Véronique Arnal

Suprafamilial relationships among Rodentia and the phylogenetic effect of removing fast-evolving nucleotides in mitochondrial, exon and intron fragments

BackgroundThe number of rodent clades identified above the family level is contentious, and to date, no consensus has been reached on the basal evolutionary relationships among all rodent families. Rodent suprafamilial phylogenetic relationships are investigated in the present study using ~7600 nucleotide characters derived from two mitochondrial genes (Cytochrome b and 12S rRNA), two nuclear exons (IRBP and vWF) and four nuclear introns (MGF, PRKC, SPTBN, THY). Because increasing the number of nucleotides does not necessarily increase phylogenetic signal (especially if the data is saturated), we assess the potential impact of saturation for each dataset by removing the fastest-evolving positions that have been recognized as sources of inconsistencies in phylogenetics.ResultsTaxonomic sampling included multiple representatives of all five rodent suborders described. Fast-evolving positions for each dataset were identified individually using a discrete gamma rate category and sites belonging to the most rapidly evolving eighth gamma category were removed. Phylogenetic tree reconstructions were performed on individual and combined datasets using Parsimony, Bayesian, and partitioned Maximum Likelihood criteria. Removal of fast-evolving positions enhanced the phylogenetic signal to noise ratio but the improvement in resolution was not consistent across different data types. The results suggested that elimination of fastest sites only improved the support for nodes moderately affected by homoplasy (the deepest nodes for introns and more recent nodes for exons and mitochondrial genes).ConclusionThe present study based on eight DNA fragments supports a fully resolved higher level rodent phylogeny with moderate to significant nodal support. Two inter-suprafamilial associations emerged. The first comprised a monophyletic assemblage containing the Anomaluromorpha (Anomaluridae + Pedetidae) + Myomorpha (Muridae + Dipodidae) as sister clade to the Castorimorpha (Castoridae + Geomyoidea). The second suprafamilial clustering identified a novel association between the Sciuromorpha (Gliridae + (Sciuridae + Aplodontidae)) and the Hystricomorpha (Ctenodactylidae + Hystricognathi) which together represents the earliest dichotomy among Rodentia. Molecular time estimates using a relaxed Bayesian molecular clock dates the appearance of the five suborders nearly contemporaniously at the KT boundary and this is congruent with suggestions of an early explosion of rodent diversity. Based on these newly proposed phylogenetic relationships, the evolution of the zygomasseteric pattern that has been used for a long time in rodent systematics is evaluated.

Phylogeography of the weasel ( Mustela nivalis ) in the western-Palaearctic region: combined effects of glacial events and human movements

The Iberian, Italian or Balkan peninsulas have been considered as refugia for numerous mammalian species in response to Quaternary climatic fluctuations in Europe. In addition to this ‘southerly refugial model’, northern refugia have also been described notably for generalist and cold-tolerant species. Here, we investigated the phylogeographic pattern of the weasel (Mustela nivalis) to assess the impact of Quaternary glaciations on the genetic structure, number and location of refugia as well as to determine the impact of human movements on the colonization of Mediterranean islands. We sequenced 1690 bp from the mitochondrial control region and cytochrome b for 88 weasels distributed throughout the western-Palaearctic region, including five Mediterranean islands. Phylogenetic analyses of combined genes produced a clear phylogeographic pattern with two main lineages. The first lineage included all of the western-continental samples (from Spain to Finland) and shows low levels of genetic structure. Demographic analysis highlighted several characteristics of an expanding group, dated approximately at 116 kiloyears (kyr; Riss glaciation). The genetic pattern suggested a northeastern-European origin from which colonization of southwestern Europe took place. The second lineage was divided into five subgroups and indicated a common origin of insular and Moroccan samples from eastern Europe. Eastern-continental weasels did not exhibit signs of sudden expansion, suggesting stable population size during the last ice ages. The time of expansion of Sicilian and Corsican populations was dated around 10 kyr ago, which supports the hypothesis of an early human intervention in the colonization of Mediterranean islands.

