Miloš Macholán

GENETIC ANALYSIS OF AUTOSOMAL AND X‐LINKED MARKERS ACROSS A MOUSE HYBRID ZONE

Abstract 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 (σ) of about 1 km/gen1/2, 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.

Phylogeny of the genus Apodemus with a special emphasis on the subgenus Sylvaemus using the nuclear IRBP gene and two mitochondrial markers: cytochrome b and 12S rRNA.

Phylogenetic relationships among 17 extant species of Murinae, with special reference to the genus Apodemus, were investigated using sequence data from the nuclear protein-coding gene IRBP (15 species) and the two mitochondrial genes cytochrome b and 12S rRNA (17 species). The analysis of the three genes does not resolve the relationships between Mus, Apodemus, and Rattus but separates Micromys from these three genera. The analysis of the two mitochondrial regions supported an association between Apodemus and Tokudaia and indicated that these two genera are more closely related to Mus than to Rattus or Micromys. Within Apodemus, the mitochondrial data sets indicated that 8 of the 9 species analyzed can be sorted into two main groups: an Apodemus group, with A. agrarius, semotus, and peninsulae, and a Sylvaemus group, with uralensis, flavicollis, alpicola, sylvaticus, and hermonensis. The position of Apodemus mystacinus is ambiguous and might be either included in Sylvaemus or considered a distinct subgenus, Karstomys, more closely related to Sylvaemus than to Apodemus. Estimation of the divergence time for these taxa suggests a separation between 7 and 8 My ago for the three groups (mystacinus and the two subgenera Apodemus and Sylvaemus). Within each subgenus, divergence times are between 5.4 and 6 My for Apodemus and between 2.2 and 3.5 My for Sylvaemus and mystacinus.

Genome-wide architecture of reproductive isolation in a naturally occurring hybrid zone between Mus musculus musculus and M. m. domesticus

Studies of a hybrid zone between two house mouse subspecies (Mus musculus musculus and M. m. domesticus) along with studies using laboratory crosses reveal a large role for the X chromosome and multiple autosomal regions in reproductive isolation as a consequence of disrupted epistasis in hybrids. One limitation of previous work has been that most of the identified genomic regions have been large. The goal here is to detect and characterize precise genomic regions underlying reproductive isolation. We surveyed 1401 markers evenly spaced across the genome in 679 mice collected from two different transects. Comparisons between transects provide a means for identifying common patterns that likely reflect intrinsic incompatibilities. We used a genomic cline approach to identify patterns that correspond to epistasis. From both transects, we identified contiguous regions on the X chromosome in which markers were inferred to be involved in epistatic interactions. We then searched for autosomal regions showing the same patterns and found they constitute about 5% of autosomal markers. We discovered substantial overlap between these candidate regions underlying reproductive isolation and QTL for hybrid sterility identified in laboratory crosses. Analysis of gene content in these regions suggests a key role for several mechanisms, including the regulation of transcription, sexual conflict and sexual selection operating at both the postmating prezygotic and postzygotic stages of reproductive isolation. Taken together, these results indicate that speciation in two recently diverged (c. 0.5 Ma) house mouse subspecies is complex, involving many genes dispersed throughout the genome and associated with distinct functions.

Reinforcement selection acting on the European house mouse hybrid zone

Behavioural isolation may lead to complete speciation when partial postzygotic isolation acts in the presence of divergent‐specific mate‐recognition systems. These conditions exist where Mus musculus musculus and M. m. domesticus come into contact and hybridize. We studied two mate‐recognition signal systems, based on urinary and salivary proteins, across a Central European portion of the mouse hybrid zone. Introgression of the genomic regions responsible for these signals: the major urinary proteins (MUPs) and androgen binding proteins (ABPs), respectively, was compared to introgression at loci assumed to be nearly neutral and those under selection against hybridization. The preference of individuals taken from across the zone regarding these signals was measured in Y mazes, and we develop a model for the analysis of the transition of such traits under reinforcement selection. The strongest assortative preferences were found in males for urine and females for ABP. Clinal analyses confirm nearly neutral introgression of an Abp locus and two loci closely linked to the Abp gene cluster, whereas two markers flanking the Mup gene region reveal unexpected introgression. Geographic change in the preference traits matches our reinforcement selection model significantly better than standard cline models. Our study confirms that behavioural barriers are important components of reproductive isolation between the house mouse subspecies.

