. It was noted that the results obtained were consistent with the assumption that the adaptation of D. melanogaster to salted fodder is largely due not to genetic changes in the experimental populations but to changes in the concomitant bacterial and yeast microbiota.     

An Experimental Test of the Relationship between Genetic Variation and Environmental Variation in Tribolium Flour Beetles

The hypothesis that a component of genetic variation for polygenic fitness traits is maintained by environmental heterogeneity was tested using an experimental system involving two species of flour beetles, Tribolium castaneum and T. confusum. Replicated populations of each species from a number of environmental treatments were analyzed for various fitness components following almost 60 generations of natural selection. Environmental differences consisted of flours of cereals commonly invaded by natural populations of these insects.—Tests for adaptation to environments were based on experiments in which populations were reared factorially on each flour, such that population treatment x flour interactions could be detected. Measurements were made of survival, growth rate, larval weight, pupal weight, developmental time, fecundity of individuals at low density and fecundity and cannibalism at high density in both fresh and conditioned media.—Flour differences were found to have significant effects on most traits. Evidence for significant genetic variation and significant genotype x environment interaction was also found. However, no evidence could be found to support the hypothesis that genetic variation was maintained by environmental heterogeneity in food resources. The absence of adaptation to the experimental treatments despite the presence of genetic variation in fitness components suggests that pleiotropy may assume an important role in determining net fitness values of polygenes.     

Periodic Selection, Infectious Gene Exchange and the Genetic Structure of E. COLI Populations

As a consequence of sequential replacements by clones of higher fitness (periodic selection), bacterial populations would be continually purged of genetic variability, and the fate of selectively neutral alleles in very large populations of bacteria would be similar to that in demes of sexually reproducing organisms with small genetically effective population sizes. The significance of periodic selection in reducing genetic variability in these clonally reproducing species is dependent on the amount of genetic exchange between clones (recombination). In an effort to determine the relationship between the rates of periodic selection, recombination and the genetically effective sizes of bacterial populations, a model for periodic selection and infectious gene exchange has been developed and its properties analyzed. It shows that, for a given periodic selection regime, genetically effective population size increases exponentially with the rate of recombination.—With the parameters of this model in the range anticipated for natural populations of E. coli, the purging effects of periodic selection on genetic variability are significant; individual populations or lineages of this bacterial species would have very small genetically effective population sizes.—Based on this result, some other a priori considerations and a review of the results of epidemiological and genetic variability studies, it is postulated that E. coli is composed of a relatively limited number of geographically widespread and genetically nearly isolated and monomorphic lineages. The implications of these considerations of the genetic structure of E. coli populations of the interpretation of protein variation and the neutral gene hypothesis are discussed.     

Unravelling genetics at the top: mountain islands or isolated belts?

Background and Aims

In mountain plant populations, local adaptation has been described as one of the main responses to climate warming, allowing plants to persist under stressful conditions. This is especially the case for marginal populations at their lowest elevation, as they are highly vulnerable. Adequate levels of genetic diversity are required for selection to take place, while high levels of altitudinal gene flow are seen as a major limiting factor potentially precluding local adaptation processes. Thus, a compromise between genetic diversity and gene flow seems necessary to guarantee persistence under oncoming conditions. It is therefore critical to determine if gene flow occurs preferentially between mountains at similar altitudinal belts, promoting local adaptation at the lowest populations, or conversely along altitude within each mountain.

Methods

Microsatellite markers were used to unravel genetic diversity and population structure, inbreeding and gene flow of populations at two nearby altitudinal gradients of Silene ciliata, a Mediterranean high-mountain cushion plant.

Key Results

Genetic diversity and inbreeding coefficients were similar in all populations. Substantial gene flow was found both along altitudinal gradients and horizontally within each elevation belt, although greater values were obtained along altitudinal gradients. Gene flow may be responsible for the homogeneous levels of genetic diversity found among populations. Bayesian cluster analyses also suggested that shifts along altitudinal gradients are the most plausible scenario.

Conclusions

Past population shifts associated with glaciations and interglacial periods in temperate mountains may partially explain current distributions of genetic diversity and population structure. In spite of the predominance of gene flow along the altitudinal gradients, local genetic differentiation of one of the lower populations together with the detection of one outlier locus might support the existence of different selection forces at low altitudes.     

