Counterselection on sex chromosomes in the Mus musculus European hybrid zone

The extent to which alleles can disperse across a hybrid zone depends on the selection they are subjected to in the hybrid genetic background or, for those that are selectively neutral, on their ability to escape from the unfavourable environment by recombination. Three markers spanning a 45 cM segment in the center of the X chromosome were used to investigate the degree to which selection against X chromosome linked genes helps to maintain the barrier to gene flow in the hybrid zone between Mus musculus domesticus and M. m. musculus in Denmark. The introgression of all the sex chromosome specific markers was more limited than that of the autosomal enzymes (Idh1, Amy, Gpd1, Pgm1, Es1, Es2, Mpi, Np1, Es10, Sod1) and the mitochondrial DNA. The cline for DXPas2, which is in the center of the X chromosome, is extremely steep and shows that certain genes located in this region are strongly selected against in the hybrid background. The clines of the other two X-linked markers, Hprt and DXPas1, and of the Y chromosome are not as abrupt and all three have similar asymmetric introgression patterns. Although the musculus variants appear to behave in much the same way as those of the autosomal genes, the domesticus variants do not introgress. The results show that X-linked and to a lesser extent Y-linked genes are more strongly selected against in the hybrid genome than the mitochondrial genome or the different autosomal loci. This suggests that co-adapted gene systems involving the sex chromosomes may play an important role in the hybrid breakdown between the two subspecies.     

Inferences of selection and migration in the Danish house mouse hybrid zone

We analysed the patterns of allele frequency change for ten diagnostic autosomal allozyme loci in the hybrid zone between the house mouse subspecies Mus musculus domesticus and M. m. musculus in central Jutland. After determining the general orientation of the clines of allele frequencies, we analysed the cline shapes along the direction of maximum gradient. Eight of the ten clines are best described by steep central steps with coincident positions and an average width of 8.9 km (support limits 7.6–12.4) flanked by tails of introgression, indicating the existence of a barrier to gene flow and only weak selection on the loci studied. We derived estimates of migration from linkage disequilibrium in the centre of the zone, and by applying isolation by distance methods to microsatellite data from some of these populations. These give concordant estimates of σ =  0.5–0.8 km generation     . The barrier to gene flow is of the order of 20 km (support limits 14–28), and could be explained by selection of a few per cent at 43–120 underdominant loci that reduces the mean fitness in the central populations to 0.45. Some of the clines appear symmetrical, whereas others are strongly asymmetrical, and two loci appear to have escaped the central barrier to gene flow, reflecting the differential action of selection on different parts of the genome. Asymmetry is always in the direction of more introgression into musculus , indicating either a general progression of domesticus into the musculus territory, possibly mediated by differential behaviour, or past movement of the hybrid zone in the opposite direction, impeded by potential geographical barriers to migration in domesticus territory.  © 2005 The Linnean Society of London, Biological Journal of the Linnean Society , 2005, 84 , 593–616.     

Inference of selection and stochastic effects in the house mouse hybrid zone

We explored the transition of 13 X-linked markers across two separate portions of the house mouse hybrid zone, asking whether such a comparison can distinguish the effects of selection from random factors. A heuristic search in the likelihood landscape revealed more complex likelihood profiles for data sampled in two-dimensional (2D) space relative to data sampled along a linear transect. Randomized resampling of localities analyzed for individual loci showed that deletion of sites away from the zone center can decrease cline width estimates whereas deletion of sites close to the center can significantly increase the width estimates. Deleting localities for all loci resulted in wider clines if the number of samples from the center was limited. The results suggest that, given the great variation in width estimates resulting from inclusion/exclusion of sampling sites, the geographic sampling design is important in hybrid zone studies and that our inferences should take into account measures of uncertainty such as support intervals. The comparison of the two transects indicates cline widths are narrower for loci in the central part of the X chromosome, suggesting selection is stronger in this region and genetic incompatibilities may have at least partly common architecture in the house mouse hybrid zone.     

