Studies to look out for -Henn and the - 2018 SMBE Symposium

[djoser-xyyman]

Henn and the - 2018 SMBE Symposium


Reconstructing the human population history of Africa
Brenna M Henn1
1UC Davis (United States)
Over twenty-five years ago, geneticists sequenced mitochondrial DNA from a diverse sample of human populations and hypothesized that all humans have a common origin in Africa 200,000 years ago.The broad outlines of this hypothesis remain remarkably unaltered, but many details of our African origin continue to be elusive. After decades of advances in human genetics, we are no longer data limited (either in terms of samples or genomic loci) but there is little consensus on most key issues. I will outline the models underlying the origin of modern humans. For example, was there a single ancestral population or multiple ancestral populations? Additionally, is there a discordance between anatomically modern humans and behaviorally modern humans? I will explore patterns of genetic diversity across Africa, and specifically focus on the complex history of southern African KhoeSan groups and adaptations to African environments. I will highlight our recent research on the evolution of skin pigmentation, malarial resistance, and infectious disease. We demonstrate that Africa continues to be an evolutionarily dynamic, heterogenous continent for human populations.


ANCESTRAL AND ADMIXTURE HISTORIES IN THE INDIAN SUBCONTINENT
Partha P Majumder1
1National Institute of Biomedical Genomics (India)
Based on the analyses of genome-scale SNP data and whole-genome sequence data from individuals drawn from a large number of extant ethnic groups, we have estimated archaic admixture contributions of Neanderthal and Denisovan genomes to extant ethnic groups in the Indian sub-continent. We have found a high level of Denisovan admixture among the Negrito tribals of Andaman and Nicobar Islands. Comparison with similar data from other Asian populations has provided clues to areas of interaction of modern humans and Denisovans. Some populations from South and Southeast Asia harbour a small proportion of ancestry from an unknown extinct hominin; this ancestry is absent from Europeans and East Asians. Our results show that that all Asian and Pacific populations share a single origin and expansion out of Africa, contradicting an earlier proposal of two independent waves of migration. Systematic analysis of genome-wide data, using multiple robust statistical methods, from individuals drawn from populations selected to represent geographic, linguistic, and ethnic diversities have revealed four major ancestries in mainland India. This contrasts with an earlier inference of two ancestries based on limited population sampling. A distinct ancestry of the populations of Andaman archipelago was identified and found to be co-ancestral to Oceanic populations. Prior to the establishment of the socially-stratified caste system in India that imposed strict rules of endogamy, there was wide admixture across tribal and caste groups which came to an abrupt end 1,900 to 4,200 years before present.

Genome wide analysis of negrito groups in Southeast Asia
Timothy Jinam1, Naruya Saitou1
1National Institute of Genetics (Japan)
The term "negrito" refers to indigenous groups in the Philippines, Malaysia and Andaman Islands who share some physical characteristics such as short stature, frizzy hair and darker skin. Genome-wide SNP analysis showed the negrito groups are phylogenetically basal to other Southeast and East Asians, but negritos also experienced substantial gene flow from these populations. SNP loci which have low Fst among all negrito groups but highly differentiated with East Asians may be associated with height, skin pigmentation and malarial resistance. We also found relatively high traces of Denisovan introgression in the Philippine Negritos, particularly in the Aeta. We will present preliminary results of whole genome sequencing analysis of 10 Philippine negritos.

Xyyman comment – if these genomes become downloaded-able….GREAT!!!!! We can do our own analysis


Human prehistoric demography revealed by polymorphic pattern of CpG transitions
Xiaoming Liu1
1School of Public Health, The University of Texas Health Science Center at Houston (United States)
Prehistoric demography of human populations is one essential piece of information to illustrate our own evolution. Despite its importance our knowledge is very limited, even for the relatively recent population dynamics during and around the Holocene. Here we inferred demographic histories from 1 to 40 thousand years ago (kya) for 24 population samples, using a newly developed model-flexible method with 36 million non-coding CpG sites genome-wide. Our results show many population growth events likely due to the Neolithic Revolution (i.e. shifting from hunting and gathering to agriculture and settlement): Han Chinese experienced a dramatic ~10 fold population growth around 8 kya to 12 kya; some South European and South Asian populations also began their long-term population growth around 10 kya but in a more gradual fashion; and British and Western European populations began their takeoff around 6-7 kya. The potential agriculture-associated population growth of Luhya in Webuye, Kenya (LWK) came relatively late (no earlier than 3 kya) compared to other African populations, in **CONTRAST TO THE ASSUMPTION **that they are the direct descendants of Bantu-speaking immigrants from West Africa. We also observed several population growth events dated before the introduction of agriculture. Our results help to paint a clearer picture of human's prehistoric demography, confirming the significant impact of agriculture to population expansion, and provide new hypotheses and directions for future research.