High Genetic Differentiation Among French Populations of the Orsini’s Viper (Vipera ursinii ursinii) Based on Mitochondrial and Microsatellite Data: Implications for Conservation Management

The Orsinis viper (Vipera ursinii) is one of the most threatened snakes in Europe due to its highly fragmented distribution and specific open environment (steppic habitat) requirement. French populations are isolated on top of mountain massifs of the southern Prealps/Alps. Mitochondrial sequences (cytochrome b) and 6 microsatellite loci have been used to estimate the levels of genetic diversity and isolation within and among 11 French fragmented populations (a total of 157 individuals). Eleven cytochrome b haplotypes with a limited divergence were observed (mean divergence between haplotypes: 0.31%). However, we detected considerable genetic differentiation among populations (global F(ST) = 0.76 and 0.26 for mitochondrial and nuclear DNA, respectively). Results indicate that 3 populations possibly went through a bottleneck and 1 population showed low genetic diversity compared with the others. Although a significant isolation by distance was detected for both markers, strong differentiation was also observed between geographically close populations, probably due to the ragged landscape that constitutes a serious barrier to gene flow owing to the limited dispersal capability of the viper. Despite some discrepancies between the 2 markers, 8 Management Units have been identified and should be considered for future management projects.

Congruent signals of population history but radically different patterns of genetic diversity between mitochondrial and nuclear markers in a mountain lizard

Historical factors, current population size, population connectivity and selective processes at linked loci contribute to shaping contemporary patterns of neutral genetic diversity. It is now widely acknowledged that nuclear and mitochondrial markers react differently to current demography as well as to past history, so the use of both types of markers is often advocated to gain insight on both historical and contemporary processes. We used 12 microsatellite loci genotyped in 13 populations of a mountain lizard (Iberolacerta bonnali) to test whether the historical scenario favoured by a previous mitochondrial study was also supported by nuclear markers and thereby evaluated the consequences of postglacial range movements on nuclear diversity. Congruent signals of recent history were revealed by nuclear and mitochondrial markers using an Approximate Bayesian computation approach, but contemporary patterns of mtDNA and nuclear DNA diversity were radically different. Although dispersal in this species is probably highly restricted at all spatial scales, colonization abilities have been historically good, suggesting capability for reestablishment of locally extinct populations except in fully disconnected habitats.

Landscape genetics in mammals

Abstract The focus of this review is on landscape genetics (LG), a relatively new discipline that arose approximately 10 years ago. LG spans the interface between population genetics and landscape ecology and thus incorporates the concepts, methods, and tools from both disciplines. On the basis of an understanding of the spatial distribution of genetic diversity, LG aims to explain how landscape and environmental characteristics influence microevolutionary processes and metapopulation dynamics, including gene flow (i.e., connectivity) and selection (i.e., local adaptations). LG is concerned with events that occurred during the recent time scale, and the individual is the operational unit. As a discipline that combines spatial genetic diversity with ecological features, LG is able to address questions relating to different evolutionary processes. We illustrate some of these here using examples taken from mammals: population structure; gene flow and the identification of barriers; fragmentation, connectivity, and corridors; local adaptation and selection; there are two different questions: applications in conservation genetics; and future developments in LG. We will then present the methods and tools commonly used in the different steps of LG analyses: the genetic and landscape sampling, the quantification of genetic variation, the characterization of spatial landscape structures, and finally, the correlation between genetic patterns and landscape features.

Genetic connectivity among osprey populations and consequences for conservation: philopatry versus dispersal as key factors

Genetic variability and population structure in osprey were studied using DNA microsatellite markers. Special emphasis was placed on the subspecies living in the Afro-Palearctic (Pandion haliaetus haliaetus). For comparative purposes, American osprey subspecies (P. h. carolinensis, P. h. ridgway) and Indo/Australian subspecies (P. h. cristatus) were included in this analysis. Twenty DNA microsatellite loci were analysed across a total of 200 individuals. Cluster analysis of genetic distances generally grouped populations of osprey in accordance with their subspecific designation and with previous results from mtDNA analysis. Ospreys from America and Australia were clearly separated from P. h. haliaetus suggesting a more ancient isolation which prevented recent gene flow across these groups. Within P. h. haliaetus, significant genetic differentiation was found between populations in northern and southern Europe, suggesting that the Afro-Palearctic group is structured into two interconnected entities (Mediterranean and continental Europe). Population structuring was supported by an assignment test and by analysis of allele-sharing among individuals. At the Mediterranean scale, no significant differences of allelic information were found between populations. Behaviours such as dispersal, migration and philopatry seem to have played simultaneously and in contrary directions in shaping the genetic structure and diversity of populations. Our results provide essential information for reconstructing gene flow and genetic variability among osprey populations at different scales, which call for caution in the proactive management and conservation of the species, namely in the Mediterranean area.

