[Show abstract][Hide abstract] ABSTRACT: The study of exploration and dispersal behaviour is a key component of conservation-related
research on any animal species. This is especially true for populations living in fragmented
habitats that are isolated or too small to be self-sustainable. In this framework the case of the
Osprey Pandion haliaetus in the Mediterranean basin is of notable interest. Despite its
favourable conservation status at a global scale, counts indicate fewer than <80 breeding
Osprey pairs in the Mediterranean area. Basic information on the spatial ecology of this
population is still lacking, limiting the implementation of conservation measures for the
species at a regional scale. In this context, we tackled the following three questions: are there
(still) exchanges among populations in the Mediterranean basin? What is the genetic distance
between individuals and between populations? At this regional level, is there a metapopulation
system between the four Mediterranean Osprey populations? We studied metapopulation
connectivity by combining ringing and GPS tracking (as direct methods for
tracking movements) and population genetic methods (both mitochondrial DNA and
microsatellite analyses, as an indirect method to investigate genetic distance between
Since 2013, >20 Mediterranean Osprey (both adults and juveniles) were tracked with
GPS/GSM tags. Data showed that connectivity between populations is potentially possible
and can take place via both adult and juvenile dispersal. Individuals from Corsica have been
tracked while travelling through Balearics, Spain, Morocco and Sardinia. In order to assess
whether populations are also interconnected by gene flow we performed microsatellite
analyses at different loci. Combining such direct and indirect methods improves basic
knowledge about adult and postnatal osprey dispersal, and will help implementing adequate
management actions and planning common and coordinated conservation measures.
26th International Ornithological Congress, Tokyo, Japan; 01/2014
[Show abstract][Hide abstract] ABSTRACT: Despite wide differences in ecology and habitats across a world-wide distributional range,
Osprey populations appear to be poorly differentiated from a morphological point of view.
The most widely accepted taxonomic arrangement recognises a single species, Pandion
haliaetus, with four subspecies classified on the basis of morphometric and plumage
characteristics: P. h. haliaetus in the Palearctic and Africa, P. h. carolinensis in North
America, P. h. ridgwayi in the Carribeans, and P. h. cristatus in the Indo-Pacific and Oceania.
Despite this, the taxonomic status is still controversial and the evolutionary history of the
species is not well understood. Here we present an extensive phylogeographic study based on
mitochondrial DNA sequence (cytochrome b) extracted from >200 samples (both fresh tissues
and ancient museum specimens) covering the totality of the world distribution for this species.
The greatest genetic divergence was found between the Americas (combining spp
carolinensis and ridgwayi) and all other populations. In the Old World, the phylogenetic
analysis revealed three different branches for birds from Palearctic-Africa, Oceania and some
birds from Indonesia. These results suggest at least 3 or 4 possible Evolutionary Signicant
Units (ESU). Contrary to current taxonomy, North American carolinensis Osprey did not
differ from ridgwayi birds from the Caribbean. In the Western Palearctic, no genetic structure
was detected between the most distant populations, from Finland to Mediterranean and the
Atlantic islands. On the other hand, the existence of a previously unknown lineage and ESU
from Indonesia remains to be confirmed by further studies. Finally, we discuss hypothetical
evolutionary scenario explaining how species distribution and differentiation took place
during the past. This work has implications for conservation strategies, not only by dening
important areas for conservation, but also by helping prevent exchanges or introductions of
individuals originating from different lineages.
26th International Ornithological Congress, Tokyo, Japan; 01/2014
[Show abstract][Hide abstract] ABSTRACT: Aim The aim of this study was to elucidate the phylogeographical pattern of taxa
composing the Vipera ursinii complex, for which the taxonomic status and the
dating of splitting events have been the subject of much debate. The objectives
were to delimit potential refugia and to date splitting events in order to suggest a
scenario that explains the diversification of this species complex.
Location Western Europe to Central Asia.
Methods Sequences of the mitochondrial cytochrome b and NADH
dehydrogenase subunit 4 (ND4) genes were analysed for 125 individuals from
46 locations throughout the distribution range of the complex. The
phylogeographical structure was investigated using Bayesian and maximum
likelihood methods. Molecular dating was performed using three calibration
points to estimate the timing of diversification.
