Patterns of morphological evolution in the mandible of the house mouse Mus musculus (Rodentia: Muridae)

Geographical variation in Eurasian red squirrel (Sciurus vulgaris L., 1758) mandibles and the issue of subspecies-level organization: a failure of history?

Sciurus vulgaris is a widespread, highly polytypic tree squirrel species, under which a large number of subspecies have been described. This study tests the robustness of the current subspecific classification by using geometric morphometrics to quantify morphological variation in mandible shape, along with canonical variates analysis to test hypotheses of morphological distinctiveness. Patterns of mandible allometry were examined in eight out of 16 currently recognized subspecies. The significance of the discriminate functions was tested statistically, and the iterative jackknife procedure was applied to evaluate stability of the subspecies-specific discriminant functions. Applying criteria that focus on shape diagnosability, rather than mean group differences, indicates that most regional subspecific groupings show intergradations and continuity in mandible shape and size and that allometric effects on mandible shape are negligible. Evidence of a distinct subspecies confined to the Iberian Peninsula (Sciurus vulgaris infuscatus) and a discrete group originating from an extinct, 19th century population in Dorset, UK were identified based on these mandibular data. All other regional subspecific groupings were not diagnosably different. These results suggest that most red squirrel subspecies might represent non-diagnosable morphological variants whose taxonomic validity seems doubtful. More generally, our results highlight the importance of applying objective, quantitative and reproducible criteria to the issue of subspecies delimitation.

A Practical Guide to Sliding and Surface Semilandmarks in Morphometric Analyses

Advances in imaging technologies, such as computed tomography (CT) and surface scanning, have facilitated the rapid generation of large datasets of high-resolution three-dimensional (3D) specimen reconstructions in recent years. The wealth of phenotypic information available from these datasets has the potential to inform our understanding of morphological variation and evolution. However, the ever-increasing ease of compiling 3D datasets has created an urgent need for sophisticated methods of capturing high-density shape data that reflect the biological complexity in form. Landmarks often do not take full advantage of the rich shape information available from high-resolution 3D specimen reconstructions, as they are typically restricted to sutures or processes that can be reliably identified across specimens and exclude most of the surface morphology. The development of sliding and surface semilandmark techniques has greatly enhanced the quantification of shape, but their application to diverse datasets can be challenging, especially when dealing with the variable absence of some regions within a structure. Using comprehensive 3D datasets of crania that span the entire clades of birds, squamates and caecilians, we demonstrate methods for capturing morphology across incredibly diverse shapes. We detail many of the difficulties associated with applying semilandmarks to comparable regions across highly disparate structures, and provide solutions to some of these challenges, while considering the consequences of decisions one makes in applying these approaches. Finally, we analyze the benefits of high-density sliding semilandmark approaches over landmark-only studies for capturing shape across diverse organisms and discuss the promise of these approaches for the study of organismal form.

Genetic vs environment influences on house mouse hybrid zone in Iran

Genetic divergence and environment influence on speciation process are the great deal studies over recent decades. One of the best ways for exploring the interaction of geography and genetics is the evaluation of hybrids in a contact zone. To understand if there is one or more hybrid zone between house mouse subspecies in Iran and what are the differences comparing these zones with European well-known hybrid zone, we performed this approach. Samples were live-trapped from Ilam city in west for sensu lato M. m. domesticus subspecies, and Neishabur city in north-east of Iran for sensu lato M. m. musculus subspecies. In five experimental groups, male and female mice of the two subspecies were crossed reciprocally to generate F1 hybrids, and then F1 offspring males and females were crossed also reciprocally between siblings to generate F2 hybrids. In the same manner as seen in European hybrid zone, hybridization between female M. m. musculus and male M. m. domesticus of all five groups showed male sterility in F1 generation, but intact female offspring. These sterile males comparing with a parent or healthy males showed low count and more abnormal sperm percentage in morphological and testis histological section studies. Comparing the results from this study with numerous studies carried out during several years on the European hybrid zone showed an equal condition of contact between two subspecies. Genetical elements have kept their same influence on postzygotic reproductive isolation more than environmental effects far from the Europe, here in Iran.

Rodent-borne diseases and their public health importance in Iran

Background

Rodents are reservoirs and hosts for several zoonotic diseases such as plague, leptospirosis, and leishmaniasis. Rapid development of industry and agriculture, as well as climate change throughout the globe, has led to change or increase in occurrence of rodent-borne diseases. Considering the distribution of rodents throughout Iran, the aim of this review is to assess the risk of rodent-borne diseases in Iran.