Genetic conflict outweighs heterogametic incompatibility in the mouse hybrid zone

BackgroundThe Mus musculus musculus/M. m. domesticus contact zone in Europe is characterised by sharp frequency discontinuities for sex chromosome markers at the centre of wider clines in allozyme frequencies.ResultsWe identify a triangular area (approximately 330 km2) where the musculus Y chromosome introgresses across this front for up to 22 km into domesticus territory. Introgression of the Y chromosome is accompanied by a perturbation of the census sex ratio: the sex ratio is significantly female biased in musculus localities and domesticus localities lacking Y chromosome introgression. In contrast, where the musculus Y is detected in domesticus localities, the sex ratio is close to parity, and significantly different from both classes of female biased localities. The geographic position of an abrupt cline in an X chromosome marker, and autosomal clines centred on the same position, seem unaffected by the musculus Y introgression.ConclusionWe conclude that sex ratio distortion is playing a role in the geographic separation of speciation genes in this section of the mouse hybrid zone. We suggest that clines for genes involved in sex-ratio distortion have escaped from the centre of the mouse hybrid zone, causing a decay in the barrier to gene flow between the two house mouse taxa.

Evolution of the house mouse

List of contributors Foreword: mice and (wo)men: an evolving relationship R. J. Berry Preface 1. The house mouse and its relatives: systematics and taxonomy Jean-Christophe Auffray and Janice Britton-Davidian 2. Phylogeny and biogeography of the genus Mus in Eurasia Hitoshi Suzuki and Ken P. Aplin 3. On the origin of the house mouse synanthropy and dispersal in the Near East and Europe: zooarchaeological review and perspectives Thomas Cucchi, Jean-Christophe Auffray and Jean-Denis Vigne 4. Origin and genetic status of Mus musculus molossinus: a typical example of reticulate evolution in the genus Mus Hiromichi Yonekawa, Jun J. Sato, Hitoshi Suzuki and Kazuo Moriwaki 5. The complex social environment of female house mice (Mus domesticus) Barbara Konig and Anna K. Lindholm 6. Development of the mouse mandible: a model system for complex morphological structures Christian Peter Klingenberg and Nicolas Navarro 7. Recognition of subspecies status mediated by androgen-binding protein (ABP) in the evolution of incipient reinforcement on the European house mouse hybrid zone Christina M. Laukaitis and Robert C. Karn 8. Mechanisms of chemical communication Pavel Stopka, Romana Stopkova and Katerina Janotova 9. The evolution of MHC diversity in house mice Dustin J. Penn and Kerstin Musolf 10. Ultrasonic vocalizations in house mice: a cryptic mode of acoustic communication Kerstin Musolf and Dustin J. Penn 11. House mouse phylogeography Francois Bonhomme and Jeremy B. Searle 12. The mouse t-haplotype: a selfish chromosome - genetics, molecular mechanism and evolution Bernhard G. Herrmann and Hermann Bauer 13. Tracing recent adaptations in natural populations of the house mouse Meike Teschke, Anna Buntge and Diethard Tautz 14. What can the Mus musculus musculus/M. m. domesticus hybrid zone tell us about speciation? Stuart J. E. Baird and Milos Macholan 15. Behaviour, ecology and speciation in the house mouse Guila Ganem 16. Chromosomal hybrid zones in the house mouse Heidi C. Hauffe, Mabel D. Gimenez and Jeremy B. Searle 17. The role of the X chromosome in house mouse speciation Ayako Oka and Toshihiko Shiroishi 18. New insights into parasitism in the house mouse hybrid zone Joelle Gouy de Bellocq, Alexis Ribas and Stuart J. E. Baird 19. Hybrid male sterility genes in the mouse subspecific crosses Jiri Forejt, Jaroslav Pialek and Zdenek Trachtulec 20. Linkage disequilibrium approaches for detecting hybrid zone movement: a study of the house mouse hybrid zone in southern Bavaria Priscilla K. Tucker, Liuyang Wang, Ken Luzynski and Katherine Teeter Index.

Assessing multilocus introgression patterns: a case study on the mouse X chromosome in central Europe.