Xyyman comment – so another debunking of the supposed Bantu expansion. No mention of Agriculture in the rest of Africa except Kenya…which was late …they say.


Population Genomic Inference from Palaeo-Neutralomes of Mediaeval Germans
Joachim Burger1, Michaela Harbeck2, Krishna R. Veeramah3
1Institute of Organismic and Molecular Evolution, Mainz University (Germany), 2SNSB Munich (Germany), 3Stony Brook University (United States)
Many modern European states trace their roots back to the Early Medieval period. To genetically better characterize this formative phase of Central European population history we have conducted a population-level analysis of people from this era, generating genomic data from 41 graves from archaeological sites in present-day Germany mostly dating to around 500 AD. We developed a novel capture array that generated high coverage (mean 72x) sequence data in all individuals from neutral regions spanning a total of 5Mb, as well as 486 functional polymorphic sites. Examination of the panel of functional loci revealed that many alleles associated with recent positive selection were already at modern-like frequencies in European populations ~1,500 years ago. Analysis of the neutralome indicates that while men generally had ancestry that closely resembles modern northern and central Europeans, women exhibit a very high genetic heterogeneity; this includes signals of genetic ancestry ranging from West Europe to East Asia. The inferred female-biased migration indicates complex demographic processes during the Early Medieval Period may have contributed in an unexpected way to the making of the modern European genetic landscape. Lastly, we used the Medieval neutralome data to generate the allele frequency spectrum (AFS) and estimate the start and rate of recent European population growth.

Xyyman comment – no Africans in Europe??!!


Distinction between ancient introgression and incomplete lineage sorting in modern human genomes
Makoto Shimada1
1Institute for Comprehensive Medical Science, Fujita Health University (Japan)
Recent advancements of massive individual human genome and high-quality ancient genomes of other hominins have provided the evidences of diverse population structure in ancestral modern human **before** out-of-Africa, as well as ancient hybridization between modern human and archaic hominins such as Neanderthals. This brings a difficulty to distinguish current haplotype origins between ancient introgression from archaic hominins and incomplete lineage sorting **before** out-of-Africa. To clarify origin of diversified haplotypes in modern human, I focused on eight loci (23 kb - 550 kb in length) containing diversified haplotypes that have been discussed whether these are exceptions of out-of-Africa model or not. As many modern human haplotypes obtained from the 1000 genomes project as possible were used for comparison in topology between phylogenetic tree and network to understand actual picture of reticulation for each locus. Using S* and EHH (Extended Haplotype Homozygosity) analyses, we examined patterns of linkage disequilibrium (LD) of haplotypes to distinguished haplotypes origins between ancient introgression and ancestral polymorphism followed by incomplete lineage sorting. These examination on LD analyses with gene genealogy showed actual state of complexity of human genome diversity and difference in origin of the diversified haplotypes among introgressed from archaic hominins whose genome sequences are available such as Neanderthal and Denisova, that from unknown other extinct hominins, and derived from ancient polymorphism **without** introgression.

Xyyman comments – so it looks like they are sort out Neanderthal and AMH doing the nasty vs sub-structure.


No Evidence for Protracted Selection Against Neandertal Alleles in Humans
Benjamin Vernot1, Martin Petr1, Svante Paabo1, Janet Kelso1
1Max-Planck-Institute for Evolutionary Anthropology (Germany)
Approximately 2% of the genomes of present-day non-Africans descends from Neandertal ancestors as a result of interbreeding between Neandertals and modern humans approximately 55,000 years ago. Negative selection against Neandertal alleles in the modern human population has been the subject of many studies. When the proportion of Neandertal DNA has been estimated in ancient modern human specimens that range in age from 45,000 years to present-day, an apparent monotonic decline over time has been observed, and interpreted to be the result of negative selection against Neandertal alleles [Yang & Fu, 2018]. Here, we use a recently sequenced Neandertal genome from Croatia [Pruefer et al 2017] to better estimate Neandertal ancestry in ancient modern human genomes. In contrast to previous results, we observe no long-term decline of Neandertal ancestry. We show that the previous observation is likely an artifact produced by migration between Europe and Africa that altered relationships between European and African populations in a time-dependent manner. With simulations using realistic recombination maps and selection coefficients, we show that selection against Neandertal alleles is likely to have occurred within the first 500 generations after introgression, i.e. prior to the age of most ancient human specimens analyzed to date. We note that our simulations **agree with other observations **supporting negative selection against Neandertal alleles, e.g. a relative depletion of Neandertal alleles around coding sequence and the presence of "deserts" of Neandertal sequence of size 10-15Mb.

