[Show abstract][Hide abstract] ABSTRACT: Mitochondrial DNA (mtDNA) haplogroup L2 originated in Western Africa but is nowadays spread across the entire continent. L2 movements were previously postulated to be related to the Bantu expansion, but L2 expansions eastwards probably occurred much earlier. By reconstructing the phylogeny of L2 (44 new complete sequences) we provide insights on the complex net of within-African migrations in the last 60 thousand years (ka). Results show that lineages in Southern Africa cluster with Western/Central African lineages at a recent time scale, whereas, eastern lineages seem to be substantially more ancient. Three moments of expansion from a Central African source are associated to L2: (1) one migration at 70-50 ka into Eastern or Southern Africa, (2) postglacial movements (15-10 ka) into Eastern Africa; and (3) the southward Bantu Expansion in the last 5 ka. The complementary population and L0a phylogeography analyses indicate no strong evidence of mtDNA gene flow between eastern and southern populations during the later movement, suggesting low admixture between Eastern African populations and the Bantu migrants. This implies that, at least in the early stages, the Bantu expansion was mainly a demic diffusion with little incorporation of local populations.
[Show abstract][Hide abstract] ABSTRACT: At the crossroads between Africa and Eurasia, Arabia is necessarily a melting pot, its peoples enriched by successive gene flow over the generations. Estimating the timing and impact of these multiple migrations are important steps in reconstructing the key demographic events in the human history. However, current methods based on genome-wide information identify admixture events inefficiently, tending to estimate only the more recent ages, as here in the case of admixture events across the Red Sea (∼8-37 generations for African input into Arabia, and 30-90 generations for "back-to-Africa" migrations). An mtDNA-based founder analysis, corroborated by detailed analysis of the whole-mtDNA genome, affords an alternative means by which to identify, date and quantify multiple migration events at greater time depths, across the full range of modern human history, albeit for the maternal line of descent only. In Arabia, this approach enables us to infer several major pulses of dispersal between the Near East and Arabia, most likely via the Gulf corridor. Although some relict lineages survive in Arabia from the time of the out-of-Africa dispersal, 60 ka, the major episodes in the peopling of the Peninsula took place from north to south in the Late Glacial and, to a lesser extent, the immediate post-glacial/Neolithic. Exchanges across the Red Sea were mainly due to the Arab slave trade and maritime dominance (from ∼2.5 ka to very recent times), but had already begun by the early Holocene, fuelled by the establishment of maritime networks since ∼8 ka. The main "back-to-Africa" migrations, again undetected by genome-wide dating analyses, occurred in the Late Glacial period for introductions into eastern Africa, whilst the Neolithic was more significant for migrations towards North Africa.
[Show abstract][Hide abstract] ABSTRACT: The emergence of more refined chronologies for climate change and archaeology in prehistoric Africa, and for the evolution of human mitochondrial DNA (mtDNA), now make it feasible to test more sophisticated models of early modern human dispersals suggested by mtDNA distributions. Here we have generated 42 novel whole-mtDNA genomes belonging to haplogroup L0, the most divergent clade in the maternal line of descent, and analysed them alongside the growing database of African lineages belonging to L0's sister clade, L1'6. We propose that the last common ancestor of modern human mtDNAs (carried by "mitochondrial Eve") possibly arose in central Africa ~180 ka, at a time of low population size. By ~130 ka two distinct groups of anatomically modern humans co-existed in Africa: broadly, the ancestors of many modern-day Khoe and San populations in the south and a second central/eastern African group that includes the ancestors of most extant worldwide populations. Early modern human dispersals correlate with climate changes, particularly the tropical African "megadroughts" of MIS 5 (marine isotope stage 5, 135-75 ka) which paradoxically may have facilitated expansions in central and eastern Africa, ultimately triggering the dispersal out of Africa of people carrying haplogroup L3 ~60 ka. Two south to east migrations are discernible within haplogroup LO. One, between 120 and 75 ka, represents the first unambiguous long-range modern human dispersal detected by mtDNA and might have allowed the dispersal of several markers of modernity. A second one, within the last 20 ka signalled by L0d, may have been responsible for the spread of southern click-consonant languages to eastern Africa, contrary to the view that these eastern examples constitute relicts of an ancient, much wider distribution.
