A new perspective on the taxonomy and systematics of Arvicolinae (Gray, 1821) and a new time-calibrated phylogeny for the clade

Background

Arvicoline rodents are one of the most speciose and rapidly evolving mammalian lineages. Fossil arvicolines are also among the most common vertebrate fossils found in sites of Pliocene and Pleistocene age in Eurasia and North America. However, there is no taxonomically robust, well-supported, time-calibrated phylogeny for the group.

Methods

Here we present well-supported hypotheses of arvicoline rodent systematics using maximum likelihood and Bayesian inference of DNA sequences of two mitochondrial genes and three nuclear genes representing 146 (82% coverage) species and 100% of currently recognized arvicoline genera. We elucidate well-supported major clades, reviewed the relationships and taxonomy of many species and genera, and critically compared our resulting molecular phylogenetic hypotheses to previously published hypotheses. We also used five fossil calibrations to generate a time-calibrated phylogeny of Arvicolinae that permitted some reconciliation between paleontological and neontological data.

Results

Our results are largely congruent with previous molecular phylogenies, but we increased the support in many regions of the arvicoline tree that were previously poorly-sampled. Our sampling resulted in a better understanding of relationships within Clethrionomyini, the early-diverging position and close relationship of true lemmings (Lemmus and Myopus) and bog lemmings (Synaptomys), and provided support for recent taxonomic changes within Microtini. Our results indicate an origin of ∼6.4 Ma for crown arvicoline rodents. These results have major implications (e.g., diversification rates, paleobiogeography) for our confidence in the fossil record of arvicolines and their utility as biochronological tools in Eurasia and North America during the Quaternary.

Biogeography of rodents in Iran: species richness, elevational distribution and their environmental correlates

Rodent biogeographic studies are disproportionately scarce in Iran, however, they are an ideal system to understand drivers of biodiversity distributions in the country. The aims of the present research are to determine (i) the pattern of rodent richness across the country, (ii) quantify their elevational distribution patterns, and (iii) explore the underlying mechanisms. To reach these goals, an updated species list was compiled based on the latest taxonomic revisions, published until December 2021. We mapped all 76 rodent species distributions to develop the first map of rodent richness in Iran. We furthermore investigated their elevational distribution patterns in the following four geographic regions based on 100 m intervals; the Zagros Mountains, north of Alborz Mountains, south of Alborz and Kopet-Dagh mountains, and central and east mountains. North-east of Iran, Zagros Mountains, Alborz Mountains, and northwestern of Iran showed the highest richness and were identified as biodiversity hotspots of rodents in the country. This study highlights the importance of past climate change as the key driver of rodent richness in Iran. We showed that rodents’ elevational distribution patterns differ among geographic regions. Areas and elevational zones with the highest species richness should be prioritized for the conservation planning of rodents in Iran.

Divergence time estimation using ddRAD data and an isolation-with-migration model applied to water vole populations of Arvicola

Molecular dating methods of population splits are crucial in evolutionary biology, but they present important difficulties due to the complexity of the genealogical relationships of genes and past migrations between populations. Using the double digest restriction-site associated DNA (ddRAD) technique and an isolation-with-migration (IM) model, we studied the evolutionary history of water vole populations of the genus Arvicola, a group of complex evolution with fossorial and semi-aquatic ecotypes. To do this, we first estimated mutation rates of ddRAD loci using a phylogenetic approach. An IM model was then used to estimate split times and other relevant demographic parameters. A set of 300 ddRAD loci that included 85 calibrated loci resulted in good mixing and model convergence. The results showed that the two populations of A. scherman present in the Iberian Peninsula split 34 thousand years ago, during the last glaciation. In addition, the much greater divergence from its sister species, A. amphibius, may help to clarify the controversial taxonomy of the genus. We conclude that this approach, based on ddRAD data and an IM model, is highly useful for analyzing the origin of populations and species.

Plague reservoir species throughout the world

Plague has been known since ancient times as a re-emerging infectious disease, causing considerable socioeconomic burden in regional hotspots. To better understand the epidemiological cycle of the causative agent of the plague, its potential occurrence, and possible future dispersion, one must carefully consider the taxonomy, distribution, and ecological requirements of reservoir-species in relation either to natural or human-driven changes (e.g. climate change or urbanization). In recent years, the depth of knowledge on species taxonomy and species composition in different landscapes has undergone a dramatic expansion, driven by modern taxonomic methods such as synthetic surveys that take into consideration morphology, genetics, and the ecological setting of captured animals to establish their species identities. Here, we consider the recent taxonomic changes of the rodent species in known plague reservoirs and detail their distribution across the world, with a particular focus on those rodents considered to be keystone host species. A complete checklist of all known plague-infectable vertebrates living in plague foci is provided as a Supporting Information table.

Photoperiod is involved in the regulation of seasonal breeding in male water voles (Arvicola terrestris)

Mammals living at temperate latitudes typically display annual cyclicity in their reproductive activity: births are synchronized when environmental conditions are most favorable. In a majority of these species, day length is the main proximate factor used to anticipate seasonal changes and to adapt physiology. The brain integrates this photoperiodic signal through key hypothalamic structures, which regulate the reproductive axis. In this context, our study aimed to characterize regulations that occur along the hypothalamo-pituitary-gonadal (HPG) axis in male fossorial water voles (Arvicola terrestris, also known as Arvicola amphibius) throughout the year and to further probe the implication of photoperiod in these seasonal regulations. Our monthly field monitoring showed dramatic seasonal changes in the morphology and activity of reproductive organs, as well as in the androgen-dependent lateral scent glands. Moreover, our data uncovered seasonal variations at the hypothalamic level. During the breeding season, kisspeptin expression in the arcuate nucleus (ARC) decreases, while RFRP3 expression in the dorsomedial hypothalamic nucleus (DMH) increases. Our follow-up laboratory study revealed activation of the reproductive axis and confirmed a decrease in kisspeptin expression in males exposed to a long photoperiod (summer condition) compared with those maintained under a short photoperiod (winter condition) that retain all features reminiscent of sexual inhibition. Altogether, our study characterizes neuroendocrine and anatomical markers of seasonal reproductive rhythmicity in male water voles and further suggests that these seasonal changes are strongly impacted by photoperiod.

