A small Cretaceous crocodyliform in a dinosaur nesting ground and the origin of sebecids.

Sebecosuchia was a group of highly specialized cursorial crocodyliforms that diversified during the Cretaceous and persist until the end of the Miocene. Their unique combination of cranial and post-cranial features indicates that they were active terrestrial predators that occupied the apex of the Late Cretaceous terrestrial ecosystems, even competing with theropod dinosaurs. Here, we report the discovery of the earliest sebecid worldwide, and the first from Eurasia, Ogresuchus furatus gen. et sp. nov., based on a semi-articulate specimen located in a titanosaurian sauropod nesting ground. The new taxon challenges current biogeographical models about the early dispersal and radiation of sebecid crocodylomorphs, and suggests an origin of the group much earlier than previously expected. Moreover, the new taxon suggests a potential convergent evolution between linages geographically isolated. Taphonomic evidences suggest that Ogresuchus died almost in the same place where fossilized, in a dinosaur nesting area. Biometric and morphologic observations lead to speculate that Ogresuchus could easily predate on sauropod hatchlings.

Allodaposuchus palustris sp. nov. from the upper cretaceous of Fumanya (South-Eastern Pyrenees, Iberian Peninsula): systematics, palaeoecology and palaeobiogeography of the enigmatic allodaposuchian crocodylians.

The controversial European genus Allodaposuchus is currently composed of two species (A. precedens, A. subjuniperus) and it has been traditionally considered a basal eusuchian clade of crocodylomorphs. In the present work, the new species A. palustris is erected on the base of cranial and postcranial remains from the lower Maastrichtian of the southern Pyrenees. Phylogenetic analyses here including both cranial and postcranial data support the hypothesis that Allodaposuchus is included within Crocodylia. The studied specimen suggests little change in postcranial skeleton along the evolutionary history of crocodylians, except for some bone elements such as the axis, the first caudal vertebra and the ilium. The specimen was found in an organic mudstone corresponding to a coastal wetland environment. Thus, A. palustris from Fumanya is the first Allodaposuchus reported in lacustrine-palustrine settings that expand the ecological range for this genus. The S-DIVA palaeobiogeographic reconstruction of ancestral area suggests that early members of Crocodylia rapidly widespread for the Northern Hemisphere landmasses no later than the Campanian, leading the apparition of endemic groups. In that way "Allodaposuchia" represents an endemic European clade probably originated in the Ibero-Armorican domain in the late Campanian and dispersed by the Southern European archipelago prior to the early Maastrichtian.

The paleoenvironment of Hispanopithecus laietanus as revealed by paleobotanical evidence from the Late Miocene of Can Llobateres 1 (Catalonia, Spain).

The early Vallesian site of Can Llobateres 1 (Vallès-Penedès Basin, Catalonia, Spain) is one of the richest localities of the European Late Miocene, having yielded the most complete remains of the fossil great ape Hispanopithecus laietanus (Primates: Hominidae). Fossil plant remains had been previously reported from this site but mostly remained unpublished. Here we describe an assemblage of plant megaremains recovered in 2010, which provides valuable paleoenvironmental data. This assemblage consists of a mixture of parautochthonous and allochthonous detached organs (leaves, stems, reproductive structures) deposited in marshy areas. The source vegetation mainly consisted of abundant reeds, palms, evergreen laurels and figs that probably grew in or near the marsh boundaries or nearby riparian forests. This environmental picture is consistent with the mammalian fauna, which shows the prevalence of humid forested environments, although somewhat more open woodlands might have been present away from the wet areas. The occurrence of mega-mesothermal taxa, together with the absence of deciduous elements, is consistent with a subtropical to warm-temperate climate. Within this mosaic environment, H. laietanus would have preferred the more humid and forested habitats, which probably were still quite common in the Vallès-Penedès during the early Vallesian. Such habitats would have provided a continuous ripe fruit supply throughout the year to these frugivorous great apes. Paleobotanical data from older sites of the same area and nearby basins show that the zonal vegetation was a warm-temperate mixed forest defined by evergreen laurels, together with leguminous trees and shrubs as well as a significant proportion of deciduous elements. Tropical and subtropical taxa would have been restricted to humid areas in the lowlands. From the late Vallesian onwards, many of these taxa disappeared from the Vallès-Penedès, whereas deciduous trees became dominant in the forested areas and wetlands, thus likely having driven Hispanopithecus to extinction in the study area.

50,000 years of genetic uniformity in the critically endangered Iberian lynx.

Low genetic diversity in the endangered Iberian lynx, including lack of mitochondrial control region variation, is thought to result from historical or Pleistocene/Holocene population bottlenecks, and to indicate poor long-term viability. We find no variability in control region sequences from 19 Iberian lynx remains from across the Iberian Peninsula and spanning the last 50,000 years. This is best explained by continuously small female effective population size through time. We conclude that low genetic variability in the Iberian lynx is not in itself a threat to long-term viability, and so should not preclude conservation efforts.

High incidence of nonslippage mechanisms generating variability and complexity in eurasian badger microsatellites.