Methodology/Principal finding

We searched Google Scholar, PubMed, Science Direct, Scientific Information Database (SID), and Magiran databases up to September 2016 to obtain articles reporting occurrence of rodent-borne diseases in Iran and extract information from them. Out of 70 known rodent-borne diseases, 34 were reported in Iran: 17 (50%) parasitic diseases, 13 (38%) bacterial diseases, and 4 (12%) viral diseases. Twenty-one out of 34 diseases were reported from both humans and rodents. Among the diseases reported in the rodents of Iran, plague, leishmaniasis, and hymenolepiasis were the most frequent. The most infected rodents were Rattus norvegicus (16 diseases), Mus musculus (14 diseases), Rattus rattus (13 diseases), Meriones persicus (7 diseases), Apodemus spp. (5 diseases), Tatera indica (4 diseases), Meriones libycus (3 diseases), Rhombomys opimus (3 diseases), Cricetulus migratorius (3 diseases), and Nesokia indica (2 diseases).

Conclusions/Significance

The results of this review indicate the importance of rodent-borne diseases in Iran. Considering notable diversity of rodents and their extensive distribution throughout the country, it is crucial to pay more attention to their role in spreading infectious diseases for better control of the diseases.

This review showed that approximately half of the known rodent-borne diseases have been reported in Iran, half of which were reported both in humans and rodents. Most of the diseases were bacterial and parasitic. Plague, leishmaniasis, and hymenolepiasis were the most frequent diseases among rodent populations. Also, this review showed that among the rodent species, three commensal ones—R. norvegicus, M. musculus, and R. rattus—play an important role in the transmission of diseases to humans in Iran. Considering repeated reports of many of these diseases in humans and rodents, and the notable diversity and extensive distribution of rodents throughout Iran, it is crucial to pay adequate attention to rodents as a source of zoonotic infectious diseases in the country.

Craniofacial shape transition across the house mouse hybrid zone: implications for the genetic architecture and evolution of between-species differences

Craniofacial shape differences between taxa have often been linked to environmental adaptation, e.g., new food sources, or have been studied in the context of domestication. Evidence for the genetic basis of such phenotypic differences to date suggests that between-species as well as between-population variation has an oligogenic basis, i.e., few loci of large effect explain most of the variation. In mice, it has been shown that within-population craniofacial variation has a highly polygenic basis, but there are no data regarding the genetic basis of between-species differences in natural populations. Here, we address this question using a phenotype-focused approach. Using 3D geometric morphometrics, we phenotyped a panel of mice derived from a natural hybrid zone between Mus musculus domesticus and Mus mus musculus and quantify the transition of craniofacial shape along the hybridization gradient. We find a continuous shape transition along the hybridization gradient and unaltered developmental stability associated with hybridization. This suggests that the morphospace between the two subspecies is continuous despite reproductive isolation and strong barriers to gene flow. We show that quantitative changes in overall genome composition generate quantitative changes in craniofacial shape; this supports a highly polygenic basis for between-species craniofacial differences in the house mouse. We discuss our findings in the context of oligogenic versus polygenic models of the genetic architecture of morphological traits.

Once upon Multivariate Analyses: When They Tell Several Stories about Biological Evolution

Geometric morphometrics aims to characterize of the geometry of complex traits. It is therefore by essence multivariate. The most popular methods to investigate patterns of differentiation in this context are (1) the Principal Component Analysis (PCA), which is an eigenvalue decomposition of the total variance-covariance matrix among all specimens; (2) the Canonical Variate Analysis (CVA, a.k.a. linear discriminant analysis (LDA) for more than two groups), which aims at separating the groups by maximizing the between-group to within-group variance ratio; (3) the between-group PCA (bgPCA) which investigates patterns of between-group variation, without standardizing by the within-group variance. Standardizing within-group variance, as performed in the CVA, distorts the relationships among groups, an effect that is particularly strong if the variance is similarly oriented in a comparable way in all groups. Such shared direction of main morphological variance may occur and have a biological meaning, for instance corresponding to the most frequent standing genetic variation in a population. Here we undertake a case study of the evolution of house mouse molar shape across various islands, based on the real dataset and simulations. We investigated how patterns of main variance influence the depiction of among-group differentiation according to the interpretation of the PCA, bgPCA and CVA. Without arguing about a method performing ‘better’ than another, it rather emerges that working on the total or between-group variance (PCA and bgPCA) will tend to put the focus on the role of direction of main variance as line of least resistance to evolution. Standardizing by the within-group variance (CVA), by dampening the expression of this line of least resistance, has the potential to reveal other relevant patterns of differentiation that may otherwise be blurred.

