Article

Genetic structure, ecological versatility, and skull shape differentiation in Arvicola water voles (Rodentia, Cricetidae)

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Abstract

Water voles from the genus Arvicola display an amazing ecological versatility, with aquatic and fossorial populations. The Southern water vole (Arvicola sapidus) is largely accepted as a valid species, as well as the newly described Arvicola persicus. In contrast, the taxonomic status and evolutionary relationships within Arvicola amphibius sensu lato had caused a long‐standing debate. The phylogenetic relationships among Arvicola were reconstructed using the mitochondrial cytochrome b gene. Four lineages within A. amphibius s.l. were identified with good support: Western European, Eurasiatic, Italian, and Turkish lineages. Fossorial and aquatic forms were found together in all well‐sampled lineages, evidencing that ecotypes do not correspond to distinct species. However, the Western European lineage mostly includes fossorial forms whereas the Eurasiatic lineage tends to include mostly aquatic forms. A morphometric analysis of skull shape evidenced a convergence of aquatic forms of the Eurasiatic lineage toward the typically aquatic shape of A. sapidus. The fossorial form of the Western European lineage, in contrast, displayed morphological adaptation to tooth‐digging behavior, with expanded zygomatic arches and proodont incisors. Fossorial Eurasiatic forms displayed intermediate morphologies. This suggests a plastic component of skull shape variation, combined with a genetic component selected by the dominant ecology in each lineage. Integrating genetic distances and other biological data suggest that the Italian lineage may correspond to an incipient species (Arvicola italicus). The three other lineages most probably correspond to phylogeographic variations of a single species (A. amphibius), encompassing the former A. amphibius, Arvicola terrestris, Arvicola scherman, and Arvicola monticola.

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... Arvicola amphibius populates aquatic habitats both in lowlands and mountains from most of Europe (excluding the Iberian Peninsula) to northwestern China 22 . Although most populations are semi-aquatic, there are also fossorial ecotypes 24,25,35 . These two ecotypes are geographically separated but may coexist in some areas of central Europe and cannot be distinguished with mitochondrial data 24 . ...
... As for the other nodes of the population tree, it should be taken into account that we have a much smaller number of samples to properly resolve them. Only one specimen was available for the central European population of A. scherman and, for A. amphibius, we only had samples from the semi-aquatic populations 24 ; we are therefore likely not to have fossorial ecotypes of A. amphibius. Hence, the estimated divergence dates and other model parameters as well as the conclusions should be taken with caution. ...
... The genome-wide data obtained here may also shed some light on the controversy about the species status of A. scherman and A. amphibius 24,25,28 , assuming that our samples are representative of both. The two taxa appeared clearly separated in the PCA ( Fig. 2A), the Structure analysis with K = 2 (Fig. 2B), and the genomic tree (Supplementary Fig. S1). ...
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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.
... Dentro de su amplia distribución, que abarca desde la Península Ibérica hasta China (Reichestein 1982), se distinguen dos ecotipos, uno vinculado a los medios acuáticos, y otro de hábitos terrestres excavadores (Ventura y Gosalbez 1988), siendo este último el que ocasiona los daños a la agricultura (Somoano 2020). Existe gran controversia en cuanto a la taxonomía de este roedor (Ventura 2007;Musser y Carleton 2005;Mahmoudi et al. 2020;Chevret et al. 2020), tendiendo los trabajos más actuales a considerar que A. amphibius, A. terrestris, A. scherman y A. monticola son distintas formas de una única especie, que sería A. amphibius (Chevret et al. 2020). No obstante, en el presente trabajo hemos preferido mantener la denominación de A. scherman, por ser la recogida en el inventario oficial de especies terrestres (MI-TECO 2020) y el utilizado en los últimos trabajos publicados sobre la misma en nuestra región (Somoano, 2020), dejando claro que nos referimos a la forma ecoetológica cavadora. ...
... Dentro de su amplia distribución, que abarca desde la Península Ibérica hasta China (Reichestein 1982), se distinguen dos ecotipos, uno vinculado a los medios acuáticos, y otro de hábitos terrestres excavadores (Ventura y Gosalbez 1988), siendo este último el que ocasiona los daños a la agricultura (Somoano 2020). Existe gran controversia en cuanto a la taxonomía de este roedor (Ventura 2007;Musser y Carleton 2005;Mahmoudi et al. 2020;Chevret et al. 2020), tendiendo los trabajos más actuales a considerar que A. amphibius, A. terrestris, A. scherman y A. monticola son distintas formas de una única especie, que sería A. amphibius (Chevret et al. 2020). No obstante, en el presente trabajo hemos preferido mantener la denominación de A. scherman, por ser la recogida en el inventario oficial de especies terrestres (MI-TECO 2020) y el utilizado en los últimos trabajos publicados sobre la misma en nuestra región (Somoano, 2020), dejando claro que nos referimos a la forma ecoetológica cavadora. ...
Article
La rata topera (Arvicola scherman) es una especie de gran interés, tanto por su papel como presa de multitud de depredadores, como por el impacto de sus daños sobre la agricultura. Las variaciones en su abundancia poblacional y el papel de los factores que la modulan han sido ampliamente estudiadas en el norte de Europa, pero hasta el momento, se carecía de esta información para las poblaciones del Pirineo. En el presente trabajo se exponen los resultados obtenidos en el plan de monitorización de la especie en Navarra desde 2016 hasta 2020, describiendo tanto los cambios de abundancia registrados, como la influencia de los factores ambientales y de gestión agroganadera analizados. Describimos una variación de la abundancia a lo largo del año, con valores significativamente mayores en primavera que en verano; y entre los 5 años de muestreo, con una abundancia significativamente mayor en 2016 y 2020. La pluviometría acumulada en los meses previos al censo y el pastoreo con ovejas han sido los factores retenidos en los modelos con influencia significativa. Ambos han ejercido un efecto positivo sobre la rata topera, aumentando su abundancia al incrementarse la pluviometría y con el aprovechamiento con ganado ovino. Se discute el papel de estos factores y otras variables de estructura del paisaje y de gestión agrícola en los cambios de abundancia poblacional de la rata topera.
