Heredity

Published by Nature Publishing Group
Publications
Using in situ hybridization to polytene salivary gland chromosomes, we have registered the co-occurrences of insertions of the four mobile elements, copia, mdg-1, I and P in the whole genomes of 17 highly-inbred lines of Drosophila melanogaster (the insertions in the centromeric regions were excluded); these elements differ in structure, DNA sequence and profile of developmental transcription. The mdg-1 and P elements tend to avoid each other on the X chromosomes but not on the autosomes; copia and mdg-1, two copia-like elements, show an excess of co-occurrences on the 2L and 3R chromosome arms but not on the X chromosomes. The pairs mdg-1/I, I/copia, I/P and copia/P do not show any kind of interaction. Populational studies are thus necessary to obtain complete accurate information on interactions between transposable elements for their sites of insertion in a genome.
 
Bacteria of the genus Wolbachia are widespread in arthropods and can induce different effects on the host such as cytoplasmic incompatibility (CI), thelytoky (T) or feminization (F). In some Wolbachia-infected hosts, no effect (N) has been found. Successful transfer of Wolbachia by microinjection from one host to an uninfected one has been established with CI, F, N-Wolbachia but not with T-Wolbachia. In this paper a transfer experiment of T-Wolbachia from the parasitoid Muscidifurax uniraptor to Drosophila simulans is described. The infection could be detected in the new host for several generations by polymerase chain reaction (PCR). However, no specific effects on the host were detected, and the bacteria were not stably maintained.
 
An official journal of the Genetics Society, Heredity publishes high-quality articles describing original research and theoretical insights in all areas of genetics. Research papers are complimented by News & Commentary articles and reviews, keeping researchers and students abreast of hot topics in the field.
 
Quercus is attractive for evolutionary studies, primarily for developing the concepts of the species, speciation and adaptation; however, remarkably little is known about levels of nucleotide polymorphism in the nuclear functional genes of this genus. This article provides the first characterization of levels of nucleotide polymorphism in 11 gene fragments in natural populations of a Quercus species, Quercus crispula Blume. Results show that the level of nucleotide variation in this oak is generally higher than that in conifers, as high as that in a European oak, but lower than that in an aspen. The level of population recombination is relatively high. Within-population inbreeding is negligible and between-population differentiation is modest. The decay of linkage disequilibrium is significantly faster in the species-wide samples and the three northernmost populations than in the other populations. Statistical tests support the hypothesis of a recent bottleneck for several populations in the southern part of Japan. The amounts and patterns of nucleotide variation, recombination and linkage disequilibrium, and genetic differentiation observed among populations of this species are contradictory to our expectations, given the recent colonization history of the northern Japan populations.
 
The Silene latifolia Y chromosome, showing genes and anonymous markers that have been identified. The deletions causing hermaphroditism (bsx mutations), and those causing complete sterility (ie early-stage anther abortion) of Y-bearing plants (asx mutations), as well as the X-43 subtelomeric sequence, are described in Farbos et al (1999) and Lardon et al (1999), and the Bgl markers are described in Donnison et al (1996). The locations of the S1X4 and S1X1 loci are inferred from the finding of a male-sterile plant (with anthers aborted late in stamen development) which has no copy of S1X4 detectable by PCR, but which appears to carry a Y chromosome, since S1X1 is present (DA Filatov, unpublished data). The estimate of a recombination fraction of 30–40% between S1X1 and S1X4 is based on unpublished data of V Laporte and V Hykelova.
Sex determination systems in plants have evolved many times from hermaphroditic ancestors (including monoecious plants with separate male and female flowers on the same individual), and sex chromosome systems have arisen several times in flowering plant evolution. Consistent with theoretical models for the evolutionary transition from hermaphroditism to monoecy, multiple sex determining genes are involved, including male-sterility and female-sterility factors. The requirement that recombination should be rare between these different loci is probably the chief reason for the genetic degeneration of Y chromosomes. Theories for Y chromosome degeneration are reviewed in the light of recent results from genes on plant sex chromosomes.
 
Reasons to consider the role of sex linkage in speciation: ( a ) Threespine sticklebacks, Gasterosteus aculeatus . Non sex-biased ecological selection on pre-existing genetic variation has led, in this case, to the spread of an autosomal variant reducing armour plating in freshwater limnetic fishes. The female in the photo (below) is fully plated, with the plates visible down the lateral line. The male (above) is the Enos Lake limnetic species, which has reduced armor. Ectodysplasin is undoubtedly the main genetic factor underlying the difference in plates between the two forms (photo credit Ernie Cooper, World Wildlife Fund Canada, ecooper@wwfcanada.org); ( b ) A male of the Hawaiian cricket Laupala paranigra . Differences in male calling song between this species and L. kohalensis are controlled by many genes of small to moderate effect, which are not disproportionately found on the X chromosome (photo credit Kerry Shaw); ( c ) A male of the fruit fly Drosophila melanogaster . Although sexual isolation between populations of this species is mainly controlled by autosomal factors, interspecific studies of D. melanogaster and the closely related D. simulans , D. mauritiana and D. sechellia reveal that the X diverges faster than autosomes, an excess of male sterility factors are recessive and they are also disproportionately located on the X chromosome (photo credit Sandra Hangartner). ( d ) A ‘typical’ hybrid between pied and collared flycatchers ( Ficedula hypoleuca and F. albicollis respectively). Its plumage pattern is intermediate with a clearly broken collar and grey-brown elements in the black back. A male species recognition plumage trait, female preference and hybrid sterility factors are all located on the Z chromosome. Such non-random accumulation of traits involved in reproductive isolation onto a single chromosome should facilitate sympatric speciation and reinforcement by reducing recombination between them. 
Recent studies of sex linkage of isolating mechanisms a
Identification of genes involved in reproductive isolation opens novel ways to investigate links between stages of the speciation process. Are the genes coding for ecological adaptations and sexual isolation the same that eventually lead to hybrid sterility and inviability? We review the role of sex-linked genes at different stages of speciation based on four main differences between sex chromosomes and autosomes; (1) relative speed of evolution, (2) non-random accumulation of genes, (3) exposure of incompatible recessive genes in hybrids and (4) recombination rate. At early stages of population divergence ecological differences appear mainly determined by autosomal genes, but fast-evolving sex-linked genes are likely to play an important role for the evolution of sexual isolation by coding for traits with sex-specific fitness effects (for example, primary and secondary sexual traits). Empirical evidence supports this expectation but mainly in female-heterogametic taxa. By contrast, there is clear evidence for both strong X- and Z-linkage of hybrid sterility and inviability at later stages of speciation. Hence genes coding for sexual isolation traits are more likely to eventually cause hybrid sterility when they are sex-linked. We conclude that the link between sexual isolation and evolution of hybrid sterility is more intuitive in male-heterogametic taxa because recessive sexually antagonistic genes are expected to quickly accumulate on the X-chromosome. However, the broader range of sexual traits that are expected to accumulate on the Z-chromosome may facilitate adaptive speciation in female-heterogametic species by allowing male signals and female preferences to remain in linkage disequilibrium despite periods of gene flow.
 