Population Genomics Reveals Genetic Divergence and Adaptive Differentiation of Chinese Sea Bass (<Emphasis Type="Italic">Lateolabrax maculatus</Emphasis>)

The marine species usually show high dispersal capabilities accompanied by high levels of gene flow. On the other hand, many physical barriers distribute along the continental marginal seas and may prevent dispersals and increase population divergence. These complexities along the continental margin generate serious challenges to population genetic studies of marine species. Chinese sea bass Lateolabrax maculatus distributes broad latitudinal gradient spanning from the tropical to the mid-temperate zones in the continental margin seas of the Northwest Pacific Ocean. Using the double digest restriction-site-associated DNA tag sequencing (ddRAD) approach, we genotyped 10,297 SNPs for 219 Chinese seabass individuals of 12 populations along the Chinese coast in the Northwest Pacific region. Genetic divergence among these populations was evaluated, and population structure was established. The results suggested that geographically distant populations in the Bohai Gulf and the Beibu Gulf retain significant genetic divergence, which are connected by a series of intermediate populations in between. The results also suggested that Leizhou Peninsula, Hainan Island, and Shandong Peninsula are major physical barriers and substantially block gene flow and genetic admixture of L. maculatus. We also investigated the potential genetic basis of local adaptation correlating with population differentiation of L. maculatus. The sea surface temperature is a significantly differentiated environmental factor for the distribution of L. maculatus. The correlation of water temperature and genetic variations in extensively distributed populations was investigated with Bayesian-based approaches. The candidate genes underlying the local selection in geographically divergent populations were identified and annotated, providing clues to understand the potential mechanisms of adaptive evolution. Overall, our genome scale population genetic analysis provided insight into population divergence and local adaptation of Chinese sea bass in the continental marginal seas along Chinese coast.     

Indirect selection of thermal tolerance during experimental evolution of Drosophila melanogaster

Natural selection alters the distribution of a trait in a population and indirectly alters the distribution of genetically correlated traits. Long‐standing models of thermal adaptation assume that trade‐offs exist between fitness at different temperatures; however, experimental evolution often fails to reveal such trade‐offs. Here, we show that adaptation to benign temperatures in experimental populations of Drosophila melanogaster resulted in correlated responses at the boundaries of the thermal niche. Specifically, adaptation to fluctuating temperatures (16–25°C) decreased tolerance of extreme heat. Surprisingly, flies adapted to a constant temperature of 25°C had greater cold tolerance than did flies adapted to other thermal conditions, including a constant temperature of 16°C. As our populations were never exposed to extreme temperatures during selection, divergence of thermal tolerance likely reflects indirect selection of standing genetic variation via linkage or pleiotropy. We found no relationship between heat and cold tolerances in these populations. Our results show that the thermal niche evolves by direct and indirect selection, in ways that are more complicated than assumed by theoretical models.     

Evolution under domestication: ongoing artificial selection and divergence of wild and managed Stenocereus pruinosus (Cactaceae) populations in the Tehuac��n Valley, Mexico

Background and Aims

The Tehuacán Valley in Mexico is a principal area of plant domestication in Mesoamerica. There, artificial selection is currently practised on nearly 120 native plant species with coexisting wild, silvicultural and cultivated populations, providing an excellent setting for studying ongoing mechanisms of evolution under domestication. One of these species is the columnar cactus Stenocereus pruinosus, in which we studied how artificial selection is operating through traditional management and whether it has determined morphological and genetic divergence between wild and managed populations.

Methods

Semi-structured interviews were conducted with 83 households of three villages to investigate motives and mechanisms of artificial selection. Management effects were studied by comparing variation patterns of 14 morphological characters and population genetics (four microsatellite loci) of 264 plants from nine wild, silvicultural and cultivated populations.

Key Results

Variation in fruit characters was recognized by most people, and was the principal target of artificial selection directed to favour larger and sweeter fruits with thinner or thicker peel, fewer spines and pulp colours others than red. Artificial selection operates in agroforestry systems favouring abundance (through not felling plants and planting branches) of the preferred phenotypes, and acts more intensely in household gardens. Significant morphological divergence between wild and managed populations was observed in fruit characters and plant vigour. On average, genetic diversity in silvicultural populations (H_E = 0·743) was higher than in wild (H_E = 0·726) and cultivated (H_E = 0·700) populations. Most of the genetic variation (90·58 %) occurred within populations. High gene flow (Nm_FST > 2) was identified among almost all populations studied, but was slightly limited by mountains among wild populations, and by artificial selection among wild and managed populations.

