Francesca Candilio

Phylogeographic refinement and large scale genotyping of human Y chromosome haplogroup E provide new insights into the dispersal of early pastoralists in the African continent.

Haplogroup E, defined by mutation M40, is the most common human Y chromosome clade within Africa. To increase the level of resolution of haplogroup E, we disclosed the phylogenetic relationships among 729 mutations found in 33 haplogroup DE Y-chromosomes sequenced at high coverage in previous studies. Additionally, we dissected the E-M35 subclade by genotyping 62 informative markers in 5,222 samples from 118 worldwide populations. The phylogeny of haplogroup E showed novel features compared with the previous topology, including a new basal dichotomy. Within haplogroup E-M35, we resolved all the previously known polytomies and assigned all the E-M35* chromosomes to five new different clades, all belonging to a newly identified subhaplogroup (E-V1515), which accounts for almost half of the E-M35 chromosomes from the Horn of Africa. Moreover, using a Bayesian phylogeographic analysis and a single nucleotide polymorphism-based approach we localized and dated the origin of this new lineage in the northern part of the Horn, about 12 ka. Time frames, phylogenetic structuring, and sociogeographic distribution of E-V1515 and its subclades are consistent with a multistep demic spread of pastoralism within north-eastern Africa and its subsequent diffusion to subequatorial areas. In addition, our results increase the discriminative power of the E-M35 haplogroup for use in forensic genetics through the identification of new ancestry-informative markers.

Stratigraphic context and paleoenvironmental significance of minor taxa (Pisces, Reptilia, Aves, Rodentia) from the late Early Pleistocene paleoanthropological site of Buia (Eritrea)

The Buia Homo site, also known as Wadi Aalad, is an East African paleoanthropological site near the village of Buia that, due to its very rich yield from the late Early Pleistocene, has been intensively investigated since 1994. In this paper, which reports on the finds of the 2010-2011 excavations, we include new fossil evidence on previously identified taxa (i.e., reptiles), as well as the very first description of the small mammal, fish and bird remains discovered. In particular, this study documents the discovery of the first African fossil of the genus Burhinus (Aves, Charadriiformes) and of the first rodent from the site. This latter is identified as a thryonomyid rodent (cane rat), a relatively common taxon in African paleoanthropological faunal assemblages. On the whole, the new occurrences documented within the Buia vertebrate assemblage confirm the occurrence of taxa characterized by strong water dependence. The paleoenvironmental characteristics of the fauna are confirmed as fully compatible with the evidence obtained through sedimentology and facies analysis, documenting the sedimentary evolution of fluvio-deltaic and lacustrine systems.

Ancient genomes document multiple waves of migration in Southeast Asian prehistory

Ancient migrations in Southeast Asia The past movements and peopling of Southeast Asia have been poorly represented in ancient DNA studies (see the Perspective by Bellwood). Lipson et al. generated sequences from people inhabiting Southeast Asia from about 1700 to 4100 years ago. Screening of more than a hundred individuals from five sites yielded ancient DNA from 18 individuals. Comparisons with present-day populations suggest two waves of mixing between resident populations. The first mix was between local hunter-gatherers and incoming farmers associated with the Neolithic spreading from South China. A second event resulted in an additional pulse of genetic material from China to Southeast Asia associated with a Bronze Age migration. McColl et al. sequenced 26 ancient genomes from Southeast Asia and Japan spanning from the late Neolithic to the Iron Age. They found that present-day populations are the result of mixing among four ancient populations, including multiple waves of genetic material from more northern East Asian populations. Science, this issue p. 92, p. 88; see also p. 31 Ancient DNA data shed light on the past 4000 years of Southeast Asian genetic history. Southeast Asia is home to rich human genetic and linguistic diversity, but the details of past population movements in the region are not well known. Here, we report genome-wide ancient DNA data from 18 Southeast Asian individuals spanning from the Neolithic period through the Iron Age (4100 to 1700 years ago). Early farmers from Man Bac in Vietnam exhibit a mixture of East Asian (southern Chinese agriculturalist) and deeply diverged eastern Eurasian (hunter-gatherer) ancestry characteristic of Austroasiatic speakers, with similar ancestry as far south as Indonesia providing evidence for an expansive initial spread of Austroasiatic languages. By the Bronze Age, in a parallel pattern to Europe, sites in Vietnam and Myanmar show close connections to present-day majority groups, reflecting substantial additional influxes of migrants.