Genetic architecture and genomic patterns of gene flow between hybridizing species of Picea

Hybrid zones provide an opportunity to study the effects of selection and gene flow in natural settings. We employed nuclear microsatellites (single sequence repeat (SSR)) and candidate gene single-nucleotide polymorphism markers (SNPs) to characterize the genetic architecture and patterns of interspecific gene flow in the Picea glauca × P. engelmannii hybrid zone across a broad latitudinal (40–60 degrees) and elevational (350–3500 m) range in western North America. Our results revealed a wide and complex hybrid zone with broad ancestry levels and low interspecific heterozygosity, shaped by asymmetric advanced-generation introgression, and low reproductive barriers between parental species. The clinal variation based on geographic variables, lack of concordance in clines among loci and the width of the hybrid zone points towards the maintenance of species integrity through environmental selection. Congruency between geographic and genomic clines suggests that loci with narrow clines are under strong selection, favoring either one parental species (directional selection) or their hybrids (overdominance) as a result of strong associations with climatic variables such as precipitation as snow and mean annual temperature. Cline movement due to past demographic events (evidenced by allelic richness and heterozygosity shifts from the average cline center) may explain the asymmetry in introgression and predominance of P. engelmannii found in this study. These results provide insights into the genetic architecture and fine-scale patterns of admixture, and identify loci that may be involved in reproductive barriers between the species.     

Testing for selection on the androgen-binding protein in the Danish mouse hybrid zone

The three peripheral subspecies of the house mouse Mus musculus have fixed specific variants of the androgen-binding protein (ABP) that have been proposed to be part of a recognition mechanism that could participate in sexual isolation between the subspecies. We tested for selection on Abpa by characterizing the pattern of Abpa introgression across a transect of the hybrid zone between M. m. musculus and M. m. domesticus in Jutland. On the musculus side, the cline for Abpa resembled that of a nearly neutral allozyme more than that of strongly selected X and Y chromosome markers. However, the high central step which displaces the tail of introgression of Abpa to higher frequencies was best accounted for by linkage to a locus under strong selection against hybrids. Still, we cannot exclude that this pattern results from weak selection against Abpa in the tail of introgression, which would be compatible with an assortative choice mechanism. On the domesticus side there was little introgression close to the hybrid zone, presumably due to a geographical barrier to migration. However, substantial frequencies of musculus alleles occurred further away, suggesting mixed colonization patterns as well as flow across the hybrid zone.  © 2005 The Linnean Society of London, Biological Journal of the Linnean Society , 2005, 84 , 447–459.     

Genetic analysis of autosomal and X-linked markers across a mouse hybrid zone

In this paper, we present results of the first comprehensive study of the introgression of both autosomal and sex-chromosome markers across the central European portion of the hybrid zone between two house mouse subspecies, Mus musculus musculus and M. m. domesticus. More than 1800 individuals sampled from 105 sites were analyzed with a set of allozyme loci (hopefully representing neutral or nearly neutral markers) and X-linked loci (which are assumed to be under selection). The zone center is best modeled as a single straight line independent of fine-scale local geographic or climatic conditions, being maintained by a balance between dispersal and selection against hybrids. The width (w) of the multilocus autosomal cline was estimated as 9.6 km whereas the estimate for the compound X-chromosome cline was about 4.6 km only. As the former estimate is comparable to that of the Danish portion of the zone (assumed to be much younger than the central European one), zone width does not appear to be related to its age. The strength (B) of the central barrier was estimated as about 20 km; with dispersal (sigma) of about 1 km/gen(1/2), this means effective selection (s*) is approximately 0.06-0.09 for autosomal loci and about 0.25 for X-linked loci. The number of loci under selection was estimated as N= 56-99 for autosomes and about 380 for X-linked loci. Finally, we highlight some potential pitfalls in hybrid zone analyses and in comparisons of different transects. We suggest that conclusions about parts of the mouse genome involved in reproductive isolation and speciation should be drawn with caution and that analytical approaches always providing some estimates should not be used without due care regarding the support or confidence of such estimates, especially if conclusions are based on the difference between these estimates. Finally, we recommend that analysis in two-dimensional space, dense sampling, and rigorous treatment of data, including inspection of likelihood profiles, are essential for hybrid zone studies.     

