The genetic basis of adaptive pigmentation variation in Drosophila melanogaster

In a broad survey of Drosophila melanogaster population samples, levels of abdominal pigmentation were found to be highly variable and geographically differentiated. A strong positive correlation was found between dark pigmentation and high altitude, suggesting adaptation to specific environments. DNA sequence polymorphism at the candidate gene ebony revealed a clear association with the pigmentation of homozygous third chromosome lines. The darkest lines sequenced had nearly identical haplotypes spanning 14.5 kb upstream of the protein-coding exons of ebony. Thus, natural selection may have elevated the frequency of an allele that confers dark abdominal pigmentation by influencing the regulation of ebony.     

Non-African populations of Drosophila melanogaster have a unique origin

Drosophila melanogaster is widely used as a model in DNA variation studies. Patterns of polymorphism have, however, been affected by the history of this species, which is thought to have recently spread out of Africa to the rest of the world. We analyzed DNA sequence variation in 11 populations, including four continental African and seven non-African samples (including Madagascar), at four independent X-linked loci. Variation patterns at all four loci followed neutral expectations in all African populations, but departed from it in all non-African ones due to a marked haplotype dimorphism at three out of four loci. We also found that all non-African populations show the same major haplotypes, though in various frequencies. A parsimonious explanation for these observations is that all non-African populations are derived from a single ancestral population having undergone a substantial reduction of polymorphism, probably through a bottleneck. Less likely alternatives involve either selection at all four loci simultaneously (including balancing selection at three of them), or admixture between two divergent populations. Small but significant structure was observed among African populations, and there were indications of differentiation across Eurasia for non-African ones. Since population history may result in non-equilibrium variation patterns, our study confirms that the search for footprints of selection in the D. melanogaster genome must include a sufficient understanding of its history.     

Patterns of microsatellite variability among X chromosomes and autosomes indicate a high frequency of beneficial mutations in non-African D. simulans

We analyzed microsatellite variability at 42 X-linked and 39 autosomal loci from African and European populations of Drosophila simulans. The African D. simulans harbored significantly more microsatellite variability than the European flies. In the European population, X-linked polymorphism was more reduced than autosomal variation, whereas there was no significant difference between chromosomes in the African population. Previous studies also observed a similar pattern but failed to distinguish between a demographic event and a selection scenario. We performed extensive computer simulations using a wide range of demographic scenarios to distinguish between the two hypotheses. Approximate summary likelihood estimates differed dramatically among X chromosomes and autosomes. Furthermore, our experimental data showed a surplus of X-linked microsatellites with a significantly reduced variability in non-African D. simulans. We conclude that our data are not compatible with a neutral scenario. Thus, the reduced variability at X-linked loci is most likely caused by selective sweeps associated with the out-of-Africa habitat expansion of D. simulans.     

Identification of X-linked quantitative trait loci affecting cold tolerance in Drosophila melanogaster and fine mapping by selective sweep analysis

Drosophila melanogaster is a cosmopolitan species that colonizes a great variety of environments. One trait that shows abundant evidence for naturally segregating genetic variance in different populations of D. melanogaster is cold tolerance. Previous work has found quantitative trait loci (QTL) exclusively on the second and the third chromosomes. To gain insight into the genetic architecture of cold tolerance on the X chromosome and to compare the results with our analyses of selective sweeps, a mapping population was derived from a cross between substitution lines that solely differed in the origin of their X chromosome: one originates from a European inbred line and the other one from an African inbred line. We found a total of six QTL for cold tolerance factors on the X chromosome of D. melanogaster. Although the composite interval mapping revealed slightly different QTL profiles between sexes, a coherent model suggests that most QTL overlapped between sexes, and each explained around 5–14% of the genetic variance (which may be slightly overestimated). The allelic effects were largely additive, but we also detected two significant interactions. Taken together, this provides evidence for multiple QTL that are spread along the entire X chromosome and whose effects range from low to intermediate. One detected transgressive QTL influences cold tolerance in different ways for the two sexes. While females benefit from the European allele increasing their cold tolerance, males tend to do better with the African allele. Finally, using selective sweep mapping, the candidate gene CG16700 for cold tolerance colocalizing with a QTL was identified.     

