Federica Crivellaro

Inter-group violence among early Holocene hunter-gatherers of West Turkana, Kenya

The nature of inter-group relations among prehistoric hunter-gatherers remains disputed, with arguments in favour and against the existence of warfare before the development of sedentary societies. Here we report on a case of inter-group violence towards a group of hunter-gatherers from Nataruk, west of Lake Turkana, which during the late Pleistocene/early Holocene period extended about 30 km beyond its present-day shore. Ten of the twelve articulated skeletons found at Nataruk show evidence of having died violently at the edge of a lagoon, into which some of the bodies fell. The remains from Nataruk are unique, preserved by the particular conditions of the lagoon with no evidence of deliberate burial. They offer a rare glimpse into the life and death of past foraging people, and evidence that warfare was part of the repertoire of inter-group relations among prehistoric hunter-gatherers.

Herders of Indian and European Cattle Share Their Predominant Allele for Lactase Persistence

Milk consumption and lactose digestion after weaning are exclusively human traits made possible by the continued production of the enzyme lactase in adulthood. Multiple independent mutations in a 100-bp region--part of an enhancer--approximately 14-kb upstream of the LCT gene are associated with this trait in Europeans and pastoralists from Saudi Arabia and Africa. However, a single mutation of purported western Eurasian origin accounts for much of observed lactase persistence outside Africa. Given the high levels of present-day milk consumption in India, together with archaeological and genetic evidence for the independent domestication of cattle in the Indus valley roughly 7,000 years ago, we sought to determine whether lactase persistence has evolved independently in the subcontinent. Here, we present the results of the first comprehensive survey of the LCT enhancer region in south Asia. Having genotyped 2,284 DNA samples from across the Indian subcontinent, we find that the previously described west Eurasian -13910 C>T mutation accounts for nearly all the genetic variation we observed in the 400- to 700-bp LCT regulatory region that we sequenced. Geography is a significant predictor of -13910*T allele frequency, and consistent with other genomic loci, its distribution in India follows a general northwest to southeast declining pattern, although frequencies among certain neighboring populations vary substantially. We confirm that the mutation is identical by descent to the European allele and is associated with the same>1 Mb extended haplotype in both populations.

The light skin allele of SLC24A5 in South Asians and Europeans shares identity by descent

Skin pigmentation is one of the most variable phenotypic traits in humans. A non-synonymous substitution (rs1426654) in the third exon of SLC24A5 accounts for lighter skin in Europeans but not in East Asians. A previous genome-wide association study carried out in a heterogeneous sample of UK immigrants of South Asian descent suggested that this gene also contributes significantly to skin pigmentation variation among South Asians. In the present study, we have quantitatively assessed skin pigmentation for a largely homogeneous cohort of 1228 individuals from the Southern region of the Indian subcontinent. Our data confirm significant association of rs1426654 SNP with skin pigmentation, explaining about 27% of total phenotypic variation in the cohort studied. Our extensive survey of the polymorphism in 1573 individuals from 54 ethnic populations across the Indian subcontinent reveals wide presence of the derived-A allele, although the frequencies vary substantially among populations. We also show that the geospatial pattern of this allele is complex, but most importantly, reflects strong influence of language, geography and demographic history of the populations. Sequencing 11.74 kb of SLC24A5 in 95 individuals worldwide reveals that the rs1426654-A alleles in South Asian and West Eurasian populations are monophyletic and occur on the background of a common haplotype that is characterized by low genetic diversity. We date the coalescence of the light skin associated allele at 22–28 KYA. Both our sequence and genome-wide genotype data confirm that this gene has been a target for positive selection among Europeans. However, the latter also shows additional evidence of selection in populations of the Middle East, Central Asia, Pakistan and North India but not in South India.

Desert Migrations: people, environment and culture in the Libyan Sahara

The Desert Migrations Project is a new interdisciplinary and multi-dimensional collaborative project between the Society for Libyan Studies and the Department of Antiquities. The geographical focus of the study is the Fazzan region of southwest Libya and in thematic terms we aim to address the theme of migration in the broadest sense, encompassing the movement of people, ideas/knowledge and material culture into and out of Fazzan, along with evidence of shifting climatic and ecological boundaries over time. The report describes the principal sub-strands of the project’s first season in January 2007, with some account of research questions, methods employed and some preliminary results. Three main sub-projects are reported on. The first concerns the improved understanding of long-term climatic and environmental changes derived from a detailed palaeoenvironmental study of palaeolake sediments. This geo-science work runs alongside and feeds directly into both archaeological sub-projects, the first relating to prehistoric activity and mobility around and between a series of palaeolakes during wetter climatic cycles; the second to the excavation of burials in the Wadi al-Ajal, exploring the changing relationship between material culture, identity and ethnicity across time, from prehistory to the early Islamic period (the span of the main cemetery zones). In addition, some rock art research and a survey of historic period sites was undertaken in the Wadi ash-Shati and Ubari sand sea.