Conclusions

Traditional management of S. pruinosus involves artificial selection, which, despite the high levels of gene flow, has promoted morphological divergence and moderate genetic structure between wild and managed populations, while conserving genetic diversity.     

Host Adaptation Is Contingent upon the Infection Route Taken by Pathogens

Evolution of pathogen virulence is affected by the route of infection. Also, alternate infection routes trigger different physiological responses on hosts, impinging on host adaptation and on its interaction with pathogens. Yet, how route of infection may shape adaptation to pathogens has not received much attention at the experimental level. We addressed this question through the experimental evolution of an outbred Drosophila melanogaster population infected by two different routes (oral and systemic) with Pseudomonas entomophila. The two selection regimes led to markedly different evolutionary trajectories. Adaptation to infection through one route did not protect from infection through the alternate route, indicating distinct genetic bases. Finally, relatively to the control population, evolved flies were not more resistant to bacteria other than Pseudomonas and showed higher susceptibility to viral infections. These specificities and trade-offs may contribute to the maintenance of genetic variation for resistance in natural populations. Our data shows that the infection route affects host adaptation and thus, must be considered in studies of host-pathogen interaction.     

Genetic Divergence and Signatures of Natural Selection in Marginal Populations of a Keystone,Long-Lived Conifer,Eastern White Pine (Pinus strobus) from Northern Ontario

Marginal populations are expected to provide the frontiers for adaptation, evolution and range shifts of plant species under the anticipated climate change conditions. Marginal populations are predicted to show genetic divergence from central populations due to their isolation, and divergent natural selection and genetic drift operating therein. Marginal populations are also expected to have lower genetic diversity and effective population size (N _e) and higher genetic differentiation than central populations. We tested these hypotheses using eastern white pine (Pinus strobus) as a model for keystone, long-lived widely-distributed plants. All 614 eastern white pine trees, in a complete census of two populations each of marginal old-growth, central old-growth, and central second-growth, were genotyped at 11 microsatellite loci. The central populations had significantly higher allelic and genotypic diversity, latent genetic potential (LGP) and N _e than the marginal populations. However, heterozygosity and fixation index were similar between them. The marginal populations were genetically diverged from the central populations. Model testing suggested predominant north to south gene flow in the study area with curtailed gene flow to northern marginal populations. Signatures of natural selection were detected at three loci in the marginal populations; two showing divergent selection with directional change in allele frequencies, and one balancing selection. Contrary to the general belief, no significant differences were observed in genetic diversity, differentiation, LGP, and N _e between old-growth and second-growth populations. Our study provides information on the dynamics of migration, genetic drift and selection in central versus marginal populations of a keystone long-lived plant species and has broad evolutionary, conservation and adaptation significance.     

The passive yet successful way of planktonic life: genomic and experimental analysis of the ecology of a free-living polynucleobacter population

Background

The bacterial taxon Polynucleobacter necessarius subspecies asymbioticus represents a group of planktonic freshwater bacteria with cosmopolitan and ubiquitous distribution in standing freshwater habitats. These bacteria comprise <1% to 70% (on average about 20%) of total bacterioplankton cells in various freshwater habitats. The ubiquity of this taxon was recently explained by intra-taxon ecological diversification, i.e. specialization of lineages to specific environmental conditions; however, details on specific adaptations are not known. Here we investigated by means of genomic and experimental analyses the ecological adaptation of a persistent population dwelling in a small acidic pond.

Findings

The investigated population (F10 lineage) contributed on average 11% to total bacterioplankton in the pond during the vegetation periods (ice-free period, usually May to November). Only a low degree of genetic diversification of the population could be revealed. These bacteria are characterized by a small genome size (2.1 Mb), a relatively small number of genes involved in transduction of environmental signals, and the lack of motility and quorum sensing. Experiments indicated that these bacteria live as chemoorganotrophs by mainly utilizing low-molecular-weight substrates derived from photooxidation of humic substances.