The use of microsatellites in population genetics is hindered by a lack of understanding of the pattern and origin of mutations, the need to develop more specific and better computational models, and a paucity of information about specific taxa and loci. We analyzed between 4 and 10 allele sequences from 10 different microsatellites in Eurasian badgers in order to determine the compliance of the sequences with stepwise mutation models and the origin of that variability which cannot be detected through standard genotyping procedures. All microsatellite loci exhibited imperfections and/or substitutions and indels in the flanking region, as well as additions or deletions of repeat units. Our data set of sequences showed a higher number of imperfect repeats than other published badger and carnivore sequences. This could be attributed to the process of loci isolation because when genetic variability is low, researchers may be more likely to use imperfect loci if these are variable in the population being studied. Locus Mel15 had 2 repetitive arrays: one was part of a polypyrimidine region of a carnivoran short interspersed nuclear element (CAN-SINE) and the other was located in an A-rich region typical of these insertions. In spite of this complexity, heterozygosity was correlated with the maximum number of repeats. Thus, although new theoretical models are being evolved to cover complex patterns of microsatellite mutation, sequencing electromorphs is needed to identify microsatellites or portions of them whose evolution can be modeled under simple models.

Phylogenetic inference and comparative evolution of a complex microsatellite and its flanking regions in carnivores.

We sequenced locus Mel 08, with complex short repetitive motifs, in 24 carnivore species belonging to five different families in order to explore mutational changes in the region in the context of locus and species evolution. This non-coding locus includes up to four different parts or repetitive motifs showing size variability. The variability consists of repeat additions and deletions; substitutions, insertions and/or deletions creating interruptions in the repeat; and substitutions, insertions and deletions in the flanking regions. The locus has different repeat expansions in different carnivore subfamilies. We hypothesize that the complexity of this locus is due to a high mutation rate at an ancestral DNA sequence and, thus, prompts the emergence of repeats at mutational hotspots. High levels of homoplasy were evident, with nine electromorphs representing 28 haplotypes never shared across species. The variability in flanking regions was informative for phylogenetic inference and their evolutionary content. Tree topologies were congruent with relevant hypotheses on current conflicts in carnivore phylogenies, such as: (i) the monophyly of Lutrinae, (ii) the paraphyly of Mustelinae, (iii) the basal position of the Eurasian badger, Meles meles , in the Mustelidae, (iv) the classification of skunks as a separate family, Mephitidae, and (v) the placement of the red panda, Ailurus fulgens , as a monotypic family, Ailuridae, at a basal position in the Musteloidea.

Eurasian otters, Lutra lutra, have a dominant mtDNA haplotype from the Iberian Peninsula to Scandinavia.

The Eurasian otter, Lutra lutra, has a Palaearctic distribution and has suffered a severe decline throughout Europe during the last century. Previous studies in this and other mustelids have shown reduced levels of variability in mitochondrial DNA, although otter phylogeographic studies were restricted to central-western Europe. In this work we have sequenced 361 bp of the mtDNA control region in 73 individuals from eight countries and added our results to eight sequences available from GenBank and the literature. The range of distribution has been expanded in relation to previous works north towards Scandinavia, east to Russia and Belarus, and south to the Iberian Peninsula. We found a single dominant haplotype in 91.78% of the samples, and six more haplotypes deviating a maximum of two mutations from the dominant haplotype restricted to a single country. Variability was extremely low in western Europe but higher in eastern countries. This, together with the lack of phylogeographical structuring, supports the postglacial recolonization of Europe from a single refugium. The Eurasian otter mtDNA control region has a 220-bp variable minisatellite in Domain III that we sequenced in 29 otters. We found a total of 19 minisatellite haplotypes, but they showed no phylogenetic information.

Radiation and phylogeography in the Japanese macaque, Macaca fuscata.

The Japanese macaque (Macaca fuscata) presumably differentiated from eastern rhesus macaque (Macaca mulatta) populations during the Pleistocene and the two species are closely related. In order to analyse speciation and subspeciation events in the Japanese macaque and to describe historical and current relationships among their populations, we sequenced and analysed a fragment of 392bp of mitochondrial DNA (mtDNA) control region in 50 individuals belonging to six populations of Japanese macaque and compared these sequences with 89 eastern rhesus macaque control region sequences from GenBank/EMBL database. There were high genetic similarities between both species and only two positions were fixed within each species, which supports the inclusion of the Japanese macaque in a single species with eastern populations of rhesus macaques. Japanese macaque ancestors colonised Japan after the separation of the two species, estimated at between 0.31 and 0.88 million years ago (Mya). The star-like phylogeny, multimodal mismatch distribution, and lack of correlation between geographic and genetic distances are in accordance with a rapid dispersion of macaques throughout the archipelago after the arrival into Japan. The species shows low genetic variation within populations and high levels of genetic differentiation among populations with no mtDNA haplotype shared across populations. Genetic distances between Yakushima macaques (Macaca fuscata yakui) and any other population of Macaca fuscata fuscata subspecies are comparable to the distances between populations of Honshu, Awajishima, and Kyushu, not supporting the classification of Yakushima macaques as a different subspecies.

Genotyping from semen of wild Japanese macaques (Macaca fuscata).

The noninvasive collection of animal cells is crucial for DNA analyses in wild populations that cannot be disturbed by capture. We describe the collection of 68 semen samples following copulation and masturbation events in wild habituated and nonhabituated troops of Japanese macaques on the protected island of Yakushima. We used this DNA to amplify 390 base pairs (bp) of the mitochondrial DNA control region in 16 individuals from eight troops, and found a monomorphic pattern in agreement with the low variability imposed by geographic isolation and female philopatry. We also amplified two microsatellite loci from samples collected after the resident males of a focal troop had copulated with different females. We found several different allele combinations in samples collected after the observed mating of a single male, indicating the presence of contaminant DNA, presumably from males that had previously mated with the same female. This discovery made it impossible to assign a given sample to a specific male except when the samples were recovered after masturbation events. Thus, it was not possible to test for kinship or estimate allele frequencies from the semen samples. The mixing of semen, and the pattern of sample collection observed in morphologically identified individuals support the notion that strong mating and sperm competition exists among resident and nonresident males.