Julien Claude

APE: Analyses of Phylogenetics and Evolution in R language

UNLABELLED Analysis of Phylogenetics and Evolution (APE) is a package written in the R language for use in molecular evolution and phylogenetics. APE provides both utility functions for reading and writing data and manipulating phylogenetic trees, as well as several advanced methods for phylogenetic and evolutionary analysis (e.g. comparative and population genetic methods). APE takes advantage of the many R functions for statistics and graphics, and also provides a flexible framework for developing and implementing further statistical methods for the analysis of evolutionary processes. AVAILABILITY The program is free and available from the official R package archive at http://cran.r-project.org/src/contrib/PACKAGES.html#ape. APE is licensed under the GNU General Public License.

A Unifying Model for the Analysis of Phenotypic, Genetic and Geographic Data

Recognition of evolutionary units (species, populations) requires integrating several kinds of data, such as genetic or phenotypic markers or spatial information in order to get a comprehensive view concerning the differentiation of the units. We propose a statistical model with a double original advantage: (i) it incorporates information about the spatial distribution of the samples, with the aim to increase inference power and to relate more explicitly observed patterns to geography and (ii) it allows one to analyze genetic and phenotypic data within a unified model and inference framework, thus opening the way to robust comparisons between markers and possibly combined analyses. We show from simulated data as well as real data that our method estimates parameters accurately and is an improvement over alternative approaches in many situations. The power of this method is exemplified using an intricate case of inter- and intraspecies differentiation based on an original data set of georeferenced genetic and morphometric markers obtained on Myodes voles from Sweden. A computer program is made available as an extension of the R package Geneland.

Ecological Correlates and Evolutionary Divergence in the Skull of Turtles: A Geometric Morphometric Assessment

Resource use and phylogeny are often correlated with morphological variation. Moreover, because biological shapes are often complex and evolve depending on several internal constraints, they must be assessed using integrative methods. We analyzed the morphological variation of the turtle skull in the context of an adaptive radiation. Our focus are turtles of the superfamily Testudinoidea, which are remarkably diverse, both in number of species and in ecology. In this study, we depict morphological variation in the turtle skull in three dimensions with respect to diet, phylogeny, and habitat using modern geometric morphometrics. Our study revealed that morphological specialization was related to both diet and habitat. Morphological variation is decomposed in regard of both resource use (habitat and diet) and phylogeny. Feeding mode depending on environment was suggested as a key factor determining morphological evolution and diversification of turtle skulls. Diet (especially durophagy) leads to parallel morphologies in different clades. Phylogeny seemed to constrain only localized features of the skull and remained of minor influence, because overall morphotypes, closely correlated with ecological factors, occurred in both clades. In conclusion, the adaptive radiation of the Testudinoidea is revealed to demonstrate a clear relationship between the skull shape and life style.

A new key locality for the Pliocene vertebrate record of Europe: the Camp dels Ninots maar (NE Spain)

A new Pliocene Konservat-Lagerstatte in north-eastern Spain is described here for the first time. It is referred to as Camp dels Ninots. The particular geological conditions of the site, which correspond to lacustrine sedimentation in a maar, made it ideal for the preservation of fossils. At present, five large mammal skeletons in anatomical connection have been recovered: three individuals of Alephis tigneresi, one of Stephanorhinus jeanvireti and one of Tapirus arvernenis, as well as isolated remains. A minimum of five individuals of the chelonian Mauremys leprosa have been recovered, some of them in anatomical connection. The rodent Apodemus atavus, the amphibians cf. Pleurodeles sp., Lissotriton aff. helveticus and Pelophylax cf. perezi and freshwater fishes (Leuciscus ?) complete the vertebrate assemblage uncovered up to the present time. The coexistence of Stephanorhinus jeanvireti and Alephis tigneresi suggests an age of about 3.2Ma for the Camp dels Ninots, near the MN15-MN16 transition. The Camp del Ninots fossil record enables one to extend the biogeographic range of some vertebrate taxa, such as Stephanorhinus jeanvireti, Tapirus arvernensis or Mauremys leprosa to the Iberian Peninsula. Taphonomic evidences of the skeletal remains indicates minimal (if any) weathering. Deposition at the lake bottom seems to have taken place in oxygen depleted layers. In this way, Camp dels Ninots is comparable to other remarkable maar sites such as Messel, the Eocene site situated in Germany.