[Show abstract][Hide abstract] ABSTRACT: A major unanswered question regarding the dispersal of modern humans around the world concerns the geographical site of the first human steps outside of Africa. The "southern coastal route" model predicts that the early stages of the dispersal took place when people crossed the Red Sea to southern Arabia, but genetic evidence has hitherto been tenuous. We have addressed this question by analyzing the three minor west-Eurasian haplogroups, N1, N2, and X. These lineages branch directly from the first non-African founder node, the root of haplogroup N, and coalesce to the time of the first successful movement of modern humans out of Africa, ∼60 thousand years (ka) ago. We sequenced complete mtDNA genomes from 85 Southwest Asian samples carrying these haplogroups and compared them with a database of 300 European examples. The results show that these minor haplogroups have a relict distribution that suggests an ancient ancestry within the Arabian Peninsula, and they most likely spread from the Gulf Oasis region toward the Near East and Europe during the pluvial period 55-24 ka ago. This pattern suggests that Arabia was indeed the first staging post in the spread of modern humans around the world.
Full-text · Article · Feb 2012 · The American Journal of Human Genetics
[Show abstract][Hide abstract] ABSTRACT: Although fossil remains show that anatomically modern humans dispersed out of Africa into the Near East ∼100 to 130 ka, genetic evidence from extant populations has suggested that non-Africans descend primarily from a single successful later migration. Within the human mitochondrial DNA (mtDNA) tree, haplogroup L3 encompasses not only many sub-Saharan Africans but also all ancient non-African lineages, and its age therefore provides an upper bound for the dispersal out of Africa. An analysis of 369 complete African L3 sequences places this maximum at ∼70 ka, virtually ruling out a successful exit before 74 ka, the date of the Toba volcanic supereruption in Sumatra. The similarity of the age of L3 to its two non-African daughter haplogroups, M and N, suggests that the same process was likely responsible for both the L3 expansion in Eastern Africa and the dispersal of a small group of modern humans out of Africa to settle the rest of the world. The timing of the expansion of L3 suggests a link to improved climatic conditions after ∼70 ka in Eastern and Central Africa rather than to symbolically mediated behavior, which evidently arose considerably earlier. The L3 mtDNA pool within Africa suggests a migration from Eastern Africa to Central Africa ∼60 to 35 ka and major migrations in the immediate postglacial again linked to climate. The largest population size increase seen in the L3 data is 3-4 ka in Central Africa, corresponding to Bantu expansions, leading diverse L3 lineages to spread into Eastern and Southern Africa in the last 3-2 ka.
Full-text · Article · Nov 2011 · Molecular Biology and Evolution
[Show abstract][Hide abstract] ABSTRACT: Because of their sensitivity and high level of discrimination, short tandem repeat (STR) maker systems are currently the method of choice in routine forensic casework and data banking, usually in multiplexes up to 15-17 loci. Constraints related to sample amount and quality, frequently encountered in forensic casework, will not allow to change this picture in the near future, notwithstanding the technological developments. In this study, we present a free online calculator named PopAffiliator ( http://cracs.fc.up.pt/popaffiliator ) for individual population affiliation in the three main population groups, Eurasian, East Asian and sub-Saharan African, based on genotype profiles for the common set of STRs used in forensics. This calculator performs affiliation based on a model constructed using machine learning techniques. The model was constructed using a data set of approximately fifteen thousand individuals collected for this work. The accuracy of individual population affiliation is approximately 86%, showing that the common set of STRs routinely used in forensics provide a considerable amount of information for population assignment, in addition to being excellent for individual identification.
Full-text · Article · Sep 2011 · Deutsche Zeitschrift für die Gesamte Gerichtliche Medizin
[Show abstract][Hide abstract] ABSTRACT: Archaeological studies have revealed cultural connections between the two sides of the Red Sea dating to prehistory. The issue has still not been properly addressed, however, by archaeogenetics. We focus our attention here on the mitochondrial haplogroup HV1 that is present in both the Arabian Peninsula and East Africa. The internal variation of 38 complete mitochondrial DNA sequences (20 of them presented here for the first time) affiliated into this haplogroup testify to its emergence during the late glacial maximum, most probably in the Near East, with subsequent dispersion via population expansions when climatic conditions improved. Detailed phylogeography of HV1 sequences shows that more recent demographic upheavals likely contributed to their spread from West Arabia to East Africa, a finding concordant with archaeological records suggesting intensive maritime trade in the Red Sea from the sixth millennium BC onwards. Closer genetic exchanges are apparent between the Horn of Africa and Yemen, while Egyptian HV1 haplotypes seem to be more similar to the Near Eastern ones.