Evidence of gene conversion associated with a selective sweep in Drosophila melanogaster

Since Drosophila melanogaster colonized Europe from tropical Africa 10 to 15 thousand years ago, it is expected that adaptation has played a major role in this species in recent times. A previously conducted multilocus scan of noncoding DNA sequences on the X chromosome in an ancestral and a derived population of D. melanogaster revealed that some loci have been affected by directional selection in the European population. We investigated if the pattern of DNA sequence polymorphism in a region surrounding one of these loci can be explained by a hitchhiking event. We found strong evidence that the studied region around the gene unc-119 was shaped by a recent selective sweep, including a valley of reduced heterozygosity of 83.4 kb, a skew in the frequency spectrum, and significant linkage disequilibrium on one side of the valley. This region, however, was interrupted by gene conversion events leading to a strong haplotype structure in the center of the valley of reduced variation.     

Inferring local adaptation from QST-FST comparisons: neutral genetic and quantitative trait variation in European populations of great snipe

We applied a phenotypic QST (PST) vs. FST approach to study spatial variation in selection among great snipe (Gallinago media) populations in two regions of northern Europe. Morphological divergence between regions was high despite low differentiation in selectively neutral genetic markers, whereas populations within regions showed very little neutral divergence and trait differentiation. QST > FST was robust against altering assumptions about the additive genetic proportions of variance components. The homogenizing effect of gene flow (or a short time available for neutral divergence) has apparently been effectively counterbalanced by differential natural selection, although one trait showed some evidence of being under uniform stabilizing selection. Neutral markers can hence be misleading for identifying evolutionary significant units, and adopting the PST-FST approach might therefore be valuable when common garden experiments is not an option. We discuss the statistical difficulties of documenting uniform selection as opposed to divergent selection, and the need for estimating measurement error. Instead of only comparing overall QST and FST values, we advocate the use of partial matrix permutation tests to analyse pairwise QST differences among populations, while statistically controlling for neutral differentiation.     

Allelic structure and distribution of 103 STR loci in a Southern Tunisian population

Genotypes of 103 short tandem repeat (STR) markers distributed at an average of 40 cM intervals throughout the genome were determined for 40 individuals from the village of BirEl Hfai (BEH). This village of approximately 31.000 individuals is localized in the south-west of Tunisia. The allele frequency distributions in BEH were compared with those obtained for individuals in the CEPH (Centre d’Etude du Polymorphisme Humain) data using a Kolmo-gorov-Smirnov two-sample test. Fourteen out of the 103 markers (13.2%) showed significant differences (P<0.05) in distribution between the two populations. Population heterogeneity in BEH was indicated by an excess of observed homozygosity deviations from Hardy-Weinberg equilibrium at 3 loci (P<0.0005). No evidence for genotypic disequilibrium was found for any of the marker pairs. This demonstrated that in spite of a high inbreeding level in the population, few markers showed evidence for a different pattern of allelic distribution compared to CEPH.     

Maximum likelihood estimation of the frequency of null alleles at microsatellite loci

We review three methods for estimating the frequency of null alleles at codominant loci (such as microsatellite loci) and present a new maximum likelihood approach. Computer simulations show that the maximum likelihood estimator has a smaller root mean squared error than previous estimators.     

