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The Sardinian dhole (Cynotherium sardous) 1 was an iconic and unique canid species that was endemic to Sardinia and Corsica until it became extinct at the end of the Late Pleistocene. 2–5 Given its peculiar dental morphology, small body size, and high level of endemism, several extant canids have been proposed as possible relatives of the Sardinian dhole, including the Asian dhole and African hunting dog ancestor. 3,6–9 Morphometric analyses 3,6,8–12 have failed to clarify the evolutionary relationship with other canids.We sequenced the genome of a ca -21,100-year-old Sardinian dhole in order to understand its genomic history and clarify its phylogenetic position. We found that it represents a separate taxon from all other living canids from Eurasia, Africa, and North America, and that the Sardinian dhole lineage diverged from the Asian dhole ca 885 ka. We additionally detected historical gene flow between the Sardinian and Asian dhole lineages, which ended approximately 500-300 ka, when the land bridge between Sardinia and mainland Italy was already broken, severing their population connectivity. Our sample showed low genome-wide diversity compared to other extant canids—probably a result of the long-term isolation—that could have contributed to the subsequent extinction of the Sardinian dhole. • The Sardinian dhole lineage diverged from the Asian dholes around 885 ka • Post-divergence gene flow between the dhole lineages ended between 560 and 310 ka • Our sample also showed a reduced genome-wide diversity • The gene flow between Lycaon and the dholes' ancestor ended around 1.05–0.83 Ma Ciucani et al. sequence the genome of a 21,100-year-old Sardinian dhole. The sample represents a different lineage from the current Asian dholes and split from them ca 885 ka. Post-divergence gene flow between the two lineages ended later— ca 560–310 ka—followed by a stable but long-term population decline and extinction of the Sardinian dhole. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

The taxonomic status of the now likely extirpated Korean Peninsula wolf has been extensively debated, with some arguing it represents an independent wolf lineage, Canis coreanus. To investigate the Korean wolf's genetic affiliations and taxonomic status, we sequenced and analysed the genomes of a Korean wolf dated to the beginning of the 20th century, and a captive wolf originally from the Pyongyang Central Zoo. Our results indicated that the Korean wolf bears similar genetic ancestry to other regional East Asian populations, therefore suggesting it is not a distinct taxonomic lineage. We identified regional patterns of wolf population structure and admixture in East Asia with potential conservation consequences in the Korean Peninsula and on a regional scale. We find that the Korean wolf has similar genomic diversity and inbreeding to other East Asian wolves. Finally, we show that, in contrast to the historical sample, the captive wolf is genetically more similar to wolves from the Tibetan Plateau; hence, Korean wolf conservation programmes might not benefit from the inclusion of this specimen. [ABSTRACT FROM AUTHOR]

The Middle Ages represented a crucial period for the evolutionary history of wolves (Canis lupus), marked by both significant ecosystem changes, especially through the degradation of wooded landscapes and heavy persecution, that drove this species to a dramatic demographic decline. In Europe, informative and well-documented wolf remains from the Medieval Ages are exceptionally rare and are mostly represented by teeth and postcranial elements. In this study, we describe a well-preserved wolf cranium dated to ca. 967–1157 AD from the Po Valley (northern Italy). The specimen was analysed through a multidisciplinary approach including CT-based, ancient DNA, and palaeopathological analyses. Morphological and genetic data supported the assignment of this sample to Canis lupus species. CT-based analyses indicated a typical wolf-like morphology falling into the extant variability of the medium-sized subspecies C. lupus italicus, whereas palaeopathological analyses indicated a severe periodontitis. Phylogenetic analyses showed that the Po valley wolf had a unique and never described mtDNA control region haplotype, testifying variability in the ancient Italian wolf, which has now been lost. This study provides the first comprehensive description of a wolf from the Middle Ages, adding useful information for a deeper knowledge about population dynamics, variability, and diseases of this species. [ABSTRACT FROM AUTHOR]

In recent years, nonhuman ancient DNA studies have begun to focus on larger sample sizes and whole genomes, offering the potential to reveal exciting and hitherto unknown answers to ongoing biological and archaeological questions. However, one major limitation to such studies is the substantial financial and time investments still required during sample screening, due to uncertainty regarding successful sample selection. This study investigates the effect of a wide range of sample properties including latitude, sample age, skeletal element, collagen preservation, and context on endogenous content and DNA damage profiles for 317 ancient and historic pinniped samples collected from across the North Atlantic and surrounding regions. Using generalised linear and mixed‐effect models, we found that a range of factors affected DNA preservation within each of the species under consideration. The most important findings were that endogenous content varied significantly within species according to context, the type of skeletal element, the collagen content and collection year. There also appears to be an effect of the sample's geographic origin, with samples from the Arctic generally showing higher endogenous content and lower damage rates. Both latitude and sample age were found to have significant relationships with damage levels, but only for walrus samples. Sex, ontogenetic age and extraction material preparation were not found to have any significant relationship with DNA preservation. Overall, skeletal element and sample context were found to be the most influential factors and should therefore be considered when selecting samples for large‐scale ancient genome studies. [ABSTRACT FROM AUTHOR]