No preview · Article · Aug 2011 · American Journal of Physical Anthropology
[Show abstract][Hide abstract] ABSTRACT: Widespread interest in the first successful Out of Africa dispersal of modern humans ∼60–80 thousand years ago via a southern
migration route has overshadowed the study of later periods of South Arabian prehistory. In this work, we show that the post-Last
Glacial Maximum period of the past 20,000 years, during which climatic conditions were becoming more hospitable, has been
a significant time in the formation of the extant genetic composition and population structure of this region. This conclusion
is supported by the internal diversification displayed in the highly resolved phylogenetic tree of 89 whole mitochondrial
genomes (71 being newly presented here) for haplogroup R0a—the most frequent and widespread haplogroup in Arabia. Additionally,
two geographically specific clades (R0a1a1a and R0a2f1) have been identified in non–Arabic speaking peoples such as the Soqotri
and Mahri living in the southern part of the Arabian Peninsula where a past refugium was identified by independent archaeological
studies. Estimates of time to the most recent common ancestor of these lineages match the earliest archaeological evidence
for seafaring activity in the peninsula in the sixth millennium BC.
Full-text · Article · Jan 2011 · Molecular Biology and Evolution
[Show abstract][Hide abstract] ABSTRACT: Genetic studies have been underway on Arabian Peninsula populations because of their pivotal geographic location for population migration and times of occurrence. To assist in better understanding population dynamics in this region, evidence is presented herein on local population structure in the Arabian Peninsula, based on Y-STR characterisation in four Arabian samples and its comparison in a broad geographical scale. Our results demonstrate that geography played an important role in shaping the genetic structure of the region around the Near-East. Populations are grouped regionally but none of these groups is significantly differentiated from others and all groups merge in the Near-East, in keeping with this important migration corridor for the human species. Focusing on the Arabian Peninsula, we show that Dubai and Oman share genetic affinities with other Near-Eastern populations, while Saudi Arabia and Yemen show a relative distinctive isolated background. Those two populations may have been kept relatively separated from migration routes, maybe due to their location in a desert area.
[Show abstract][Hide abstract] ABSTRACT: The introduction of mitochondrial DNA (mtDNA) investigation in forensic genetics allowed to obtaining results from ancient, residual and degraded samples, enlarging extensively the possibility of applying genetic analyses to difficult forensic cases. However, the particular characteristics of mtDNA brought some conceptual and statistical challenges to forensic genetics, namely: the uniparental (maternal) transmission implies lineage instead of individual characterization, so that mtDNA can be more informative in excluding rather than in including a suspect; the absence of recombination in mtDNA renders impossible to apply the product rule for estimation of match probabilities, so that evaluations are limited to the frequency of a certain haplotype in a database; most of mtDNA haplotypes are unique or very low frequent, implying that databases must have a considerable number of individuals in order to be informative; heterogeneity in mutation rates between mtDNA positions and heteroplasmy must be taken into account when evaluating if diverse haplotypes can come from the same individual. Typically, the mtDNA survey in forensic genetics is performed by sequencing two hypervariable regions in the control region or D-loop. Some databases, reporting haplotypes in diverse populations, are publically available for forensic purposes. Recently, information from other polymorphisms located in the coding region is being also added to forensic analyses, which allows to inferring more securely the haplogroup to which the haplotype belongs. This phylogenetic information can be very informative for quality purposes, helping in detecting possible mix-up of samples and in checking haplogroup defining polymorphisms. Lately, the mtDNA screening is being enlarged to the total control region (~1200bp), and in the near future to the complete molecule. Such amount of information, in such a short period of time, will challenge forensic genetics in maintaining its strict quality-control of sequences and in being efficient to updating online databases for match evaluation.
[Show abstract][Hide abstract] ABSTRACT: A major effort must be put in East and sub-Saharan African mtDNA diversity characterisation for the construction of an informative database. We contribute 102 new HVRI+HVRII Sudanese sequences. As expected this sample is highly diverse, mainly constituted of unique haplotypes (2.07% random match probability for HVRI alone), 72.5% of which belong to sub-Saharan haplogroups.
No preview · Article · Aug 2008 · Forensic Science International Genetics Supplement Series
[Show abstract][Hide abstract] ABSTRACT: 249 entire mtDNA control region sequences were generated and analyzed in a population sample from Dubai, one of the seven United Arab Emirates. The control region was amplified in one piece and sequenced with different sequencing primers. Sequence evaluation was performed twice and validated by a third senior mtDNA scientist. Phylogenetic analyses were used for quality assurance purposes and for the determination of the haplogroup affiliation of the samples. Upon publication, the population data are going to be available in the EMPOP database (www.empop.org).
[Show abstract][Hide abstract] ABSTRACT: The aim of the study is to demonstrate the power obtained by combining autosomal and Y chromosome STRs in certain case scenarios. Although autosomal STRs are in use and highly informative, Y STRs are extremely useful and provide additional information that could not be provided by autosomal STRs alone.
Preview · Article · Apr 2004 · International Congress Series