The relation between the successive generations of inbreeding and the number of loci homozygous. (a) Frequency at which a certain number of alleles (0–6) can be expected to be homozygous. Starting at the top from an outbred individual with nine successive generations of sibmating as we move down the panels. (b) The relationship between number of loci homozygous and the inbreeding coefficient. The successive points starting from bottom left show the increase in the mean inbreeding coefficient over successive generations of sibmating.
The relationship between clutch size and number of homozygous loci. Tree 1, circles and dashed lines; tree 2, triangles and dotted lines; tree 3, squares and solid lines; Model 1, heavy lines; Model 2, thinner lines.
Mixed mating systems are somewhat of an enigma as most models predict that organisms should either inbreed when inbreeding depression is low, or outbreed when inbreeding depression is high. Many wasps mix routine inbreeding with a little random mating. This random mating is most common when all local sibmating opportunities are exhausted and dispersal is the only way males can further increase their fitness. The males of the pollinating fig wasp, Platyscapa awekei, are slightly different in that they disperse before all sibmating opportunities have been exhausted. To see if this is a response to inbreeding depression we quantify inbreeding depression by comparing females' life time reproductive success to their heterozygosity at multiple microsatellite loci. We find that a female wasp's heterozygosity is an accurate predictor of her inbreeding coefficient and that P. awekei females actually seem to suffer from outbreeding depression and possibly from a little inbreeding depression. Male dispersal is thus not a means to effect the optimal mating system, but more likely a mechanism to reduce competition among brothers. The number of mature offspring a female produces depends on her own heterozygosity and not on that of the offspring, and may be determined by egg and gall quality.
 
Eukaryotic genomes contain a large proportion of repetitive DNA sequences, mostly transposable elements (TEs) and tandem repeats. These repetitive sequences often colonize specific chromosomal (Y or W chromosomes, B chromosomes) or subchromosomal (telomeres, centromeres) niches. Sex chromosomes, especially non-recombining regions of the Y chromosome, are subject to different evolutionary forces compared with autosomes. In non-recombining regions of the Y chromosome repetitive DNA sequences are accumulated, representing a dominant and early process forming the Y chromosome, probably before genes start to degenerate. Here we review the occurrence and role of repetitive DNA in Y chromosome evolution in various species with a focus on dioecious plants. We also discuss the potential link between recombination and transposition in shaping genomes.
 
Flow cytometric DNA histograms from a sample of (a) female and (b) male wasps. The number of nuclei with different levels of fluorescence (relative nuclear DNA content) is shown; the mean value of fluorescence and the coefficient of variation are given above the peak. Two major peaks of nuclei can be observed: on the left is the internal standard D. melanogaster, on the right is E. hispida. Females and males show similar nuclear DNA content (2.44- and 2.45-fold the standard, respectively); no peak for haploid nuclei occurs in male wasps. Similar results were obtained from all replicates of the experiment (data not shown).
Cardinium is a bacterial symbiont infecting many species of arthropods, and is associated with manipulation of host reproduction. Cardinium is the causal agent of asexual reproduction, or thelytoky, in the chalcidoid parasitoid wasp Encarsia hispida. Feeding antibiotics to the infected adult females results in uninfected male offspring. Here, we show that these males are diploid. Diploid males are extremely unusual in the large hymenopteran superfamily Chalcidoidea, and, to our knowledge, have never before been associated with symbiont infection in this group. These findings indicate that at least in E. hispida, diploidy restoration is a necessary condition but not sufficient to elicit female development. Cardinium is required to feminize diploid male embryos and thus must interact with elements of the host sex determination system. In addition, our data suggest that Cardinium is necessary for the fertility of E. hispida; antibiotic curing of Cardinium reduces offspring production of adult females.
 
The process of speciation has puzzled scientists for decades, but only recently they have they been able to reveal the genetic basis of reproductive isolation. Much emphasis has been on Haldane's rule, the observation that the heterogametic sex often suffers more from hybridization than the homogametic sex. Most research on Haldane's rule has focused on diploid organisms with chromosomal sex determination. We argue that species lacking chromosomal sex determination, such as haplodiploids, also follow Haldane's rule and thus should be included in the definition of this rule. We provide evidence for Haldane's rule in Nasonia wasps and describe how haplodiploids can be used to test the different theories that have been proposed to explain Haldane's rule. We discuss how the faster-male and faster-X theories can shape speciation differently in haplodiploids compared to diploids.
 
Chromosome-by-chromosome analysis of quantitative variation in the red forewing band
Mimicry has had a significant historical influence as a tractable system for studying adaptation and is known to play a role in speciation. Here, we discuss recent theoretical treatment of adaptive walks to local adaptive peaks and contrast this with the adaptive landscape of mimicry. Evolution of novel Müllerian mimicry patterns almost certainly involves substitution of a major mutation to provide an initial similarity to the model, such that major gene effects are expected to an even greater degree than for other adaptive traits. The likelihood of large adaptive peak shifts in mimicry evolution may therefore promote speciation. In addition, mimicry adaptive peaks are determined by the local abundance of particular patterns and may be more fluid than the case for other traits. It will therefore be of considerable interest to test empirically the distribution of effect sizes fixed during mimicry evolution. Here, we show the feasibility of this by presenting a preliminary quantitative trait locus (QTL) analysis of Heliconius colour patterns. This shows that a number of modifier loci of different effect sizes influence forewing band morphology. We also show multiple pleiotropic effects of major Heliconius patterning loci and discuss the likelihood of multiple substitutions at the same loci in pattern evolution, which would inflate the importance of major loci in QTL analysis of the gene effect sizes. Analyses such as these have the potential to uncover the genetic architecture of both within and between species adaptive differences.
 
This paper examines patterns of heritability and genetic covariance between traits in the genus Drosophila. Traits are divided into the categories, morphology, behaviour, physiology and life history. Early theoretical analyses suggested that life history traits should have heritabilities that are lower than those in other categories. Variable pleiotrophy, environmental variation, mutation and niche variation may, however, maintain high heritabilities. In Drosophila the heritabilities of life history traits are lower than morphological or physiological traits but may exceed 20 per cent. The pattern of variation in the heritability of behavioural traits is similar to that of life history traits. Genetic covariance between morphological traits and between morphological and life history traits are all positive but those between life history traits have variable sign. Negative covariance between traits supports the variable pleiotropy hypothesis but other factors such as environmental heterogeneity, or mutation cannot be excluded.
 
Characteristics of nine nuclear microsatellite loci in Sorbus domestica with primer sequence, number of alleles observed and their size range, annealing temperature (T a ) and corresponding reference
Precise empirical data on current gene flow by pollen, both with respect to distance and abundance, is crucial to understand whether habitat fragments are functionally connected. Based on a large-scale inventory ( approximately 100 km(2)) in which all individuals of a naturally scattered forest tree (Sorbus domestica) were mapped, we inferred current gene flow by pollen using genetic paternity analysis. We detected an extensive network of effective pollen transfer. Although short pollen flow distances were most abundant, 10% of the assigned pollen donors were more than 2 km away from their female mating partners, and 1.8% were even at a distance of 12-16 km. This latter pollen flow shows that current long-distance gene flow over a fragmented landscape clearly occurs. Pollen dispersal was well described by a fat-tailed inverse curve. Using parentage analysis of established trees, maternally inherited chloroplast markers and diameter at breast height measurements as an indicator of individual tree age, we were able to infer regular seed dispersal distances over several hundred metres up to more than 10 km. We conclude that in temperate, insect-pollinated and animal-dispersed tree species such as S. domestica, fragmented subpopulations are functionally connected by gene flow through both pollen and seed.
 
The mutation rate at 54 perfect (uninterrupted) dinucleotide microsatellite loci is estimated by direct genotyping of 96 Arabidopsis thaliana mutation accumulation lines. The estimated rate differs significantly among motif types with the highest rate for AT repeats (2.03 x 10(-3) per allele per generation), intermediate for CT (3.31 x 10(-4)), and lowest for CA (4.96 x 10(-5)). The average mutation rate per generation for this sample of loci is 8.87 x 10(-4) (s.e.=2.57 x 10(-4)). There is a strong effect of initial repeat number, particularly for AT repeats, with mutation rate increasing with the length of the microsatellite locus in the progenitor line. Controlling for motif and initial repeat number, chromosome 4 exhibited an elevated mutation rate relative to other chromosomes. The great majority of mutations were gains or losses of a single repeat. Generally, the data are consistent with the stepwise mutation model of microsatellite evolution. Several lines exhibited multiple step changes from the progenitor sequence, but it is unclear whether these are multi-step mutations or multiple single-step mutations. A survey of dinucleotide repeats across the entire Arabidopsis genome indicates that AT repeats are most abundant, followed by CT, and CA.
 
