Biology subjects

Bochaton, C.

Publications and source records attributed to Bochaton, C..

8 recordsLinked to original sources

bioRxiv2026

A comprehensive identification protocol for postcranial bones of Southeast Asian Ruminantia. Part 2: Morphological criteria for small and medium-sized species

The taxonomic identification of postcranial elements from small and medium-sized ruminants represents a significant challenge in zooarchaeological and Late Quaternary paleontological studies, particularly in biodiversity-rich regions such as continental Southeast Asia. This study presents a comprehensive osteological reference framework for the small and medium-sized Ruminantia of this region, based on a comparative sample of 228 specimens representing 14 species across three families (Bovidae, Cervidae, and Moschidae). Osteological characters were first described on a small initial specimen set and subsequently scored across the full sample. Although a small number of character states were found to be unique to specific taxa, most proved highly variable, limiting their individual identification potential. To address this, a Random Forest and a Naive Bayes classifier were applied to assess the discriminatory power of character combinations across four taxonomic ranks (Family, Subfamily, Genus, and Species) on independent bones. Both approaches performed similarly, achieving mean identification accuracies of 87-86% at the family level, 69% at the subfamily level, 50% at the genus level, and 35-33% at the species level. The Naive Bayes models were further deployed as an interactive web application, allowing users to perform bone identification based on any combination of observable character states from a single anatomical element. Our results highlight the limits of morphological identification of postcranial elements in this taxonomic and biogeographic context, while demonstrating that a transparent, reproducible, and statistically grounded approach can still represent a significant step forward for zooarchaeological and Late Quaternary paleontological studies in Southeast Asia and beyond.

zoology↗

bioRxiv2026

A comprehensive identification protocol for postcranial bones of Southeast Asian Ruminantia. Part 3: Morphological criteria for large-sized species

Postcranial remains of large-bodied ruminants are abundant in the Late Quaternary record of continental Southeast Asia, yet their taxonomic attribution remains one of the least resolved problems in the zooarchaeology of this biodiversity-rich region. We address it here with an osteological identification protocol covering the six large ruminant species of the mainland: Bubalus bubalis, Bos javanicus, Bos sauveli, Bos gaurus, Budorcas taxicolor and Rusa unicolor, built from a comparative sample of 109 skeletons. A total of 148 discrete characters over 27 skeletal elements representing 442 states were defined on a restricted set of individuals, then scored across the entire sample. Most proved remarkably stable within taxa with 80.0% of the character/taxon combinations showing a dominant state at a frequency above 95%, and a substantial number of states occurred in a single family, subfamily, genus or species. Character combinations for taxonomic identification were then evaluated by the use of two supervised machine learning methods, a random forest model and a naive Bayes classifier at each of four taxonomic ranks. The two behaved almost identically, with mean accuracies of 95-94% for families, 93% for subfamilies, 89% for genera and 76% for species; only the three closely related and unevenly sampled species of Bos resisted consistent separation. The weighted naive Bayes models are distributed as a standalone web application in which any combination of states observed on a single element returns attribution probabilities for every rank. Together these results offer a transparent and statistically explicit alternative to expert judgement for the identification of Late Quaternary postcranial mammal remains, in Southeast Asia and elsewhere.

zoology↗

bioRxiv2025

A comprehensive identification protocol for postcranial bones of Southeast Asian Ruminantia. Part 1: Osteometry

AO_SCPLOWBSTRACTC_SCPLOWTaxonomic identification of animal bone remains from archaeological and paleontological contexts is usually conducted by comparison with modern skeletal specimens, an approach that is relatively straightforward in temperate or insular regions. In contrast, it is more challenging in continental tropical areas, where rich biodiversity makes it difficult to assemble exhaustive modern references. This situation is well illustrated in continental Southeast Asia, where studies of large mammal assemblages have largely focused on teeth and cranial elements, while postcranial remains are rarely investigated. To address this issue, we established an osteometric reference dataset of the limb bones from Southeast Asian ruminant species and analyzed both the potential of raw measurements and osteometric ratios to identify the different taxa. The results reveal significant differences between genera and species, allowing size-based grouping and precise taxonomic identification in some cases. These data were subsequently used to develop an easy-to-use identification tool based solely on measurements. The performance of this tool was tested against previously published datasets, allowing confirmation of existing results, and discussion of potential biases associated with identification based on measurements alone. This new methodological framework provides a solid foundation to be combined with qualitative morphological criteria to enhance the precision and robustness of the taxonomic identifications of subfossil bones from continental southeast Asia.