Results Eighty-nine haplotypes were observed from the concatenation of the two
genes. Phylogenetic inferences supported two main groups, referred to in this
study as the ‘ursinii clade’ and the ‘renardi clade’, within which several subclades
were identified. Samples from Greece (Vipera ursinii graeca) represented the first
split within the V. ursinii complex. In addition, three main periods of
diversification were revealed, mainly during the Pleistocene (2.4–2.0 Ma,
1.4 Ma and 1.0–0.6 Ma).
Main conclusions The present distribution of the V. ursinii complex seems to
have been shaped by Quaternary climatic fluctuations, and the Balkan, Caucasus
and Carpathian regions are identified in this study as probable refugia. Our
results support a south–north pattern of colonization, in contrast to the north–
south colonization previously proposed for this complex. The biogeographical
history of the V. ursinii complex corroborates other biogeographical studies that
have revealed an east–west disjunction (situated near the Black Sea) within a
species complex distributed throughout the Palaearctic region.
Journal of Biogeography 10/2012; · 4.97 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The evolution of the southern African faunal assemblages is thought to
have been largely influenced by climatic oscillations of the
Plio-Pleistocene. These fluctuations presumably had a major impact in
the form of vicariant diversification of taxa by causing simultaneous
speciation/cladogenetic events due to habitat fragmentation. We aimed to
test this hypothesis by comparing the timing of diversification observed
for several rodent lineages with three peaks of aridification described
at approximately 2.8, 1.7 and 1.0 Mya. Our study included nine rodent
taxa (Nannomys, Aethomys, Otomys, Myotomys, Rhabdomys and Mastomys for
the Muridae, Saccostomus for the Nesomyidae, Cryptomys for the
Bathyergidae, and Xerus for the Sciuridae) that showed intrageneric
mitochondrial cytochrome b cladogenesis during the last 5 Ma.
Phylogenetic analysis performed with maximum likelihood and Bayesian
methods supported the monophyly of all subgenera and genera. Most
diversifications are also well supported and in agreement with
previously published studies. Divergence dates between lineages were
estimated using a Bayesian relaxed molecular clock and the 7 Myr split
between different Apodemus species as well as the divergence between
Tatera and Gerbillurus at 6.3 Myr were used as calibration points. Our
results did not provide any convincing evidence of a correspondence
between rodent diversification events and peaks in aridity during the
Plio-Pleistocene. The nearly perfect linear correlation between
cladogenesis and time, during the last 5 Myr, strongly suggests that the
diversification of southern African rodent lineages is driven by complex
interactions between different factors, including life history, climatic
changes, and topographic barriers.
[Show abstract][Hide abstract] ABSTRACT: The Orsini's 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.
The Journal of heredity 12/2010; 102(1):67-78. · 1.97 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: 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.
[Show abstract][Hide abstract] ABSTRACT: The 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 approximately 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.
Taxonomic 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).
The 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.
[Show abstract][Hide abstract] ABSTRACT: Nuclear DNA intron sequences are increasingly used to investigate evolutionary relationships among closely related organisms. The phylogenetic usefulness of intron sequences at higher taxonomic levels has, however, not been firmly established and very few studies have used these markers to address evolutionary questions above the family level. In addition, the mechanisms driving intron evolution are not well understood. We compared DNA sequence data derived from three presumably independently segregating introns (THY, PRKC I and MGF) across 158 mammalian species. All currently recognized extant eutherian mammalian orders were included with the exception of Cingulata, Dermoptera and Scandentia. The total aligned length of the data was 6366 base pairs (bp); after the exclusion of autapomorphic insertions, 1511 bp were analyzed. In many instances the Bayesian and parsimony analyses were complementary and gave significant posterior probability and bootstrap support (>80) for the monophyly of Afrotheria, Euarchontoglires, Laurasiatheria and Boreoeutheria. Apart from finding congruent support when using these methods, the intron data also provided several indels longer than 3 bp that support, among others, the monophyly of Afrotheria, Paenungulata, Ferae and Boreoeutheria. A quantitative analysis of insertions and deletions suggested that there was a 75% bias towards deletions. The average insertion size in the mammalian data set was 16.49 bp +/- 57.70 while the average deletion was much smaller (4.47 bp +/- 14.17). The tendency towards large insertions and small deletions is highlighted by the observation that out of a total of 17 indels larger than 100 bp, 15 were insertions. The majority of indels (>60% of all events) were 1 or 2 bp changes. Although the average overall indel substitution rate of 0.00559 per site is comparable to that previously reported for rodents and primates, individual analyses among different evolutionary lineages provide evidence for differences in the formation rate of indels among the different mammalian groups.