A comparison of nuclear and mitochondrial cline shapes in a hybrid zone in the Sceloporus grammicus complex (Squamata; Phrynosomatidae)

The F5 and FM2 chromosome races of the Sceloporus grammicus complex form a hybrid zone in the Mexican state of Hidalgo. Previous studies of this zone have assessed genetic structure by averaging estimates of shape and width across three diagnostic chromosome markers. This approach is likely to mask subtle differences in cline shape among loci (e.g. selected vs. neutral), and obscure any displacement of cline centres (if present). Here we use maximum likelihood methods to construct the best fitting individual clines for three chromosomal markers, and also add two new markers; the mitochondrial DNA (mtDNA) locus, and the nuclear ribosomal DNA (rDNA) repeat. For each locus, hybrid zone models were fitted by cline shape and width, and the position and number of segments describing the centre of the zone. Pairwise comparisons between all clines revealed concordance between chromosomes 2 and 6, but significant discordance in cline structure among all other paired combinations. The concordance of chromosomes 2 and 6 suggests that these clines are maintained by genome-wide forces. The discordance of the chromosome 1 cline suggests an influence of asymmetric introgression, while the mtDNA cline is probably influenced by selection and drift. The rDNA locus reveals a pattern best explained by either extreme asymmetric introgression or gene conversion. The structure of zone indicates that genome-wide processes and locus specific selective forces as well as drift, are operating to different degrees on different loci. The locus-by-locus approach used here permits a finer discrimination among possible mechanisms responsible for the maintenance of the individual clines.     

THE VARIABLE GENOMIC ARCHITECTURE OF ISOLATION BETWEEN HYBRIDIZING SPECIES OF HOUSE MICE

Studies of the genetics of hybrid zones can provide insight into the genomic architecture of species boundaries. By examining patterns of introgression of multiple loci across a hybrid zone, it may be possible to identify regions of the genome that have experienced selection. Here, we present a comparison of introgression in two replicate transects through the house mouse hybrid zone through central Europe, using data from 41 single nucleotide markers. Using both genomic and geographic clines, we found many differences in patterns of introgression between the two transects, as well as some similarities. We found that many loci may have experienced the effects of selection at linked sites, including selection against hybrid genotypes, as well as positive selection in the form of genotypes introgressed into a foreign genetic background. We also found many positive associations of conspecific alleles among unlinked markers, which could be caused by epistatic interactions. Different patterns of introgression in the two transects highlight the challenge of using hybrid zones to identify genes underlying isolation and raise the possibility that the genetic basis of isolation between these species may be dependent on the local population genetic make-up or the local ecological setting.     

Steep clines within a highly permeable genome across a hybrid zone between two subspecies of the European rabbit

Maintenance of genetic distinction in the face of gene flow is an important aspect of the speciation process. Here, we provide a detailed spatial and genetic characterization of a hybrid zone between two subspecies of the European rabbit. We examined patterns of allele frequency change for 22 markers located on the autosomes, X‐chromosome, Y‐chromosome and mtDNA in 1078 individuals sampled across the hybrid zone. While some loci revealed extremely wide clines (w ≥ 300 km) relative to an estimated dispersal of 1.95–4.22 km/generation, others showed abrupt transitions (w ≈ 10 km), indicating localized genomic regions of strong selection against introgression. The subset of loci showing steep clines had largely coincident centers and stepped changes in allele frequency that did not co‐localize with any physical barrier or ecotone, suggesting that the rabbit hybrid zone is a tension zone. The steepest clines were for X‐ and Y‐chromosome markers. Our results are consistent with previous inference based on DNA sequence variation of individuals sampled in allopatry in suggesting that a large proportion of each genome has escaped the overall barrier to gene flow in the middle of the hybrid zone. These results imply an old history of hybridization and high effective gene flow and anticipate that isolation factors should often localize to small genomic regions.     