Comparative phylogeography of amphibians and reptiles in Algeria suggests common causes for the east-west phylogeographic breaks in the Maghreb

A series of phylogeographic studies in the Maghreb identified a repeated pattern of deep genetic divergence between an eastern (Tunisia) and western (Morocco) lineage for several taxa but lack of sampling in Algeria made it difficult to know if the range limits between the eastern and western lineages were shared among taxa or not. To address this question, we designed a comparative phylogeographic study using 8 reptile and 3 amphibian species with wide distribution in the Maghreb as models. We selected species where previous studies had identified an East-West phylogeographic divide and collected sampled in Algeria to 1) examine whether the simple East-West divergence pattern still holds after filling the sampling gap in Algeria or if more complex diversity patterns emerge; 2) if the E-W pattern still holds, test whether the limits between the E and W clades are shared between species, suggesting that common historical process caused the E-W divergences; 3) if E-W limits are shared between species, use information on the age of the divergence to identify possible geological or climatic events that could have triggered these E-W differentiations. We found that the E-W pattern was generally maintained after additional sampling in Algeria and identified two common disjunction areas, one around the Algeria-Morocco border, the other one in Kabylia (central Algeria), suggesting that common historical mechanisms caused the E-W divergences in the Maghreb. Our estimates for the times to most common recent ancestors to the E and W clades span a wide range between the Messinian salinity crisis and the Plio-Pleistocene limit (except for one older split), suggesting different origins for the initial divergences and subsequent preservation of the E and W lineages in common climatic refugia in the west and the east of the Maghreb.

Conservation Below the Species Level: Suitable Evolutionarily Significant Units among Mountain Vipers (the Montivipera raddei complex) in Iran

Northern and western mountains of Iran are among the most important biodiversity and endemism hot spots for reptiles in the Middle East. Among herpetofauna, the montivipers represent an emblematic and fragmented endemic group for which estimating their level of genetic differentiation and defining conservation priorities is urgently needed. Here, we present the most comprehensive phylogenetic study on the Montivipera raddei species group comprising all 5 known taxa, among which 3 are endemic to Iran. Based on 2 mitochondrial genes, phylogenetic and phylogeographic analyses revealed 3 major lineages each presenting very contrasting distribution areas. The Iranian montivipers are highly structured in clades showing low genetic diversity and corresponding to high altitude summits. Molecular dating revealed the role of Quaternary paleo-climatic oscillations and altitudinal movements of montivipers in shaping genetic diversity and differentiation of these sky-island taxa. In addition, the best scenario of historical biogeography allowed identifying 3 possible refugial areas in Iran most likely arising by vicariance. Based on our mitochondrial results and pending additional data, we recognize 3 candidate species among the M. raddei complex: M. raddei, Montivipera latifii, and Montivipera kuhrangica that are coherent with their geographical distribution. We propose that the most appropriate evolutionary significant units for conservation of the montivipers are represented by 13 units among which 6 are recognized as high priority. Finally, we suggest some recommendations to the IUCN as well as to the Iranian conservation policies with respect to conservation prioritization.

The contrasting genetic patterns of two sympatric flying fox species from the Comoros and the implications for conservation

Pteropus livingstonii and Pteropus seychellensis comorensis are endemic fruit bat species that are among the most threatened animals in the Comoros archipelago. Both species are pollinators and seed dispersers of native and cultivated plants and are thus of crucial importance for the regeneration of natural forests as well as for cultivated plantations. However, these species are subject to strong anthropogenic pressures and face one of the highest rates of natural habitat loss reported worldwide. Yet little is known about the population genetic structure of these two species, making it difficult to define relevant conservation strategies. In this study, we investigated for the two flying fox species (1) the level of genetic diversity within islands, as well as across the archipelago and (2) the genetic structure between the two islands (Anjouan and Mohéli) for P. livingstonii and between the four islands of the archipelago (Anjouan, Mohéli, Grande Comore and Mayotte) for P. s. comorensis using mitochondrial and microsatellite markers. The results revealed contrasting patterns of genetic structure, with P. s. comorensis showing low genetic structure between islands, whereas P. livingstonii exhibited high levels of inter-island genetic differentiation. Overall, the genetic analyses showed low genetic diversity for both species. These contrasting genetic patterns may be the result of different dispersal patterns and the populations’ evolutionary histories. Our findings lead us to suggest that in terms of conservation strategy, the two populations of P. livingstonii (on Anjouan and Mohéli islands) should be considered as two separate management units. We recommend focusing conservation efforts on the Anjouan population, which is the largest, exhibits the highest genetic diversity, and suffers the greatest anthropogenic pressure. As for P. s. comorensis, its four populations could be considered as a single unit for conservation management purposes. For this species, we recommend protecting roosting trees to reduce population disturbance.