A collaborative backbone resource for comparative studies of subterranean evolution: The World Asellidae database.

Transition to novel environments, such as groundwater colonization by surface organisms, provides an excellent research ground to study phenotypic evolution. However, interspecific comparative studies on evolution to groundwater life are few because of the challenge in assembling large ecological and molecular resources for species-rich taxa comprised of surface and subterranean species. Here, we make available to the scientific community an operational set of working tools and resources for the Asellidae, a family of freshwater isopods containing hundreds of surface and subterranean species. First, we release the World Asellidae database (WAD) and its web application, a sustainable and FAIR solution to producing and sharing data and biological material. WAD provides access to thousands of species occurrences, specimens, DNA extracts and DNA sequences with rich metadata ensuring full scientific traceability. Second, we perform a large-scale dated phylogenetic reconstruction of Asellidae to support phylogenetic comparative analyses. Of 424 terminal branches, we identify 34 pairs of surface and subterranean species representing independent replicates of the transition from surface water to groundwater. Third, we exemplify the usefulness of WAD for documenting phenotypic shifts associated with colonization of subterranean habitats. We provide the first phylogenetically controlled evidence that body size of males decreases relative to that of females upon groundwater colonization, suggesting competition for rare receptive females selects for smaller, more agile males in groundwater. By making these tools and resources widely accessible, we open up new opportunities for exploring how phenotypic traits evolve in response to changes in selective pressures and trade-offs during groundwater colonization.

The biocultural origins and dispersal of domestic chickens.

Though chickens are the most numerous and ubiquitous domestic bird, their origins, the circumstances of their initial association with people, and the routes along which they dispersed across the world remain controversial. In order to establish a robust spatial and temporal framework for their origins and dispersal, we assessed archaeological occurrences and the domestic status of chickens from ∼600 sites in 89 countries by combining zoogeographic, morphological, osteometric, stratigraphic, contextual, iconographic, and textual data. Our results suggest that the first unambiguous domestic chicken bones are found at Neolithic Ban Non Wat in central Thailand dated to ∼1650 to 1250 BCE, and that chickens were not domesticated in the Indian Subcontinent. Chickens did not arrive in Central China, South Asia, or Mesopotamia until the late second millennium BCE, and in Ethiopia and Mediterranean Europe by ∼800 BCE. To investigate the circumstances of their initial domestication, we correlated the temporal spread of rice and millet cultivation with the first appearance of chickens within the range of red junglefowl species. Our results suggest that agricultural practices focused on the production and storage of cereal staples served to draw arboreal red junglefowl into the human niche. Thus, the arrival of rice agriculture may have first facilitated the initiation of the chicken domestication process, and then, following their integration within human communities, allowed for their dispersal across the globe.

Unexpected morphological diversity in ancient dogs compared to modern relatives.

Dogs are among the most variable species today, but little is known about the morphological variability in the early phases of their history. The Neolithic transition to farming may have resulted in an early morphological diversification as a result of changes in the anthropic environment or intentional selection on specific morphologies. Here, we describe the variability and modularity in mandible form by comparing 525 dog mandibles from European archaeological sites ranging from 8100 to 3000 cal. BC to a reference sample of modern dogs, wolves, and dingoes. We use three-dimensional geometric morphometrics to quantify the form of complete and fragmented mandibles. We demonstrate that an important morphological variability already existed before the Bronze Age in Europe, yet the largest, smallest, most brachycephalic or dolichocephalic extant dogs have no equivalent in the archaeological sample, resulting in a lower variation compared to modern relatives. The covariation between the anterior and posterior parts of the mandible is lower in archaeological dogs, suggesting a low degree of intentional human selection in early periods. The mandible of modern and ancient dogs differs in functionally important areas, possibly reflecting differences in diet, competition, or the implication of ancient dogs in hunting or defence.

Feeding sites promoting wildlife-related tourism might highly expose the endangered Yunnan snub-nosed monkey (Rhinopithecus bieti) to parasite transmission.