Conclusions

Evolutionary genome streamlining resulted in a highly passive lifestyle so far only known among free-living bacteria from pelagic marine taxa dwelling in environmentally stable nutrient-poor off-shore systems. Surprisingly, such a lifestyle is also successful in a highly dynamic and nutrient-richer environment such as the water column of the investigated pond, which was undergoing complete mixis and pronounced stratification in diurnal cycles. Obviously, metabolic and ecological versatility is not a prerequisite for long-lasting establishment of abundant bacterial populations under highly dynamic environmental conditions. Caution should be exercised when generalizing the obtained insights into the ecology and adaptation of the investigated lineage to other Polynucleobacter lineages.     

Divergent Selection and Local Adaptation in Disjunct Populations of an Endangered Conifer,Keteleeria davidiana var. formosana (Pinaceae)

The present study investigated the genetic diversity, population structure, F _ST outliers, and extent and pattern of linkage disequilibrium in five populations of Keteleeria davidiana var. formosana, which is listed as a critically endangered species by the Council of Agriculture, Taiwan. Twelve amplified fragment length polymorphism primer pairs generated a total of 465 markers, of which 83.74% on average were polymorphic across populations, with a mean Nei’s genetic diversity of 0.233 and a low level of genetic differentiation (approximately 6%) based on the total dataset. Linkage disequilibrium and HICKORY analyses suggested recent population bottlenecks and inbreeding in K. davidiana var. formosana. Both STRUCTURE and BAPS observed extensive admixture of individual genotypes among populations based on the total dataset in various clustering scenarios, which probably resulted from incomplete lineage sorting of ancestral variation rather than a high rate of recent gene flow. Our results based on outlier analysis revealed generally high levels of genetic differentiation and suggest that divergent selection arising from environmental variation has been driven by differences in temperature, precipitation, and humidity. Identification of ecologically associated outliers among environmentally disparate populations further support divergent selection and potential local adaptation.     

Population structure of the malaria vector Anopheles sinensis (Diptera: Culicidae) in China: two gene pools inferred by microsatellites

Background

Anopheles sinensis is a competent malaria vector in China. An understanding of vector population structure is important to the vector-based malaria control programs. However, there is no adequate data of A. sinensis population genetics available yet.

Methodology/Principal Findings

This study used 5 microsatellite loci to estimate population genetic diversity, genetic differentiation and demographic history of A. sinensis from 14 representative localities in China. All 5 microsatellite loci were highly polymorphic across populations, with high allelic richness and heterozygosity. Hardy–Weinberg disequilibrium was found in 12 populations associated with heterozygote deficits, which was likely caused by the presence of null allele and the Wahlund effect. Bayesian clustering analysis revealed two gene pools, grouping samples into two population clusters; one includes six and the other includes eight populations. Out of 14 samples, six samples were mixed with individuals from both gene pools, indicating the coexistence of two genetic units in the areas sampled. The overall differentiation between two genetic pools was moderate (F _ST = 0.156). Pairwise differentiation between populations were lower within clusters (F _ST = 0.008–0.028 in cluster I and F _ST = 0.004–0.048 in cluster II) than between clusters (F _ST = 0.120–0.201). A reduced gene flow (Nm = 1–1.7) was detected between clusters. No evidence of isolation by distance was detected among populations neither within nor between the two clusters. There are differences in effective population size (Ne = 14.3-infinite) across sampled populations.

Conclusions/Significance

Two genetic pools with moderate genetic differentiation were identified in the A. sinensis populations in China. The population divergence was not correlated with geographic distance or barrier in the range. Variable effective population size and other demographic effects of historical population perturbations could be the factors affecting the population differentiation. The structured populations may limit the migration of genes under pressures/selections, such as insecticides and immune genes against malaria.     

Genetic diversity and natural selection in wild fruit flies revealed by whole-genome resequencing

We characterized 26 wild fruit flies comparative population genomics from six different altitude and latitude locations by whole genome resequencing. Genetic diversity was relatively higher in Ganzi and Chongqing populations. We also found 13 genes showing selection signature between different altitude flies and variants related to hypoxia and temperature stimulus, were preferentially selected during the flies evolution. One of the most striking selective sweeps found in all high altitude flies occurred in the region harboring Hsp70Aa and Hsp70Ab on chromosome 3R. Interestingly, these two genes are involved in GO terms including response to hypoxia, unfolded protein, temperature stimulus, heat, oxygen levels. Mutation in HPH gene, a candidate gene in the hypoxia inducible factor pathway, might contributes to hypoxic high-altitude adaptation. Intriguingly, some of the selected genes, primarily utilized in humans, were involved in the response to hypoxia, which could imply a conserved molecular mechanisms underlying high-altitude adaptation between insects and humans.     