... In the taxonomic review of this genus by Musser and Carleton (2005), three species were accepted: the southwestern water vole, A. sapidus Miller, 1908 (semiaquatic); the montane water vole, Arvicola scherman (Shaw, 1801) (fossorial); and the European water vole, Arvicola amphibius (Linnaeus, 1758) (semiaquatic or mostly semiaquatic). Although A. sapidus is widely accepted as a valid species, recent studies based on analyses of genetic data have given rise to controversy on the taxonomy of the formerly accepted A. terrestris (for details, see Chevret et al., 2020;Kryštufek et al., 2015;Mahmoudi et al., 2020;Pardiñas et al., 2017;Ventura & Casado-Cruz, 2011 and references therein). As for the Iberian populations analyzed in the present study, according to these new results, fossorial water voles from the Pyrenees could be attributed to A. amphibius sensu lato (Kryštufek et al., 2015), Arvicola monticola (Mahmoudi et al., 2020;Pardiñas et al., 2017) or A. amphibius (Chevret et al., 2020). ...
... Although A. sapidus is widely accepted as a valid species, recent studies based on analyses of genetic data have given rise to controversy on the taxonomy of the formerly accepted A. terrestris (for details, see Chevret et al., 2020;Kryštufek et al., 2015;Mahmoudi et al., 2020;Pardiñas et al., 2017;Ventura & Casado-Cruz, 2011 and references therein). As for the Iberian populations analyzed in the present study, according to these new results, fossorial water voles from the Pyrenees could be attributed to A. amphibius sensu lato (Kryštufek et al., 2015), Arvicola monticola (Mahmoudi et al., 2020;Pardiñas et al., 2017) or A. amphibius (Chevret et al., 2020). Since this point remains unsolved, we decided to follow the taxonomic arrangement by Musser and Carleton (2005) to clearly distinguish between typical fossorial (A. ...
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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 post‐weaning femur form changes between Arvicola sapidus (semi‐aquatic) and A. 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.
... Dentro de su amplia distribución, que abarca desde la Península Ibérica hasta China (Reichestein 1982), se distinguen dos ecotipos, uno vinculado a los medios acuáticos, y otro de hábitos terrestres excavadores (Ventura y Gosalbez 1988), siendo este último el que ocasiona los daños a la agricultura (Somoano 2020). Existe gran controversia en cuanto a la taxonomía de este roedor (Ventura 2007;Musser y Carleton 2005;Mahmoudi et al. 2020;Chevret et al. 2020), tendiendo los trabajos más actuales a considerar que A. amphibius, A. terrestris, A. scherman y A. monticola son distintas formas de una única especie, que sería A. amphibius (Chevret et al. 2020). No obstante, en el presente trabajo hemos preferido mantener la denominación de A. scherman, por ser la recogida en el inventario oficial de especies terrestres (MI-TECO 2020) y el utilizado en los últimos trabajos publicados sobre la misma en nuestra región (Somoano, 2020), dejando claro que nos referimos a la forma ecoetológica cavadora. ...
... Dentro de su amplia distribución, que abarca desde la Península Ibérica hasta China (Reichestein 1982), se distinguen dos ecotipos, uno vinculado a los medios acuáticos, y otro de hábitos terrestres excavadores (Ventura y Gosalbez 1988), siendo este último el que ocasiona los daños a la agricultura (Somoano 2020). Existe gran controversia en cuanto a la taxonomía de este roedor (Ventura 2007;Musser y Carleton 2005;Mahmoudi et al. 2020;Chevret et al. 2020), tendiendo los trabajos más actuales a considerar que A. amphibius, A. terrestris, A. scherman y A. monticola son distintas formas de una única especie, que sería A. amphibius (Chevret et al. 2020). No obstante, en el presente trabajo hemos preferido mantener la denominación de A. scherman, por ser la recogida en el inventario oficial de especies terrestres (MI-TECO 2020) y el utilizado en los últimos trabajos publicados sobre la misma en nuestra región (Somoano, 2020), dejando claro que nos referimos a la forma ecoetológica cavadora. ...
Article
Full-text available
Resumen: La rata topera (Arvicola scherman) es una especie de gran interés, tanto por su papel como presa de multitud de depredadores, como por el impacto de sus daños sobre la agricultura. Las variaciones en su abundancia poblacional y el papel de los factores que la modulan han sido ampliamente estudiadas en el norte de Europa, pero hasta el momento, se carecía de esta información para las poblaciones del Pirineo. En el presente trabajo se exponen los resultados obtenidos en el plan de monitorización de la especie en Navarra desde 2016 hasta 2020, describiendo tanto los cambios de abundancia registrados, como la influencia de los factores ambientales y de gestión agroganadera analizados. Describimos una variación de la abundancia a lo largo del año, con valores significativamente mayores en primavera que en verano; y entre los 5 años de muestreo, con una abundancia significativamente mayor en 2016 y 2020. La pluviometría acumulada en los meses previos al censo y el pastoreo con ovejas han sido los factores retenidos en los modelos con influencia significativa. Ambos han ejercido un efecto positivo sobre la rata topera, aumentando su abundancia al incrementarse la pluviometría y con el aprovechamiento con ganado ovino. Se discute el papel de estos factores y otras variables de estructura del paisaje y de gestión agrícola en los cambios de abundancia poblacional de la rata topera. Abstract: The Fossorial Water Vole (Arvicola scherman) is a species of great interest, both because of its role as prey for a wide variety of predators, and the damages on agriculture. The variation in its population abundance and the factors that modulate it have been widely studied in northern Europe, but they are rather unknown for Pyrenean populations. Here we show the results obtained in the monitoring plan for the species in Navarra from 2016 to 2020, describing both the inter- and intra-annual changes in population abundance, as well as the effect of environmental factors and agricultural management. We found intra-annual variation in its abundance, with significantly higher values in spring than in summer. Interannually, there was a significantly higher abundance both in 2016 and 2020. The accumulated rainfall in the three months prior to sampling and grazing with sheep were the two most important factors that explain variation in population abundance. Both factors had a positive effect on the Fossorial Water Vole, so that its abundance increased with wetter months before sampling and in areas where sheep were present. The role of these factors and other variables of landscape and agricultural management in the changes of abundance of this rodent are also discussed.
... The taxonomic revision by Musser and Carleton (2005) recognized the following species of Arvicola: the southwestern water vole, Arvicola sapidus Miller, 1908 (semiaquatic), the montane water vole, Arvicola scherman (Shaw, 1801) (fossorial), and the European water vole, A. amphibius (Linnaeus, 1758) (semiaquatic or mostly semiaquatic). Although several studies do not support this taxonomic configuration (for details see Ventura & Casado-Cruz, 2011 and references therein; Chevret et al., 2020;Mahmoudi et al., 2020) we followed that taxonomy in the present work in order to clearly distinguish a typical fossorial morphotype from a typical semiaquatic one (A. sapidus). ...