Dispersal in the course of an invasion

Invasive species receive attention as manifestations of global ecological change and because of the effects that they may have on other organisms. They are commonly discussed in the context of the ecological perturbations or the human activities that permitted the invasion. There is also evidence, that there is an intrinsic component to biological invasions in that evolutionary changes of the invaders themselves can facilitate or limit invasions (Lee 2002; Urban et al. 2007; Van Bocxlaer et al. 2010). Hence, teasing apart whether environmental change or changes of the organism foster invasions is an interesting field of research. Ample evidence for plants and animals documents that ecological change and human activities trigger range expansions and invasions, but questions regarding evolutionary change of invaders remain less explored although there are several reasons to believe it matters. Firstly, rapid evolutionary change is possible in time-frames relevant for contemporary biological invasions(Hendry et al. 2007). Furthermore, population genetic modelling suggests that there are circumstances where the range expansion and colonization of empty spaces in the course of an invasion can induce evolutionary change in a way that is specific to invaders: the process of repeated founding out of marginal populations in the course of a range expansion can shift allele frequencies and has been referred to as allele surfing, which not only affects neutral genetic variance, but also fitness relevant traits (Klopfstein et al. 2006; Travis et al. 2007; Burton & Travis 2008). Importantly, this process poses a null model for evolutionary inference in invasive populations. It predicts conspicuous allele frequency changes in an expanding metapopulation unless migration homogenizes the gene pool. Despite this relevance, ideas about allele surfing rely heavily on modelling although some experimental evidence comes from studies that document the segregation of genetic variants in growing plaques of bacteria (Hallatschek et al. 2007). To date, little empirical data is available that would reveal the migration processes that affect the establishment of gene pools at invasion fronts in natural systems. This aspect sets the study of Bronnenhuber et al. (2011) apart. They quantify migration behind the expansion front of an invading fish and thus provide important baseline data for the interpretation of the emerging patterns of genetic differentiation.     

Intron sequences of arginine kinase in an intertidal snail suggest an ecotype-specific selective sweep and a gene duplication

Many species with restricted gene flow repeatedly respond similarly to local selection pressures. To fully understand the genetic mechanisms behind this process, the phylogeographic history of the species (inferred from neutral markers) as well as the loci under selection need to be known. Here we sequenced an intron in the arginine kinase gene (Ark), which shows strong clinal variation between two locally adapted ecotypes of the flat periwinkle, Littorina fabalis. The ‘small-sheltered'' ecotype was almost fixed for one haplotype, H1, in populations on both sides of the North Sea, unlike the ‘large-moderately exposed ecotype'', which segregated for ten different haplotypes. This contrasts with neutral markers, where the two ecotypes are equally variable. H1 could have been driven to high frequency in an ancestral population and then repeatedly spread to sheltered habitats due to local selection pressures with the colonization of both sides of the North Sea, after the last glacial maximum (∼18 000 years ago). An alternative explanation is that a positively selected mutation, in or linked to Ark, arose after the range expansion and secondarily spread through sheltered populations throughout the distribution range, causing this ecotype to evolve in a concerted fashion. Also, we were able to sequence up to four haplotypes consistently from some individuals, suggesting a gene duplication in Ark.     

用SSR研究栲树群体遗传结构

利用微卫星（SSR）分子标记对福建省内4个栲树（Castanopsis fargesii Franch.）群体遗传结构进行了研究。SSR标记揭示了栲树群体丰富的遗传变异：平均等位基因数A＝9.0,平均有效等位基因数Ne=4.8,平均期望杂合度He=0.65,而群 具有较低的Fst值（Fst=0.031）。SSR每个位点的等位基因频率分布在栲树群体间都存在显或极显差异,表明根据SSR等位基因频率分布亦能了解各体的分化。SSR标记使栲树群体中一些稀有等位基因得以表现,54个SSR等位基因中有15个等位基因仅出现在1个或2个群体中,且频率较低,在遗传多样性保护中更应注重保护这些稀有的等位变异。     

Relative migration rates and local adaptation in a mosquito-protozoan interaction

Theory predicts that the direction of local adaptation depends on the relative migration rates of hosts and parasites. Here we measured relative migration rates and tested for local adaptation in the interaction between a tree hole mosquito (Ochlerotatus sierrensis) and a protozoan parasite (Lambornella clarki). We found strong support for the hypothesis that the host migrates more than its parasite. Hosts colonized artificial tree holes in the field at a much higher rate than the parasite. Field releases of the parasite demonstrated that it colonizes and persists in natural tree holes where it was previously absent, suggesting that parasite distribution is limited by its migratory ability. Although the host migrates more than its parasite, we found no evidence for local adaptation by hosts and some evidence for local adaptation by parasites. Other life history traits of the host and parasite may also influence patterns in local adaptation, particularly parasite virulence and host dormancy.     