The Genomic Formation of South and Central Asia

The genetic formation of Central and South Asian populations has been unclear because of an absence of ancient DNA. To address this gap, we generated genome-wide data from 362 ancient individuals, including the first from eastern Iran, Turan (Uzbekistan, Turkmenistan, and Tajikistan), Bronze Age Kazakhstan, and South Asia. Our data reveal a complex set of genetic sources that ultimately combined to form the ancestry of South Asians today. We document a southward spread of genetic ancestry from the Eurasian Steppe, correlating with the archaeologically known expansion of pastoralist sites from the Steppe to Turan in the Middle Bronze Age (2300-1500 BCE). These Steppe communities mixed genetically with peoples of the Bactria Margiana Archaeological Complex (BMAC) whom they encountered in Turan (primarily descendants of earlier agriculturalists of Iran), but there is no evidence that the main BMAC population contributed genetically to later South Asians. Instead, Steppe communities integrated farther south throughout the 2nd millennium BCE, and we show that they mixed with a more southern population that we document at multiple sites as outlier individuals exhibiting a distinctive mixture of ancestry related to Iranian agriculturalists and South Asian hunter-gathers. We call this group Indus Periphery because they were found at sites in cultural contact with the Indus Valley Civilization (IVC) and along its northern fringe, and also because they were genetically similar to post-IVC groups in the Swat Valley of Pakistan. By co-analyzing ancient DNA and genomic data from diverse present-day South Asians, we show that Indus Periphery-related people are the single most important source of ancestry in South Asia—consistent with the idea that the Indus Periphery individuals are providing us with the first direct look at the ancestry of peoples of the IVC—and we develop a model for the formation of present-day South Asians in terms of the temporally and geographically proximate sources of Indus Periphery-related, Steppe, and local South Asian hunter-gatherer-related ancestry. Our results show how ancestry from the Steppe genetically linked Europe and South Asia in the Bronze Age, and identifies the populations that almost certainly were responsible for spreading Indo-European languages across much of Eurasia. One Sentence Summary Genome wide ancient DNA from 357 individuals from Central and South Asia sheds new light on the spread of Indo-European languages and parallels between the genetic history of two sub-continents, Europe and South Asia.

The early Pleistocene vertebrate fauna of Mulhuli-Amo (Buia area, Danakil Depression, Eritrea)

