To add detail to the genetic map of Arabidopsis lyrata, and compare it with that of A. thaliana, we have developed many additional markers in the A. lyrata linkage groups, LG1 and LG2, corresponding to A. thaliana chromosome 1. We used a newly developed method for marker development for single nucleotide polymorphisms present in gene sequences, plus length differences, to map genes in an A. lyrata family, including variants in several genes close to the A. thaliana centromere 1, providing the first data on the location of an A. lyrata centromere; we discuss the implications for the evolution of chromosome 1 of A. thaliana. With our larger marker density, large rearrangements between the two Arabidopsis species are excluded, except for a large inversion on LG2. This was previously known in Capsella; its presence in A. lyrata suggests that, like most other rearrangements, it probably arose in the A. thaliana lineage. Knowing that marker orders are similar, we can now compare homologous, non-rearranged map distances to test the prediction of more frequent crossing-over in the more inbreeding species. Our results support the previous conclusion of similar distances in the two species for A. lyrata LG1 markers. For LG2 markers, the distances were consistently, but non-significantly, larger in A. lyrata. Given the two species' large DNA content difference, the similarity of map lengths, particularly for LG1, suggests that crossing-over is more frequent across comparable physical distances in the inbreeder, A. thaliana, as predicted.

Weak selection is maintaining the Drosophila americana X/4 fusion chromosomal frequency cline. The gene(s) harbouring the advantageous variant(s) that is responsible for the establishment and maintenance of this chromosomal frequency gradient must be located in a region of the X and/or 4th chromosome that is genetically isolated between the X/4 fusion and non-fusion forms. The limits of these regions must thus be determined before an attempt is made to identify these genes. For this purpose, the correspondence between the D. virilis X and 4th chromosome genome scaffolds sequence and the D. americana gene order was established. Polymorphism levels and patterns at seven genes located at the base of the D. americana X chromosome, as well as three genes located at the base of the 4th chromosome, were analysed. The data suggest that the D. americana X/4 fusion is no more than 29000 years old. At the base of the X chromosome, there is suppression of recombination within X/4 fusion and non-fusion chromosomes, and little recombination between the two chromosomal forms. Apparent fixed silent and replacement differences are found in three of seven genes analysed located at the base of the X chromosome. There is no evidence for suppression of recombination between fusion and non-fusion chromosomes at the base of the 4th chromosome. The advantageous variant responsible for the establishment in frequency and maintenance of the X/4 fusion is thus inferred to be in the D. americana X centromere–inversion Xc basal breakpoint region.

The comparison of the genetic differentiation of quantitative traits (QST) and molecular markers (FST) can inform on the strength and spatial heterogeneity of selection in natural populations, provided that markers behave neutrally. However, selection may influence the behaviour of markers in selfing species with strong linkage disequilibria among loci, therefore invalidating this test of detection of selection. We address this issue by monitoring the genetic differentiation of five microsatellite loci (FST) and nine quantitative traits (QST) in experimental metapopulations of the predominantly selfing species Arabidopsis thaliana, that evolved during eight generations. Metapopulations differed with respect to population size and selection heterogeneity. In large populations, the genetic differentiation of neutral microsatellites was much larger under heterogeneous selection than under uniform selection. Using simulations, we show that this influence of selection heterogeneity on FST can be attributable to initial linkage disequilibria among loci, creating stronger genetic differentiation of QTL than expected under a simple additive model with no initial linkage. We found no significant differences between FST and QST regardless of selection heterogeneity, despite a demonstrated effect of selection on QST values. Additional data are required to validate the role of mating system and linkage disequilibria in the joint evolution of neutral and selected genetic differentiation, but our results suggest that FST/QST comparisons can be conservative tests to detect selection in selfing species.

The enzyme aldehyde dehydrogenase (ALDH) is essential for ethanol metabolism in mammals, converting the highly toxic intermediate acetaldehyde to acetate. The role of ALDH in Drosophila has been debated, with some authors arguing that, at least in larvae, acetaldehyde detoxification is carried out mainly by alcohol dehydrogenase (ADH), the enzyme responsible for converting ethanol to acetaldehyde. Here, we report the creation and characterization of four null mutants of Aldh, the putative structural locus for ALDH. Aldh null larvae and adults are poisoned by ethanol concentrations easily tolerated by wild-types; their ethanol sensitivity is in fact comparable to that of Adh nulls. The results refute the view that ALDH plays only a minor role in ethanol detoxification in larvae, and suggest that Aldh and Adh may be equally important players in the evolution of ethanol resistance in fruit-breeding Drosophila.