... scherman the relatively smaller size of the humerus is associated with its smaller body size, which seems to be an adaptation to reduce the digging cost. However, this hypothesis seems to not be supported within A. amphibius s.l., since clear size differences were not detected between aquatic and fossorial forms (Chevret et al., 2020). This discordance is probably linked to the greater morphological heterogeneity (morphotypes and ages) within the sample of A. amphibus s.l. ...
Article
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.
... Despite this, the detection of localized, endemic taxa is indeed pivotal to preserve them. The ongoing habitat loss and human environmental exploitation represents the main cause of the global biodiversity loss [17], and several rodent species are strictly linked to vulnerable habitats [8,[18][19][20]. Amongst those, the harvest mouse Micromys minutus, the smallest European rodent, shows a wide distribution from Northern Spain to Japan [21]. ...
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The Italian peninsula represented one of the main glacial refugia during climatic oscillations of the Pleistocene, currently being a biodiversity hotspot. In this work, we analysed for the first time the genetic diversity of harvest mouse populations in Italy, and we compared them with those of the rest of Eurasia. Mitochondrial cytochrome-b gene was amplified from 12 samples from throughout the Italian range. We recorded a very low genetic diversity, in line with the rest of the harvest mouse range. In the comparative phylogenetic tree, Northern Italy samples clustered together as a sister group of the rest of Europe, whereas those from Central Italy clustered with Central Europe samples. Harvest mice have recently conquered Southern Europe, i.e., possibly at the start of the Holocene. The global genetic homogeneity might be due to accidental human-mediated introductions or to the sharp decline of the habitat of the harvest mouse, which may in turn have caused severe bottlenecks in the populations of this small rodent.
... Unit II: one left lower m1. Description and discussion: recent works have shown that the Iranian phylogroup of water voles can be considered a valid species, named Arvicola persicus (Fig. 3.4) (Chevret et al. 2020;Mahmoudi et al. 2020). We chose to follow Maul et al. (2020) in using the name Arvicola ex. ...
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Located at the crossroads between Africa, Europe and Asia, the Southern Caucasus is a prime location to study occupations by H. heidelbergensis, H. neanderthalensis and anatomically modern humans. Azokh Cave is an important site for the understanding of human evolution in its archaeological, palaeontological, environmental and ecological context. The main objective of this work is to use rodents to infer the climatic and environmental conditions that prevailed during the formation of the site. The small-mammal remains come from the archaeological excavation campaigns carried out in Azokh 1 in 2003, 2005, 2014, 2015 and 2018; they are from Unit V, Units III–IV and Unit II. The small-mammal assemblage is composed of at least 13 taxa: seven arvicoline, two cricetine, two gerbilline, one dipodid and one murine species. Units III–IV do not yield enough material to draw palaeoclimatic inferences. The palaeoclimatic conditions for Units V and II, ascertained by means of the bioclimatic model, suggest temperatures and precipitation similar to nowadays; the climate seems to be relatively warm-temperate in both units. The palaeoenvironmental reconstruction by means of habitat weighting points to an environment mainly composed of desert and steppe habitats, as well as portions of grassland and forest. This interpretation differs from that inferred from the large-mammal and archaeobotanical data, which indicate a woodland environment. These differences could be explained by the origin of the accumulation. There was no evidence of a major palaeoenvironmental or palaeoclimatic change between the Middle and Late Pleistocene layers, indicating favourable conditions throughout the study period.
... However, stakeholders in such systems are often protagonists of endless debates about regulation adoption and management decisions, which each of them advocating the control of one among many possible population targets and subsequent options for management. This debating is the case in the Jura mountains where massive outbreaks of a grassland vole species, the montane water vole, Arvicola amphibius (formerly A. terrestris (Chevret et al., 2020)), occur with 5-to 6-year cycles and population densities exceeding 500-1,000 ind.ha −1 . High-density peaks propagate over grasslands under the form of a traveling wave (Berthier et al., 2014;Giraudoux, 1997). ...
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Voles can reach high densities with multiannual population fluctuations of large amplitude, and they are at the base of predator communities in Northern Eurasia and Northern America. This status places them at the heart of management conflicts wherein crop protection and health concerns are often raised against conservation issues. Here, a 20‐year survey describes the effects of large variations in grassland vole populations on the densities and the daily theoretical food intakes (TFI) of vole predators based on roadside counts. Our results show how the predator community responded to prey variations of large amplitude and how it reorganized with the increase in a dominant predator, here the red fox, which likely negatively impacted hare, European wildcat, and domestic cat populations. This population increase did not lead to an increase in the average number of predators present in the study area, suggesting compensations among resident species due to intraguild predation or competition. Large variations in vole predator number could be clearly attributed to the temporary increase in the populations of mobile birds of prey in response to grassland vole outbreaks. Our study provides empirical support for more timely and better focused actions in wildlife management and vole population control, and it supports an evidence‐based and constructive dialogue about management targets and options between all stakeholders of such socio‐ecosystems.
... Detailed taxonomical and morphological analyses were based on: Nadachowski (1984) and Luzi and López-García (2019) for Microtus agrestis and M. arvalis lower dentition; Nores et al. (1982), Pemán (1983) and Barti (2006) for Neomys mandibles; Pasquier (1974) and Nores (1988) for Apodemus dentition; and Niethammer (1990) for Talpa humeri. The taxonomic classification followed the systematics proposed by Wilson et al. (2016Wilson et al. ( , 2017 and Chevret et al. (2020) for rodents, and Wilson and Mittermeier (2018) for shrews and moles. ...
Article
La Güelga Cave (Asturias, NW Spain) contains a stratigraphic succession dating from 47.2 ± 2.2 to 38.6 ± 0.5 cal kyr BP. Evidence of Mousterian, Châtelperronian and Aurignacian occupations in the succession documents the transition from Neanderthals to Early Modern Humans. To better understand the palaeoenvironmental context of this transition, we analyzed a rich small-mammal assemblage, comprising a minimum number of 2227 individuals and 20 taxa, in a high-resolution stratigraphic context, using the Bioclimatic Model, the Habitat Weighting Method, and biodiversity measures. Results identify a climate-cooling phase at the end of the Mousterian occupations (~45 ka), which transformed a mosaic of patchy forest and humid meadows into a more arid open landscape. Another cooling event, matching Heinrich stadial 4 (H4), coincided with the arrival of the Aurignacians (~39 ka). Comparison with regional and global records shows that the alternating cool-wet and arid events documented at La Güelga Cave are coeval with the advance and retreat of the Picos de Europa glaciers, and with global climatic events recorded in marine and ice cores. The impact of these environmental changes on the human cultural and biologic transitions is discussed.