Molecular Phylogenetics and Evolution 04/2007; 42(3):827-37. · 4.02 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Reg proteins are expressed in various organs and are involved in cancers and neurodegenerative diseases. They display a typical C-type lectin-like domain but possess additional highly conserved amino acids. By studying human databases and Expressed Sequence Tags library, we identified a new member called PAP IB. Using probabilistic approaches, we established a phylogenetic tree of eighteen Reg proteins. The dendogram showed that they constitute a superfamily composed of three distinct families (FI to FIII) of paralogues that resulted from duplication. We therefore focused on two proteins, REG Ialpha and PAP IB, belonging to the more closely related FI and FII families, respectively. REG Ialpha and PAP IB share 50% sequence identity. After cloning PAP IB, however, we found that it was expressed almost only in pancreas, unlike REG Ialpha, whose expression is ubiquitous. In addition, by building a model of the structure of PAP IB based on the X-ray structure of REG Ialpha, we observed that the two proteins displayed distinctive surface charge distribution, which may lead to different ligands binding. In spite of their common fold that should result in closely related functions, REG Ialpha and PAP IB are a good example of duplication and divergence, probably with the acquisition of new functions, thus participating in the evolution of the protein repertoire.
Biochimica et Biophysica Acta 04/2005; 1727(3):177-87. · 4.66 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The phylogenetic relationships among the Gliridae (order Rodentia) were assessed using 3430 nucleotides derived from three nuclear fragments (beta-spectrin non-erythrocytic 1, thyrotropin and lecithin cholesterol acyl transferase) and one mitochondrial gene (12S rRNA). We included 14 glirid species, representative of seven genera of the three recognized subfamilies (Graphiurinae, Glirinae and Leithiinae) in our analysis. The molecular data identified three evolutionary lineages that broadly correspond to the three extant subfamilies. However, the data suggest that the genus Muscardinus, previously regarded as falling within the Glirinae, should be included in the Leithiinae. Molecular dating using local molecular clocks and partitioned datasets allowed an estimate of the timing of cladogenesis within the glirids. Graphiurus probably diverged early in the group's evolution (40-50 Myr ago) and the three subfamilies diverged contemporaneously, probably in Europe. The radiation within Graphiurus is more recent, with the colonization of Africa by this lineage estimated at ca. 8-10 Myr ago.
Proceedings of the Royal Society B: Biological Sciences 10/2003; 270(1527):1947-55. · 5.29 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: 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.
Molecular Phylogenetics and Evolution 03/2002; 22(2):220-33. · 4.02 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: A major question in rhinocerotid phylogenetics concerns the position of the Sumatran rhinoceros (Dicerorhinus sumatrensis) with regard to the other extant Asian (Rhinoceros unicornis and R. sondaicus) and African (Diceros bicornis and Ceratotherium simum) species. We have examined this particular question through the phylogenetic analysis of the complete sequences of the mitochondrial 12S rRNA and cytochrome b genes. Three additional perissodactyls (one tapir and two equids) plus several outgroup cetartiodactyls were included in the analysis. The analysis identified a basal rhinocerotid divergence between the African and the Asian species, with the Sumatran rhinoceros forming the sister group of the genus Rhinoceros. We estimate the Asian and African lineages to have diverged at about 26 million years before present.
