Genetic distinction between contiguous urban and rural multimammate mice in Tanzania despite gene flow.

Special conditions are required for genetic differentiation to arise at a local geographical scale in the face of gene flow. The Natal multimammate mouse, Mastomys natalensis, is the most widely distributed and abundant rodent in sub-Saharan Africa. A notorious agricultural pest and a natural host for many zoonotic diseases, it can live in close proximity to humans and appears to compete with other rodents for the synanthropic niche. We surveyed its population genetic structure across a 180-km transect in central Tanzania along which the landscape varied between agricultural land in a rural setting and natural woody vegetation, rivers, roads and a city (Morogoro). We sampled M. natalensis across 10 localities and genotyped 15 microsatellite loci from 515 individuals. Hierarchical STRUCTURE analyses show a K-invariant pattern distinguishing Morogoro suburbs (located in the centre of the transect) from nine surrounding rural localities. Landscape connectivity analyses in Circuitscape and comparison of rainfall patterns suggest that neither geographical isolation nor natural breeding asynchrony could explain the genetic differentiation of the urban population. Using the isolation-with-migration model implemented in IMa2, we inferred that a split between suburban and rural populations would have occurred recently (<150 years ago) with higher urban effective population density consistent with an urban source to rural sink of effective migration. The observed genetic differentiation of urban multimammate mice is striking given the uninterrupted distribution of the animal throughout the landscape and the high estimates of effective migration (2Ne M = 3.0 and 29.7), suggesting a strong selection gradient across the urban boundary.

The evolutionary history of hepaciviruses.

In the search for natural reservoirs of hepatitis C virus (HCV), a broad diversity of non-human viruses within the Hepacivirus genus has been uncovered. However, the evolutionary dynamics that shaped the diversity and timescale of hepaciviruses evolution remain elusive. To gain further insights into the origins and evolution of this genus, we screened a large dataset of wild mammal samples (n = 1,672) from Africa and Asia, and generated 34 full-length hepacivirus genomes. Phylogenetic analysis of these data together with publicly available genomes emphasizes the importance of rodents as hepacivirus hosts and we identify 13 rodent species and 3 rodent genera (in Cricetidae and Muridae families) as novel hosts of hepaciviruses. Through co-phylogenetic analyses, we demonstrate that hepacivirus diversity has been affected by cross-species transmission events against the backdrop of detectable signal of virus-host co-divergence in the deep evolutionary history. Using a Bayesian phylogenetic multidimensional scaling approach, we explore the extent to which host relatedness and geographic distances have structured present-day hepacivirus diversity. Our results provide evidence for a substantial structuring of mammalian hepacivirus diversity by host as well as geography, with a somewhat more irregular diffusion process in geographic space. Finally, using a mechanistic model that accounts for substitution saturation, we provide the first formal estimates of the timescale of hepacivirus evolution and estimate the origin of the genus to be about 22 million years ago. Our results offer a comprehensive overview of the micro- and macroevolutionary processes that have shaped hepacivirus diversity and enhance our understanding of the long-term evolution of the Hepacivirus genus.

Genetic structure and contrasting selection pattern at two major histocompatibility complex genes in wild house mouse populations.

The mammalian major histocompatibility complex (MHC) is a tightly linked cluster of immune genes, and is often thought of as inherited as a unit. This has led to the hope that studying a single MHC gene will reveal patterns of evolution representative of the MHC as a whole. In this study we analyse a 1000-km transect of MHC variation traversing the European house mouse hybrid zone to compare signals of selection and patterns of diversification at two closely linked MHC class II genes, H-2Aa and H-2Eb. We show that although they are 0.01 cM apart (that is, recombination is expected only once in 10 000 meioses), disparate evolutionary patterns were detected. H-2Aa shows higher allelic polymorphism, faster allelic turnover due to higher mutation rates, stronger positive selection at antigen-binding sites and higher population structuring than H-2Eb. H-2Eb alleles are maintained in the gene pool for longer, including over separation of the subspecies, some H-2Eb alleles are positively and others negatively selected and some of the alleles are not expressed. We conclude that studies on MHC genes in wild-living vertebrates can give substantially different results depending on the MHC gene examined and that the level of polymorphism in a related species is a poor criterion for gene choice.

Coevolutionary relationship between helminth diversity and MHC class II polymorphism in rodents.

Parasite-mediated selection on major histocompatibility complex (MHC) genes has mainly been explored at the intraspecific level, although many molecular studies have revealed trans-species polymorphism. Interspecific patterns of MHC diversity might reveal factors responsible for the long-term evolution of MHC polymorphism. We hypothesize that host taxa harbouring high parasite diversity should exhibit high levels of MHC genetic diversity. We test this assumption using data on rodent species and their helminth parasites compiled from the literature. Controlling for similarity due to common descent, we present evidence indicating that high helminth species richness in rodent species is associated with increased MHC class II polymorphism. Our results are consistent with the idea that parasites sharing a long-term coevolutionary history with their hosts are the agents of selection explaining MHC polymorphism.

Phylogeny of the Trichostrongylina (Nematoda) inferred from 28S rDNA sequences.

We produced a molecular phylogeny of species within the order Strongylida (bursate nematodes) using the D1 and D2 domains of 28S rDNA, with 23 new sequences for each domain. A first analysis using Caenorhabditis elegans as an outgroup produced a tree with low resolution in which three taxa (Dictyocaulus filaria, Dictyocaulus noerneri, and Metastrongylus pudendotectus) showed highly divergent sequences. In a second analysis, these three species and C. elegans were removed and an Ancylostomatina, Bunostomum trigonocephalum, was chosen (on the basis of previous morphological analyses) as the outgroup for an analysis of the phylogenetic relationships between and within the Strongylina (strongyles) and Trichostrongylina (trichostrongyles). A very robust tree was obtained. The Trichostrongylina were monophyletic, but the Strongylina were paraphyletic, though this requires confirmation. Within the Trichostrongylina, the three superfamilies defined from morphological characters are confirmed, with the Trichostrongyloidea sister group to a clade including the Molineoidea and Heligmosomoidea. Within the Trichostrongyloidea, the Cooperiidae, Trichostrongylidae, and Haemonchidae were polytomous, the Haemonchinae were monophyletic, but the Ostertagiinae were paraphyletic. The sister-group relationships between Molineoidea and Heligmosomoidea were unsuspected from previous morphological analysis. No unequivocal morphological synapomorphy could be found for the grouping Molineoidea + Heligmosomoidea, but none was found which contradicted it.