Mulhuli-Amo is an early Pleistocene locality of the Buia area in the Dandiero Basin (Danakil Depression, Eritrea) already known for the presence of Homo remains and stone tools. Recent surface surveys lead to the retrieval of a rich vertebrate fauna that is here described for the first time in order to contribute to the palaeoenvironmental background to the Homo layers of the basin. The following 14 taxa (two fishes, four reptiles, one bird, and nine mammals) were identified: Clarias (Clarias) sp., ?Cichlidae indet., Crocodylus sp., Pelusios sinuatus, Varanus niloticus, Python gr. P. sebae, Ardeotis kori, Palaeoloxodon cf. P. recki, Ceratotherium simum, Equus cf. E. quagga, Hippopotamus gorgops, Kolpochoerus majus, Bos cf. B. buiaensis, and Kobus cf. K. ellipsiprymnus. With the exception of a fish and the bird that were identified at Mulhuli-Amo for the first time, the whole fauna is fully congruent with the taxa already described for the neighbouring locality of Uadi Aalad and confirms, in agreement with all the other proxies, an early Pleistocene age and the former presence of moist grassed habitats adjacent to persistent water. RIASSUNTO [I vertebrati del Pleistocene inferiore di Mulhuli-Amo (area di Buia, Depressione Dancala, Eritrea)] Il Progetto Buia nasce nel 1994 come un progetto di ricognizione geologica finalizzato allo studio della geologia regionale di un’area circa 20 Km a sud di Buia nella Dancalia settentrionale (Eritrea) ma, già a partire dalle prime missioni, il rinvenimento di resti umani associati a strumenti litici e ad una ricca fauna di vertebrati ha ampliato notevolmente le prospettive di ricerca. I primi resti umani sono stati identificati nel 1995 in un livello della località Uadi Aalad attribuito al Subcrono Jaramillo e datato a circa 1.0 Ma. Successivamente, a partire dal dicembre 2000, ulteriori resti umani sono stati ritrovati a Mulhuli-Amo, una località lontana circa 5 Km dalla prima, già conosciuta per un eccezionale accumulo di strumenti litici e di resti di vertebrati. In questo lavoro viene descritta per la prima volta in modo unitario la fauna vertebrata non umana rinvenuta in superficie a Mulhuli-Amo. Complessivamente, sono stati identificati i seguenti 14 taxa: Clarias (Clarias) sp., ?Cichlidae indet., Crocodylus sp., Pelusios sinuatus, Varanus niloticus, Python gr. P. sebae, Ardeotis kori, Palaeoloxodon cf. P. recki, Ceratotherium simum, Equus cf. E. quagga, Hippopotamus gorgops, Kolpochoerus majus, Bos cf. B. buiaensis, Kobus cf. K. ellipsiprymnus. L’associazione faunistica è pienamente congruente con quella di Uadi Aalad e, nonostante sia meno diversificata di questa, presenta alcuni elementi di novità (?Cichlidae indet., Ardeotis kori). Alcuni mammiferi (Palaeoloxodon cf. P. recki, E. cf. E. quagga, H. gorgops, K. majus, B. cf. B. buiaensis) confermano l’attribuzione della fauna al Pleistocene inferiore finale. Da un punto di vista ambientale, l’associazione faunistica suggerisce la presenza di raccolte permanenti d’acqua circondate da praterie umide, in netto contrasto con gli ambienti attuali estremamente aridi.

The Biocultural Evolution in the Osmore Valley: Morphological Dental Traits in Pre-Inca Populations

Abstract Bioarchaeological studies on population dynamics in the pre-Inca Osmore Valley (Peru) have shown a level of biological affinity between colonies in the valley (Chen Chen) and the people in the Tiwanaku state, suggesting the Tiwanaku expansion brought about the foundation of two colonies and settlements in the Central Osmore Valley (Chen Chen) and perhaps along the coast where, according to some theories, they may have given rise to the Chiribaya. Conversely, archaeological data suggest an absence of cultural contact between the Tiwanaku and the Wari outposts in the Upper Valley. The present study investigates 46 dental nonmetric traits in seven pre-Inca groups to provide a geographically expanded view by comparing sites from the coastal region and the Upper Osmore Valley with groups representing the Wari and Moche cultures. Multivariate statistical analyses indicate that the Tiwanaku colony of Chen Chen shows affinity with the Wari and Moche samples, but not with the later coastal Chiribaya collection. Despite the lack of a true Tiwanaku comparative sample, this evidence suggests a biological interaction between ethnically diverse groups in the region. However caution must be taken with any final interpretation.Bioarchaeological studies on population dynamics in the pre-Inca Osmore Valley (Peru) have shown a level of biological affinity between colonies in the valley (Chen Chen) and the people in the Tiwanaku state, suggesting the Tiwanaku expansion brought about the foundation of two colonies and settlements in the Central Osmore Valley (Chen Chen) and perhaps along the coast where, according to some theories, they may have given rise to the Chiribaya. Conversely, archaeological data suggest an absence of cultural contact between the Tiwanaku and the Wari outposts in the Upper Valley. The present study investigates 46 dental nonmetric traits in seven pre-Inca groups to provide a geographically expanded view by comparing sites from the coastal region and the Upper Osmore Valley with groups representing the Wari and Moche cultures. Multivariate statistical analyses indicate that the Tiwanaku colony of Chen Chen shows affinity with the Wari and Moche samples, but not with the later coastal Chiribaya collection. Despite the lack of a true Tiwanaku comparative sample, this evidence suggests a biological interaction between ethnically diverse groups in the region. However caution must be taken with any final interpretation.