The processes that have shaped the extraordinary species diversity in neotropical rainforests are poorly understood, and knowledge about the patterns of genetic diversity across species' ranges is scarce, in contrast to other regions of the globe. We have conducted a range-wide study of genetic diversity in a plant endemic to the Brazilian Atlantic Rainforest, Vriesea gigantea (Bromeliaceae), based on a combined data set of nuclear microsatellites and chloroplast (cp) DNA markers typed in 429 plants from 13 populations. The results indicate a strong negative correlation between genetic diversity and population latitude, consistent with historical forest expansion from the northern half of the present distribution range. A deep phylogeographic split exists between the Brazilian states of São Paulo and Rio de Janeiro at ca. 23 degrees S latitude, probably reflecting past population isolation within more than one glacial refuge during the climatic changes of the Pleistocene. A comparison of genetic structures at cpDNA and nuclear markers revealed a pollen/seed flow ratio of more than 3:1, thus indicating an important role of the pollinating animals (that is, bats) in shaping the population genetic structure of this species. Diversity was reduced for cpDNA markers in the island populations off the coast, and reduced diversity and increased differentiation were observed for both nuclear and cpDNA at the edges of the species' range. The link between patterns of genetic and species diversity supports the hypothesis that both were shaped by the same biogeographic processes, triggered by the climatic oscillations of the Pleistocene.
 
False positive rates obtained from the analysis of 100 independent sets of 1000 unlinked loci
Importance of the choice of the number of groups and demes used in simulations when computing P-values
Human genome diversity project (HGDP) short term repeat (STR) data. Joint distribution of FST (computed as ST) against heterozygosity. Black open circles correspond to observed STR loci, whereas grey dots are simulated loci under either (a) finite island model or (b) hierarchical island model. Significant loci (P<0.01) are shown as large black dots in (b).
Sticklebacks short term repeat (STR) data. Joint distribution of FST (computed either as FST or ST) against heterozygosity. Black open circles correspond to observed STR loci, whereas grey dots are simulated loci under either (a and b) the finite island model, or (c) the hierarchical island model. Significant loci at 1% level of significance are shown as large black dots in (c).
Human STR loci found significant at the 1% level of significance with closest known genes
Patterns of genetic diversity between populations are often used to detect loci under selection in genome scans. Indeed, loci involved in local adaptations should show high F(ST) values, whereas loci under balancing selection should rather show low F(ST) values. Most tests of selection based on F(ST) use a null distribution generated under a simple island model of population differentiation. Although this model has been shown to be robust, many species have a more complex genetic structure, with some populations sharing a recent ancestry or due to the presence of barriers to gene flow between different parts of a species range. In this paper, we propose the use of a hierarchical island model, in which demes exchange more migrants within groups than between groups, to generate the joint distribution of genetic diversity within and between populations. We show that tests not accounting for a hierarchical structure, when it exists, do generate a large excess of false positive loci, whereas the hierarchical island model is robust to uncertainties about the exact number of groups and demes per group in the system. Our approach also explicitly takes into account the mutational process, and does not just rely on allele frequencies, which is important for short tandem repeat (STR) data. An application to human and stickleback STR data sets reveals a much lower number of significant loci than previously obtained under a non-hierarchical model. The elimination of false positive loci from genome scans should allow us to better determine on which specific class of genes selection is operating.
 
An official journal of the Genetics Society, Heredity publishes high-quality articles describing original research and theoretical insights in all areas of genetics. Research papers are complimented by News & Commentary articles and reviews, keeping researchers and students abreast of hot topics in the field.
 
Knowledge about the extent and patterns of linkage disequilibrium (LD) can provide important insights into demographic processes and strategies to identify the genetic basis of complex phenotypes in wild populations. However, data on the extent and patterns of LD from non-model vertebrate species from the wild are still scarce. We conducted so far the most extensive and detailed examination of LD in a pedigreed wild bird population using genotypes from 97 autosomal and 6 gonosomal microsatellites and a recently established linkage map of Siberian jays (Perisoreus infaustus). Analysis of syntenic marker pairs showed high levels of LD that extended over tens of centimorgans or several megabases and generally decayed as an increasing function of intermarker distance. In addition, significant LD was also very common between nonsyntenic markers. Patterns of LD varied across different linkage groups possibly because of the differences in chromosomal structure (macro-, micro-, and Z-chromosome). In particular, the level of LD was significantly lower on the Z-chromosome than on the autosomes at comparable genetic distances. In general, the high levels and extent of LD in this population are likely owing to its relatively small size, significant intrapopulation genetic structure, and occurrence of inbreeding. Whatever the cause, the long-range LD between syntenic loci suggests that LD mapping of phenotypic traits in this population using low-density markers maps is feasible. However, the frequent occurrence of LD between nonsyntenic markers suggests that the combined use of linkage and LD methods is needed to reduce the likelihood of false-positive associations between marker loci and traits of ecological and evolutionary interest.
 
An official journal of the Genetics Society, Heredity publishes high-quality articles describing original research and theoretical insights in all areas of genetics. Research papers are complimented by News & Commentary articles and reviews, keeping researchers and students abreast of hot topics in the field.
 
Cave fish provide a model system for exploring the genetic basis of regressive evolution. A proposal that regressive evolution (for example, eye loss) may result from pleiotropy, by selection on constructive traits (for example, improved taste) has received considerable recent interest as it contradicts the theory that regressive evolution results from neutral evolution. In this study, these theories are reviewed by placing the classical and molecular genetic studies of cave fish in a common framework. Sequence data and the wide range of intermediate sized eyes in hybrids between surface and cave fish suggest that currently there is no strong evidence supporting the notion that structural eye genes have been afflicted by destructive mutations. The hedgehog genes, which are suggested to reduce the primordial eye cup size in cavefish by expanded expression, are also not mutated. The as yet unidentified 'eye genes' revealed by crossing experiments seem primarily responsible for eye regression and determine eye development through hedgehog. Hybrids between different eye-reduced cave populations developing large 'back to surface eyes' support this. In such eyes, hh expression is restored by complementary restitution because of the recombination of 'eye genes', which were subjected to different destructive mutations in separately evolving cave fish populations. All regressive and constructive cave fish traits can be considered to result from genetic modules, each showing a comparable pattern of expression. The constructive and regressive modules are shown to inherit independently from each other, which does not support the view that eye regression is a spin off effect of the improvement of beneficial traits through pleiotropy.
 