The typical life cycle of an aphid is cyclical parthenogenesis which involves the alternation of sexual and asexual reproduction. However, aphid life cycles, even within a species, can encompass everything on a continuum from obligate sexuality, through facultative sexuality to obligate asexuality. Loss of the sexual cycle in aphids is frequently associated with the introduction of a new pest and can occur for a number of environmental and genetic reasons. Here we investigate loss of sexual function in Sitobion aphids in Australia. Specifically, we aimed to determine whether an absence of sexual reproduction in Australian Sitobion results from genetic loss of sexual function or environmental constraints in the introduced range. We addressed our aims by performing a series of breeding experiments. We found that some lineages have genetically lost sexual function while others retain sexual function and appear environmentally constrained to asexuality. Further, in our crosses, using autosomal and X-linked microsatellite markers, we identified processes deviating from normal Mendelian segregation. We observed strong deviations in X chromosome transmission through the sexual cycle. Additionally, when progeny genotypes were examined across multiple loci simultaneously we found that some multilocus genotypes are significantly over-represented in the sample and that levels of heterozygosity were much higher than expected at almost all loci. This study demonstrates that strong biases in the transmission of X chromosomes through the sexual cycle are likely to be widespread in aphids. The mechanisms underlying these patterns are not clear. We discuss several possible alternatives, including mutation accumulation during periods of functional asexuality and genetic imprinting.

Latitudinal variation of the polymorphic sn-glycerol-3-phosphate (α-Gpdh) locus in Drosophila melanogaster has been characterized on several continents; however, apparent clinal patterns are potentially confounded by linkage with an inversion, close associations with other genetic markers that vary clinally, and a tandem α-Gpdh pseudogene. Here we compare clinal patterns in α-Gpdh with those of other linked markers by testing field flies from eastern Australian locations collected in two separate years. The α-Gpdh variation exhibited a consistent non-linear cline reflecting an increase in the α-GpdhF allele at extreme latitudes. This pattern was not influenced by the In(2L)t inversion wherein this locus is located, nor was it influenced by the presence of the α-Gpdh pseudogene, whose presence was ubiquitous and highly variable among populations. The α-Gpdh pattern was also independent of a cline in allozyme frequencies at the alcohol dehydrogenase (Adh) locus, and two length polymorphisms in the Adh gene. These results suggest clinal selection at the α-Gpdh locus that is partially or wholly unrelated to linear climatic gradients along the eastern coast of Australia.

The sex comb on the forelegs of Drosophila males is a secondary sexual trait, and the number of teeth on these combs varies greatly within and between species. To understand the relationship between the intra- and interspecific variation, we performed quantitative trait locus (QTL) analyses of the intraspecific variation in sex-comb tooth number. We used five mapping populations derived from two inbred Drosophila simulans strains that were divergent in the number of sex-comb teeth. Although no QTLs were detected on the X chromosome, we identified four QTLs on the second chromosome and three QTLs on the third chromosome. While identification and estimated effects of the second-chromosome QTLs depend on genetic backgrounds, significant and consistent effects of the two third-chromosome QTLs were found in two genetic backgrounds. There were significant epistatic interactions between a second-chromosome QTL and a third-chromosome QTL, as well as between two second-chromosome QTLs. The third-chromosome QTLs are concordant with the locations of the QTLs responsible for the previously observed differences in sex-comb tooth number between D. simulans and D. mauritiana.

Drosophila pseudoobscura has been intensively studied by evolutionary biologists for over 70 years. The recent publication of the genome sequence not only permits studies of comparative genomics with other dipterans but also opens the door to identifying genes associated with adaptive traits or speciation or testing for the signature of natural selection across the genome. Information on regional rates of recombination, localization of inversion breakpoints distinguishing it from its sibling species D. persimilis, and known polymorphic markers may be useful in such studies. Here, we present a molecular linkage map of four of the five major chromosome arms of D. pseudoobscura. In doing so, we order and orient several sequence contig groups, localize the inversion breakpoints on chromosome 2 to intervals of 200 kilobases, and identify one error in the published sequence assembly. Our results show that regional recombination rates in D. pseudoobscura are much higher than in D. melanogaster and significantly higher even than in D. persimilis. Furthermore, we detect a non-significant positive correlation between recombination rate and published DNA sequence variation. Finally, the online Appendix presents 200 primer sequence pairs for molecular markers that can be used for mapping of quantitative trait loci, of which 125 are known to be polymorphic within or between species.