An increasing number of studies have found that the implementation of feeding sites for wildlife-related tourism can affect animal health, behaviour and reproduction. Feeding sites can favour high densities, home range overlap, greater sedentary behaviour and increased interspecific contacts, all of which might promote parasite transmission. In the Yunnan snub-nosed monkey (Rhinopithecus bieti), human interventions via provisioning monkeys at specific feeding sites have led to the sub-structuring of a group into genetically differentiated sub-groups. The fed subgroup is located near human hamlets and interacts with domesticated animals. Using high-throughput sequencing, we investigated Entamoeba species diversity in a local host assemblage strongly influenced by provisioning for wildlife-related tourism. We identified 13 Entamoeba species or lineages in faeces of Yunnan snub-nosed monkeys, humans and domesticated animals (including pigs, cattle, and domestic chicken). In Yunnan snub-nosed monkeys, Entamoeba prevalence and OTU richness were higher in the fed than in the wild subgroup. Entamoeba polecki was found in monkeys, pigs and humans, suggesting that this parasite might circulates between the wild and domestic components of this local social-ecological system. The highest proportion of faeces positive for Entamoeba in monkeys geographically coincided with the presence of livestock and humans. These elements suggest that feeding sites might indirectly play a role on parasite transmission in the Yunnan snub-nosed monkey. The implementation of such sites should carefully consider the risk of creating hotspots of disease transmission, which should be prevented by maintaining a buffer zone between monkeys and livestock/humans. Regular screenings for pathogens in fed subgroup are necessary to monitor transmission risk in order to balance the economic development of human communities dependent on wildlife-related tourism, and the conservation of the endangered Yunnan snub-nosed monkey.

Masticatory system integration in a commensal canid: interrelationships between bones, muscles and bite force in the red fox.

The jaw system in canids is essential for defence and prey acquisition. However, how it varies in wild species in comparison with domestic species remains poorly understood, yet is of interest in terms of understanding the impact of artificial selection. Here, we explored the variability and interrelationships between the upper and lower jaws, muscle architecture and bite force in the red fox (Vulpes vulpes). We performed dissections and used 3D geometric morphometric approaches to quantify jaw shape in 68 foxes. We used a static lever model and bite force estimates were compared with in vivo measurements of 10 silver foxes. Our results show strong relationships exist between cranial and mandible shape, and between cranial or mandible shape on the one hand and muscles or estimated bite force on the other hand, confirming the strong integration of the bony and muscular components of the jaw system. These strong relationships are strongly driven by size. The functional links between shape and estimated bite force are stronger for the mandible, which probably reflects its greater specialisation towards biting. We then compared our results with data previously obtained for dogs (Canis lupus familiaris) to investigate the effect of domestication. Foxes and dogs differ in skull shape and muscle physiological cross-sectional area (PCSA). They show a similar amount of morphological variation in muscle PCSA, but foxes show lower variation in cranial and mandible shape. Interestingly, the patterns of covariation are not stronger in foxes than in dogs, suggesting that domestication did not lead to a disruption of the functional links of the jaw system.

New mitogenomic lineages in Papio baboons and their phylogeographic implications.

OBJECTIVES: Incomplete and/or biased sampling either on a taxonomic or geographic level can lead to delusive phylogenetic and phylogeographic inferences. However, a complete taxonomic and geographical sampling is often and for various reasons impossible, particularly for widespread taxa such as baboons (Papio spp.). Previous studies on baboon phylogeography identified several sampling gaps, some of which we fill by investigating additional material including samples from museum specimens. MATERIALS AND METHODS: We generated 10 new mitochondrial genomes either via conventional PCR and subsequent Sanger sequencing from two blood samples or via high-throughput shotgun sequencing from degraded DNA extracted from eight museum specimens. Phylogenetic relationships and divergence times among baboon lineages were determined using maximum-likelihood and Bayesian inferences. RESULTS: We identified new mitochondrial lineages in baboons from Central Africa (Chad, the Central African Republic), from the Mahale, and the Udzungwa Mountains (Tanzania), with the latter likely representing a case of mitochondrial capture from sympatric kipunjis (Rungwecebus kipunji). We also found that the mitochondrial clades of olive baboons found in Ivory Coast and Tanzania extend into Niger and the Democratic Republic of Congo, respectively. Moreover, an olive baboon from Sierra Leone carries a mitochondrial haplotype usually found in Guinea baboons, suggesting gene flow between these two species. DISCUSSION: The extension of the geographic sampling by including samples from areas difficult to visit or from populations that are most likely extirpated has improved the geographic and temporal resolution of the mitochondrial phylogeny of baboons considerably. Our study also shows the great value of museum material for genetic analyses even when DNA is highly degraded.