The Influence of Natural Barriers in Shaping the Genetic Structure of Maharashtra Populations

Background The geographical position of Maharashtra state makes it rather essential to study the dispersal of modern humans in South Asia. Several hypotheses have been proposed to explain the cultural, linguistic and geographical affinity of the populations living in Maharashtra state with other South Asian populations. The genetic origin of populations living in this state is poorly understood and hitherto been described at low molecular resolution level. Methodology/Principal Findings To address this issue, we have analyzed the mitochondrial DNA (mtDNA) of 185 individuals and NRY (non-recombining region of Y chromosome) of 98 individuals belonging to two major tribal populations of Maharashtra, and compared their molecular variations with that of 54 South Asian contemporary populations of adjacent states. Inter and intra population comparisons reveal that the maternal gene pool of Maharashtra state populations is composed of mainly South Asian haplogroups with traces of east and west Eurasian haplogroups, while the paternal haplogroups comprise the South Asian as well as signature of near eastern specific haplogroup J2a. Conclusions/Significance Our analysis suggests that Indian populations, including Maharashtra state, are largely derived from Paleolithic ancient settlers; however, a more recent (∼10 Ky older) detectable paternal gene flow from west Asia is well reflected in the present study. These findings reveal movement of populations to Maharashtra through the western coast rather than mainland where Western Ghats-Vindhya Mountains and Narmada-Tapti rivers might have acted as a natural barrier. Comparing the Maharastrian populations with other South Asian populations reveals that they have a closer affinity with the South Indian than with the Central Indian populations.

Detecting Genetic Isolation in Human Populations: A Study of European Language Minorities

The identification of isolation signatures is fundamental to better understand the genetic structure of human populations and to test the relations between cultural factors and genetic variation. However, with current approaches, it is not possible to distinguish between the consequences of long-term isolation and the effects of reduced sample size, selection and differential gene flow. To overcome these limitations, we have integrated the analysis of classical genetic diversity measures with a Bayesian method to estimate gene flow and have carried out simulations based on the coalescent. Combining these approaches, we first tested whether the relatively short history of cultural and geographical isolation of four “linguistic islands” of the Eastern Alps (Lessinia, Sauris, Sappada and Timau) had left detectable signatures in their genetic structure. We then compared our findings to previous studies of European population isolates. Finally, we explored the importance of demographic and cultural factors in shaping genetic diversity among the groups under study. A combination of small initial effective size and continued genetic isolation from surrounding populations seems to provide a coherent explanation for the diversity observed among Sauris, Sappada and Timau, which was found to be substantially greater than in other groups of European isolated populations. Simulations of micro-evolutionary scenarios indicate that ethnicity might have been important in increasing genetic diversity among these culturally related and spatially close populations.

DMP III: Pleistocene and Holocene palaeonvironments and prehistoric occupation of Fazzan, Libyan Sahara

The palaeoanthropological and geomorphological sub-projects of the Desert Migrations Project (DMP) focus on the Pleistocene and early Holocene environment and prehistory of Fazzan so as to assess the timing and extent of hominin and human movement across the Sahara through time. This paper reports on the findings of the 2008 field season, with a focus on the prehistoric evidence along the northern margin of the Ubari sand sea. The geomorphological record of the area preserves evidence of at least five past episodes of lake formation. The exact chronology of these, as well as the spatial extent of these lakes, remains the focus of further study. The archaeological record of hominin and human occupation of Fazzan prior to the establishment of the Garamantian civilisation is extraordinarily rich. Between 2007 and 2008, the DMP palaeoanthropological project surveyed thirty-five localities along the northern margin of the Ubari sand sea, recording a range of assemblages spanning all Palaeolithic industries. Most of the archaeological remains found consisted of stone-tools, while grinding stones were comparatively restricted geographically. Mode 1/Oldowan tools were found at two localities, contrasting with the widespread presence of Mode 2/Acheulean, Mode 3/Middle Stone Age and Mode 5/microlithic artefacts. This indicates that, although hominin presence in the area is probably earlier than previously thought, populations were comparatively sparse until the Middle Pleistocene. Twenty-one localities within the Ubari sand sea, as well as seven south of the Messak Settafet were also surveyed between 2007 and 2008. The detailed study of the lithics from these areas will be carried out next year, but preliminary results stress the different nature of the assemblages found within interdune corridors — very low frequency of cores, no Mode 1 and extremely rare Mode 2 lithics (found at a single locality). The 2009 field season will focus on obtaining further samples of palaeolake sediments for dating, on the evidence of Mode 1 assemblages south of the Messak, as well as on the refining of the archaeological indicators that may distinguish the different phases of hominin and human occupation of Fazzan during the Later Pleistocene and Holocene.