Sampled sites, distribution of Lissotriton helveticus and L. vulgaris and location of the zone of sympatry (from IUCN, 2008). The outlet shows the study site where we investigated patterns of introgression at a local scale (BD CARTHAGE IGN, Paris, France 2005). White circles indicate sampled sites where only L. helveticus were found and black triangles indicate sampled sites with only L. vulgaris . Grey rectangles indicate syntopic sites. Stars indicate the locations of hybrids as reported in the literature (a, Griffiths et al ., 1987; b,c, Arntzen et al ., 1998; d,e, Beebee et al ., 1999; f, Schlu  ̈ pmann et al ., 1999). 
Scatterplot of the two first axes of a factorial correspondence analysis based on multilocus analysis of 927 Lissotriton helveticus (open circles) and 343 L. vulgaris (black filled triangles) sampled over the breeding ranges of the two species. The dotted and plain ellipsoids represent 99% confidence intervals for L. helveticus and L. vulgaris, respectively. Grey open squares represent L. helveticus -like hybrids and grey filled squares L. vulgaris -like hybrids. The two asterisks indicate the L. helveticus like hybrid with a L. vulgaris mitochondrial DNA and the L. vulgaris like hybrid with a L. helveticus mitochondrial DNA. 
Distribution of ancestry estimates from STRUCTURE analysis (proportion of individual genomes derived from Lissotriton vulgaris) in L. helveticus and in L. vulgaris in different ecological contexts.
Pairwise associations within-genomes, k 0,2 (corresponding 
Scatterplot of the two first axes of a principal component analysis based on phenotypic traits measured in ( a ) 240 males and ( b ) 320 females of Lissotriton helveticus (white circles) and L. vulgaris (black triangles) sampled in the Loire valley. Note that dotted and plain ellipsoids represent 99% confidence intervals for L. helveticus and L. vulgaris , respectively. 
Species that overlap over a large part of their range and habitat requirements are challenging for the study of speciation and hybridization. In this respect, the study of broadscale introgressive hybridization has raised recent interest. Here we studied hybridization between two closely related amphibians Lissotriton helveticus and Lissotriton vulgaris that reproduce over a wide sympatric zone. We used mitochondrial and microsatellite markers on 1272 individuals in 37 sites over Europe to detect hybrids at the individual-level and to analyse Hardy-Weinberg and linkage disequilibria at the population-level. Morphological traits showed a strong bimodal distribution. Consistently, hybrid frequency was low (1.7%). We found asymmetric introgression with five times more hybrids in L. vulgaris than in L. helveticus, a pattern probably explained by an unequal effective population size in a study part wherein L. helveticus numerically predominates. Strikingly, significant levels of introgression were detected in 73% of sites shared by both species. Our study showed that introgression is widespread but remains confined to the sites where the two species reproduce at the same time. This pattern may explain why these species remain genetically distinct over a broad sympatric zone.
 
Relationship between genetic (FST/(1-FST)) and geographic distance (km) for all 35 population-year combinations (all dots, black line: —; Mantel r=0.29, P<0.0001) and excluding two outlier populations (SAN07 and LAG01) identified by the DPR analysis (excluding filled dots, dashed line: - - - -; Mantel r=0.26, P<0.0001).
Intercepts and slopes of the decomposed pairwise regressions for each population
DPR analyses. (a) Average residuals and 95% CIs from the regression in  (b–d) DPR of genetic (FST/(1-FST) versus geographic distance (km) for each of the 35 population-year combinations. Each of the two ‘true’ outlier populations was regressed with the 33 non-outlier populations (b), whereas each of the 33 non-outlier populations was regressed with the other 32 populations showing statistically significant (c) and non-significant (d) regressions.
Correlation biplot of PC1 (8.62% of the total variance) versus PC2 (6.69% of the total variance) showing the loadings of each population sampled in a given year on both PCs and color coded according to basin (PC, principal component).
Relationship between genetic (FST/(1-FST) and geographic distance (km) in each sampling year. The linear regression model and P-value of the Mantel test are also shown in each panel. For 2001 and 2007, pairwise comparisons involving the two previously identified ‘overall’ outlier populations (LAG01 in 2001 and SAN07 in 2007) are indicated by asterisks.
Gene flow has the potential to both constrain and facilitate adaptation to local environmental conditions. The early stages of population divergence can be unstable because of fluctuating levels of gene flow. Investigating temporal variation in gene flow during the initial stages of population divergence can therefore provide insights to the role of gene flow in adaptive evolution. Since the recent colonization of Lake Lesjaskogsvatnet in Norway by European grayling (Thymallus thymallus), local populations have been established in over 20 tributaries. Multiple founder events appear to have resulted in reduced neutral variation. Nevertheless, there is evidence for local adaptation in early life-history traits to different temperature regimes. In this study, microsatellite data from almost a decade of sampling were assessed to infer population structuring and its temporal stability. Several alternative analyses indicated that spatial variation explained 2-3 times more of the divergence in the system than temporal variation. Over all samples and years, there was a significant correlation between genetic and geographic distance. However, decomposed pairwise regression analysis revealed differing patterns of genetic structure among local populations and indicated that migration outweighs genetic drift in the majority of populations. In addition, isolation by distance was observable in only three of the six years, and signals of population bottlenecks were observed in the majority of samples. Combined, the results suggest that habitat-specific adaptation in this system has preceded the development of consistent population substructuring in the face of high levels of gene flow from divergent environments.
 
An illustration of the nested nature of plasmids and their bacterial hosts. Different sub-populations may harbour different densities of plasmids. If a gene involved in cooperation is carried on a plasmid, this will affect the relatedness between individuals in a patch (because of relatedness being measured at a focal locus, in this case on a plasmid). Thus, sub-populations A and D have high plasmid relatedness, whereas sub-populations C and B have low plasmid relatedness. Relatedness is influenced by local cell density and migration between sub-populations and, in the case of loci on plasmids, relatedness changed because of the degree of horizontal gene transfer (see Box 2 and for details).
The effect of horizontal gene transfer rate β on genetic relatedness between individuals within a patch, measured at loci with transfer rate β. The equation follows from that described in Box 2, where m=0.1, N=50 and s=0. In the absence of any HGT (that is, β=0) for the parameters chosen, r=0.079 (shown by the dotted line).
Although similar to any other organism, prokaryotes can transfer genes vertically from mother cell to daughter cell, they can also exchange certain genes horizontally. Genes can move within and between genomes at fast rates because of mobile genetic elements (MGEs). Although mobile elements are fundamentally self-interested entities, and thus replicate for their own gain, they frequently carry genes beneficial for their hosts and/or the neighbours of their hosts. Many genes that are carried by mobile elements code for traits that are expressed outside of the cell. Such traits are involved in bacterial sociality, such as the production of public goods, which benefit a cell's neighbours, or the production of bacteriocins, which harm a cell's neighbours. In this study we review the patterns that are emerging in the types of genes carried by mobile elements, and discuss the evolutionary and ecological conditions under which mobile elements evolve to carry their peculiar mix of parasitic, beneficial and cooperative genes.
 
The high mortality and widespread impact of malaria have resulted in this disease being the strongest evolutionary selective force in recent human history, and genes that confer resistance to malaria provide some of the best-known case studies of strong positive selection in modern humans. I begin by reviewing JBS Haldane's initial contribution to the potential of malaria genetic resistance in humans. Further, I discuss the population genetics aspects of many of the variants, including globin, G6PD deficiency, Duffy, ovalocytosis, ABO and human leukocyte antigen variants. Many of the variants conferring resistance to malaria are 'loss-of-function' mutants and appear to be recent polymorphisms from the last 5000-10 000 years or less. I discuss estimation of selection coefficients from case-control data and make predictions about the change for S, C and G6PD-deficiency variants. In addition, I consider the predicted joint changes when the two β-globin alleles S and C are both variable in the same population and when there is a variation for α-thalassemia and S, two unlinked, but epistatic variants. As more becomes known about genes conferring genetic resistance to malaria in humans, population genetics approaches can contribute both to investigating past selection and predicting the consequences in future generations for these variants.
 