The Tol2 element of the medaka fish Oryzias latipes is a member of the hAT (hobo/Activator/Tam3) transposable element family. There is evidence for rapid expansion in the genome and throughout the species in the past but a high spontaneous transposition rate is not observed with current fish materials, suggesting that the Tol2 element and its host species have already acquired an interactive mechanism to control the transposition frequency. DNA methylation is a possible contributing factor, given its involvement with many other transposable elements. We therefore soaked embryos in 5-azacytidine, a reagent that causes reduction in the DNA methylation level, and examined amounts of PCR products reflecting the somatic excision frequency, obtaining direct evidence that exposure promotes Tol2 excision. Our results thus suggest that methylation of the genome DNA is a factor included in the putative mechanisms of control of transposition of the Tol2 element.

In drosophilid flies, male recombination and neo-sex chromosome formation are rare. Following the genotyping of full-sib families with 20 microsatellite markers and subsequent cytological work, we found evidence of both male recombination and neo-sex chromosome formation in Scaptodrosophila hibisci. As far as we are aware, this is the first report of male recombination and neo-sex chromosome formation co-occurring in a drosophilid fly. Two autosomal loci, Sh29c and Sh90, showed aberrant segregation of male parental alleles. We describe how an autosomal fission followed by fusion of one of the autosomal fragments to the Y chromosome to create a Y1Y2X1X2/X1X1X2X2 sex determination system provides the most parsimonious explanation of the patterns we observe. Male recombination was observed in three families, including autosomal linkage groups and the Y1/X2 linkage group. In addition to the X1 linkage group, two autosomal linkage groups were identified.

We propose a simple approach, the multiplicative background correction, to solve a perplexing problem in spotted microarray data analysis: correcting the foreground intensities for the background noise, especially for spots with genes that are weakly expressed or not at all. The conventional approach, the additive background correction, directly subtracts the background intensities from foreground intensities. When the foreground intensities marginally dominate the background intensities, the additive background correction provides unreliable estimates of the differential gene expression levels and usually presents M–A plots with ‘fishtails’ or fans. Unreliable additive background correction makes it preferable to ignore the background noise, which may increase the number of false positives. Based on the more realistic multiplicative assumption instead of the conventional additive assumption, we propose to logarithmically transform the intensity readings before the background correction, with the logarithmic transformation symmetrizing the skewed intensity readings. This approach not only precludes the ‘fishtails’ and fans in the M–A plots, but provides highly reproducible background-corrected intensities for both strongly and weakly expressed genes. The superiority of the multiplicative background correction to the additive one as well as the no background correction is justified by publicly available self-hybridization datasets.

Human-mediated bioinvasions provide the opportunity to study the early stages of contact between formerly allopatric, divergent populations of a species. However, when invasive and resident populations are morphologically similar, it may be very difficult to assess their distribution in the field, as well as the extent of ecological overlap and genetic exchanges between invasive and resident populations. We here illustrate the use of data obtained from a set of eight microsatellite markers together with Bayesian clustering methods to document invasions in a group of major tropical pests, Bemisia tabaci, which comprises several morphologically indistinguishable biotypes with different agronomic impacts. We focus on the island of La Réunion, where an invasive biotype (B) has recently been introduced and now interacts with the resident biotype (Ms). The temporal and spatial distribution, host-plant range and genetic structure of both biotypes are investigated. We showed (i) that, without prior information, clustering methods separate two groups of individuals that can safely be identified as the B and Ms biotypes; (ii) that the B biotype has invaded all regions of the island, and showed no signs of genetic founder effect relative to the Ms biotype; (iii) that the B and Ms biotypes coexist in sympatry throughout most of their geographical ranges, although they tend to segregate into different host plants; and finally (iv) that asymmetrical and locus-specific introgression occurs between the two biotypes when they are in syntopy.