... A. sapidus is strictly aquatic, whereas A. monticola is fossorial, and A. amphibius and A. italicus include both aquatic and fossorial morphotypes (Kryštufek et al. 2015). However, the discussion regarding the number of existing recent Arvicola species is still under debate, as, e.g., Chevret et al. (2020) do not accept A. monticola as a separate species. ...
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The (palaeo)biogeography of water voles is a puzzle that is not solved in detail yet. Extant species of the genus Arvicola cover a vast geographic area of the Palearctic. In this study, we collected morphometric data of extant and fossil Arvicola from Israel at the southern fringe of the water vole distribution area. The dental evolution of water voles is characterised by certain clear trends in the first lower molar (m1) related to crown height, tooth length, the proportion of the anteroconid-complex, and enamel differentiation. Trans-regional correlation of the latter trend shows that it did not develop completely synchronously in all the geographic areas of water voles' distribution, i.e., not at the same evolutionary rate. Based on the size and geographic distribution, we tentatively consider the Israeli material to belong to an A. persicus group, which facilitates the possibility of future taxonomic subdivision. Among the Israeli material, Late Pleistocene remains from Nahal Mahanayeem Outlet (NMO) show a very particular morphology of the first lower molar compared to samples from other localities in Israel and western Asia, which-in our opinion-justifies the establishment of a new species Arvicola nahalensis n. sp.
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Robust identification of species and significant evolutionary units (ESUs) is essential to implement appropriate conservation strategies for endangered species. However, definitions of species or ESUs are numerous and sometimes controversial, which might lead to biased conclusions, with serious consequences for the management of endangered species. The hazel dormouse, an arboreal rodent of conservation concern throughout Europe is an ideal model species to investigate the relevance of species identification for conservation purposes. This species is a member of the Gliridae family, which is protected in Europe and seriously threatened in the northern part of its range. We assessed the extent of genetic subdivision in the hazel dormouse by sequencing one mitochondrial gene (cytb) and two nuclear genes (BFIBR, APOB) and genotyping 10 autosomal microsatellites. These data were analysed using a combination of phylogenetic analyses and species delimitation methods. Multilocus analyses revealed the presence of two genetically distinct lineages (approximately 11 % cytb genetic divergence, no nuclear alleles shared) for the hazel dormouse in Europe, which presumably diverged during the Late Miocene. The phylogenetic patterns suggests that Muscardinus avellanarius populations could be split into two cryptic species respectively distributed in western and central-eastern Europe and Anatolia. However, the comparison of several species definitions and methods estimated the number of species between 1 and 10. Our results revealed the difficulty in choosing and applying an appropriate criterion and markers to identify species and highlight the fact that consensus guidelines are essential for species delimitation in the future. In addition, this study contributes to a better knowledge about the evolutionary history of the species.
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We characterized eighteen water voles, Arvicola amphibius (s.l.), from five populations along the Italian peninsula by means of mtDNA cytochrome b (Cytb) sequences. The samples included aquatic voles and one fossorial population from northern Italy. The standard karyotype of four voles from one central Italian population was also analysed and was identical to the one found in other populations outside Italy. Phylogenetic analyses, including vole Cytb haplotypes from the entire range, indicated the existence of a wellsupported and highly divergent Italian lineage (4.3%), sister to all the other haplotypes. The fossorial voles are not genetically differentiated from the aquatic voles from a nearby population and belong to the same taxon. Given the high Cytb divergence and the results of previous investigations on allozymes and hybrid fertility, we believe that the Italian population of water voles belongs to a distinct species, Arvicola italicus Savi, 1838, with the type locality near Pisa, although a morphological assessment of the entire skull is necessary to define it.
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The terminal Pleistocene and Early Holocene, a period from 15 000 to 18 000 Before Present (BP), was critical in establishing the current Holarctic fauna, with temperate-climate species largely replacing cold-adapted ones at midlatitudes. However, the timing and nature of this process remain unclear for many taxa, a point that impacts on current and future management strategies. Here, we use an ancient DNA dataset to test more directly postglacial histories of the water vole (Arvicola amphibius, formerly A. terrestris), a species that is both a conservation priority and a pest in different parts of its range. We specifically examine colonization of Britain, where a complex genetic structure can be observed today. Although we focus on population history at the limits of the species’ range, the inclusion of additional European samples allows insights into European postglacial colonization events and provides a molecular perspective on water vole taxonomy. © 2016 The Author(s) Published by the Royal Society. All rights reserved.
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African mole-rats are fossorial rodents that consist of five chisel-tooth digging genera (Heterocephalus, Heliophobius, Georychus, Fukomys, and Cryptomys) and one scratch digger (Bathyergus). They are characterized by striking physiological, morphological, and behavioral adaptations intimately related to their subterranean life. The influence of their mode of life in shaping the cranial morphology has yet to be evaluated in comparison to other Ctenohystrica, especially fossorial genera,which include the subterranean genera Spalacopus and Ctenomys. In our study, we seek to determine to what extent subterranean life affects the morpho-functional properties of the skull among fossorial ctenohystricans. 3D geometric morphometric analyses were performed on 277 skulls, encompassing 63 genera of Ctenohystrica, and complemented by biomechanical studies. African mole-rats and other subterranean Ctenohystrica, especially chisel-tooth diggers, have a short snout, a wide cranium with enlarged zygomatic arches, and a strongly hystricognathous mandible. Even if convergences are also manifest between most fossorial Ctenohystrica, subterranean rodents departed from the main ctenohystrican allometric trends in having a skull shape less size-dependent, but under stronger directional selection with intense digging activity as a major constraint. African mole-rats, notably chisel-tooth diggers, show important mechanical advantage for the temporalis muscles favoring higher forces at the bite point, while mechanical advantage of the superficial masseter muscles is lower compared to other Ctenohystrica. If subterranean species can be clearly discriminated based on their skull morphology, the intrinsic mosaic of anatomical characters of each genus (e.g., skull, teeth, and muscles) can be understood only in the light of their ecology and evolutionary history.
