Biology subjects

Cucchi, T.

Publications and source records attributed to Cucchi, T..

3 recordsLinked to original sources

bioRxiv2022

Can growth in captivity alter the calcaneal microanatomy of a wild ungulate?

AO_SCPLOWBSTRACTC_SCPLOWReduced mobility associated with captivity induces changes in biomechanical stress on the skeleton of domesticated animals. Due to bone plasticity, bones morphology and internal structure can respond to these new biomechanical stresses over individuals lifetime. In a context where documenting early process of animal domestication is challenging, this study will test the hypothesis that change in mobility patterns during a wild ungulates life will alter the internal structure of its limb bones and provide a proof of concept for the application of this knowledge in Zooarchaeology. Using the calcaneus as a phenotypic marker through qualitative and quantitative 3D microanatomical analyses, we relied on a comparative study across wild boars (Sus scrofa) populations from controlled experimental conditions with different mobility patterns (natural habitat, large pen, and stall) and archaeological specimens collected from middle and late Mesolithic as surrogate for the norm of reaction in European wild boar phenotype before the spread of agriculture and domestic pigs. Results provide evidence for compressive and tensile forces as the main elements affecting the variation in the cortical thickness along the calcaneus. Furthermore, changes in the internal structure of the calcaneus between mobility patterns are observed but their intensity is not directly associated with the degree of mobility restriction and only weakly impacted by the size or weight of the individuals. Despite having greater bone volume, the calcaneus of the Mesolithic wild boars displays a very similar microanatomy compared to the present-day hunted or captive wild boars. These results suggest that calcaneal microanatomy is more affected by population differences than by locomotor variation. For all these reasons, this preliminary study doesnt support the use of microanatomy of the calcaneus as an indicator of change in locomotor behaviour induced by captivity in the archaeological record.

developmental biology↗

bioRxiv2021

Palaeogenomic analysis of black rat (Rattus rattus) reveals multiple European introductions associated with human economic history

The distribution of the black rat (Rattus rattus) has been heavily influenced by its association with humans. The dispersal history of this non-native commensal rodent across Europe, however, remains poorly understood, and different introductions may have occurred during the Roman and medieval periods. Here, in order to reconstruct the population history of European black rats, we generated a de novo genome assembly of the black rat, 67 ancient black rat mitogenomes and 36 ancient nuclear genomes from sites spanning the 1st-17th centuries CE in Europe and North Africa. Analyses of mitochondrial DNA confirm that black rats were introduced into the Mediterranean and Europe from Southwest Asia. Genomic analyses of the ancient rats reveal a population turnover in temperate Europe between the 6th and 10th centuries CE, coincident with an archaeologically attested decline in the black rat population. The near disappearance and re-emergence of black rats in Europe may have been the result of the breakdown of the Roman Empire, the First Plague Pandemic, and/or post-Roman climatic cooling.

evolutionary biology↗

bioRxiv2020

Deep learning for species identification of modern and fossil rodent molars

Reliable identification of species is a key step to assess biodiversity. In fossil and archaeological contexts, genetic identifications remain often difficult or even impossible and morphological criteria are the only window on past biodiversity. Methods of numerical taxonomy based on geometric morphometric provide reliable identifications at the specific and even intraspecific levels, but they remain relatively time consuming and require expertise on the group under study. Here, we explore an alternative based on computer vision and machine learning. The identification of three rodent species based on pictures of their molar tooth row constituted the case study. We focused on the first upper molar in order to transfer the model elaborated on modern, genetically identified specimens to isolated fossil teeth. A pipeline based on deep neural network automatically cropped the first molar from the pictures, and returned a prediction regarding species identification. The deep-learning approach performed equally good as geometric morphometrics and, provided an extensive reference dataset including fossil teeth, it was able to successfully identify teeth from an archaeological deposit that was not included in the training dataset. This is a proof-of-concept that such methods could allow fast and reliable identification of extensive amounts of fossil remains, often left unstudied in archaeological deposits for lack of time and expertise. Deep-learning methods may thus allow new insights on the biodiversity dynamics across the last 10.000 years, including the role of humans in extinction or recent evolution.

zoology↗