The aim of this paper is to combine different but complementary approaches to check the neutrality of a given locus in a selected population. Analysis was undertaken through the polymorphism's evolution compared with that predicted under the effect of drift and through the analysis of the variance components of the measured traits, considering the effect of the locus as either a fixed or a random effect. This study deals with the case of the MHC locus, using both data from experimental lines of chicken selected for three different criteria of immune response, and frequencies of the genotyped haplotypes over time. Both the evolution of the polymorphism and the variance components approach have led to the conclusion that the MHC locus has an effect on the trait affecting antibody production against the Newcastle disease virus. Results have also highlighted the interest in using various methods in the case of low allelic frequencies. However, none of the common hypotheses, overdominance or frequency-dependent selection, was sufficient to explain the observed variation of the MHC polymorphism, which was displayed by the temporal variation of the allelic frequencies.

Many biological processes, from cellular metabolism to population dynamics, are characterized by particular allometric scaling relationships between rate and size (power laws). A statistical model for mapping specific quantitative trait loci (QTLs) that are responsible for allometric scaling laws has been developed. We present an improved model for allometric mapping of QTLs based on a more general allometry equation. This improved model includes two steps: (1) use model II regression analysis to estimate the parameters underlying universal allometric scaling laws, and (2) substitute the estimated allometric parameters in the mixture-based mapping model to obtain the estimation of QTL position and effects. This model has been validated by a real example for a mouse F2 progeny, in which two QTLs were detected on different chromosomes that determine the allometric relationship between growth rate and body weight.

To comprehensively investigate the genetic architecture of growth and obesity, we performed Bayesian analyses of multiple epistatic quantitative trait locus (QTL) models for body weights at five ages (12 days, 3, 6, 9 and 12 weeks) and body composition traits (weights of two fat pads and five organs) in mice produced from a cross of the F1 between M16i (selected for rapid growth rate) and CAST/Ei (wild-derived strain of small and lean mice) back to M16i. Bayesian model selection revealed a temporally regulated network of multiple QTL for body weight, involving both strong main effects and epistatic effects. No QTL had strong support for both early and late growth, although overlapping combinations of main and epistatic effects were observed at adjacent ages. Most main effects and epistatic interactions had an opposite effect on early and late growth. The contribution of epistasis was more pronounced for body weights at older ages. Body composition traits were also influenced by an interacting network of multiple QTLs. Several main and epistatic effects were shared by the body composition and body weight traits, suggesting that pleiotropy plays an important role in growth and obesity.

Coordinated expression of embryo and endosperm tissues is required for proper seed development. The coordination among these two tissues is controlled by the interaction between multiple genes expressed in the embryo and endosperm genomes. In this article, we present a statistical model for testing whether quantitative trait loci (QTL) active in different genomes, diploid embryo and triploid endosperm, epistatically affect a trait expressed on the endosperm tissue. The maximum likelihood approach, implemented with the EM algorithm, was derived to provide the maximum likelihood estimates of the locations of embryo- and endosperm-specific QTL and their main effects and epistatic effects. This model was used in a real example for rice in which two QTL, one from the embryo genome and the other from the endosperm genome, exert a significant interaction effect on gel consistency on the endosperm. Our model has successfully detected Waxy, a candidate gene in the embryo genome known to regulate one of the major steps of amylose biosynthesis in the endosperm. This model will have great implications for agricultural and evolutionary genetic research.

The observation of high mitochondrial mutation rates in human pedigrees has led to the question of how such an asexual genetic system can survive the accumulation of slightly deleterious mutations caused by Muller's ratchet. I define a null model to quantify in unprecedented detail the threat from extinction caused by Muller's ratchet. This model is general enough to explore the biological significance of Muller's ratchet in various species where its operation has been suspected. For increased precision over a wide range of parameter space I employ individual-based simulations run by evolution@home, the first global computing system for evolutionary biology. After compiling realistic values for the key parameters in human mitochondrial DNA (mtDNA) I find that a surprisingly large range of biologically realistic parameter combinations would lead to the extinction of the human line over a period of 20 million years – if accepted wisdom about mtDNA and Muller's ratchet is correct. The resulting genomic decay paradox complements a similar threat from extinction due to mutation accumulation in nuclear DNA and suggests evaluation of unconventional explanations for long-term persistence. A substantial list of potential solutions is given, including compensatory back mutations, mutation rate heterogeneity and occasional recombination in mtDNA. Future work will have to explore which of these actually solves the paradox. Nonetheless, the results presented here provide yet another reason to minimize anthropogenic increase of mutation rates.