Inferences from a rapidly moving hybrid zone

Anartia fatima and Anartia amathea (Lepidoptera: Nymphalidae) are sister taxa whose ranges abut in a narrow hybrid zone in eastern Panama. At the center of the zone, hybrids are abundant, although deviations from Hardy-Weinberg and linkage disequilibria are strong, due in part to assortative mating. We measured differences across the zone in four wing color-pattern characters, three allozyme loci, and mitochondrial haplotype. Wing pattern, allozyme, and mitochondrial clines were coincident (i.e., had the same positions) and concordant (i.e.. all markers had similar cline shapes, about 28 km wide). Repeated samples demonstrated that the hybrid zone has been moving eastwards at an average rate of 2.5 km/year over the past 20 years, accompanied by an equivalent movement of the mtDNA cline. No introgression of mtDNA haplotypes were found in the 'wake" of the moving cline, as might be expected for a neutral marker. The concordance of morphological and mtDNA clines between 1994 and 2000, in spite of hybrid zone movement, suggests strong epistasis between the mitochondrial genome and nuclear loci. Cline movement is achieved mainly by pure fatima immigrating into amathea populations; hybrids had little effect, and were presumably outcompeted by fitter pure fatima genotypes. This movement can be explained if random dispersal of 7-19 km x gen(1/2) is coupled with a competitive advantage to A. fatima genomes of 2-5%. Hybrid zone motion is equivalent to Phase III of Wright's shifting balance. Hybrid zone movement has rarely been considered likely in the past, but our results show that it may be more important in biogeography and evolution than generally realized.     

Chromosomal and allelic variation in Drosophila americana: selective maintenance of a chromosomal cline.

Geographically structured genetic variation, as represented by clines and hybrid zones, offers unique opportunities to study adaptation and speciation in natural populations. A hybrid zone has been reported between Drosophila americana americana and Drosophila americana texana, two taxa that are distinguished solely by the arrangement of their X and 4th chromosomes. In this study, samples of D. americana were collected along a latitudinal transect across the inferred hybrid zone, and the frequency of the alternative chromosomal arrangements is reported. These data illustrate that the alternative chromosomal arrangements are distributed along a shallow cline over a broad geographic region, and that the frequency of the arrangements is tightly correlated with latitude. Allelic variants at 13 RFLP loci in three genes on chromosome 4 exhibit no evidence of association with the cline. Presence of a cline for the chromosomal arrangements, as well as a general absence of geographic structure for variation at these genes, is interpreted as evidence that natural selection is responsible for the maintenance of this chromosomal cline. Furthermore, these results demonstrate that taxonomic subdivision of D. americana is unwarranted, because it exists as a cohesive species that is segregating a chromosomal fusion.     

Differential patterns of introgression across the X chromosome in a hybrid zone between two species of house mice

A complete understanding of the speciation process requires the identification of genomic regions and genes that confer reproductive barriers between species. Empirical and theoretical research has revealed two important patterns in the evolution of reproductive isolation in animals: isolation typically arises as a result of disrupted epistatic interactions between multiple loci and these disruptions map disproportionately to the X chromosome. These patterns suggest that a targeted examination of natural gene flow between closely related species at X-linked markers with known positions would provide insight into the genetic basis of speciation. We take advantage of the existence of genomic data and a well-documented European zone of hybridization between two species of house mice, Mus domesticus and M. musculus, to conduct such a survey. We evaluate patterns of introgression across the hybrid zone for 13 diagnostic X-linked loci with known chromosomal positions using a maximum likelihood model. Interlocus comparisons clearly identify one locus with reduced introgression across the center of the hybrid zone, pinpointing a candidate region for reproductive isolation. Results also reveal one locus with high frequencies of M. domesticus alleles in populations on the M. musculus side of the zone, suggesting the possibility that positive selection may act to drive the spread of alleles from one species on to the genomic background of the other species. Finally, cline width and cline center are strongly positively correlated across the X chromosome, indicating that gene flow of the X chromosome may be asymmetrical. This study highlights the utility of natural populations of hybrids for mapping speciation genes and suggests that the middle of the X chromosome may be important for reproductive isolation between species of house mice.     

Comparing clines on molecular and phenotypic traits in hybrid zones: a window on tension zone models

The study of zones of secondary contact provides insight into the maintenance of reproductive isolation. Tension zone theory supplies powerful tools for assessing how dispersal and selection shape hybrid zones. We present a multimodal analysis of phenotypic clines in conjunction with clines at molecular markers in a hybrid zone between Larus glaucescens and Larus occidentalis. We developed a new method to analyze simultaneously clines of quantitative traits and molecular data. Low linkage disequilibrium and the lack of coincidence between clines at six microsatellites, a mitochondrial DNA region, and two phenotypic traits indicated introgression. However, the hypothesis of neutral diffusion was rejected based on evidence that all of the clines were concordant and narrower than expected for neutral clines, indicating some indirect selection. The analysis of phenotypic variance gave evidence of restricted phenotypic introgression and together with the bimodal distribution of phenotypes suggested that disruptive selection is acting across the hybrid zone, especially on the coloration of bare parts. Multimodal analysis of phenotypic clines also highlighted a shift between the peak of intermediates and the cline center, left behind by hybrid zone motion. High-resolution analysis of phenotypes distribution thus proved useful for detecting hybrid zone movement even without temporal data.     

