X-Linked Signature of Reproductive Isolation in Humans is Mirrored in a Howler Monkey Hybrid Zone.

Reproductive isolation is a fundamental step in speciation. While sex chromosomes have been linked to reproductive isolation in many model systems, including hominids, genetic studies of the contribution of sex chromosome loci to speciation for natural populations are relatively sparse. Natural hybrid zones can help identify genomic regions contributing to reproductive isolation, like hybrid incompatibility loci, since these regions exhibit reduced introgression between parental species.

Multiple forms of selection shape reproductive isolation in a primate hybrid zone.

Speciation occurs when populations diverge and become reproductively isolated from each other. Natural selection is commonly accepted to play a large role in this process, and it has been widely assumed that reproductive isolation often results as a by-product of divergence driven by adaptation in allopatry. When such populations come into secondary contact, reinforcement can act to strengthen reproductive isolation, but the frequency and importance of this process are still unknown.

Effect of coffee agriculture management on the population structure of a forest dwelling rodent ().

Most of the natural habitat in tropical regions exists as scattered fragments embedded in a matrix of different agricultural uses. As a result of this agricultural expansion, habitat loss and fragmentation have become the main drivers of biodiversity loss. Understanding the long-term effects of agricultural management on populations is of great importance for the development of successful conservation strategies.

Phylogenomic Insights into Mouse Evolution Using a Pseudoreference Approach.

Comparative genomic studies are now possible across a broad range of evolutionary timescales, but the generation and analysis of genomic data across many different species still present a number of challenges. The most sophisticated genotyping and down-stream analytical frameworks are still predominantly based on comparisons to high-quality reference genomes. However, established genomic resources are often limited within a given group of species, necessitating comparisons to divergent reference genomes that could restrict or bias comparisons across a phylogenetic sample.

Functional organization of the genome may shape the species boundary in the house mouse.

Genomic features such as rate of recombination and differentiation have been suggested to play a role in species divergence. However, the relationship of these phenomena to functional organization of the genome in the context of reproductive isolation remains unexplored. Here, we examine genomic characteristics of the species boundaries between two house mouse subspecies (Mus musculus musculus/M.

The uncharacterized gene 1700093K21Rik and flanking regions are correlated with reproductive isolation in the house mouse, Mus musculus.

Reproductive barriers exist between the house mouse subspecies, Mus musculus musculus and M. m. domesticus, members of the Mus musculus species complex, primarily as a result of hybrid male infertility, and a hybrid zone exists where their ranges intersect in Europe.

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 Haldane's rule. Recent work suggests that a major force maintaining the species barrier acts through sperm traits.

The contribution of the Y chromosome to hybrid male sterility in house mice.

Hybrid sterility in the heterogametic sex is a common feature of speciation in animals. In house mice, the contribution of the Mus musculus musculus X chromosome to hybrid male sterility is large. It is not known, however, whether F1 male sterility is caused by X-Y or X-autosome incompatibilities or a combination of both.

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.

Adaptive evolution and effective population size in wild house mice.

Estimates of the proportion of amino acid substitutions that have been fixed by selection (α) vary widely among taxa, ranging from zero in humans to over 50% in Drosophila. This wide range may reflect differences in the efficacy of selection due to differences in the effective population size (N(e)). However, most comparisons have been made among distantly related organisms that differ not only in N(e) but also in many other aspects of their biology.

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.

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.

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.

The endothelial-specific regulatory mutation, Mvwf1, is a common mouse founder allele.

Mvwf1 is a cis-regulatory mutation previously identified in the RIIIS/J mouse strain that causes a unique tissue-specific switch in the expression of an N-acetylgalactosaminyltransferase, B4GALNT2, from intestinal epithelium to vascular endothelium. Vascular B4galnt2 expression results in aberrant glycosylation of von Willebrand Factor (VWF) and accelerated VWF clearance from plasma. We now report that 13 inbred mouse strains share the Mvwf1 tissue-specific switch and low VWF phenotype, including five wild-derived strains.

Genome-wide patterns of gene flow across a house mouse hybrid zone.

Hybrid zones between closely related species or subspecies provide useful settings for studying the genetic architecture of speciation. Using markers distributed throughout the mouse genome, we use a hybrid zone between two recently diverged species of house mice (Mus musculus and Mus domesticus) as a natural mapping experiment to identify genomic regions that may be involved in reproductive isolation. Using cline analysis we document a nearly 50-fold variation in level of introgression among markers.

Inefficient purifying selection: the mammalian Y chromosome in the rodent genus Mus.

Two related genes with potentially similar functions, one on the Y chromosome and one on the X chromosome, were examined to determine if they evolved differently because of their chromosomal positions. Six hundred fifty-seven base pairs of coding sequence of Jarid1d (Smcy) on the Y chromosome and Jarid1c (Smcx) on the X chromosome were sequenced in 13 rodent taxa. An analysis of replacement and silent substitutions, using a counting method designed for samples with small evolutionary distances, showed a significant difference between the two genes.