paleontology↗

bioRxiv2025

Archaeological Bone Assemblages Trace Changes in Turtle and Tortoise Diversity in Continental Southeast Asia

Among tropical regions, continental Southeast Asia is a major hotspot of biodiversity. However, due to rapid urban expansion and severe deforestation, this area is recognized as one of the top global conservation priorities. As in other tropical regions, the prevailing idea is that the decline of local biodiversity in this region is a direct result of the overwhelming environmental changes that have occurred over the last 80 years. However, paleoecological data indicate that tropical forests have been exploited by human populations since at least the Late Pleistocene, and forest clearance for farming began several thousand years ago. To gain a complete overview of the long-term evolution of vertebrate fauna in continental Southeast Asia, it is necessary to investigate the past. This task is currently out of reach, mainly due to the lack of paleontological and historical studies regarding small animals, including emblematic taxa like turtles. Indeed, although some evidence suggests that the biodiversity of turtles in continental Southeast Asia may have changed over the last millennia, the paucity of historical records and archaeological assemblages studies currently precludes further assessment of the potential effect of past environmental changes, including potential human disturbances. The present study consists of a paleontological analysis of turtle bone assemblages collected from four prehistoric sites in Thailand and Cambodia. The aim is to test the hypothesis of changes in turtle biodiversity over the last 10,000 years. Our results indicate that turtle assemblages in most areas have experienced only limited changes across the Holocene, except for Laang Spean in Cambodia. However, a few rare taxa may represent extirpated or extinct species of Testudinidae in continental Southeast Asia at an unknown time during the Holocene. We also observed significant changes in the geographic distribution of some genera, such as Batagur, Cyclemys, and Amyda. The fact that turtle fauna has been rather resilient and unchanged for several millennia shows that past human impact in most investigated areas had limited effects on these taxa. The strong modifications observed in Cambodia could, however, serve as a warning about the potential fate of turtle biodiversity in this region if further loss of natural environments occurs.

paleontology↗

bioRxiv2024

CTCF-DEPENDENT INSULATION OF Hoxb13 AND THE HETEROCHRONIC CONTROL OF TAIL LENGTH

In mammals, tail length is controlled by several genetic determinants, amongst which Hox13 genes located at the posterior extremities of Hox clusters, whose main function are to terminate the extension of the body axis. In this view, the precise timing in the transcriptional activation of these genes may impact upon body length. Unlike other Hox clusters, HoxB lacks all posterior genes between Hoxb9 and Hoxb13, two genes separated by a ca. 70 kb large DNA segment containing an unusually high number of CTCF sites, suggesting it isolates Hoxb13 from the rest of the cluster, thereby delaying its negative impact on trunk extension. We deleted the spacer DNA to induce a potential heterochronic gain of function of Hoxb13 at physiological concentration and observed a shortening of the tail as well as other abnormal phenotypes, which were all rescued by inactivating Hoxb13 in-cis with the deletion. A comparable gain of function was observed in mutant ES cells grown as pseudo-embryos in vitro, which allowed us to examine in details the importance of both the number and the orientation of CTCF sites in the insulating activity of the DNA spacer. A short cassette containing all the CTCF sites was sufficient to insulate Hoxb13 from the rest of HoxB and additional modifications of this CTCF cassette showed that two CTCF sites in convergent orientations are already capable of importantly delaying Hoxb13 activation in these conditions. We discuss the relative importance of genomic distance versus number and orientation of CTCF sites in preventing Hoxb13 to be activated too early during trunk extension and hence to modulate tail length.