Demographic histories, isolation and social factors as determinants of the genetic structure of alpine linguistic groups

Great European mountain ranges have acted as barriers to gene flow for resident populations since prehistory and have offered a place for the settlement of small, and sometimes culturally diverse, communities. Therefore, the human groups that have settled in these areas are worth exploring as an important potential source of diversity in the genetic structure of European populations. In this study, we present new high resolution data concerning Y chromosomal variation in three distinct Alpine ethno-linguistic groups, Italian, Ladin and German. Combining unpublished and literature data on Y chromosome and mitochondrial variation, we were able to detect different genetic patterns. In fact, within and among population diversity values observed vary across linguistic groups, with German and Italian speakers at the two extremes, and seem to reflect their different demographic histories. Using simulations we inferred that the joint effect of continued genetic isolation and reduced founding group size may explain the apportionment of genetic diversity observed in all groups. Extending the analysis to other continental populations, we observed that the genetic differentiation of Ladins and German speakers from Europeans is comparable or even greater to that observed for well known outliers like Sardinian and Basques. Finally, we found that in south Tyroleans, the social practice of Geschlossener Hof, a hereditary norm which might have favored male dispersal, coincides with a significant intra-group diversity for mtDNA but not for Y chromosome, a genetic pattern which is opposite to those expected among patrilocal populations. Together with previous evidence regarding the possible effects of “local ethnicity” on the genetic structure of German speakers that have settled in the eastern Italian Alps, this finding suggests that taking socio-cultural factors into account together with geographical variables and linguistic diversity may help unveil some yet to be understood aspects of the genetic structure of European populations.

DMP VI: preliminary results from 2009 fieldwork on the human prehistory of the Libyan Sahara

Th is paper reports on the work carried out during the 2009 fi eld season of the prehistory sub-theme of the Desert Migrations Project. Th e work consisted of detailed survey and small-scale excavations in two wadis that drain the Messak Settafet, near the town of Jarma. Both wadis were found to contain evidence of Palaeolithic and Neolithic occupation, as well as of having been used as migratory routes between the Ubari and Murzuq sand seas. One of the wadis (WJAR-E-O1) was surveyed intensely along a few kilometers of its tributary margins. Th is revealed archaeological material ranging from Oldowan (Mode 1) to historic. Th e distribution of the various industries and structures had a distinct spatial patterning; the Palaeolithic scatters were spatially discrete, but Holocene remains were often found superimposed on earlier industries. Among the fi nds were a spatially discrete Oldowan assemblage, an extensive Acheulean industry which included the exploitation of fossil wood as raw material, the identifi cation of at least fi ve major outcrops of fossil trees, and a number of more recent structures dating from Neolithic to Islamic times and consisting of graves, cairns, rock engravings, and stone features. Middle Stone Age lithics, so predominant over the surface of the Messak plateau, were absent. Th e second wadi (WJAR-W-02) was geomorphologically diff erent, being comparatively narrow and deeply incised, and containing a number of terraces on the wadi bed resulting from cut and infi ll processes in the past. Th e surface of these terraces contained an extensive Aterian lithic industry, while evidence of late Holocene use of the area was also recorded in the form of Tifi nagh inscriptions, rock engravings, cairns and graves. Besides mapping the archaeological distributions, a number of trenches were dug at the edge of the river terraces. Th ese revealed an in situ stratigraphic sequence, within which Aterian lithics were found at a depth of >1 m. Samples for OSL dating were taken. Overall, the work of the 2009 fi eld season was extremely successful in that, besides the fascinating range of archaeological material recorded and studied, it provided important insights into the role of the north-south wadis that cross the Messak, the southern boundary of the area being explored by the DMP, and their diff erential use in prehistory.

Unravelling the distinct strains of Tharu ancestry

The northern region of the Indian subcontinent is a vast landscape interlaced by diverse ecologies, for example, the Gangetic Plain and the Himalayas. A great number of ethnic groups are found there, displaying a multitude of languages and cultures. The Tharu is one of the largest and most linguistically diverse of such groups, scattered across the Tarai region of Nepal and bordering Indian states. Their origins are uncertain. Hypotheses have been advanced postulating shared ancestry with Austroasiatic, or Tibeto-Burman-speaking populations as well as aboriginal roots in the Tarai. Several Tharu groups speak a variety of Indo-Aryan languages, but have traditionally been described by ethnographers as representing East Asian phenotype. Their ancestry and intra-population diversity has previously been tested only for haploid (mitochondrial DNA and Y-chromosome) markers in a small portion of the population. This study presents the first systematic genetic survey of the Tharu from both Nepal and two Indian states of Uttarakhand and Uttar Pradesh, using genome-wide SNPs and haploid markers. We show that the Tharu have dual genetic ancestry as up to one-half of their gene pool is of East Asian origin. Within the South Asian proportion of the Tharu genetic ancestry, we see vestiges of their common origin in the north of the South Asian Subcontinent manifested by mitochondrial DNA haplogroup M43.