A mutant Thr-239-Ileu at the α2-tubulin gene was found to confer resistance to dinitroanilines, a family of mitosis-disrupting herbicides. However, mutations affecting microtubule polymerization and cell division are expected to impact growth and reproduction, that is, the fitness of a resistant weed or the yield of a tolerant crop, although it has not been demonstrated yet. This study was designed to test this hypothesis for the growth and reproduction of near-isogenic resistant and susceptible materials that were created in F(2) and F(3) generations after a Setaria viridis x S. italica cross. Differential growth was noticeable at the very onset of seedling growth. The homozygous resistant plants, grown both in a greenhouse cabinet and in the field, were smaller and had lower 1000-grain weight and therefore a lower yield. This fitness penalty is certainly due to modified cell division kinetics. Although the presence of the mutant allele accounted for 20% yield losses, there were also measurable benefits of dinitroaniline resistance, and these benefits are discussed.
 
Female morph frequencies (%) in populations of I. elegans and I. graellsii in Europe. The figure shows the range of I. elegans (map a ; Dijkstra and Lewington, 2006), and the frequencies of the three female colour morphs, namely the androchrome (gray), infuscans (clear gray) and infuscans–obsoleta morph (black) at each population. The frequencies of the eastern European populations of I. elegans in the Ukraine and in Poland are shown in map b and of Iberian populations of I. elegans and I. graellsii in map c . The line across Iberia indicates the rough distribution of I. elegans and I. graellsii , with I. elegans being most frequent above the line and I. graellsii below the line. For details of each population, see Table 1. A full color version of this figure is available at the Heredity journal online. 
Frequencies of female colour morphs in natural populations of Ischnura elegans and I. graellsii
Genetic variation at microsatellite loci for each population of I. elegans and I. graellsii
Degree of differentiation (F ST ) between I. elegans populations for six neutral loci (above diagonal) and for the colour locus (below diagonal)
Disentangling the relative importance and potential interactions of selection and genetic drift in driving phenotypic divergence of species is a classical research topic in population genetics and evolutionary biology. Here, we evaluate the role of stochastic and selective forces on population divergence of a colour polymorphism in seven damselfly species of the genus Ischnura, with a particular focus on I. elegans and I. graellsii. Colour-morph frequencies in Spanish I. elegans populations varied greatly, even at a local scale, whereas more similar frequencies were found among populations in eastern Europe. In contrast, I. graellsii and the other five Ischnura species showed little variation in colour-morph frequencies between populations. F(ST)-outlier analyses revealed that the colour locus deviated strongly from neutral expectations in Spanish populations of I. elegans, contrasting the pattern found in eastern European populations, and in I. graellsii, where no such discrepancy between morph divergence and neutral divergence could be detected. This suggests that divergent selection has been operating on the colour locus in Spanish populations of I. elegans, whereas processes such as genetic drift, possibly in combination with other forms of selection (such as negative frequency-dependent selection), appear to have been present in other regions, such as eastern Europe. Overall, the results indicate that both selective and stochastic processes operate on these colour polymorphisms, and suggest that the relative importance of factors varies between geographical regions.
 
A coalescent argument is used to derive the effective size in simple models with recurrent local extinctions. Several alternative methods of derivation of this result are given and compared to earlier analyses of this problem. The different methods described in this paper all give the same result, which differs from earlier ones. For two published sets of estimates of demographic parameters, metapopulation structure appears to result in a moderate reduction of effective size relative to total adult population size.
 
Typical life cycle of homobasidiomycetes (mushrooms, a), of ascomycetes (b) and of Microbotrum (c), with location of presyngamy vs postsyngamy reproductive barriers.
Evolution of presyngamic and postsyngamic reproductive compatibility with genetic distance in basidiomycetes
Evolution of presyngamic and postsyngamic reproductive compatibility in ascomycetes
Reproductive isolation is an essential ingredient of speciation, and much has been learned in recent years about the evolution of reproductive isolation and the genetics of reproductive barriers in animals and plants. Fungi have been neglected on these aspects, despite being tractable model eukaryotes. Here, we used a model fitting approach to look at the importance of different barriers to gene flow to explain the decrease of reproductive compatibility with genetic distance in fungi. We found support for the occurrence of reinforcement in the presyngamy compatibility among basidiomycetes. In contrast, no evidence for reinforcement was detected in ascomycetes, concurring with the idea that host/habitat adaptation in this group can pleiotropically cause reproductive isolation. We found no evidence of a snowballing accumulation of postsyngamic reproductive incompatibilities in either ascomycetes or the complex of anther smut fungi. Together with previous studies, our results suggest that ecologically based barriers to gene flow and karyotypic differences may have an important role in hybrid inviability and sterility in fungi. Interestingly, hybrid sterility appeared to evolve faster than hybrid inviability in fungi.
 
Genealogies of a sample under a bottleneck model. (a) Two lineages escape a moderate bottleneck and coalesce further back in the past. (b) All the remaining lineages coalesce during a severe bottleneck. A full color version of this figure is available at the Heredity journal online.
Scaled SFS under a bottleneck model. The scaled SFS is the ratio of the SFS and the expected SFS for a model of constant population size. A sample of 100 chromosome of 50 000 bp long was simulated for a population of 10 000 present-day diploid individuals. (a) Recombination rate of 1.5 × 10−8 per site and per generation as well as a mutation rate of 1.2 × 10−8 per site and per generation was used (Scally and Durbin, 2012). Each curve corresponds to the ratio between the observed SFS under a bottleneck model and the expected SFS under a standard neutral model with constant population size. The color of the curves indicates the onset of the bottleneck, in units of four times the present-day population size. Each bottleneck lasted 1000 generations and the strength of the bottleneck measures the reduction in population size during the bottleneck: 80% reduction (left panel) or 95% reduction (right panel). A total of 20 000 simulations per model were performed with the software ms (Hudson, 2002).
Mean of Tajima’s D as a function of the time since the onset of the bottleneck. Average values of Tajima’s D over 20 000 replicate simulations of bottleneck models, for an 80% reduction in population size (left panel) and a 95% reduction in population size (right panel). Different chromosomes are considered: autosome (A, solid line), X chromosome (X, dashed line) and mitochondrion (mt, dash-dotted line). The bottleneck lasted 1000 generations for all models, and the onset of the bottleneck varies, as indicated on the x axis (given in units of four times the present-day population size). The simulated samples are composed of 100 segments of 50 000 bp (the recombination rate is 1.5 × 10−8 per site and per generation), with a mutation rate of 1.2 × 10−8 per site and per generation, and they are randomly sampled from a present-day population of 10 000 diploid individuals. mtDNA segments are also 50 000 bp long, but they are non-recombining and the mutation rate is 2.5 × 10−6. Time is measured in units of 4 N generations.
LD measures and analytic approximations. A sample of 100 chromosomes (of length 500 kb) was simulated for a constant population size model of 10 000 diploid individuals assuming a recombination rate of 1.5 × 10−8 per site and per generation, and a mutation rate of 1.2 × 10−8 per site and per generation. Only pairs of segregating sites with genetic distance <0.25 cM were considered. At least 10 million simulated pairs of segregating sites were grouped into 500 equally spaced bins according to their genetic distance between 0 and 0.25 cM. The product of allele frequencies, D2 values and r2 values were averaged across all pairs of segregating sites in each bin. The Ohta and Kimura (1971) expectation was computed following Equation (7). The McEvoy et al. (2011) approximation corresponds to 1/(2+ρ).
Effect of different models of population structure and different sampling strategies on Tajima’s D. Average values of Tajima’s D over 100 000 replicate simulations of divergence models with global sampling (left panel), island models with local sampling (central panel) and island models with global sampling (right panel), as function of the number of demes. The simulated samples are composed of 100 chromosomes (of length 50 000 bp), with a mutation rate of 1.2 × 10−8 per site and per generation and a recombination rate of 1.5 × 10−8 per site and per generation. In all models, the demes are of size 10 000 present-day diploid individuals, and n represents the number of demes. In the local sampling scheme, all chromosomes are sampled from one deme only. In the global sampling schemes, however, the chromosomes are sampled from all the demes, with an almost equal number of chromosomes within each deme (plus or minus one chromosome). No migration is allowed in the divergence model, whereas a migration rate of 1 × 10−3 migrants/generation is assumed in the island model.
Reconstructing historical variation of population size from sequence and single-nucleotide polymorphism (SNP) data is valuable for understanding the evolutionary history of species. Changes in the population size of humans have been thoroughly investigated, and we review different methodologies of demographic reconstruction, specifically focusing on human bottlenecks. In addition to the classical approaches based on the site-frequency spectrum (SFS) or based on linkage disequilibrium, we also review more recent approaches that utilize atypical shared genomic fragments, such as identical by descent or homozygous segments between or within individuals. Compared with methods based on the SFS, these methods are well suited for detecting recent bottlenecks. In general, all these various methods suffer from bias and dependencies on confounding factors such as population structure or poor specification of the mutational and recombination processes, which can affect the demographic reconstruction. With the exception of SFS-based methods, the effects of confounding factors on the inference methods remain poorly investigated. We conclude that an important step when investigating population size changes rests on validating the demographic model by investigating to what extent the fitted demographic model can reproduce the main features of the polymorphism data.Heredity advance online publication, 20 February 2013; doi:10.1038/hdy.2012.120.
 