Male-driven evolution in closely related species of the mouse genus Mus.

Recently, other researchers have found that closely related primate species had a lower male-to-female mutation rate ratio (alpha) than distantly related species. To determine if this is a general phenomenon affecting other mammalian orders, eleven species or subspecies of the rodent genus Mus and two outgroup species were compared. Intron sequences from a gene in the nonrecombining region of the Y chromosome Jarid1d (Smcy) and its X chromosomal gametolog, Jarid1c (Smcx), were analyzed in a phylogenetic context.

Positive selection for indel substitutions in the rodent sperm protein catsper1.

Catsper1 is a voltage-gated calcium channel located in the plasma membrane of the sperm tail and is necessary for sperm motility and fertility in mice. We here examine the evolutionary pattern of Catsper1 from nine species of the rodent subfamily Murinae of family Muridae. We show that the rate of insertion/deletion (indel) substitutions in exon 1 of the gene is 4-15 times that in introns or neutral genomic regions, suggesting the presence of strong positive selection that promotes fixations of indel mutations in exon 1.

Evolutionary strata on the mouse X chromosome correspond to strata on the human X chromosome.

Lahn and Page previously observed that genes on the human X chromosome were physically arranged along the chromosome in "strata," roughly ordered by degree of divergence from related genes on the Y chromosome. They hypothesized that this ordering results from a historical series of suppressions of recombination along the mammalian Y chromosome, thereby allowing formerly recombining X and Y chromosomal genes to diverge independently. Here predictions of this hypothesis are confirmed in a nonprimate mammalian order, Rodentia, through an analysis of eight gene pairs from the X and Y chromosomes of the house mouse, Mus musculus.

Differential rates of evolution for the ZFY-related zinc finger genes, Zfy, Zfx, and Zfa in the mouse genus Mus.

A comparative study of the last exon of the zinc finger genes Zfx, Zfy, and Zfa from species of mice in the genus Mus was conducted to assess the extent of gene-specific and chromosome-specific effects on the evolutionary patterns among related X-, Y-, and autosomal-linked genes. Phylogenetic analyses of 29 sequences from Zfx, Zfa, and Zfy from 10 taxa were performed to infer relatedness among the zinc finger loci, and codon-based maximum likelihood analyses were conducted to assess evolutionary pattern among genes. Five models of nucleotide sequence evolution were applied and compared using a likelihood ratio test.

Tests for positive selection on immune and reproductive genes in closely related species of the murine genus mus.

We examine variation among species of Mus in four genes involved in reproduction and the immune response for evidence of positive selection: the sperm recognition gene Zp-3, the testis-determining locus Sry, the testicular cell surface matrix protein Tcp-1, and the immune system protein beta(2) m. We use likelihood ratio tests in the context of a well-supported phylogeny to determine whether models that allow for positively selected sites fit the sequences better than models that assume purifying selection. We then apply a Bayesian approach to identify particular sites in each gene that have a high posterior probability of being under positive selection.

Phylogenetic relationships in the genus mus, based on paternally, maternally, and biparentally inherited characters.

Several species in the rodent genus Mus are used as model research organisms, but comparative studies of these mice have been hampered by the lack of a well-supported phylogeny. We used DNA sequences from six genes representing paternally, maternally, and biparentally inherited regions of the genome to infer phylogenetic relationships among 10 species of Mus commonly used in laboratory research. Our sample included seven species from the subgenus Mus; one species each from the subgenera Pyromys, Coelomys, and Nannomys; and representatives from three additional murine genera, which served as outgroups in the phylogenetic analyses.

Molecular Phylogeny and Biogeography of the Native Rodents of Madagascar (Muridae: Nesomyinae): A Test of the Single-Origin Hypothesis.

Complete nucleotide sequences from the mitochondrial cytochrome b gene (1143 bp) were used to investigate the phylogenetic relationships among the native rodents of Madagascar. Specifically, this study examines whether the nine genera of nesomyines form a monophyletic group relative to other Old World murids. All nine of the nesomyine genera, including multiple individuals from 15 of the 21 described species, were included in the analysis, and their monophyly was assessed relative to the murid subfamilies Mystromyinae, Petromyscinae, Dendromurinae, Cricetomyinae, Murinae, Rhizomyinae, and Calomyscinae.

ABRUPT CLINE FOR SEX CHROMOSOMES IN A HYBRID ZONE BETWEEN TWO SPECIES OF MICE.

We compared the patterns of movement of sex chromosomal and autosomal loci along a 160 km transect across a zone of hybridization between M. domesticus and M. musculus in southern Germany and western Austria using seven genetic markers.