Genetic Organization and Adaptive Response of Allozymes to Ecological Variables in FUNDULUS HETEROCLITUS

Populations of Fundulus heteroclitus, (Cyprinodontidae) a widespread coastal marine fish, were studied in control and artificially heated environments on the North Shore of Long Island, New York to determine (1) patterns of variation in biochemical phenotypes and (2) the extent to which this variation reflected adaptation to environmental characteristics.—Variation at three of twelve polymorphic isoenzyme loci from the warm water population was beyond the range of variation among control populations, and resembled those determined for populations living at more southern latitudes. Hence, these differences were interpreted as adaptations to warm environments. Significant differences in allele frequencies and zygotic proportions at ten of twelve isoenzyme loci were found associated with differences in environments, sexes, and/or age classes. These data strongly support the view that protein polymorphisms are adaptive.—Several observations suggested that selection acts upon multilocus phenotypes rather than upon those of single loci. Several di-locus phenotypic distributions were demonstrated to be nonrandom, and those that exhibited similar patterns of dependence over years were postulated to be maintained by selection. Highly heterozygous fish exhibited superior viability when cohorts were compared over successive years.—The consequences of the polygynous mating system in this species for maintaining genetic variation and for allowing rapid evolutionary response to a variable environment are discussed.     

Evolution of outcrossing in experimental populations of Caenorhabditis elegans

Caenorhabditis elegans can reproduce exclusively by self-fertilization. Yet, males can be maintained in laboratory populations, a phenomenon that continues to puzzle biologists. In this study we evaluated the role of males in facilitating adaptation to novel environments. For this, we contrasted the evolution of a fitness component exclusive to outcrossing in experimental populations of different mating systems. We introgressed a modifier of outcrossing into a hybrid population derived from several wild isolates to transform the wild-type androdioecious mating system into a dioecious mating system. By genotyping 375 single-nucleotide polymorphisms we show that the two populations had similar standing genetic diversity available for adaptation, despite the occurrence of selection during their derivation. We then performed replicated experimental evolution under the two mating systems from starting conditions of either high or low levels of diversity, under defined environmental conditions of discrete non-overlapping generations, constant density at high population sizes (N = 10⁴), no obvious spatial structure and abundant food resources. During 100 generations measurements of sex ratios and male competitive performance showed: 1) adaptation to the novel environment; 2) directional selection on male frequency under androdioecy; 3) optimal outcrossing rates of 0.5 under androdioecy; 4) the existence of initial inbreeding depression; and finally 5) that the strength of directional selection on male competitive performance does not depend on male frequencies. Taken together, these results suggest that androdioecious males are maintained at intermediate frequencies because outcrossing is adaptive.     

Fine-scale genetic breaks driven by historical range dynamics and ongoing density-barrier effects in the estuarine seaweed Fucus ceranoides L.

Background

In the laboratory, the Drosophila melanogaster heat shock protein Hsp90 can buffer the phenotypic effects of genetic variation. Laboratory experiments either manipulate Hsp90 activity pharmacologically, or they induce mutations with strong effects in the gene Hsp83, the single-copy fly gene encoding Hsp90. It is unknown whether observations from such laboratory experiments are relevant in the wild.

Results

We here study naturally occurring mutations in Hsp83, and their effects on fitness and phenotypic buffering in flies derived from wild populations. We examined more than 4500 flies from 42 Drosophila populations distributed world-wide for insertions or deletions of mobile DNA in or near the Hsp83 gene. The insertions we observed occur at low population frequencies, and reduce Hsp83 gene expression. In competition experiments, mutant flies performed much more poorly than wild-type flies. Mutant flies were also significantly less fecund and shorter-lived than wild-type flies, as well as less well buffered against cryptic deleterious variation, as we show through inbreeding experiments. Specifically, in Hsp83 mutant flies female fecundity dropped to much lower levels after inbreeding than in wild-type flies. At even slightly elevated temperatures, inbred mutant Hsp83 populations went extinct, whereas inbred wild-type populations persisted.