Weeds are among the greatest pests of agriculture, causing billions of dollars in crop losses each year. As crop field management practices have changed over the past 12 000 years, weeds have adapted in turn to evade human removal. This evolutionary change can be startlingly rapid, making weeds an appealing system to study evolutionary processes that occur over short periods of time. An understanding of how weeds originate and adapt is needed for successful management; however, relatively little emphasis has been placed on genetically characterizing these systems. Here, we review the current literature on agricultural weed origins and their mechanisms of adaptation. Where possible, we have included examples that have been genetically well characterized. Evidence for three possible, non-mutually exclusive weed origins (from wild species, crop-wild hybrids or directly from crops) is discussed with respect to what is known about the microevolutionary signatures that result from these processes. We also discuss what is known about the genetic basis of adaptive traits in weeds and the range of genetic mechanisms that are responsible. With a better understanding of genetic mechanisms underlying adaptation in weedy species, we can address the more general process of adaptive evolution and what can be expected as we continue to apply selective pressures in agroecosystems around the world.Heredity advance online publication, 28 November 2012; doi:10.1038/hdy.2012.104.
 
Distribution of mutational effects according to parameters used for the Mukai and the CGD scenarios. We show with squares the distribution of mutational effects for the Mukai scenario with β=1 and =0.05, and with circles, the distribution for the CGD scenario with β=2.3 and =0.264.
Conservation programmes aim at minimising the loss of genetic diversity, which allows populations to adapt to potential environmental changes. This can be achieved by calculating how many offspring every individual should contribute to the next generation to minimise global coancestry. However, an undesired consequence of this strategy is that it maintains deleterious mutations, compromising the viability of the population. In order to avoid this, optimal contributions could be combined with inbred matings, to expose and eliminate recessive deleterious mutations by natural selection in a process known as purging. Although some populations that have undergone purging experienced reduced inbreeding depression, this effect is not consistent across species. Whether purging by inbred matings is efficient in conservation programmes depends on the balance between the loss of diversity, the initial decrease in fitness and the reduction in mutational load. Here we perform computer simulations to determine whether managing a population by combining optimal contributions with inbred matings improves its long-term viability while keeping reasonable levels of diversity. We compare the management based on genealogical information with management based on molecular data to calculate coancestries. In the scenarios analysed, inbred matings never led to higher fitness and usually maintained lower diversity than random or minimum coancestry matings. Replacing genealogical with molecular coancestry can maintain a larger genetic diversity but can also lead to a lower fitness. Our results are strongly dependent on the mutational model assumed for the trait under selection, the population size during management and the reproductive rate.Heredity advance online publication, 16 January 2013; doi:10.1038/hdy.2012.119.
 
Location of study populations of Lychnis flos-cuculi in Switzerland. Grey lines mark ditches and other water bodies with flowing water; grey areas indicate forested areas.
Coordinates (according to Swiss national grid), sample and population size, allelic richness (A R ), expected heterozygosity (H E ), observed heterozygosity (H O ) and inbreeding coefficient (F IS ) of the study populations of Lychnis flos-cuculi
of regression on distance matrices analyses on the effects of landscape variables on the genetic differentiation F ST among the study populations of Lychnis flos-cuculi in Switzerland using different corridor widths
Understanding the relationship between structural and functional connectivity is essential for successful restoration and conservation management, particularly in intensely managed agricultural landscapes. We evaluated the relationship between structural and functional connectivity of the wetland plant Lychnis flos-cuculi in a fragmented agricultural landscape using landscape genetic and network approaches. First, we studied the effect of structural connectivity, such as geographic distance and various landscape elements (forest, agricultural land, settlements and ditch verges), on gene flow among populations as a measurement of functional connectivity. Second, we examined the effect of structural graph-theoretic connectivity measures on gene flow among populations and on genetic diversity within populations of L. flos-cuculi. Among landscape elements, forests hindered gene flow in L. flos-cuculi, whereas gene flow was independent of geographic distance. Among the structural graph-theoretic connectivity variables, only intrapopulation connectivity, which was based on population size, had a significant positive effect on gene flow, that is, more gene flow took place among larger populations. Unexpectedly, interpopulation connectivity of populations, which takes into account the spatial location and distance among populations, did not influence gene flow in L. flos-cuculi. However, higher observed heterozygosity and lower inbreeding was observed in populations characterised by higher structural interpopulation connectivity. This finding shows that a spatially coherent network of populations is significant for maintaining the genetic diversity of populations. Nevertheless, lack of significant relationships between gene flow and most of the structural connectivity measures suggests that structural connectivity does not necessarily correspond to functional connectivity.Heredity advance online publication, 20 November 2013; doi:10.1038/hdy.2013.120.
 
Spatial autocorrelation analyses of 12 allozyme loci were used to compare genetic structure within populations of two varieties of Pinus clausa. P. clausa var. immuginata populations tend to be uneven-aged, with continuous recruitment in small gaps created by wind damage, whereas P. clausa var. clausa populations are more even-aged, with recruitment postdating periodic canopy fires. Three var. immuginata populations and three matched pairs of var. clausa populations, including both a mature and a nearby recently burned population, were examined. Aggregation of multilocus genotypes at small distances was evident in all young var. clausa populations. Little inbreeding was apparent among juveniles or adults in these populations; their genetic structure is likely to have resulted from limited seed dispersal. Genotypes were not significantly spatially structured in nearby matched mature populations. Genetic structure was less evident in var. immuginata populations. Aggregated genotypes were only apparent in the population where patches included juveniles of similar ages; dense juvenile clumps in the other two var. immuginata populations comprised a variety of ages. Interannual variability in allele frequencies of surviving seedlings may account for the absence of genetic structure in these populations.
 
For many organisms the ability to cold acclimate with the onset of seasonal cold has major implications for their fitness. In insects, where this ability is widespread, the physiological changes associated with increased cold tolerance have been well studied. Despite this, little work has been done to trace changes in gene expression during cold acclimation that lead to an increase in cold tolerance. We used an RNA-Seq approach to investigate this in two species of the Drosophila virilis group. We found that the majority of genes that are differentially expressed during cold acclimation differ between the two species. Despite this, the biological processes associated with the differentially expressed genes were broadly similar in the two species. These included: metabolism, cell membrane composition, and circadian rhythms, which are largely consistent with previous work on cold acclimation/cold tolerance. In addition, we also found evidence of the involvement of the rhodopsin pathway in cold acclimation, a pathway that has been recently linked to thermotaxis. Interestingly, we found no evidence of differential expression of stress genes implying that long-term cold acclimation and short-term stress response may have a different physiological basis.Heredity advance online publication, 11 February 2015; doi:10.1038/hdy.2015.6.
 
