Ancestry of victims of 1755 Lisbon earthquake based on tooth morphology.

The present investigation comprises the characterization of skeletal remains recovered from the 2004 archaeological excavations carried out in the Cloister's Southwest Wing of the Academy of Sciences of Lisbon, attributed to the 1755 earthquake. Among the remains, many teeth were found. Our goal is to use dental morphological characteristics to assess the geographic ancestry of the combined sample using the methods of biodistance and web-based application of the Arizona State University Dental Anthropology System 2. The crown and root traits of the ASUDAS were scored in a sample of 1068 disarticulated teeth, 65 skulls, 138 adult and 42 sub-adult jaws. Eight characteristics of 34 specimens (7 skulls and 27 jaws) were analyzed using rASUDAS2. Results demonstrate that 73.5% of this sample can be assigned to Western Eurasian ancestry, with the remaining 26.5% divided between Sub-Saharan Africa, non-Arctic and Arctic America, and East Asia. Euclidean and Bray-Curtis distance measures were used to put this Portuguese sample in a world context. From both distance matrixes, cluster analyses were used to generate dendrograms. Based on Bray-Curtis values, Portugal is closest to Western Europe, followed by India and Eastern Europe. For the tree based on Euclidean distances, India is the first to join Portugal, followed by Eastern and Western Europe. Therefore, on both an individual and group level, the Portuguese sample is most closely tied to Western Eurasia. However, there may be other ancestries in the sample, such as Sub-Saharan Africa, due to non-European migrants in Portugal along with the African slave trade to Brazil that reached its peak in 18th century Lisbon.

Revising the recent evolutionary history of equids using ancient DNA.

The rich fossil record of the family Equidae (Mammalia: Perissodactyla) over the past 55 MY has made it an icon for the patterns and processes of macroevolution. Despite this, many aspects of equid phylogenetic relationships and taxonomy remain unresolved. Recent genetic analyses of extinct equids have revealed unexpected evolutionary patterns and a need for major revisions at the generic, subgeneric, and species levels. To investigate this issue we examine 35 ancient equid specimens from four geographic regions (South America, Europe, Southwest Asia, and South Africa), of which 22 delivered 87-688 bp of reproducible aDNA mitochondrial sequence. Phylogenetic analyses support a major revision of the recent evolutionary history of equids and reveal two new species, a South American hippidion and a descendant of a basal lineage potentially related to Middle Pleistocene equids. Sequences from specimens assigned to the giant extinct Cape zebra, Equus capensis, formed a separate clade within the modern plain zebra species, a phenotypicically plastic group that also included the extinct quagga. In addition, we revise the currently recognized extinction times for two hemione-related equid groups. However, it is apparent that the current dataset cannot solve all of the taxonomic and phylogenetic questions relevant to the evolution of Equus. In light of these findings, we propose a rapid DNA barcoding approach to evaluate the taxonomic status of the many Late Pleistocene fossil Equidae species that have been described from purely morphological analyses.

The genomic history and global expansion of domestic donkeys.

Donkeys transformed human history as essential beasts of burden for long-distance movement, especially across semi-arid and upland environments. They remain insufficiently studied despite globally expanding and providing key support to low- to middle-income communities. To elucidate their domestication history, we constructed a comprehensive genome panel of 207 modern and 31 ancient donkeys, as well as 15 wild equids. We found a strong phylogeographic structure in modern donkeys that supports a single domestication in Africa ~5000 BCE, followed by further expansions in this continent and Eurasia and ultimately returning to Africa. We uncover a previously unknown genetic lineage in the Levant ~200 BCE, which contributed increasing ancestry toward Asia. Donkey management involved inbreeding and the production of giant bloodlines at a time when mules were essential to the Roman economy and military.