Male sterility thermal thresholds in Drosophila: D. simulans appears more cold-adapted than its sibling D. melanogaster

Numerous different criteria may be used for analysing species thermal adaptation. We compared male sterility thresholds in the two most investigated cosmopolitan siblings, D. melanogaster and D. simulans. A survey of various populations from Europe and North Africa evidenced consistent differences between the two species, and a detailed analysis was made on flies from Marrakech. Sharp sterility thresholds were observed in both species but at different temperatures: D. simulans appeared more tolerant to cold than its sibling (difference 1°C) but more sensitive to heat (difference 1.5°C). When transferred to an optimum temperature of 21°C, D. simulans males, sterilized by a low temperature, recovered more rapidly than males of D. melanogaster; the reverse was true on the high temperature side. The analysis of progeny number also revealed the better tolerance of D. simulans males to cold but a lesser tolerance to heat. From these observations, we might expect that D. simulans should be more successful in cold temperate countries than its sibling, while ecological observations point to the contrary. Our data clearly show the difficulty of comparing ecophysiological data to field observations, and also the need of extensive comparative life history studies in closely related species.     

High mutation rate of TPE repeats: a microsatellite in the putative transposase of the hobo element in Drosophila melanogaster

The hobo transposable element contains a polymorphic microsatellite sequence located in its coding region, the TPE repeats. Previous surveys of natural populations of Drosophila melanogaster have detected at least seven different hobo transposons. These natural populations are geographically structured with regard to TPE polymorphism, and a scenario has been proposed for the invasion process. Natural populations have recently been completely invaded by hobo elements with three TPE repeats. New elements then appeared by mutation, triggering a new stage of invasion by other elements. Since TPE polymorphism appeared over a short period of time, we focused on estimating the mutation rate of these TPE repeats. We used transgenic lines harboring three TPE and/or five TPE hobo elements that had been evolving for at least 16 generations to search for a new TPE repeat polymorphism. We detected three mutants, with four, seven, and eight TPE repeats, respectively. The estimated mutation rate of the TPE repeats is therefore higher than that of neutral microsatellites in D. melanogaster (4.2 x 10-4 versus 6.5 x 10-6). The role of the transposition mechanism and the particular structure of the TPE repeats of the hobo element in this increase in the mutation rate are discussed.     

Evidence for local adaptation in neighbouring Daphnia populations: a laboratory transplant experiment

1. We tested whether two neighbouring Daphnia galeata populations (from Lake Blankaart and Fish Pond), separated only by 5 m of land and with the occasional exchange of water were genetically differentiated in allozyme markers and life history traits. Allozyme electrophoresis revealed that the populations differed in allelic as well as in genotypic composition. 2. In a laboratory transplant experiment, in which animals of four clones of each of the populations were raised in the water of both ponds, survival in Blankaart water was high for both the Blankaart and Fish Pond clones, whereas survival in Fish Pond water was high for the Fish Pond clones, but low for the Blankaart clones. 3. Fish Pond clones produced fewer neonates than Blankaart clones when cultured in Blankaart water. High egg mortality was observed for animals that were raised in Blankaart water, and this egg mortality was higher for Fish Pond clones than for Blankaart clones. 4. Our results provide evidence for genetic differentiation between Daphnia populations inhabiting neighbouring water bodies and suggest local adaptation to environmental conditions other than direct predation.     

A population genomic approach to map recent positive selection in model species

Based on nearly complete genome sequences from a variety of organisms data on naturally occurring genetic variation on the scale of hundreds of loci to entire genomes have been collected in recent years. In parallel, new statistical tests have been developed to infer evidence of recent positive selection from these data and to localize the target regions of selection in the genome. These methods have now been successfully applied to Drosophila melanogaster , humans, mice and a few plant species. In genomic regions of normal recombination rates, the targets of positive selection have been mapped down to the level of individual genes.     

Study of local correlations in bacterial genes for use in the framework of hidden Markov models

Computer-aided search for genes often relies on mathematical models based on the notion of hidden Markov chain. Here I propose using the selective correlation ratio to determine the local relationship required for compilation of such models. The case when a gene is presented as an amino acid sequence was calculated on the example of 11 annotated genomes. A number of nonexplicit relationships (presumably related to the properties of protein α-helix) have been revealed, which allows specific recommendations for constructing the models.