Cytonuclear discordance among Southeast Asian black rats (Rattus rattus complex)

Black rats are major invasive vertebrate pests with severe ecological, economic and health impacts. Remarkably, their evolutionary history has received little attention, and there is no firm agreement on how many species should be recognized within the black rat complex. This species complex is native to India and Southeast Asia. According to current taxonomic classification, there are three taxa living in sympatry in several parts of Thailand, Cambodia and Lao Peoples Democratic Republic, where this study was conducted: two accepted species (Rattus tanezumi, Rattus sakeratensis) and an additional mitochondrial lineage of unclear taxonomic status referred to here as ‘Rattus R3’. We used extensive sampling, morphological data and diverse genetic markers differing in rates of evolution and parental inheritance (two mitochondrial DNA genes, one nuclear gene and eight microsatellite loci) to assess the reproductive isolation of these three taxa. Two close Asian relatives, Rattus argentiventer and Rattus exulans, were also included in the genetic analyses. Genetic analyses revealed discordance between the mitochondrial and nuclear data. Mitochondrial phylogeny studies identified three reciprocally monophyletic clades in the black rat complex. However, studies of the phylogeny of the nuclear exon interphotoreceptor retinoid‐binding protein gene and clustering and assignation analyses with eight microsatellites failed to separate R. tanezumi and R3. Morphometric analyses were consistent with nuclear data. The incongruence between mitochondrial and nuclear (and morphological) data rendered R. tanezumi/R3 paraphyletic for mitochondrial lineages with respect to R. sakeratensis. Various evolutionary processes, such as shared ancestral polymorphism and incomplete lineage sorting or hybridization with massive mitochondrial introgression between species, may account for this unusual genetic pattern in mammals.

Dating cryptodiran nodes: Origin and diversification of the turtle superfamily Testudinoidea

The superfamily Testudinoidea is the most diverse and widely distributed clade of extant turtles. Surprisingly, despite an extensive fossil record, and increasing amount of molecular data available, the temporal origin of this group is still largely unknown. To address this issue, we used a comprehensive molecular dataset to perform phylogenetic and molecular dating analyses, as well as seven fossil constraints to calibrate the ages of the nodes in the phylogeny. The molecular dataset includes the complete mitochondrial genomes of 37 turtle species, including newly sequenced mitochondrial genomes of Phrynops hilarii, Emys orbicularis, Rhinoclemmys punctularia, and Chelonoidis nigra, and four nuclear markers. Our results revealed that the earliest divergences within crown testudinoids occurred around 95.0 Mya, in the early Late Cretaceous, earlier than previously reported, raising new questions about the historical biogeography of this group.

Morphometrics Parallel Genetics in a Newly Discovered and Endangered Taxon of Galápagos Tortoise

Galápagos tortoises represent the only surviving lineage of giant tortoises that exhibit two different types of shell morphology. The taxonomy of Galápagos tortoises was initially based mainly on diagnostic morphological characters of the shell, but has been clarified by molecular studies indicating that most islands harbor monophyletic lineages, with the exception of Isabela and Santa Cruz. On Santa Cruz there is strong genetic differentiation between the two tortoise populations (Cerro Fatal and La Reserva) exhibiting domed shell morphology. Here we integrate nuclear microsatellite and mitochondrial data with statistical analyses of shell shape morphology to evaluate whether the genetic distinction and variability of the two domed tortoise populations is paralleled by differences in shell shape. Based on our results, morphometric analyses support the genetic distinction of the two populations and also reveal that the level of genetic variation is associated with morphological shell shape variation in both populations. The Cerro Fatal population possesses lower levels of morphological and genetic variation compared to the La Reserva population. Because the turtle shell is a complex heritable trait, our results suggest that, for the Cerro Fatal population, non-neutral loci have probably experienced a parallel decrease in variability as that observed for the genetic data.

First Clarkforkian equivalent Land Mammal Age in the latest Paleocene basal Sparnacian facies of Europe: fauna, flora, paleoenvironment and (bio)stratigraphy.