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The evolutionary history of the genus Megadontomys, a group of mice allopatrically distributed along the cool-humid forest in the highlands of Mexico, is controversial. In this study, we examined phylogenetic relationships within the genus using sequences data from the complete mitochondrial cytochrome b gene. This information also allowed us to corroborate species limits, geographic boundaries of taxonomic entities and assess genetic variation within each taxon. The results of the phylogenetic analyses based on maximum likelihood, Bayesian inference and maximum parsimony were largely congruent in that M. nelsoni and M. thomasi were more closely related relative to M. cryophilus. These results are concordant with previous studies based on morphology and allozyme variation. However, testing of the alternative hypothesis of a closer evolutionary affinity between M. nelsoni M. cryophilus did not produce a significantly less likely tree. The lack of unambiguous support towards one of these previously proposed contending hypotheses is congruent with the alternative scenario of an almost simultaneous diversification of the three species. Application of the phylogenetic species concept and the genetic species concept supports the recognition of three distinct taxonomic entities at the specific level. M. nelsoni inhabits the Sierra Madre Oriental (Hidalgo, Veracruz, and Puebla) including the Sierra Mazateca (Oaxaca); M. cryophilus is restricted to the Sierra de Juarez (Oaxaca); and M. thomasi occurs in portions of the Sierra Madre del Sur (Guerrero) and the Sierra Mixteca (Oaxaca). Our data show that M. thomasi is formed by two genetically distinct lineages that potentially may represent distinct Evolutionary Significant Units.
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Background Rodents of the genus Mus represent one of the most valuable biological models for biomedical and evolutionary research. Out of the four currently recognized subgenera, Nannomys (African pygmy mice, including the smallest rodents in the world) comprises the only original African lineage. Species of this subgenus became important models for the study of sex determination in mammals and they are also hosts of potentially dangerous pathogens. Nannomys ancestors colonized Africa from Asia at the end of Miocene and Eastern Africa should be considered as the place of their first radiation. In sharp contrast with this fact and despite the biological importance of Nannomys, the specimens from Eastern Africa were obviously under-represented in previous studies and the phylogenetic and distributional patterns were thus incomplete.ResultsWe performed comprehensive genetic analysis of 657 individuals of Nannomys collected at approximately 300 localities across the whole sub-Saharan Africa. Phylogenetic reconstructions based on mitochondrial (CYTB) and nuclear (IRBP) genes identified five species groups and three monotypic ancestral lineages. We provide evidence for important cryptic diversity and we defined and mapped the distribution of 27 molecular operational taxonomic units (MOTUs) that may correspond to presumable species. Biogeographical reconstructions based on data spanning all of Africa modified the previous evolutionary scenarios. First divergences occurred in Eastern African mountains soon after the colonization of the continent and the remnants of these old divergences still occur there, represented by long basal branches of M. (previously Muriculus) imberbis and two undescribed species from Ethiopia and Malawi. The radiation in drier lowland habitats associated with the decrease of body size is much younger, occurred mainly in a single lineage (called the minutoides group, and especially within the species M. minutoides), and was probably linked to aridification and climatic fluctuations in middle Pliocene/Pleistocene.Conclusions We discovered very high cryptic diversity in African pygmy mice making the genus Mus one of the richest genera of African mammals. Our taxon sampling allowed reliable phylogenetic and biogeographic reconstructions that (together with detailed distributional data of individual MOTUs) provide a solid basis for further evolutionary, ecological and epidemiological studies of this important group of rodents.
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A b s t r a c t . The increasing use of phylogeographic studies, based on mitochondrial DNA, in European mammals not only provides the genetic structure of the populations and a reconstruction of the evolutionary history of each taxon but is also useful in identifying cryptic species and areas that may represent conservation priorities. We reviewed the published data (about 60 articles) reporting phylogeographic studies, based on sequences of mtDNA genes, in order to identify those populations representing putative species, not yet formally described among European mammal species of all orders, with the exception of Chiroptera. A DNA taxonomic approach and the value of subspecies are also discussed in relation to conservation activities.
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Since its introduction in 2001, MrBayes has grown in popularity as a software package for Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) methods. With this note, we announce the release of version 3.2, a major upgrade to the latest official release presented in 2003. The new version provides convergence diagnostics and allows multiple analyses to be run in parallel with convergence progress monitored on the fly. The introduction of new proposals and automatic optimization of tuning parameters has improved convergence for many problems. The new version also sports significantly faster likelihood calculations through streaming single-instruction-multiple-data extensions (SSE) and support of the BEAGLE library, allowing likelihood calculations to be delegated to graphics processing units (GPUs) on compatible hardware. Speedup factors range from around 2 with SSE code to more than 50 with BEAGLE for codon problems. Checkpointing across all models allows long runs to be completed even when an analysis is prematurely terminated. New models include relaxed clocks, dating, model averaging across time-reversible substitution models, and support for hard, negative, and partial (backbone) tree constraints. Inference of species trees from gene trees is supported by full incorporation of the Bayesian estimation of species trees (BEST) algorithms. Marginal model likelihoods for Bayes factor tests can be estimated accurately across the entire model space using the stepping stone method. The new version provides more output options than previously, including samples of ancestral states, site rates, site d(N)/d(S) rations, branch rates, and node dates. A wide range of statistics on tree parameters can also be output for visualization in FigTree and compatible software.
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PhyML is a phylogeny software based on the maximum-likelihood principle. Early PhyML versions used a fast algorithm performing nearest neighbor interchanges to improve a reasonable starting tree topology. Since the original publication (Guindon S., Gascuel O. 2003. A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52:696-704), PhyML has been widely used (>2500 citations in ISI Web of Science) because of its simplicity and a fair compromise between accuracy and speed. In the meantime, research around PhyML has continued, and this article describes the new algorithms and methods implemented in the program. First, we introduce a new algorithm to search the tree space with user-defined intensity using subtree pruning and regrafting topological moves. The parsimony criterion is used here to filter out the least promising topology modifications with respect to the likelihood function. The analysis of a large collection of real nucleotide and amino acid data sets of various sizes demonstrates the good performance of this method. Second, we describe a new test to assess the support of the data for internal branches of a phylogeny. This approach extends the recently proposed approximate likelihood-ratio test and relies on a nonparametric, Shimodaira-Hasegawa-like procedure. A detailed analysis of real alignments sheds light on the links between this new approach and the more classical nonparametric bootstrap method. Overall, our tests show that the last version (3.0) of PhyML is fast, accurate, stable, and ready to use. A Web server and binary files are available from http://www.atgc-montpellier.fr/phyml/.