Eurasian house mouse (Mus musculus L.) differentiation at microsatellite loci identifies the Iranian plateau as a phylogeographic hotspot

Background

The phylogeography of the house mouse (Mus musculus L.), an emblematic species for genetic and biomedical studies, is only partly understood, essentially because of a sampling bias towards its most peripheral populations in Europe, Asia and the Americas. Moreover, the present-day phylogeographic hypotheses stem mostly from the study of mitochondrial lineages. In this article, we complement the mtDNA studies with a comprehensive survey of nuclear markers (19 microsatellite loci) typed in 963 individuals from 47 population samples, with an emphasis on the putative Middle-Eastern centre of dispersal of the species.

Results

Based on correspondence analysis, distance and allele-sharing trees, we find a good coherence between geographical origin and genetic make-up of the populations. We thus confirm the clear distinction of the three best described peripheral subspecies, M. m. musculus, M. m. domesticus and M. m. castaneus. A large diversity was found in the Iranian populations, which have had an unclear taxonomic status to date. In addition to samples with clear affiliation to M. m. musculus and M. m. domesticus, we find two genetic groups in Central and South East Iran, which are as distinct from each other as they are from the south-east Asian M. m. castaneus. These groups were previously also found to harbor distinct mitochondrial haplotypes.

Conclusion

We propose that the Iranian plateau is home to two more taxonomic units displaying complex primary and secondary relationships with their long recognized neighbours. This central region emerges as the area with the highest known diversity of mouse lineages within a restricted geographical area, designating it as the focal place to study the mechanisms of speciation and diversification of this species.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-015-0306-4) contains supplementary material, which is available to authorized users.

Use of a natural hybrid zone for genomewide association mapping of craniofacial traits in the house mouse

The identification of the genes involved in morphological variation in nature is still a major challenge. Here, we explore a new approach: we combine 178 samples from a natural hybrid zone between two subspecies of the house mouse (Mus musculus domesticus and Mus musculus musculus), and high coverage of the genome (~ 145K SNPs) to identify loci underlying craniofacial shape variation. Due to the long history of recombination in the hybrid zone, high mapping resolution is anticipated. The combination of genomes from subspecies allows the mapping of both, variation within subspecies and inter-subspecific differences, thereby increasing the overall amount of causal genetic variation that can be detected. Skull and mandible shape were measured using 3D landmarks and geometric morphometrics. Using principal component axes as phenotypes, and a linear mixed model accounting for genetic relatedness in the mapping populations, we identified nine genomic regions associated with skull shape and 10 with mandible shape. High mapping resolution (median size of significant regions = 148 kb) enabled identification of single or few candidate genes in most cases. Some of the genes act as regulators or modifiers of signalling pathways relevant for morphological development and bone formation, including several with known craniofacial phenotypes in mice and humans. The significant associations combined explain 13% and 7% of the skull and mandible shape variation, respectively. In addition, a positive correlation was found between chromosomal length and proportion of variation explained. Our results suggest a complex genetic architecture for shape traits and support a polygenic model.

Lines of least resistance and genetic architecture of house mouse (Mus musculus) mandible shape

Evolution along "lines of least resistance (LLR)" is a well-established phenomenon, which is ultimately based on variational properties of the developmental system. However, it has remained unclear which aspects of development are responsible for observed distributions of variation. This article suggests that house mouse mandible shape may present an opportunity for future research in this field. The genetic architecture of mouse mandible shape has been investigated in the laboratory, and its evolution has been surveyed in studies on natural variation. Here, I ask whether evolutionary diversification of mandible shape follows "LLR" by comparing principal directions of genetic and evolutionary variation, and I assess the potential contribution of specific genomic regions to evolutionary divergence along these directions. The role of two aspects of development, QTL number (presumably reflecting mutational target size) and canalization, is comparatively assessed. Overall, our results demonstrate a strong tendency of genetic and evolutionary systems to vary along similar directions, suggesting that mandible shape evolves along LLR at the level of populations, subspecies and species. At the level of genetic factors, effects bearing similarity to directions of evolution are significantly overrepresented, providing support for the mutational target size hypothesis. A role for canalization is not supported by a clear correlation between directions of evolution and size of genetic effects; however, the evidence for canalization remains ambiguous. These results provide some insights into how the developmental system may shape the variational properties of genetic systems and thus influence the direction of evolution.