We review some recently published results on sex chromosomes in a diversity of species. We focus on several fish and some plants whose sex chromosomes appear to be 'young', as only parts of the chromosome are nonrecombining, while the rest is pseudoautosomal. However, the age of these systems is not yet very clear. Even without knowing what proportions of their genes are genetically degenerate, these cases are of great interest, as they may offer opportunities to study in detail how sex chromosomes evolve. In particular, we review evidence that recombination suppression occurs progressively in evolutionarily independent cases, suggesting that selection drives loss of recombination over increasingly large regions. We discuss how selection during the period when a chromosome is adapting to its role as a Y chromosome might drive such a process.
 
Comparison of the new method of QTL mapping with the logistic regression analysis 
Mean and standard deviation (STD) of the estimated threshold values and QTL effect under various levels of QTL size 
Mean and standard deviation (STD) of the estimated threshold values and QTL effect for various shapes of phenotypic distribution 
Mean and standard deviation (STD) of the estimated threshold values and QTL effect for various sample sizes (n) 
Many disease resistance traits in plants have a polygenic background and the disease phenotypes are modified by environmental factors. As a consequence, the phenotypic values usually show a quantitative variation. The phenotypes of such disease traits, however, are often measured in discrete but ordered categories. These traits are called ordinal traits. In terms of disease resistance, they are called quantitative resistance traits, as opposed to qualitative resistance traits, and are controlled by the quantitative resistance loci (QRL). Classical quantitative trait locus mapping methods are not optimal for ordinal trait analysis because the assumption of normal distribution is violated. Methods for mapping binary trait loci are not suitable either because there are more than two categories in ordinal traits. We developed a maximum likelihood method to map these QRL. The method is implemented via a multicycle expectation-conditional-maximization (ECM) algorithm under the threshold model, where we can estimate both the QRL effects and the thresholds that link the disease liability and the categorical phenotype. The method is verified in simulated data under various combinations of the parameters. An SAS program is available to implement the multicycle ECM algorithm. The program can be downloaded from our website at www.statgen.ucr.edu.
 
The greater white-toothed shrew (C. russula) range in the West Palaearctic and the eight sampled localities. (1) Tunisia (Kneiss Island); (2) Tunisia (Aïn Draham); (3) Pantelleria Island (Montagna grande); (4) Sardinia (S. Pietru); (5) Spain (Heyos del Espino); (6) Spain (Eugi); (7) Spain (Montseny); and (8) Belgium (Meròn).
R2 repeated motif variants sequenced in the C. russula specimens
Bootstrap consensus tree obtained from the UPGMA cluster of the Kimura 2-parameter model for the right domain of the C. russula control region. The different tandem repeated motifs R2 (see Table 1) are shown as they should have appeared in the different lineages (black boxes) and, inside the northeast-African group, in the different demes (grey boxes). Along the tree, the new R2 variants are added to the previous and keep themselves within the clade.
A short segment (135 bp) of the control region and a partial sequence (394 bp) of the 12S-rRNA gene in the mitochondrial DNA of Crocidura russula were analyzed in order to test a previous hypothesis regarding the presence of a gene flow disruption in northern Africa. This breakpoint would have separated northeast-African C. russula populations from the European (plus the northwest-African) populations. The analysis was carried out on specimens from Tunisia (C. r. cf agilis), Sardinia (C. r. ichnusae), and Pantelleria (C. r. cossyrensis), and on C. r. russula from Spain and Belgium. Two C. russula lineages were identified; they both shared R2 tandem repeated motifs of the same length (12 bp), but not the same primary structure. These simple sequence repeats were present in 12-23 copies in the right domain of the control region. Within the northeast-African populations, a polymorphism of repeat variants, not yet found in Europe, was recorded. A neighbor-join tree, which was built by sequences of the conserved 12S-rRNA gene, separated the two sister groups; it permitted us to date a divergence time of 0.5 Myr. Our data discriminated two different mitochondrial lineages in accordance with the previous morphological and karyological data. Ecoclimatic barriers formed during the Middle Pleistocene broke the range of ancestral species in the Eastern Algeria (Kabile Mountains), leading to two genetically separate and modern lineages. The northeast-African lineage can today be located in Tunisia, Pantelleria, and Sardinia. The northwest-African lineage (Morocco and West Algeria), reaching Spain by anthropogenic introduction, spread over north Europe in modern times. The Palaearctic C. russula species is monophyletic, but a taxonomical revision (ie, to provide a full species rank for the northeast taxa and to put in synonymy some insular taxa) is required.
 
Hybrid zones are found wherever two populations distinguishable on the basis of heritable characters overlap spatially and temporally and hybridization occurs. If hybrids have lower fitness than the parental types a tension zone may emerge, in which there is a barrier to gene flow between the two parental populations. Here we discuss a hybrid zone between two honeybee subspecies, Apis mellifera capensis and A. m. scutellata and argue that this zone is an example of a tension zone. This tension zone is particularly interesting because A. m. capensis can be a lethal social parasite of A. m. scutellata. However, despite its parasitic potential, A. m. capensis appears to be unable to increase its natural range unassisted. We propose three interlinked mechanisms that could maintain the South African honeybee hybrid zone: (1) low fitness of intercrossed and genetically mixed colonies arising from inadequate regulation of worker reproduction; (2) higher reproductive success of A. m. scutellata via both high dispersal rates into the hybrid zone and increased competitiveness of males, countered by (3) the parasitic nature of A. m. capensis.
 
Meiotic cells of zebrafish have been prepared to show synaptonemal complexes (SCs) by light and electron microscopy. Completely paired SCs from both spermatocytes and oocytes were measured to produce an SC karyotype. The SC karyotype resembles the somatic karyotype of zebrafish and has no recognisable sex bivalent. Measurements of total SC length indicate that SCs grow longer and develop centromeres during pachytene. Oocytes consistently have longer SCs than spermatocytes, presumably correlated with the reported higher recombination frequency in females than in males.
 
Different partial-diallel designs considered in our simulations. Shaded cells indicate crosses that are included in the analysis. (a) Half diallel; (b) SRR; (c) DRR; (d) FCT.
Expected and observed variance components in the F 2 generation
Power of different partial-diallel designs to detect an additive QTL that contributes 7.5% of the phenotypic variance, expressed as the proportion of simulations (out of 1000) in which the completely linked marker showed a significant association with the phenotype at the =0.05 level. Each diallel design was analyzed with 10, 25, 50, 100, and 200 numbers of F2 individuals per family, yielding different total experimental sizes for the designs that include different numbers of families. Results are shown for one of the two specified QTL, under purely nonadditive polygene action. (a) Comparison of designs at equal numbers of individuals per family; (b) Comparison of designs at equal total experimental sizes.
Analysis of quantitative trait loci (QTL) affecting complex traits is often pursued in single-cross experiments. For most purposes, including breeding, some assessment is desired of the generalizability of the QTL findings and of the overall genetic architecture of the trait. Single-cross experiments provide a poor basis for these purposes, as comparison across experiments is hampered by segregation of different allelic combinations among different parents and by context-dependent effects of QTL. To overcome this problem, we combined the benefits of QTL analysis (to identify genomic regions affecting trait variation) and classic diallel analysis (to obtain insight into the general inheritance of the trait) by analyzing multiple mapping families that are connected via shared parents. We first provide a theoretical derivation of main (general combining ability (GCA)) and interaction (specific combining ability (SCA)) effects on F(2) family means relative to variance components in a randomly mating reference population. Then, using computer simulations to generate F(2) families derived from 10 inbred parents in different partial-diallel designs, we show that QTL can be detected and that the residual among-family variance can be analyzed. Standard diallel analysis methods are applied in order to reveal the presence and mode of action (in terms of GCA and SCA) of undetected polygenes. Given a fixed experiment size (total number of individuals), we demonstrate that QTL detection and estimation of the genetic architecture of polygenic effects are competing goals, which should be explicitly accounted for in the experimental design. Our approach provides a general strategy for exploring the genetic architecture, as well as the QTL underlying variation in quantitative traits.
 
