Population Dynamics in Italian Canids between the Late Pleistocene and Bronze Age

Coyotes can do 'puppy dog eyes' too: comparing interspecific variation in Canis facial expression muscles

Facial expressions are critical for non-verbal communication. The Canis genus epitomizes the interplay between behaviour and morphology in the evolution of non-verbal communication. Recent work suggests that the levator anguli oculi medialis (LAOM) muscle is unique to dogs (Canis familiaris) within the Canis genus and evolved due to domestication. The LAOM raises the inner eyebrows, resulting in the 'puppy dog eyes' expression. Here, we test whether the LAOM is a derived trait in dogs by (i) examining the facial expression muscles of a closely related and ancestral wild Canis species, the coyote (C. latrans) and (ii) comparing our results with other Canis and canid taxa. We discover that coyotes have a well-developed LAOM like dogs, which differs from the modified/absent LAOM in grey wolves. Our findings challenge the hypothesis that the LAOM developed due to domestication. We suggest that the LAOM is a basal trait that was lost in grey wolves. Additionally, we find inter- and intraspecific variations in the size of the muscles of the outer ear, forehead, lips and rostrum, indicating potential adaptations related to sensory perception, communication and individual-level functional variations within canids. Together, this research expands our knowledge of facial expressions, their evolution and their role in communication.

Ancient DNA re-opens the question of the phylogenetic position of the Sardinian pika Prolagus sardus (Wagner, 1829), an extinct lagomorph

Palaeogenomics is contributing to refine our understanding of many major evolutionary events at an unprecedented resolution, with relevant impacts in several fields, including phylogenetics of extinct species. Few extant and extinct animal species from Mediterranean regions have been characterised at the DNA level thus far. The Sardinian pika, Prolagus sardus (Wagner, 1829), was an iconic lagomorph species that populated Sardinia and Corsica and became extinct during the Holocene. There is a certain scientific debate on the phylogenetic assignment of the extinct genus Prolagus to the family Ochotonidae (one of the only two extant families of the order Lagomorpha) or to a separated family Prolagidae, or to the subfamily Prolaginae within the family Ochotonidae. In this study, we successfully reconstructed a portion of the mitogenome of a Sardinian pika dated to the Neolithic period and recovered from the Cabaddaris cave, an archaeological site in Sardinia. Our calibrated phylogeny may support the hypothesis that the genus Prolagus is an independent sister group to the family Ochotonidae that diverged from the Ochotona genus lineage about 30 million years ago. These results may contribute to refine the phylogenetic interpretation of the morphological peculiarities of the Prolagus genus already described by palaeontological studies.

The extinct Sicilian wolf shows a complex history of isolation and admixture with ancient dogs

The Sicilian wolf remained isolated in Sicily from the end of the Pleistocene until its extermination in the 1930s-1960s. Given its long-term isolation on the island and distinctive morphology, the genetic origin of the Sicilian wolf remains debated. We sequenced four nuclear genomes and five mitogenomes from the seven existing museum specimens to investigate the Sicilian wolf ancestry, relationships with extant and extinct wolves and dogs, and diversity. Our results show that the Sicilian wolf is most closely related to the Italian wolf but carries ancestry from a lineage related to European Eneolithic and Bronze Age dogs. The average nucleotide diversity of the Sicilian wolf was half of the Italian wolf, with 37-50% of its genome contained in runs of homozygosity. Overall, we show that, by the time it went extinct, the Sicilian wolf had high inbreeding and low-genetic diversity, consistent with a population in an insular environment.

Evolutionary history of the extinct wolf population from France in the context of global phylogeographic changes throughout the Holocene

Phylogeographic patterns in large mammals result from natural environmental factors and anthropogenic effects, which in some cases include domestication. The grey wolf was once widely distributed across the Holarctic, but experienced phylogeographic shifts and demographic declines during the Holocene. In the 19th-20th centuries, the species became extirpated from large parts of Europe due to direct extermination and habitat loss. We reconstructed the evolutionary history of the extinct Western European wolves based on the mitogenomic composition of 78 samples from France (Neolithic-20th century) in the context of other populations of wolves and dogs worldwide. We found a close genetic similarity of French wolves from ancient, medieval and recent populations, which suggests the long-term continuity of maternal lineages. MtDNA haplotypes of the French wolves showed large diversity and fell into two main haplogroups of modern Holarctic wolves. Our worldwide phylogeographic analysis indicated that haplogroup W1, which includes wolves from Eurasia and North America, originated in Northern Siberia. Haplogroup W2, which includes only European wolves, originated in Europe ~35 kya and its frequency was reduced during the Holocene due to an expansion of haplogroup W1 from the east. Moreover, we found that dog haplogroup D, currently restricted to Europe and the Middle East, was nested within the wolf haplogroup W2. This suggests European origin of haplogroup D, probably as a result of an ancient introgression from European wolves. Our results highlight the dynamic evolutionary history of European wolves during the Holocene, with a partial lineage replacement and introgressive hybridization with local dog populations.

Being a Dog: A Review of the Domestication Process

The process of canine domestication represents certainly one of the most interesting questions that evolutionary biology aims to address. A "multiphase" view of this process is now accepted, with a first phase during which different groups of wolves were attracted by the anthropogenic niche and a second phase characterized by the gradual establishment of mutual relationships between wolves and humans. Here, we provide a review of dog (Canis familiaris) domestication, highlighting the ecological differences between dogs and wolves, analyzing the molecular mechanisms which seem to have influenced the affiliative behaviors first observed in Belyaev's foxes, and describing the genetics of ancient European dogs. Then, we focus on three Mediterranean peninsulas (Balkan, Iberian and Italian), which together represent the main geographic area for studying canine domestication dynamics, as it has shaped the current genetic variability of dog populations, and where a well-defined European genetic structure was pinpointed through the analysis of uniparental genetic markers and their phylogeny.