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Recent genetic studies have challenged the traditional view that the ancestors of British Celtic people spread from central Europe during the Iron Age and have suggested a much earlier origin for them as part of the human recolonization of Britain at the end of the last glaciation. Here we propose that small mammals provide an analogue to help resolve this controversy. Previous studies have shown that common shrews (Sorex araneus) with particular chromosomal characteristics and water voles (Arvicola terrestris) of a specific mitochondrial (mt) DNA lineage have peripheral western/northern distributions with striking similarities to that of Celtic people. We show that mtDNA lineages of three other small mammal species (bank vole Myodes glareolus, field vole Microtus agrestis and pygmy shrew Sorex minutus) also form a 'Celtic fringe'. We argue that these small mammals most reasonably colonized Britain in a two-phase process following the last glacial maximum (LGM), with climatically driven partial replacement of the first colonists by the second colonists, leaving a peripheral geographical distribution for the first colonists. We suggest that these natural Celtic fringes provide insight into the same phenomenon in humans and support its origin in processes following the end of the LGM.
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Comparison of post-weaning ontogenetic changes in bone structures between phylogenetically close species with different ecology and types of locomotion can provide a broader picture of the role that function can play in growth patterns. Since the skulls of water voles of genus Arvicola exhibit an important morphological variation associated with underground or semi-aquatic habitats, we compare postnatal ontogenetic changes in the mandible of A. sapidus (semi-aquatic) and A. scherman (fossorial). A total of 15 two-dimensional landmarks were digitized on 271 mandibles from collection specimens for geometric morphometric analyses. We compared allometric and phenotypic trajectories, ontogenetic form changes, and estimated bite force between these two taxa. Results revealed that in young individuals of both species, important shape changes occur in the angular and condylar processes. Conversely, the mandible shows significant interspecific differences in size and shape, the orientation of allometric and phenotypic trajectories, and estimated bite force. Across the post-weaning ontogeny, A. scherman shows respect to A. sapidus an increased diastema, a lower ramus, a ventral and caudal expansion of the condylar process, and a dorsal expansion of the angular process. Likewise, a comparatively higher estimated bite force was found in A. scherman. All these differences seem to be concomitant with the mechanical stress and functional constraints associated with persistent excavation activity in fossorial water voles.
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Closed form representations of the gradients and an approximation to the Hessian are given for an asymptotic approximation to the log likelihood function of a multidimensional autoregressive moving average Gaussian process. Their use for the numerical maximization of the likelihood function is discussed. It is shown that the procedure described by Hannan for the estimation of the parameters of one dimensional autoregressive moving average processes is equivalent to a three stage realization of one step of the Newton Raphson procedure for the numerical maximization of the likelihood function, using the gradient and the approximate Hessian. This makes it straightforward to extend the procedure to the multidimensional case. The use of the block Toeplitz type characteristic of the approximate Hessian is pointed out.
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The time scales of evolutionary and ecological studies tend to converge, as evidenced by studies that have shown contemporary evolution can occur as fast as ecological processes. This opens new questions regarding variation of characters usually considered to change mostly along an evolutionary time scale, such as morphometric traits, including osteological and dental features such as mandibles and teeth of mammals. Using two-dimensional geometric morphometric approach, we questioned whether such features can change on a seasonal and local basis, in relation to the ecological dynamics of the populations. Our model comprised populations of house mice (Mus musculus domesticus) in two contrasted situations in mainland Western Europe: a feral population vs. two close commensal populations. Mitochondrial DNA (D-loop) provided insight into the diversity and dynamics of the populations.
Chapter
The mathematical/statistical software platform R has seen an immense increase in popularity within the last decade. Its main advantages are its flexibility, a large repository of freely available extensions, its open-source nature and a thriving community. This tutorial gives an introduction into landmark/surface-mesh based statistical shape analysis in R – specifically using the packages Morpho and Rvcg . Beginning with examples based on sparse sets of anatomical landmarks, the tutorial will go on dealing with surface and curve landmarks and more challenging tasks such as mesh manipulations and surface registration. Apart from statistical analyses, emphasis will also be put on comprehensive visualization of the results. Extensive examples and code snippets are provided to allow the reader to easily replicate the analyses.
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Haplotype networks are an intuitive method for visualising relationships between individual genotypes at the population level. Here, we present popart, an integrated software package that provides a comprehensive implementation of haplotype network methods, phylogeographic visualisation tools and standard statistical tests, together with publication-ready figure production. popart also provides a platform for the implementation and distribution of new network-based methods – we describe one such new method, integer neighbour-joining. The software is open source and freely available for all major operating systems.
Article
Ventura, J. and Casado-Cruz, M. 2011. Post-weaning ontogeny of the mandible in fossorial water voles: ecological and evolutionary implications. —Acta Zoologica (Stockholm) 92: 12–20. Geometric morphometrics was applied to the mandible of fossorial water voles (Arvicola terrestris monticola) to determine size and shape variations in this structure during post-weaning ontogeny. The sample consisted of collection specimens obtained in the Aran Valley (Spain), which were grouped into six age classes. Mandible size and shape did not differ significantly between sexes, but between age classes. Mandible size accounted significantly for the shape variation. After the size-related differences were removed, the mandible shape did not show significant sexual dimorphism but differences by age remained significant. The main shape changes occur between the third and tenth weeks of life and are related to the shift from suckling to a herbivorous diet. Although mandible shape was less remodelled after that age, an appreciable variation also occurs during adulthood. Age-related changes lead to enhancing the digging potential of the mandible, which in adults becomes a robust structure with an increased surface and stronger crests for muscle insertion. As part of the mandible shape variation was not related to the size-dependent adjustment and diet does not vary significantly between juvenile and adult voles, shape changes that occur during adulthood can be related to the mechanical stress derived from digging activities.
Article
In the late Oligocene and early Miocene of North America, beavers (Castoridae) diversified into two lineages of burrowing specialists, the Palaeocastorinae and Migmacastorinae. Although common in the fossil record, artefactual evidence of burrowing beaver habits is rare and thus the ecology of most species is unknown. Living fossorial rodents display three distinct digging modes: scratch, chisel-tooth, and head-lift digging. We used a geometric morphometric approach to examine how digging behaviors are reflected in the craniodental shape of a broad sample of extant rodents, and then used the results to infer the digging modes of 18 extinct beaver species. Ecomorphological analyses revealed differences in skull shape related to digging habits, which can be used to discriminate the digging modes of extant rodents. Extant rodents with similar digging habits show convergent morphology, suggesting this method could be applied to extinct rodents, regardless of ancestry, to accurately infer their locomotor ecologies. The Oligocene to Miocene radiation of burrowing beavers included specialized chisel-tooth and head-lift digging species, which likely filled similar roles to living fossorial and subterranean species. Climate changes toward cooler, drier, and more open habitats correspond with the diversification of burrowing beavers. The subsequent radiation of other fossorially adapted rodent species likely led to competition with, and the extinction of, burrowing beavers.