GENOMIC AND MORPHOLOGICAL ANALYSIS OF A SEMIPERMEABLE AVIAN HYBRID ZONE SUGGESTS ASYMMETRICAL INTROGRESSION OF A SEXUAL SIGNAL

Hybrid zones are geographic regions where differentiated taxa meet and potentially exchange genes. Increasingly, genomic analyses have demonstrated that many hybrid zones are semipermeable boundaries across which introgression is highly variable. In some cases, certain alleles penetrate across the hybrid zone in only one direction, recombining into the alternate genome. We investigated this phenomenon using genomic (genotyping‐by‐sequencing) and morphological (plumage reflectance spectrophotometry) analyses of the hybrid zone between two subspecies of the red‐backed fairy‐wren (Malurus melanocephalus) that differ conspicuously in a sexual signal, male back plumage color. Geographic cline analyses revealed a highly variable pattern of differential introgression, with many narrow coincident clines combined with several significantly wider clines, suggesting that the hybrid zone is a semipermeable tension zone. The plumage cline was shifted significantly into the genomic background of the orange subspecies, consistent with sexual selection driving asymmetrical introgression of red plumage alleles across the hybrid zone. This interpretation is supported by previous experimental work demonstrating an extra‐pair mating advantage for red males, but the role of genetic dominance in driving this pattern remains unclear. This study highlights the potential for sexual selection to erode taxonomic boundaries and promote gene flow, particularly at an intermediate stage of divergence.     

SPATIO‐TEMPORAL CHANGES IN THE STRUCTURE OF AN AUSTRALIAN FROG HYBRID ZONE: A 40‐YEAR PERSPECTIVE

Spatio‐temporal studies of hybrid zones provide an opportunity to test evolutionary hypotheses of hybrid zone maintenance and movement. We conducted a landscape genetics study on a classic hybrid zone of the south‐eastern Australian frogs, Litoria ewingii and Litoria paraewingi. This hybrid zone has been comprehensively studied since the 1960s, providing the unique opportunity to directly assess changes in hybrid zone structure across time. We compared both mtDNA and male advertisement call data from two time periods (present and 1960s). Clinal analysis of the coincidence (same center) and concordance (same width) of these traits indicated that the center of the hybrid zone has shifted 1 km south over the last 40 years, although the width of the zone and the rate of introgression remained unchanged. The low frequency of hybrids, the strong concordance of clines within a time period, and the small but significant movement across the study period despite significant anthropogenic changes through the region, suggest the hybrid zone is a tension zone located within a low‐density trough. Hybrid zone movement has not been considered common in the past but our findings highlight that it should be considered a crucial component to our understanding of evolution.     

WHERE ARE THE WORMY MICE? A REEXAMINATION OF HYBRID PARASITISM IN THE EUROPEAN HOUSE MOUSE HYBRID ZONE

Wormy mice in a hybrid zone have been interpreted as evidence of low hybrid fitness, such that parasites contribute to species separation. However, because of its natural heterogeneity, observations of parasite load must be numerous with good field area coverage. We sampled 689 mice from 107 localities across the Bavaria-Bohemia region of the European house mouse hybrid zone and calculated their hybrid indices using 1401 diagnostic single nucleotide polymorphisms (SNPs). We tested whether hybrids have greater or lesser diversity and load of parasite helminths than additive expectations, performing load analyses on the four most common taxa. We found hybrids have significantly reduced diversity and load of each of the commonest helminths; rarer helminths further support reduced load. Although within-locality comparisons have little power, randomization tests show the repeated pattern is unlikely to be due to local parasite heterogeneity, and simulations show a patch of low parasite diversity is unlikely to fall by chance just so in the field area, such that it produces the observed effects. Our data therefore contradict the idea that helminths reduce hybrid fitness through increased load. We discuss a vicariant Red Queen model that implies immune genes tracking parasites will escape Dobzhansky-Muller incompatibilities, generating hybrid variants untargeted by parasites.     