On the traces of lost identities: chronological, anthropological and taphonomic analyses of the Late Neolithic/Early Eneolithic fragmented and commingled human remains from the Farneto rock shelter (Bologna, northern Italy)

The present study examines the prehistoric human skeletal remains retrieved starting from the 1920s in the deposit of the Farneto rock shelter, situated in the area of the 'Parco dei Gessi Bolognesi e Calanchi dell'Abbadessa' (San Lazzaro di Savena, Bologna, northern Italy). An exact dating and a reliable interpretation of the assemblage had not been reached so far because of the lack of contextual data useful for dating purposes, the inaccurate recovery procedures of the remains and their state of preservation. In fact, the skeletal remains from the Farneto rock shelter are highly fragmented and commingled, whereas reliable information about their original position and their recovery procedures are not available. Despite these difficulties, radiocarbon analyses allowed the precise dating of the remains to a final phase of the Neolithic and an early phase of the Eneolithic period in Emilia Romagna (northern Italy). The study of the assemblage enabled to clarify the use of the context for funerary purposes. Moreover, the anthropological and taphonomic analyses of the skeletal remains shed light on the biological profile of the individuals and on some events that occurred after their death. In particular, the analysis of perimortem lesions highlighted the existence of intentional interventions related to corpse treatment, referable to dismembering/disarticulation and scarnification, i.e. cleaning of bones from soft tissues. Finally, the comparison with other Italian and European Neo/Eneolithic funerary contexts enabled a better understanding of these complex ritual practices.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12520-023-01727-2.

Museomics Provides Insights into Conservation and Education: The Instance of an African Lion Specimen from the Museum of Zoology “Pietro Doderlein”

Innovative technological approaches are crucial to enhance naturalistic museum collections and develop information repositories of relevant interest to science, such as threatened animal taxa. In this context, museomics is an emerging discipline that provides a novel approach to the enhancement and exploitation of these collections. In the present study, the discovery of a neglected lion skeleton in the Museum of Zoology “Pietro Doderlein” of the University of Palermo (Italy) offered the opportunity to undertake a multidisciplinary project. The aims of the study consisted of the following: (i) adding useful information for museographic strategies, (ii) obtaining a new genetic data repository from a vulnerable species, (iii) strengthening public awareness of wildlife conservation, and (iv) sharing new learning material. The remains of the lion were examined with a preliminary osteological survey, then they were restored by means of 3D printing of missing skeletal fragments. Phylogenetic analyses based on cytochrome b sequence clearly indicate that the specimen belongs to the Central Africa mitochondrial clade. At the end of the study, the complete and restored skeleton was exhibited, along with all of the information and data available from this project. This study shows a useful approach for the restoration and enhancement of a museum specimen, with important opportunities for preserving biodiversity and driving specific conservation policies, but also for providing Life Science learning material.

The Sequence Analysis of Mitochondrial DNA Revealed Some Major Centers of Horse Domestications: The Archaeologist's Cut

The question about the time and the place of horse domestication, a process which had a profound impact on the progress of mankind, is disputable. According to the most widely accepted hypothesis, the earliest domestication of the horse happened in the western parts of the Eurasian steppes, between the Northern Black Sea region and present-day Kazakhstan and Turkmenistan. It seems that it occurred not earlier than the first half and most probably during the middle (even the last third) of the fourth millennium BC (from ∼ 5.5 kya). The next steps of large-scale horse breeding occurred almost simultaneously in Eurasia and North Africa due to the development of the social structure of human communities. On the other hand, the morphological differences between wild and domestic animals are rather vague and the genetic introgression between them is speculative. In this review, we have tried to gather all available scientific data on the existing possible hypotheses for the earliest domestication of the horse, as well as to highlight some data on the most plausible ones. This is due to the frequency of some significant data on the frequency of strictly defined mitotypes in different historical periods of human civilizations existing in the same periods.

The gut microbiome buffers dietary adaptation in Bronze Age domesticated dogs

In an attempt to explore the role of the gut microbiome during recent canine evolutionary history, we sequenced the metagenome of 13 canine coprolites dated ca. 3,600–3,450 years ago from the Bronze Age archaeological site of Solarolo (Italy), which housed a complex farming community. The microbiome structure of Solarolo dogs revealed continuity with that of modern dogs, but it also shared some features with the wild wolf microbiome, as a kind of transitional state between them. The dietary niche, as also inferred from the microbiome composition, was omnivorous, with evidence of consumption of starchy agricultural foods. Of interest, the Solarolo dog microbiome was particularly enriched in sequences encoding alpha-amylases and complemented a low copy number of the host amylase gene. These findings suggest that Neolithic dogs could have responded to the transition to a starch-rich diet by expanding microbial functionalities devoted to starch catabolism, thus compensating for delayed host response.

•

Ancient DNA of Bronze Age canine coprolites from Solarolo was sequenced

•

Solarolo dogs share gut microbiome features with modern wolves and dogs

•

The gut microbiome of Solarolo dogs shows high number of reads for alpha-amylase

•

Neolithic canine gut microbiome complemented delay in host genome adaptation