Field study reveals morphological and neuroendocrine correlates of seasonal breeding in female water voles, Arvicola terrestris

Seasonally breeding mammals display timely physiological switches between reproductive activity and sexual rest, which ensure synchronisation of births at the most favourable time of the year. These switches correlate with seasonal changes along the hypothalamo-pituitary-gonadal axis, but they are primarily orchestrated at the hypothalamic level through environmental control of KISS1-dependent GnRH release. Our field study shows that births of fossorial water voles, Arvicola terrestris, are concentrated between March and October, which indicates the existence of an annual reproductive cycle in this species. Monthly field monitoring for over a year further reveals dramatic seasonal changes in the morphology of the ovary, uterus and lateral scent glands, which correlate with the reproductive status. Finally, we demonstrate seasonal variation in kisspeptin expression within the hypothalamic arcuate nucleus. Altogether, this study demonstrates a marked rhythm of seasonal breeding in the water vole and we speculate that this is governed by seasonal changes in photoperiod.

Postnatal ontogeny of the femur in fossorial and semiaquatic water voles in the 3D-shape space

Water voles of the genus Arvicola constitute an excellent subject to investigate to which extent function affects postnatal developmental growth of limb structures in phylogenetically close species. We performed a comparative analysis of postweaning femur form changes between Arvicola sapidus (semiaquatic) and Arvicola scherman (fossorial) using three-dimensional landmark-based geometric morphometrics. In both species, we observed greater femur robustness in juvenile individuals than in adult ones, probably due to the accommodation of high loads on the bone during initial locomotor efforts. Significant interspecific differences were also found in the femur size and shape of adult specimens, as well as in the postnatal allometric and phenotypic trajectories. In terms of phenotypic variation, fossorial water voles show relatively wider third and lesser trochanters, and greater femur robustness than A. sapidus, characters associated to the digging activity. In contrast, A. sapidus displays a slight increase of the greater trochanter in comparison with A. scherman, which is seemingly an adaptive response for enhancing propulsion through the water. Results evidence that certain morphological traits and differences between A. sapidus and A. scherman in the allometric and phenotypic trajectories of the femur are associated with their different locomotor mode.

A taxonomic revision of fat dormice, genus Glis (Rodentia)

We address in this study the taxonomic status of the two major phylogenetic lineages of fat dormice, genus Glis. These lineages show unique mutations at 43 positions of the cytochrome b alignment and are classified as two distinct species, the European fat dormouse Glis glis (Linnaeus, C. [1766]. Systema naturae per regna tria naturae, secundum classes, ordines, genera, species, cum characteribus, differentiis synonymis, locis, Vol. 1. Laurentii Salvii, Holmiae [Stockholm]) and the Iranian fat dormouse Glis persicus (Erxleben, I.C.P. [1777]. Systema regni animalis per classes, ordines, genera, species, varietates cum synonymia et historia animalium. Classis I. Mammalia. Impensis Weygandianis, Lipsia [Leipzig]). The European dormouse is widespread in Europe, Asia Minor and the Caucasus, while the Iranian dormouse occupies the southern Caspian coast in Iran. Ranges are presumably delimited in Azerbaijan by rivers Kura and Aras. The two species differ categorically in size of the glans penis, size and shape of the baculum and in width of the posterior extension of the premaxilla. The Iranian fat dormouse has on average a more blackish distal half of the tail, a higher count for abdominal nipples, and a longer maxillary tooth-row. Intraspecific structuring in G. glis indicates a taxonomic complexity which is not yet understood and requires a comprehensive systematic revision. To define the nominal taxon objectively we designate voucher PMS 27369 (Slovenian Museum of Natural History) as the neotype for G. glis, therefore restricting the type locality for the species to Mt. Krim in Slovenia.

Three-dimensional geometric morphometric analysis of the humerus: Comparative postweaning ontogeny between fossorial and semiaquatic water voles (Arvicola)

Different types of locomotion in phylogenetically close rodent species can lead to significantly different growth patterns of certain skeletal structures. In the present study, we compared the allometric and phenotypic trajectories of the humerus in semiaquatic (Arvicola sapidus) and fossorial (Arvicola scherman) water vole taxa, using three-dimensional geometric morphometrics, to investigate the relationships between functional and ontogenetic differences. Results revealed shared humerus traits between A. sapidus and A. scherman, specifically an expansion of the epicondylar and deltopectoral crests along postnatal ontogeny. In both species, the humerus of young specimens is more robust than in adults, possibly as a compensatory response for lower bone stiffness. However, significant interspecific differences were detected in all components of allometric and phenotypic trajectories. Noticeably divergent allometric trajectories were observed, probably as a result of different functional pressures exerted on this bone. Important differences in the form of the adult humerus between taxa were also found, particularly in features located in muscle insertion zones. Furthermore, the allometric regression revealed certain shape variation not associated with size in A. scherman, suggesting mechanical stress produced by the persistent digging activity during adulthood. A. scherman is a chisel-tooth digger that shares several traits in the humerus morphology with scratch-digger rodent species. Nevertheless, these shared characteristics are less pronounced in fossorial water voles, which is congruent with the different implications of the forelimb in the digging activity in these two types of diggers.