Multilocus hybrid zone (HZ) studies predate genomics by decades. The power of early methods is becoming apparent and now large datasets are commonplace. Relating introgression along a chromosome to evolutionary process is challenging: although reduced introgression regions may indicate speciation genes, this pattern may be obscured by asymmetric introgression of linked invasive genes. Further, HZ movement may form salients and leave islands in its wake. Bartons concordance was proposed 24 years ago for assessing introgression where geographic patterns are complex. The geographic axis of introgression is replaced with the hybrid index. We compare this, a recently proposed genomic clines approach, and two‐dimensional (2D) geographic analyses, for 24 X chromosome loci of 2873 mice from the central‐European house mouse HZ. In 2D, 14 loci show linear contact, seven precisely matching previous studies. Four show introgression islands to the east of the zone, suggesting past westward zone movement, two show westward salients. Bartons concordance both recovers and refines this information. A region of reduced introgression on the central X is supported, despite X centromere‐proximal male‐biased westward introgression matching a westward 2D geographic salient. Genomic clines results are consistent regarding introgression asymmetries, but otherwise more difficult to interpret. Evidence for genetic conflict is discussed.

Sperm-related phenotypes implicated in both maintenance and breakdown of a natural species barrier in the house mouse

The house mouse hybrid zone (HMHZ) is a species barrier thought to be maintained by a balance between dispersal and natural selection against hybrids. While the HMHZ is characterized by frequency discontinuities for some sex chromosome markers, there is an unexpected large-scale regional introgression of a Y chromosome across the barrier, in defiance of Haldanes rule. Recent work suggests that a major force maintaining the species barrier acts through sperm traits. Here, we test whether the Y chromosome penetration of the species barrier acts through sperm traits by assessing sperm characteristics of wild-caught males directly in a field laboratory set up in a Y introgression region of the HMHZ, later calculating the hybrid index of each male using 1401 diagnostic single nucleotide polymorphisms (SNPs). We found that both sperm count (SC) and sperm velocity were significantly reduced across the natural spectrum of hybrids. However, SC was more than rescued in the presence of the invading Y. Our results imply an asymmetric advantage for Y chromosome introgression consistent with the observed large-scale introgression. We suggest that selection on sperm-related traits probably explains a large component of patterns observed in the natural hybrid zone, including the Y chromosome penetration.

Measures of linkage disequilibrium among neighbouring SNPs indicate asymmetries across the house mouse hybrid zone

Theory predicts that naturally occurring hybrid zones between genetically distinct taxa can move over space and time as a result of selection and/or demographic processes, with certain types of hybrid zones being more or less likely to move. Determining whether a hybrid zone is stationary or moving has important implications for understanding evolutionary processes affecting interactions in hybrid populations. However, direct observations of hybrid zone movement are difficult to make unless the zone is moving rapidly. Here, evidence for movement in the house mouse Mus musculus domesticus × Mus musculus musculus hybrid zone is provided using measures of LD and haplotype structure among neighbouring SNP markers from across the genome. Local populations of mice across two transects in Germany and the Czech Republic were sampled, and a total of 1301 mice were genotyped at 1401 markers from the nuclear genome. Empirical measures of LD provide evidence for extinction and (re)colonization in single populations and, together with simulations, suggest hybrid zone movement because of either geography‐dependent asymmetrical dispersal or selection favouring one subspecies over the other.

ALLOZYME VARIATION AND SYSTEMATICS OF THE GENUS APODEMUS (RODENTIA: MURIDAE) IN ASIA MINOR AND IRAN

Abstract Starch gel electrophoresis at 36 presumptive loci was used to study genetic variation and systematic status of 110 wood mice (genus Apodemus) from 19 sites scattered across Anatolia, Armenia, and Iran. Seventeen loci were monomorphic and fixed for the same allele among populations, whereas 19 loci were found to be polymorphic or discriminant among samples. The following species were determined in the material: A. flavicollis, A. uralensis, A. hermonensis, and a taxon provisionally called Apodemus cf. hyrcanicus. The study material was compared with previously analyzed samples from western Anatolia, increasing the total material to 245 specimens from 31 localities. In general, the pattern of variation and level of genetic differentiation within and among species were comparable between western and eastern samples. Intraspecific genetic distances were low, ranging from 0 to 0.051, but interspecific distances were an order of magnitude higher. Similarly, neighbor-joining trees showed negligible differentiation between populations of individual species and no sign of intraspecific structuring. A. uralensis seems to prefer humid sites, whereas A. hermonensis and A. flavicollis also occur in drier places. Individuals referred to Apodemus cf. hyrcanicus were limited to lowlands south of the Caspian Sea. Problems associated with the systematic relationships and taxonomy of A. falzfeini–fulvipectus–hermonensis–arianus and A. cf. hyrcanicus from northern Iran are briefly discussed.