Article
Species are generally described from morphological features, but there is growing recognition of sister forms that show substantial genetic differentiation without obvious morphological variation and may therefore be considered 'cryptic species'. Here, we investigate the field vole (Microtus agrestis), a Eurasian mammal with little apparent morphological differentiation but which, on the basis of previous sex-linked nuclear and mitochondrial DNA (mtDNA) analyses, is subdivided into a Northern and a Southern lineage, sufficiently divergent that they may represent two cryptic species. These earlier studies also provided limited evidence for two major mtDNA lineages within Iberia. In our present study, we extend these findings through a multilocus approach. We sampled 163 individuals from 46 localities, mainly in Iberia, and sequenced seven loci, maternally, paternally and biparentally inherited. Our results show that the mtDNA lineage identified in Portugal is indeed a distinct third lineage on the basis of other markers as well. In fact, multilocus coalescent-based methods clearly support three separate evolutionary units that may represent cryptic species: Northern, Southern and Portuguese. Divergence among these units was inferred to have occurred during the last glacial period; the Portuguese lineage split occurred first (estimated at c. 70 000 bp), and the Northern and Southern lineages separated at around the last glacial maximum (estimated at c. 18 500 bp). Such recent formation of evolutionary units that might be considered species has repercussions in terms of understanding evolutionary processes and the diversity of small mammals in a European context.
Article
Species identification through noninvasive sampling is increasingly used in animal conservation genetics, given that it obviates the need to handle free-living individuals. Noninvasive sampling is particularly valuable for elusive and small species such as rodents. Although rodents are not usually assumed to be the most obvious target for conservation, of the 21 species or near-species present in Iberia, three are considered endangered and declining, while several others are poorly studied. Here, we develop a genetic tool for identifying all rodent species in Iberia by noninvasive genetic sampling. To achieve this purpose, we selected one mitochondrial gene [cytochrome b (cyt-b)] and one nuclear gene [interphotoreceptor retinoid-binding protein (IRBP)], which we first sequenced using tissue samples. Both genes allow for the phylogenetic distinction of all species except the sibling species Microtus lusitanicus and Microtus duodecimcostatus. Overall, cyt-b showed higher resolution than IRBP, revealing a clear barcoding gap. To allow these markers to be applied to noninvasive samples, we selected a short highly diagnostic fragment from each gene, which we used to obtain sequences from faeces and bones from owl pellets. Amplification success for the cyt-b and IRBP fragment was 85% and 43% in faecal and 88% and 64% in owl-pellet DNA extractions, respectively. The method allows the unambiguous identification of the great majority of Iberian rodent species from noninvasive samples, with application in studies of distribution, spatial ecology and population dynamics, and for conservation.
Article
The Quaternary cold periods in Europe are thought to have heavily influenced the amount and distribution of intraspecific genetic variation in both animals and plants. The phylogeographies of 10 taxa, including mammals (Ursus arctos, Sorex spp., Crocidura suaveolens, Arvicola spp.), amphibians (Triturus spp.), arthropods (Chorthippus parallelus), and plants (Abies alba, Picea abies, Fagus sylvatica, Quercus spp.), were analysed to elucidate general trends across Europe. Only a small degree of congruence was found amongst the phylogeographies of the 10 taxa, but the likely postglacial colonization routes exhibit some similarities. A Brooks parsimony analysis produced an unrooted area phylogram, showing that: (i) the northern regions were colonized generally from the Iberic and Balkanic refugia; and (ii) the Italian lineages were often isolated due to the presence of the Alpine barrier. The comparison of colonization routes highlighted four main suture-zones where lineages from the different refugia meet. Some of the intraspecific genetic distances among lineages indicated a prequaternary divergence that cannot be connected to any particular cold period, but are probably related mainly to the date of arrival of each taxon in the European continent. As a consequence, molecular genetics so far appears to be of limited use in dating Quaternary events.
Article
The respective roles of the phylogenetic and ecological components in an adaptive radiation are tested on a sample of Old World rats and mice (Muridae, Murinae). Phylogeny was established on nuclear and mitochondrial genes and reconstructed by maximum likelihood and Bayesian methods. This phylogeny is congruent with previous larger scale ones recently published, but includes some new results: Bandicota and Nesokia are sister taxa and Micromys would be closely related to the Rattus group. The ecological diversification is investigated through one factor, the diet, and the mandible outline provides the morphological marker. Elliptic and radial Fourier transforms are used for quantifying size and shape differences among species. Univariate size and shape parameters indicate that phylogeny is more influential on size than diet, and the reverse occurs for shape and robust patterns are recognized by multivariate analyses of the data sets provided by the Fourier methods. Omnivorous and herbivorous groups are well separated despite some overlapping, as well as are other Murinae with a specialized diet (insects, seeds). Phylogeny is also influential as shown by the segregation of several groups (Praomys, Arvicanthini, Rattus, Apodemus). Allometric shape variation was investigated, and although present it does not overwhelm effects of either phylogeny or diet. Massive mandibles characterize herbivorous Murinae and slender mandibles, the insectivorous ones. A strong angular process relative to the coronoid process characterizes seedeaters, and the reverse characterized Murinae with a diet based largely on animal matter. Such changes in morphology are clearly in relation with the functioning of the mandible, and with the forces required by the nature of the food: the need of a stronger occlusal force in herbivorous species would explain massive mandibles, and an increase of the grasping and piercing function of incisors in insectivorous species would explain slender mandibles.