This paper attempts to explain how the different heterogametic mechanisms of sex determination, such as male and female heterogamety, can arise from a single ancestor. We study this problem by first building and analysing some models and then comparing the models to relevant data from animals. Based on these comparisons, the models appear to be useful for understanding how sex determining mechanisms evolve. Some results of the models include:A mutant sex determiner invading a population of male or female heterogamety creates the potential for the evolution of a new heterogametic sex determining mechanism.Certain mutants will lead to a new system of male heterogamety whereas others will lead to a new system of female heterogamety.These changes take place through an intermediate population characterised by multigenic sex determination. In some cases the multigenic mechanism is stable and will not revert to male or female heterogamety. The success of the invading mutant depends upon both (i) the relative viabilities of the different genotypes, and (ii) the segregation ratio of the X and Y in males; the population primary sex ratio is otherwise maintained at 1/2.The models show how the different systems of genic balance arise and how sex determiners can become inherited autosomally.
 
Value of Fisher tests associated with the GCA and SCA and probabilities (%) 
Comparison of parents for estimated GCA 
Rank correlations between general combining abilities for the different traits (associated probabilities) (first trial: upper half; second trial: lower half) 
The genetic parameters of several agronomic traits were estimated in Coffea canephora in a triangular diallel with six parents and in a partial diallel with 18 parents. The yield data came from harvests obtained over 14 years divided into an initial 6-year cycle, a second cycle of 5 years after cutting back and a third cycle of 3 years after topping. Risk incidence was also observed over several years. The general combining abilities (GCA) were the principal sources of variation for the various traits considered. Parents derived from the Yangambi selections (Democratic Republic of Congo) proved to be best for yields in the three cropping cycles. The rank correlations between the GCA of the various traits indicated that first-cycle production was still not enough to predict the GCA for yield over 14 years. Susceptibility to leaf anthracnose and to drought could lead to modifications in successive classifications, with a more significant impact on production during the first cycle. The differences in susceptibility to Coffee Berry Borers had an impact on yield, which increased in line with coffee tree age. There was a rather good relation between inherent values and values in parent combinations and it was thus possible to choose parents on their own performance.
 
Genetic variation was studied in quantitative traits and molecular markers in six natural Scandinavian populations of Arabidopsis thaliana. Only two of the populations had several molecular marker haplotypes and significant between-family variance components in quantitative traits. There was no genetic variation in the other four populations. The differentiation between the populations was high in both molecular markers and quantitative traits, with FST estimates of above 0.60 in almost all traits. The patterns of variation of the neutral markers and morphological and phenological traits were consistent in all the analyses, as opposed to what has been found in predominantly outcrossing species. The general picture of the level and distribution of genetic variance agrees with the information from other predominantly inbreeding species.
 
Various subspecies of the house mouse (Mus musculus sensu lato) are known to have contributed to its worldwide expansion. However, the origin of mice on some larger islands such as Madagascar has remained unknown, with several sources being possible. In order to classify the Malagasy house mouse, individuals were trapped in 13 different localities distributed throughout the island. For 33 individuals the control region (D-Loop) of the mitochondrial DNA was partially sequenced and 21 males were typed for a Zfy-2 polymorphism of the Y chromosome. Malagasy mt DNA lineages constitute a narrow monophyletic group which suggests a recent and probably single origin, and are very close to the gentilulus mitochondrial lineages from Yemen. This was supported by the fact that all the males have the domesticus type Y chromosome, like gentilulus. From these results, it can be inferred that the Malagasy house mice originate probably from the Arabian peninsula in a single colonisation wave, unlike its human population. Our results provide a better molecular description of the Yemeni-Malagasy mitochondrial clade which clearly belongs to the Mus musculus radiation.
 
An electrophoretic salivary amylase variant in the recombinant inbred mouse strain BXD-16 segregated in crosses as an allele at the salivary amylase locus. No other strain was found with the same combination of electrophoretic types of salivary and pancreatic amylase, and no sign of contamination by foreign genes from other strains was found. The variant therefore seems to have arisen during the inbreeding of the strain by a genetic alteration in the amylase complex. Purified variant amylase had a lower heat stability and an altered net charge of one or more CNBr fragments, but had the same size distribution of peptides from restricted proteolysis and CNBr cleavage as salivary amylase from the progenitor strains. Radioactive pulse labelling of the variant amylase showed that its relative rate of synthesis was the same as that in the progenitor strains. The variant is therefore, most likely, the result of a missense mutation that has altered the structure of all the salivary amylase produced in the strain. This indicates that only a single structural gene for the enzyme is expressed in the strain BXD-16.
 
Sex-biased dispersal, where individuals of one sex stay or return to their natal site (or group) to breed while individuals of the other sex are prone to disperse, is a wide-spread pattern in vertebrate organisms. In general, mammals exhibit male-biased dispersal whereas birds exhibit female-bias. Dispersal estimates are often difficult to obtain from direct field observations. Here we describe different methods for inferring sex-specific dispersal using population genetic tools and discuss the problems they can raise. We distinguish two types of methods: those based on bi-parental markers (eg comparison of male/female relatedness, F(st) and assignment probabilities) and those relying on the comparison between markers with different modes of inheritance (eg mtDNA markers and microsatellites). Finally, we discuss statistical problems that are encountered with these different methods (eg pseudoreplication, problems due to the comparison of distinct markers). While the genetic methods to detect sex-biased dispersal are now relatively well developed, their interpretation can prove problematic due to the confounding effects of factors such as the mating system of the species. Moreover, the relative power of these methods is not well known and requires further investigation.
 
An official journal of the Genetics Society, Heredity publishes high-quality articles describing original research and theoretical insights in all areas of genetics. Research papers are complimented by News & Commentary articles and reviews, keeping researchers and students abreast of hot topics in the field.
 
Eurya emarginata (Thunb.) Makino (Theaceae) is a dioecious, insect-pollinated tree, which combines sexual reproduction and clonal spread. It is narrowly distributed in coastal areas from southern China, along southern Korea, and extending to central and southern Japan. We used allozyme loci and spatial autocorrelation statistics to examine the clonal structure and the spatial distribution of allozyme polymorphisms of sexually reproduced individuals in a study population (70 m x 120 m area) in Korea. The population maintains moderate levels of allozyme variability (mean He=0.133), and multilocus genotypic diversity is high (mean DG=0. 992). The frequency of clones was 0.377 (90/239), and the mean clone-pair distance was very large (35.06 m +/- 1.91 m [SE]), indicating that clones can form at long distances away from their ancestors. In addition, it was found that genetic patch width was at least 24 m. However, join-count statistics for the total number of unlike joins showed that, contrary to expectation for such species, clonal reproduction does not contribute substantially to genetic isolation by distance neither among the sexually reproduced individuals nor the whole population. In contrast, limits to seed and pollen dispersal create substantial levels of genetic structure.
 
Top-cited authors
Francois Rousset
  • Université de Montpellier
Michel Raymond
  • Université de Montpellier
Derek Roff
  • University of California, Riverside
Deborah Charlesworth
  • The University of Edinburgh
Chris Haley
  • The University of Edinburgh