Dog domestication is still largely unresolved due to time-gaps in the sampling of regions. Ancient Italian canids are particularly understudied, currently represented by only a few specimens. In the present study, we sampled 27 canid remains from Northern Italy dated between the Late Pleistocene and Bronze Age to assess their genetic variability, and thus add context to dog domestication dynamics. They were targeted at four DNA fragments of the hypervariable region 1 of mitochondrial DNA. A total of 11 samples had good DNA preservation and were used for phylogenetic analyses. The dog samples were assigned to dog haplogroups A, C and D, and a Late Pleistocene wolf was set into wolf haplogroup 2. We present our data in the landscape of ancient and modern dog genetic variability, with a particular focus on the ancient Italian samples published thus far. Our results suggest there is high genetic variability within ancient Italian canids, where close relationships were evident between both a ~24,700 years old Italian canid, and Iberian and Bulgarian ancient dogs. These findings emphasize that disentangling dog domestication dynamics benefits from the analysis of specimens from Southern European regions. [ABSTRACT FROM AUTHOR]

Evidence of maternal care and childbirth events in the past are rare in the archaeological record and are difficult to recognize. To combat this, we analyzed thirteen double burials potentially related to childbirth death events, thereby containing an adult and a perinate. The specimens were excavated from the archaeological area identified as "Forlì Campus" (Forlì, Italy), that dated to 17th-18th centuries AD and was adjacent to a hospital in use at that time. This period witnessed the development of medical techniques and novel approaches in obstetrics in Europe, with the introduction of lying-in hospitals and maternity wards. We here tested if the double burials were ascribable to childbirth death events and thus represent the first reported cases of the hospitalization of childbirth in the history of medicine. A multidisciplinary analysis was undertaken to achieve this aim, combining anthropology, archaeology, paleopathology and archaeogenetics. In five burials the adult individual was recognized as a female in fertile age and the non-adult individual was assigned as perinate. Mitochondrial DNA analysis highlighted different haplotypes among the individuals of these burials, and these results, combined with the archaeological and anthropological data do not support a possible maternal relationship between them. This study is novel in testing the hypotheses of childbirth deaths, through a reliable approach in the interpretation of these archaeological contexts. The analysis of ancient DNA in this particular application proves a useful strategy to support and complete the interpretation of archaeological and anthropological data, showing that a general assumption of mother/child relations within such burials can be misleading. • Childbirth deaths in the past are difficult to recognize in the archaeological record. • Double burials containing a female in childbearing age and a perinate were analyzed. • Mitochondrial DNA analysis highlighted different haplotypes. • The results do not support a possible maternal relationship between them. • A general assumption of mother/child relations within such burials can be misleading. [ABSTRACT FROM AUTHOR]

Three principal methods are under discussion as possible pathways to "true" de-extinction; i.e., back-breeding, cloning, and genetic engineering. 1,2 Of these, while the latter approach is most likely to apply to the largest number of extinct species, its potential is constrained by the degree to which the extinct species genome can be reconstructed. We explore this question using the extinct Christmas Island rat (Rattus macleari) as a model, an endemic rat species that was driven extinct between 1898 and 1908. 3–5 We first re-sequenced its genome to an average of >60× coverage, then mapped it to the reference genomes of different Rattus species. We then explored how evolutionary divergence from the extant reference genome affected the fraction of the Christmas Island rat genome that could be recovered. Our analyses show that even when the extremely high-quality Norway brown rat (R. norvegicus) is used as a reference, nearly 5% of the genome sequence is unrecoverable, with 1,661 genes recovered at lower than 90% completeness, and 26 completely absent. Furthermore, we find the distribution of regions affected is not random, but for example, if 90% completeness is used as the cutoff, genes related to immune response and olfaction are excessively affected. Ultimately, our approach demonstrates the importance of applying similar analyses to candidates for de-extinction through genome editing in order to provide critical baseline information about how representative the edited form would be of the extinct species. • Evolutionary divergence limits the completeness of extinct species genomes • The extinct Christmas Island rat was re-sequenced to ca. 60× coverage • Nevertheless, 4.85% of the Norway brown rat genome remains absent after mapping • Absences are not random; immune response and olfaction are excessively affected Lin et al. explore how evolutionary divergence constrains the potential of de-extinction, using the Christmas Island rat as a model. Although 95% of its genome is recovered when re-sequenced at high depth, regions that remain unmapped to the reference likely have significant consequences for any attempt at de-extinction using genome editing. [ABSTRACT FROM AUTHOR]