Investigating the impact of captivity and domestication on limb bone cortical morphology: an experimental approach using a wild boar model.

The lack of bone morphological markers associated with the human control of wild animals has prevented the documentation of incipient animal domestication in archaeology. Here, we assess whether direct environmental changes (i.e. mobility reduction) could immediately affect ontogenetic changes in long bone structure, providing a skeletal marker of early domestication. We relied on a wild boar experimental model, analysing 24 wild-born specimens raised in captivity from 6 months to 2 years old. The shaft cortical thickness of their humerus was measured using a 3D morphometric mapping approach and compared with 23 free-ranging wild boars and 22 pigs from different breeds, taking into account sex, mass and muscle force differences. In wild boars we found that captivity induced an increase in cortical bone volume and muscle force, and a topographic change of cortical thickness associated with muscular expression along a phenotypic trajectory that differed from the divergence induced by selective breeding. These results provide an experimental proof of concept that changes in locomotor behaviour and selective breeding might be inferred from long bones morphology in the fossil and archaeological record. These trends need to be explored in the archaeological record and further studies are required to explore the developmental changes behind these plastic responses.

Bite force and its relationship to jaw shape in domestic dogs.

Previous studies based on two-dimensional methods have suggested that the great morphological variability of cranial shape in domestic dogs has impacted bite performance. Here, we used a three-dimensional biomechanical model based on dissection data to estimate the bite force of 47 dogs of various breeds at several bite points and gape angles. In vivo bite force for three Belgian shepherd dogs was used to validate our model. We then used three-dimensional geometric morphometrics to investigate the drivers of bite force variation and to describe the relationships between the overall shape of the jaws and bite force. The model output shows that bite force is rather variable in dogs and that dogs bite harder on the molar teeth and at lower gape angles. Half of the bite force is determined by the temporal muscle. Bite force also increased with size, and brachycephalic dogs showed higher bite forces for their size than mesocephalic dogs. We obtained significant covariation between the shape of the upper or lower jaw and absolute or residual bite force. Our results demonstrate that domestication has not resulted in a disruption of the functional links in the jaw system in dogs and that mandible shape is a good predictor of bite force.

The mark of captivity: plastic responses in the ankle bone of a wild ungulate (Sus scrofa).

Deciphering the plastic (non-heritable) changes induced by human control over wild animals in the archaeological record is challenging. We hypothesized that changes in locomotor behaviour in a wild ungulate due to mobility control could be quantified in the bone anatomy. To test this, we experimented with the effect of mobility reduction on the skeleton of wild boar (Sus scrofa), using the calcaneus shape as a possible phenotypic marker. We first assessed differences in shape variation and covariation in captive-reared and wild-caught wild boars, taking into account differences in sex, body mass, available space for movement and muscle force. This plastic signal was then contrasted with the phenotypic changes induced by selective breeding in domestic pigs. We found that mobility reduction induces a plastic response beyond the shape variation of wild boars in their natural habitat, associated with a reduction in the range of locomotor behaviours and muscle loads. This plastic signal of captivity in the calcaneus shape differs from the main changes induced by selective breeding for larger muscle and earlier development that impacted the pigs' calcaneus shape in a much greater extent than the mobility reduction during the domestication process of their wild ancestors.

Rabbits and the Specious Origins of Domestication.