The complex ontogenetic trajectory of mandibular shape in a laboratory mouse

The mouse mandible is a popular model system that continues to be the focus of studies in evo-devo and other fields. Yet, little attention has been given to the role of postnatal growth in producing the adult form. Using cleared and stained specimens, we describe the timing of tooth and jaw development and changes in jaw size and shape from postnatal day 1 (p1) through weaning to adulthood. We found that tooth development is relatively advanced at birth, and that the functional adult dentition is in place by p15 (just before the start of weaning). Shape analysis showed that the trajectory of mandible shape changes direction at least twice between birth and adulthood, at p7 and p15. At each stage there are changes in shape to all tooth- and muscle-bearing regions and, at each change of direction, all of these regions change their pattern of growth. The timing of the changes in direction in Mus suggests there are signals that redirect growth patterns independently of changes in function and loading associated with weaning and jaw muscle growth. A better understanding of these signals and how they produce a functionally integrated mandible may help explain the mechanisms guiding evolutionary trends and patterns of plasticity and may also provide valuable clues to therapeutic manipulation of growth to alleviate the consequences of trauma or disease.

Jaw growth in the absence of teeth: the developmental morphology of edentulous mandibles using the p63 mouse mutant

Mammalian tooth and jaw development must be coordinated well enough that these systems continue to function together properly throughout growth, thus optimizing an animal's survival and fitness, as well as a species' success. The persistent question is how teeth and jaws remain developmentally and functionally viable despite sometimes monumental evolutionary changes to tooth and jaw shape and size. Here we used the p63 mouse mutant to test the effect of tooth development - or the lack thereof - on normal mandible developmental morphology. Using 3D geometric morphometrics, we compared for the first time mandible shape among mice with normal tooth and jaw development against p63 double knock-out mice, with failed tooth development but apparently normal jaw development. Mandible shape differed statistically between toothless (p63(-/-) ) and toothed (p63(+/-) , p63(+/+) ) mice as early as embryonic day (E) 18. As expected, most of the shape difference in the p63(-/-) mandibles was due to underdeveloped alveolar bone related to arrested odontogenesis in these E18-aged mice. Mandible shape did not differ statistically between p63(+/-) and p63(+/+) adult mice, which showed normal tooth development. Our results support the idea of a gene regulatory network that is exclusive to the mandible and independent of the dentition. This study also underscores the biomechanical impact of the teeth on the developing alveolar bone. Importantly, this work shows quantitatively that the p63 mutant is an apt model with which to study mandible morphogenesis in isolation of odontogenesis to clarify developmental relationships between the teeth and jaws.

Invasive house mice facing a changing environment on the Sub-Antarctic Guillou Island (Kerguelen Archipelago)

Adaptation to new environments is a key feature in evolution promoting divergence in morphological structures under selection. The house mouse (Mus musculus domesticus) introduced on the Sub-Antarctic Guillou Island (Kerguelen Archipelago) had and still has to face environmental conditions that likely shaped the pattern and pace of its insular evolution. Since mouse arrival on the island, probably not more than two centuries ago, ecological conditions dramatically differed from those available to their Western European commensal source populations. In addition, over the last two decades, the plant and animal communities of Guillou Island were considerably modified by the eradication of rabbits, the effects of climate change and the spread of invasive species detrimental to native communities. Under such a changing habitat, the mouse response was investigated using a morphometric quantification of mandible and molar tooth, two morphological structures related to food processing. A marked differentiation of the insular mice compared with their relatives from Western Europe was documented for both mandibles and molar shapes. Moreover, these shapes changed through the 16 years of the record, in agreement with expectations of drift for the molar, but more than expected by chance for the mandible. These results suggest that mice responded to the recent changes in food resources, possibly with a part of plastic variation for the mandible prone to bone remodelling. This pattern exemplifies the intricate interplay of evolution, ecology and plasticity that is a probable key of the success of such an invasive rodent facing pronounced shifts in food resources exploitation under a changing environment.