The Paleocene-Eocene Thermal Maximum (PETM) is correlated with the first occurrences of earliest modern mammals in the Northern Hemisphere. The latest Paleocene Clarkforkian North American Land Mammal Age, that has yielded rodents and carnivorans, is the only exception to this rule. However, until now no pre-PETM localities have yielded modern mammals in Europe or Asia. We report the first Clarkforkian equivalent Land Mammal Age in the latest Paleocene deposits of the basal Sparnacian facies at Rivecourt, in the north-central part of the Paris Basin. The new terrestrial vertebrate and macroflora assemblages are analyzed through a multidisciplinary study including sedimentologic, stratigraphic, isotopic, and palynological aspects in order to reconstruct the paleoenvironment and to evaluate biochronologic and paleogeographic implications. The mammals are moderately diverse and not abundant, contrary to turtles and champsosaurs. The macroflora is exceptional in preservation and diversity with numerous angiosperms represented by flowers, fruits, seeds and wood preserved as lignite material, revealing an abundance of Arecaceae, Betulaceae, Icacinaceae, Menispermaceae, Vitaceae and probably Cornaceae. Results indicate a Late Paleocene age based on carbon isotope data, palynology and vertebrate occurrences such as the choristoderan Champsosaurus, the arctocyonid Arctocyon, and the plesiadapid Plesiadapis tricuspidens. However, several mammal species compare better with the earliest Eocene. Among these, the particular louisinid Teilhardimys musculus, also recorded from the latest Paleocene of the Spanish Pyrenees, suggests a younger age than the typical MP6 reference level. Nevertheless, the most important aspect of the Rivecourt fauna is the presence of dental remains of a rodent and a “miacid” carnivoran, attesting to the presence of two modern mammalian orders in the latest Paleocene of Europe. Interestingly, these two groups are also the only modern groups recorded from the latest Paleocene of North America, making Rivecourt the first direct equivalent to the Clarkforkian Land Mammal Age outside of North America.

Basilochelys macrobios n. gen. and n. sp., a large cryptodiran turtle from the Phu Kradung Formation (latest Jurassic-earliest Cretaceous) of the Khorat Plateau, NE Thailand

Abstract A large cryptodiran turtle, Basilochelys macrobios n. gen. n. sp. is described from the latest Jurassic–earliest Cretaceous Phu Kradung Formation of NE Thailand, on the basis of skull, shell and other postcranial elements. Basilochelys presents a combination of primitive and derived characters. The derived characters include sculptured skull roof and shell surface; deeply embedded canalis caroticus internus; foramen posterius canalis carotici interni completely surrounded by pterygoid; neural formula of 6>4<6<6<6<6; anteroposteriorly expanded eleventh and twelfth marginal scutes extending onto the suprapygal and costal plates; narrow vertebral scutes; plastron sutured to the carapace, with large and wide anterior and posterior lobes, long and narrow bridge, very narrow axillary and inguinal notch; wide entoplastron; humeropectoral sulcus located on the posterior part of the entoplastron; anal notch absent. This taxon is placed in Trionychoidae and considered as the most basal member of that group.

Habitat fragmentation alters the properties of a host-parasite network: rodents and their helminths in South-East Asia

1. While the effects of deforestation and habitat fragmentation on parasite prevalence or richness are well investigated, host-parasite networks are still understudied despite their importance in understanding the mechanisms of these major disturbances. Because fragmentation may negatively impact species occupancy, abundance and co-occurrence, we predict a link between spatiotemporal changes in habitat and the architecture of host-parasite networks. 2. For this, we used an extensive data set on 16 rodent species and 29 helminth species from seven localities of South-East Asia. We analysed the effects of rapid deforestation on connectance and modularity of helminth-parasite networks. We estimated both the degree of fragmentation and the rate of deforestation through the development of land uses and their changes through the last 20 to 30 years in order to take into account the dynamics of habitat fragmentation in our statistical analyses. 3. We found that rapid fragmentation does not affect helminth species richness per se but impacts host-parasite interactions as the rodent-helminth network becomes less connected and more modular. 4. Our results suggest that parasite sharing among host species may become more difficult to maintain with the increase of habitat disturbance.