Rabbits are commonly thought to have been domesticated in ∼AD600 by French monks. Using historical and archaeological records, and genetic methods, we demonstrate that this is a misconception and the general inability to date domestication stems from both methodological biases and the lack of appreciation of domestication as a continuum.

The enigma of the dog mummy from ancient Egypt and the origin of 'Rhipicephalus sanguineus'.

BACKGROUND: Ticks belonging to the Rhipicephalus sanguineus group are amongst the most important vectors of pathogenic microorganisms to dogs and humans. However, the taxonomy of this species group is still the subject of debate, especially because there is no type specimen or reliable morphological description for Rhipicephalus sanguineus sensu stricto. Recently, a comprehensive morphological and genetic study on representative tick specimens from Europe, Africa, Americas, and Oceania, revealed the existence of at least four morphologically and genetically distinct species under the name 'R. sanguineus' infesting dogs from different countries. METHODS: Herein, we examined morphologically tick specimens retrieved on a dog mummy from Ancient Egypt (ca. 1st century - 4th century A.D.). The dog mummy and associated ticks were found during an archaeological expedition conducted in El Deir. RESULTS: Scanning electron micrographs allowed us to assess their identity as belonging to the R. sanguineus group. In addition on the basis of the scutal punctation pattern, spiracular plates, width of dorsal tail of spiracular plates relative to the adjacent festoon, female genital aperture, male adanal plates and accessory shields, these ticks were tentatively identified as Rhipicephalus sp. II (=temperate species). CONCLUSIONS: It can be concluded that R. sanguineus group ticks have infested dogs living in the Mediterranean region since ancient times. This finding represents the oldest record of ticks on any animal species and adds a new piece in the complex puzzle regarding tick parasitism on dogs and humans and their role as vectors of pathogens.

Brief communication: a cranial morphometric assessment of the taxonomic affinities of Trachypithecus auratus (E. Geoffroy, 1812 primates: Colobinae) with a reassessment of the T. auratus type specimen.

The debate over the taxonomic position and affinities of Trachypithecus auratus has been ongoing since its identification by E. Geoffroy Saint-Hilaire in 1812. The type specimen of this species is housed in Muséum national d'Histoire naturelle in Paris (MNHN-ZM 2005-912). This point is debated due to the complex and fluctuating taxonomy of Southeast Asian Colobinae (Brandon-Jones et al.: Int J Primatol 25 (2004) 97-164) and to the fact that this individual is represented by a mounted skeleton. By means of 3D medical imaging methodologies we describe for the first time the cranial anatomy of the specimen MNHN-ZM 2005-912 and compare it with other Trachypithecus species, in order to test the molecular systematic hypotheses for affinities among the T. auratus-T. cristatus group. We ascertain the taxonomic attribution of this individual to the species Trachypithecus auratus species. The most diagnostic characters shared by the type specimen and Trachypithecus auratus compared to other species of Trachypithecus are the rounded orbits and the straight facial profile. We then try to clarify the inconsistencies concerning the geographical provenance of the type. The island of Java appears to be the most probable locality from a cluster analysis based on linear morphometry. After this approach and a discriminant analysis, a northeastern Javanese provenance of this specimen, as proposed by Brandon-Jones et al. (Int J Primatol 25 (2004) 97-164) is dubious. Finally we provide 3D models of the skull and the endocast, and a list of cranial landmark coordinates of the holotype for future research.

Archaeology: a lion found in the Egyptian tomb of Maïa.

Lions are mentioned by classical scholars and in pharaonic inscriptions as being among the sacred animals that were bred and buried in the Nile valley. And yet no specimens have been found in Egypt - until the excavation of the Bubasteion necropolis at Saqqara. Here we describe a complete skeleton, once a mummy, of a male lion (Panthera leo) that was discovered there, buried among the cats' catacombs created during the last centuries bc and occupying the much older tomb of Maïa, wet-nurse to the king Tutankhamun (from the New Kingdom, fourteenth century bc). This important find at a site that was dedicated to the feline goddess Bastet (also known as Bubastis) confirms the status of the lion as a sacred animal during the Late and Greek periods.