Evolution of insect-plant relationships: chemical constraints, coadaptation, and concordance of insect/plant traits

Co-adaptations, co-evolution, and co-speciation between herbivores and their host plants have been topics of interest for several decades. Difficulties in deciphering these relationships as well as physiological, biochemical, and ecological adaptations of herbivorous insects themselves are discussed here in relation to biotic and abiotic environmental factors that create temporal as well as spatial mosaics of genetic variation. Hybridization was shown in swallowtail butterflies (Papilio) (Lepidoptera: Papilionidae) to produce some trait concordance, but mostly independent geographic trait clines (physiological, biochemical, and morphological). Strong and extensive genetic introgression of Liriodendron tulipifera detoxification abilities was documented northward across the hybrid zone, presumably as a result of regional climate warming only during the last 3–4 years. These and other genetic novelties produced by hybridization may be important in speciation processes, and they also emphasize the difficulties identifying appropriate taxonomic classifications for discussing any species concept. Host plant detoxification abilities (as `key innovations') are shown capable of rapid movement between different polyphagous herbivore species independently of the host plant availability and well beyond the insect species geographical range distribution. Part of the difficulty associated with ecologically categorizing herbivore species and identifying affiliated adaptations for host plant use may be related to independent movement of various `species-diagnostic' traits. Climate-driven local selection regimes could help generate the dynamic variation observed for co-adapted, co-evolved, or non-adapted genotypes, and may produce the confusing and changing patterns of geographic mosaics seen within and among closely related herbivores. Experimental analyses of several factors that could explain the asymmetrical shapes of trait clines across the hybrid zone for tiger swallowtail butterflies are discussed.     

Dobzhansky–Muller incompatibilities,dominance drive,and sex‐chromosome introgression at secondary contact zones: A simulation study

Dobzhansky–Muller (DM) incompatibilities involving sex chromosomes have been proposed to account for Haldane's rule (lowered fitness among hybrid offspring of the heterogametic sex) as well as Darwin's corollary (asymmetric fitness costs with respect to the direction of the cross). We performed simulation studies of a hybrid zone to investigate the effects of different types of DM incompatibilities on cline widths and positions of sex‐linked markers. From our simulations, X‐Y incompatibilities generate steep clines for both X‐linked and Y‐linked markers; random effects may produce strong noise in cline center positions when migration is high relative to fitness costs, but X‐ and Y‐centers always coincide strictly. X‐autosome and Y‐autosome incompatibilities also generate steep clines, but systematic shifts in cline centers occur when migration is high relative to selection, as a result of a dominance drive linked to Darwin's corollary. Interestingly, sex‐linked genes always show farther introgression than the associated autosomal genes. We discuss ways of disentangling the potentially confounding effects of sex biases in migration, we compare our results to those of a few documented contact zones, and we stress the need to study independent replicates of the same contact zone.     

Reduced introgression of the Y chromosome between subspecies of the European rabbit (Oryctolagus cuniculus) in the Iberian Peninsula

The role of the Y chromosome in speciation is unclear. Hybrid zones provide natural arenas for studying speciation, as differential introgression of markers may reveal selection acting against incompatibilities. Two subspecies of the European rabbit (Oryctolagus cuniculus) form a hybrid zone in the Iberian Peninsula. Previous work on mitochondrial DNA (mtDNA), Y- and X-linked loci revealed the existence of two divergent lineages in the rabbit genome and that these lineages are largely subspecies-specific for mtDNA and two X-linked loci. Here we investigated the geographic distribution of the two Y chromosome lineages by genotyping two diagnostic single nucleotide polymorphisms in a sample of 353 male rabbits representing both subspecies, and found that Y chromosome lineages are also largely subspecies-specific. We then sequenced three autosomal loci and discovered considerable variation in levels of differentiation at these loci. Finally, we compared estimates of population differentiation between rabbit subspecies at 26 markers and found a surprising bimodal distribution of F(ST)values. The vast majority of loci showed little or no differentiation between rabbit subspecies while a few loci, including the SRY gene, showed little or no introgression across the hybrid zone. Estimates of population differentiation for the Y chromosome were surprisingly high given that there is male-biased dispersal in rabbits. Taken together, these data indicate that there is a clear dichotomy in the rabbit genome and that some loci remain highly differentiated despite extensive gene flow following secondary contact.