Article
The Palaearctic genus Arvicola includes two species: the south-western water vole A. sapidus, and the northern water vole A. terrestris. The latter has semiaquatic and/or subterranean populations, while populations of A. sapidus are always semiaquatic. According to the current phylogenetic and palaeontological data, adaptation to semiaquatic life is plesiomorphic for the genus Arvicola. We studied the ontogenetic allometry of skull and long bones of the semiaquatic A. sapidus, a semiaquatic population of A. terrestris (A. t. italicus), and two fossorial populations of A. terrestris (A. t. scherman and A. t. monticola). Animals from fossorial populations were smaller than were those from semiaquatic populations. We found that most of the ontogenetic allometric exponents of characters linked to digging in the skull and in the long bones were significantly higher in A. t. monticola, a fossorial clade, than they were in the semiaquatic populations. On the other hand, there may have been an evolutionary lag between invasion of the hypogeic habitat and the acquisition of fossorial adaptations in A. t. scherman. We showed statistically that the morphological differences linked to the invasion of a hypogeic habitat are already present in juvenile animals and, according to these results, suggest that these morphological differences are the direct expression of genetic changes rather than the outcome of epigenetic factors of mechanical origin. Moreover, we tried to ascertain whether the apomorphic shape of the skull and long bones in the fossorial populations of A. terrestris (compared with the primitive condition that would have been retained by the semiaquatic A. sapidus) are the outcome of a heterochronic process. Optimization by squared change parsimony supported the hypothesis of an apomorphic reduction of body size linked to the invasion of the subterranean habitat. The comparison of the ontogenetic trajectories of both skull shape and long bone shape suggested that a heterochronic process was involved in this morphological transformation. By using the ‘clock model’ method, this mechanism was identified as ‘accelerated dwarfism’ affecting both the skull and long bones. © 2006 The Linnean Society of London, Biological Journal of the Linnean Society, 2006, 87, 381–391.
Article
Morphometrics, a new branch of statistics, combines tools from geometry, computer graphics and biometrics in techniques for the multivariate analysis of biological shape variation. Although medical image analysts typically prefer to represent scenes by way of curving outlines or surfaces, the most recent developments in this associated statistical methodology have emphasized the domain of landmark data: size and shape of configurations of discrete, named points in two or three dimensions. This paper introduces a combination of Procrustes analysis and thin-plate splines, the two most powerful tools of landmark-based morphometrics, for multivariate analysis of curving outlines in samples of biomedical images. The thin-plate spline is used to assign point-to-point correspondences, called semi-landmarks, between curves of similar but variable shape, while the standard algorithm for Procrustes shape averages and shape coordinates is altered to accord with the ways in which semi-landmarks formally differ from more traditional landmark loci. Subsequent multivariate statistics and visualization proceed mainly as in the landmark-based methods. The combination provides a range of complementary filters, from high pass to low pass, for effects on outline shape in grouped studies. The low-pass version is based on the spectrum of the spline, the high pass, on a familiar special case of Procrustes analysis. This hybrid method is demonstrated in a comparison of the shape of the corpus callosum from mid-sagittal sections of MRI of 25 human brains, 12 normal and 13 with schizophrenia.
Article
Reconstructing phylogenies from intraspecific data (such as human mitochondrial DNA variation) is often a challenging task because of large sample sizes and small genetic distances between individuals. The resulting multitude of plausible trees is best expressed by a network which displays alternative potential evolutionary paths in the form of cycles. We present a method ("median joining" [MJ]) for constructing networks from recombination-free population data that combines features of Kruskal's algorithm for finding minimum spanning trees by favoring short connections, and Farris's maximum-parsimony (MP) heuristic algorithm, which sequentially adds new vertices called "median vectors", except that our MJ method does not resolve ties. The MJ method is hence closely related to the earlier approach of Foulds, Hendy, and Penny for estimating MP trees but can be adjusted to the level of homoplasy by setting a parameter epsilon. Unlike our earlier reduced median (RM) network method, MJ is applicable to multistate characters (e.g., amino acid sequences). An additional feature is the speed of the implemented algorithm: a sample of 800 worldwide mtDNA hypervariable segment I sequences requires less than 3 h on a Pentium 120 PC. The MJ method is demonstrated on a Tibetan mitochondrial DNA RFLP data set.
Article
Nucleotide sequence data from the mitochondrial 12S rRNA and cytochrome b genes were used to analyze phylogenetic relationships among sciurognath rodents. Our sample taxa included representatives of 11 sciurognath and 3 hystricognath families with two marsupial species, Didelphis virginiana and Macropus robustus, as outgroups. The dataset was analyzed using both maximum-parsimony (weighted and unweighted) and likelihood methods. Three suprafamilial groupings are strongly supported: Geomyidae + Heteromyidae (Geomyoidea), Sciuridae + Aplodontidae (Sciuroidea), and Pedetidae + Anomaluridae (Anomaluroidea). Although moderately supported, two sister group relationships were identified between Gliridae and Sciuroidea and between Castor and Geomyoidea. In contrast to previous nuclear DNA evidence, the evolutionary affinities between Ctenodactylidae and Hystricognathi (Ctenohystrica) and between Muridae and Dipodidae (Myodonta) are not supported by the mitochondrial data. Molecular divergence dates based on the combined data were estimated for suprafamilial groupings and are discussed in the light of current morphological and paleontological interpretations of rodent phylogeny.
Article
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.
Article
We sequenced 965 base pairs of the mitochondrial DNA cytochrome b from 102 woodmice (Apodemus sylvaticus) collected from 40 European localities. The aims of the study were to answer the following questions. (i) Did the Mediterranean peninsulas play a role as refuge for woodmice? (ii) Is genetic variability of A. sylvaticus higher in the Mediterranean region compared with northern Europe? (iii) Are the patterns of the postglacial colonization of Europe by woodmice similar to those presently recognized for other European species? The results provide a clear picture of the impact of the Quaternary glaciations on the genetic and geographical structure of the woodmouse. Our analyses indicate a higher genetic variability of woodmice in the Mediterranean peninsulas compared to northern Europe, suggesting a role of the former as refuge regions for this small mammal. An original pattern of postglacial colonization is proposed where the Iberian and southern France refuge populations colonized almost all European regions. The Sicilian population appears to be very differentiated and highly variable. This emphasizes the importance of this island as a 'hot spot' for the intraspecific genetic diversity of the woodmouse. Finally, woodmice in North Africa originated from southwestern Europe, most probably as a result of a recent anthropogenic introduction.
Tpsdig v.2. Ver. 2.16: Ecology and evolution
  • F. J. Rohlf
Handbook of the mammals of the world. Volume 7. Rodents II
  • U. Pardiñas
  • D. Ruelas
  • L. Bradley
  • R. Bradley
  • N. Ordonez
  • B. Kryštufek
  • M. J. Brito
Le campagnol terrestre en Suisse: Biologie et systématique (Mammalia Rodentia)
  • J. Morel