Conclusions

Our work shows that Hsp90, a regulator of the stress response and of signaling, helps buffer deleterious variation in fruit flies derived from wild population, and that its buffering role becomes even more important under heat stress.     

The Genetical Response to Natural Selection by Varied Environments. IV. Gametic Disequilibrium in Spatially Varied Environments

Gametic disequilibria between allozyme loci were related to spatial variation of the environment in caged populations of Drosophila melanogaster . Two experiments, one with flies collected at "Chateau Tahbilk," South Australia, and the other with flies from "Groningen," The Netherlands, were sampled at generations 16 and 32. Spatial variation of the environment was stimulated using three food media. Eight polymorphic allozyme loci were used to estimate gametic disequilibria from digenic combinations of allotypes. All populations were duplicated within an environment and maintained at about 2500 adults. Standardized gametic disequilibria were compared by a weighted least squares analysis of the z-transformed statistical correlation of allele frequencies. Gametic disequilibria were strongly dependent upon food niche and food-niche interactions. The effects also varied with sampling time and were similar in duplicate populations. Gametic disequilibria were most often detected in the "Groningen"-derived populations and their strength was not strongly associated with recombination fraction. Many of the disequilibria concerned unlinked loci. The strength of selection was probably considerable and populations were evolving genetic architectures which reflected niche selection by the different foods without marked genetic isolation between foods; gene frequencies did not vary between niches within a population cage.     

Genetic analysis of population differentiation and adaptation in Leuciscus waleckii

Demographic events and natural selection both influence animal phenotypic and genetic variation; exploring the effects of demography and selection on population divergence is of great significance in evolutionary biology. To uncover the causes behind the patterns of genetic differentiation and adaptation among six populations of Leuciscus waleckii from Dali Basin (two populations, alkaline vs. freshwater) and Amur Basin (four populations, freshwater rivers vs. alkaline lake), a set of 21 unlinked polymorphic microsatellite markers and two mitochondrial DNA sequences (Cytb and D-loop) were applied to examine whether populations from different environments or habitats have distinct genetic differentiation and whether alkalinity is the major factor that caused population divergence. Bayesian analysis and principal component analysis as well as haplotype network analysis showed that these populations are primarily divided into two groups, which are congruent with geographic separation but not inconsistent with the habitat environment (alkalinity). Using three different approaches, outlier detection indicated that one locus, HLJYL017, may be under directional selection and involved in local adaptation processes. Overall, this study suggested that demographic events and selection of local environmental conditions including of alkalinity are jointly responsible for population divergence. These findings constitute an important step towards the understanding of the genetic basis of differentiation and adaptation, as well as towards the conservation of L. waleckii.     

The age and evolution of an antiviral resistance mutation in Drosophila melanogaster

What selective processes underlie the evolution of parasites and their hosts? Arms-race models propose that new host-resistance mutations or parasite counter-adaptations arise and sweep to fixation. Frequency-dependent models propose that selection favours pathogens adapted to the most common host genotypes, conferring an advantage to rare host genotypes. Distinguishing between these models is empirically difficult. The maintenance of disease-resistance polymorphisms has been studied in detail in plants, but less so in animals, and rarely in natural populations. We have made a detailed study of genetic variation in host resistance in a natural animal population, Drosophila melanogaster, and its natural pathogen, the sigma virus. We confirm previous findings that a single (albeit complex) mutation in the gene ref(2)P confers resistance against sigma and show that this mutation has increased in frequency under positive selection. Previous studies suggested that ref(2)P polymorphism reflects the progress of a very recent selective sweep, and that in Europe during the 1980s, this was followed by a sweep of a sigma virus strain able to infect flies carrying this mutation. We find that the ref(2)P resistance mutation is considerably older than the recent spread of this viral strain and suggest that—possibly because it is recessive—the initial spread of the resistance mutation was very slow.     