Molecular Phylogenetics and Evolution 05/2001; 19(1):34-44. · 4.02 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Gliridae is a small family of rodents including three subfamilies: the Eurasian Glirinae (with three genera) and Leithiinae (with four genera) and the African Graphiurinae (with a single genus). Phylogenetic relationships among these eight genera are not fully resolved based on morphological characters. Moreover, the genus Graphiurus is characterized by numerous peculiar features (morphological characters and geographical distribution), raising the question of its relationships to the family Gliridae. The phylogenetic position of Graphiurus and the intra-Gliridae relationships are here addressed by a molecular analysis of 12S RNA and cytochrome b mitochondrial gene sequences for six glirid genera. Phylogenetic analyses are performed with three construction methods (neighbor-joining, maximum parsimony and maximum likelihood) and tests of alternative topologies with respect to the most likely. Our analyses reveal that Graphiurus is clearly a member of the Gliridae, refuting the hypothesis that the family could be paraphyletic. Among Gliridae, phylogenetic relationships are poorly resolved: the Leithiinae could be monophyletic, there is no support for the subfamily Glirinae, and the closest relative of Graphiurus is not identified. The inclusion of Graphiurus among Gliridae allows us to postulate that its hystricomorphous condition has been achieved convergently with other hystricomorphous rodents.
Journal of Mammalian Evolution 02/1999; 6(1):67-83. · 2.63 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Suiformes (Artiodactyla) traditionally includes three families: Suidae, Tayassuidae, and Hippopotamidae but the monophyly of this suborder has recently been questioned from molecular data. A maximum parsimony analysis of molecular, morphological, and combined data was performed on the same set of taxa including representatives of the three Artiodactyla suborders (Suiformes, Ruminantia, and Tylopoda) and Perissodactyla as outgroup. Mitochondrial (cytochrome b and 12S rRNA) sequence comparisons support the monophyly of Suina (Suidae and Tayassuidae) and Ancodonta (Hippopotamidae) but not the monophyly of Suiformes. Inversely, our preliminary morphological analysis supports the monophyly of Suiformes whereas relationships among the three families are not resolved. The combined data set does not resolve the relationships between Suina, Ancodonta, and Ruminantia. These results are discussed in relation to morphological characters and paleontological data. Some improvements are suggested to clarify the morphological definition of Suiformes and relationships among them.
Molecular Phylogenetics and Evolution 07/1998; 9(3):528-32. · 4.02 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: A data set of complete mitochondrial cytochrome b and 12S rDNA sequences is presented here for 17 representatives of Artiodactyla and Cetacea, together with potential outgroups (two Perissodactyla, two Carnivora, two Tethytheria, four Rodentia, and two Marsupialia). We include seven sequences not previously published from Hippopotamidae (Ancodonta) and Camelidae (Tylopoda), yielding a total of nearly 2.1 kb for both genes combined. Distance and parsimony analyses of each gene indicate that 11 clades are well supported, including the artiodactyl taxa Pecora, Ruminantia (with low 12S rRNA support), Tylopoda, Suina, and Ancodonta, as well as Cetacea, Perissodactyla, Carnivora, Tethytheria, Muridae, and Caviomorpha. Neither the cytochrome b nor the 12S rDNA genes resolve the relationships between these major clades. The combined analysis of the two genes suggests a monophyletic Cetacea +Artiodactyla clade (defined as "Cetartiodactyla"), whereas Perissodactyla, Carnivora, and Tethytheria fall outside this clade. Perissodactyla could represent the sister taxon of Cetartiodactyla, as deduced from resampling studies among outgroup lineages. Cetartiodactyla includes five major lineages: Ruminantia, Tylopoda, Suina, Ancodonta, and Cetacea, among which the phylogenetic relationships are not resolved. Thus, Suiformes do not appear to be monophyletic, justifying their split into the Suina and Ancodonta infraorders. An association between Cetacea and Hippopotamidae is supported by the cytochrome b gene but not by the 12S rRNA gene. Calculation of divergence dates suggests that the Cetartiodactyla could have diverged from other Ferungulata about 60 MYA.
Molecular Biology and Evolution 06/1997; 14(5):550-9. · 14.31 Impact Factor