developmental biology↗

bioRxiv2023

Zooarchaeological investigation of the Hoabinhian exploitation of reptiles and amphibians in Thailand and Cambodia with a focus on the Yellow-Headed tortoise (Indotestudo elongata (Blyth, 1854))

While non-marine turtles are almost ubiquitous in the archaeological record of Southeast Asia, their zooarchaeological examination has been inadequately pursued within this tropical region. This gap in research hinders a complete comprehension of past human subsistence strategies and economies, as only a limited number of comprehensive studies encompassing all the taxa found in archaeological sites have been conducted thus far. This constraint becomes particularly significant in relation to prehistoric hunter-gatherer populations, who might have extensively utilized inland chelonian taxa. In order to initiate a new approach to the study of past human-turtle interactions in Southeast Asia, we propose an in-depth zooarchaeological analysis of turtle bone remains recovered from four Hoabinhian Hunter-gatherer archaeological assemblages located in Thailand and Cambodia, dating from the Late Pleistocene to the first half of the Holocene. Our study focuses on the bone remains attributed to the Yellow-headed Tortoise (Indotestudo elongata) as it is the most represented taxon in archaeological assemblages in the region of study. For this species, we developed osteometric equations enabling the estimation of the carapace size of the archaeological individuals. This allowed us to study the size structure of the archaeological populations at different sites and to reveal the human exploitation strategies of these animals. We observed a significant taphonomic homogeneity among the studied assemblages, along with similarities in the diversity of hunted reptile and amphibian taxa as well as the size of the exploited tortoises. These findings suggest consistent subsistence behaviors across distinct sites, despite their varying environmental conditions, and raise the possibility of cultural similarities across different periods and regions. Additionally, we provide a baseline for future zooarchaeological studies and a methodological framework for the detailed analysis of archaeological turtle bones in continental Southeast Asia.

paleontology↗

bioRxiv2022

Sequential And Directional Insulation By Conserved CTCF Sites Underlies The Hox Timer In Pseudo-Embryos

During development, Hox genes are activated in a time sequence following their relative positions on their clusters, leading to the proper identities of structures along the rostral to caudal axis. To understand the mechanism operating this Hox timer, we used ES-cells derived stembryos and show that the core of the process involves the start of transcription at the 3 part of the cluster, following Wnt signaling, and the concomitant loading of cohesin complexes on the transcribed DNA segments, i.e., with an asymmetric distribution along the gene cluster. Chromatin extrusion then occurs with successively more posterior CTCF sites acting as transient insulators, thus generating a progressive time-delay in the activation of more 5-located genes due to long-range contacts with a flanking TAD. Mutant stembryos support this model and reveal that the iterated presence of evolutionary conserved and regularly spaced intergenic CTCF sites control the precision and the pace of this temporal mechanism.

developmental biology↗

bioRxiv2019

Constrained Transcriptional Polarity In The Organization Of Mammalian Hox Gene Clusters

In many animal species with a bilateral symmetry, Hox genes are clustered either at one or at several genomic loci. This organization has a functional relevance, as the transcriptional control applied to each gene depends upon its relative position within the gene cluster. It was previously noted that vertebrate Hox clusters display a much higher level of genomic organization than their invertebrate counterparts. The former are always more compact than the latter, they are generally devoid of repeats and of interspersed genes, and all genes are transcribed by the same DNA strand, suggesting that particular factors constrained these clusters towards a tighter structure during the evolution of the vertebrate lineage. Here we investigate the importance of uniform transcriptional orientation by engineering several alleles within the HoxD cluster such as to invert one or several transcription unit(s), with or without a neighboring CTCF site. We observe that the association between the tight structure of mammalian Hox clusters and their regulation makes inversions likely detrimental to the proper implementation of this complex genetic system. We propose that the consolidation of Hox clusters in vertebrates, including transcriptional polarity, evolved in conjunction with the emergence of global gene regulation via the flanking regulatory landscapes, to optimize a coordinated response of selected subsets of target genes in cis.

developmental biology↗