The future of molecular evolution

Antony Dean explores the past, present and future of evolutionary theory and our continuing efforts to explain biological patterns in terms of molecular processes and mechanisms.There are just two questions to be asked in evolution: how are things related, and what makes them differ? Lamarck was the first biologist—he invented the word—to address both. In his Philosophie Zoologique (1809) he suggested that the relationships among species are better described by branching trees than by a simple ladder, that new species arise gradually by descent with modification and that they adapt to changing environments through the inheritance of acquired characteristics. Much that Lamarck imagined has since been superseded. Following Wallace and Darwin, we now envision that species belong to a single highly branched tree and that natural selection is the mechanism of adaptation. Nonetheless, to Lamarck we owe the insight that pattern is produced by process and that both need mechanistic explanation.Questions of pattern, process and mechanism pervade the modern discipline of molecular evolution. The field was established when Zuckerkandl & Pauling (1965) noted that haemoglobins evolve at a roughly constant rate. Their “molecular evolutionary clock” forever changed our view of evolutionary history. Not only were seemingly intractable relationships resolved—for example, whales are allies of the hippopotamus—but also the eubacterial origins of eukaryotic organelles were firmly established and a new domain of life was discovered: the Archaea.Yet, different genes sometimes produce different trees. Golding & Gupta (1995) resolved two-dozen conflicting protein trees by suggesting that Eukarya arose following massive horizontal gene transfer between Bacteria and Archaea. Whole genome sequencing has since revealed so many conflicts that horizontal gene transfer seems characteristic of prokaryote evolution. In higher animals—where horizontal transfer is sufficiently rare that the tree metaphor remains robust—rapid and inexpensive whole genome sequencing promises to provide a wealth of data for population studies. The patterns of migration, admixture and divergence of species will be soon addressed in unprecedented detail.Sequence analyses are also used to infer processes. A constant molecular clock originally buttressed the neutral theory of molecular evolution (Kimura, 1985). The clock has since proven erratic, while the neutral theory now serves as a null hypothesis for statistical tests of ‘selection''. In truth, most tests are also sensitive to demographic changes. The promise of ultra-high throughput sequencing to provide genome-wide data should help dissect selection, which targets particular genes, from demography, which affects all the genes in a genome, although weak selection and ancient adaptations will remain undetected.In the functional synthesis (Dean & Thornton, 2007), molecular biology provides the experimental means to test evolutionary inferences decisively. For example, site-directed mutagenesis can be used to introduce putatively selected mutations into reconstructed ancestral sequences, the gene products are then expressed and purified and their functional properties determined in vitro. In microbial species, homologous recombination is used routinely to replace wild-type with engineered genes, enabling organismal phenotypes and fitnesses to be determined in vivo. The vision of Zuckerkandl & Pauling (1965) that by “furnishing probable structures of ancestral proteins, chemical paleogenetics will in the future lead to deductions concerning molecular functions as they were presumably carried out in the distant evolutionary past” is now a reality.If experimental tests of evolutionary inferences open windows on past mechanisms, directed evolution focuses on the mechanisms without attempting historical reconstruction. Today''s ‘fast-forward'' molecular breeding experiments use mutagenic PCR to generate vast libraries of variation and high throughput screens to identify rare novel mutants (Romero & Arnold, 2009; Khersonsky & Tawfik, 2010). Among numerous topics explored are: the role of intragenic recombination in furthering adaptation, the number and location of mutations in protein structures, the necessity—or lack thereof—of broadening substrate specificity before a new function is acquired, the evolution of robustness, and the alleged trade-off between stability and catalytic efficiency. Few, however, have approached the detail found in those classic studies of evolved β-galactosidase (Hall, 2003) that revealed how the free-energy profile of an enzyme-catalysed reaction evolved. Even further removed from natural systems are catalytic RNAs that, by combining phenotype and genotype within the same molecule, allow evolution to proceed in a lifeless series of chemical reactions. Recently, two RNA enzymes that catalyse each other''s synthesis were shown to undergo self-sustained exponential amplification (Lincoln & Joyce, 2009). Competition for limiting tetranucleotide resources favours mutants with higher relative fitness—faster replication—demonstrating that adaptive evolution can occur in a chemically defined abiotic genetic system.Lamarck was the first to attempt a coherent explanation of biological patterns in terms of processes and mechanisms. That his legacy can still be discerned in the vibrant field of molecular evolution would no doubt please him as much as it does us in promising extraordinary advances in our understanding of the mechanistic basis of molecular adaptation.