Xyyman comment: - So Paabo is at it again. And again makes a stupid comment like “We note that our simulations **agree with other observations **supporting negative selection against Neandertal alleles’ But careful now. The title used “Protracted”. Also agreeing with Lazaridis ..Basal Eurasian diluted “Neanderthal” DNA in Europeans.


Insights into the population history of the "Hidden Ones": From oral history to genome-wide analysis
Hiba Babiker1, Abbie Hantgan1, Johann-Mattis List1, Jeffrey Heath2, Russell Gray1
1Max Planck Institute for the Science of Human History (Germany), 2University of Michigan (United States)
Africa contains nearly one-third of the world's languages, and its populations have the highest genetic diversity. The depiction of genetic diversity in Africa is critical for reconstructing modern human origins and demographic history. Exploring the linguistic diversity in Africa is reframing current classification system regarding language families and isolates. The sub-Saharan fringe in Western Africa is becoming ripe for extensive research in linguistics, genetics, archaeology and cultural evolution. However, some populations are under-represented in multifaceted studies. Our research focuses on the Dogon and Bangande populations of the Bandiagara Escarpment in Central Eastern Mali who claim a "Mande" origin and a collective Dogon ethnicity. We used genome-wide data to understand the genetic structure of these populations and the evolutionary forces that shaped their genomes. We also leveraged lexical data representing the languages spoken by these populations to document historical contacts. We used state of the art analyses in population genetics and computational linguistics as well as simulation modelling. My talk will explore recent findings and will discuss the impact of cultural and geographical barriers on gene flow and population admixture. These findings shed light on the co-evolution of languages and genes. The results highlight the importance of interdisciplinary research in depicting the complex linguistic and genetic histories, hence, decoding unanswered questions in the human history.

Xyyman comment: - Computational linguistics is new. They are finally getting around to West Africans diversity


New Insights into the Genetic Basis and Evolutionary History of Lactase Persistence in Africa
Alessia Ranciaro1, Michael C. Campbell2, Elizabeth Eyerman1, Simon Thompson1, William Beggs1, Sununguko Wata Mpoloka3, Gaonyadiwe George Mokone4, Thomas Nyambo5, Dawit Wolde Meskel6, Gurja Belay6, Meredith Yeager7, Stephen Chanock8, Sarah A Tishkoff1, 9
1University of Pennsylvania (United States), 2Howard University (United States), 3University of Botswana (Botswana), 4University of Botswana School of Medicine (Botswana), 5Muhimbili University of Health and Allied Sciences (Tanzania), 6Addis Ababa University (Ethiopia), 7 National Cancer Institute (United States), 8Leidos Biomedical Research Inc (United States), 9University of Pennsylvania (United States)
Lactase persistence (LP) is a recent adaptive trait in humans that evolved mainly in populations practicing milk production.Prior studies of African populations have identified **novel **common variants in intron 13 of the MCM6 gene (a known candidate enhancer region for LCT) associated with LP primarily in pastoralists. While these variants account for a large proportion of the phenotypic variance, there may be additional polymorphisms that contribute to the LP trait. To test this hypothesis, we resequenced 555 bp of intron 13 of MCM6 in 1588 African individuals from diverse populations in Ethiopia, Tanzania and Botswana. We also genotyped these same individuals using the Illumina Omni 5M SNP array, and integrated our sequencing data with the 5M genotype data to detect signatures of selection. In addition, we performed the lactose tolerance test for a subset of 457 individuals. Based on our analyses, we identified for the** first time** the presence of the C-14010 and G-13915 variants in the Hadza hunter-gatherers from Tanzania. We also observed the G-13915 variant in the Burunge and Maasai populations from Tanzania, which has never previously been reported. Furthermore, we confirmed the presence of the G-13907 and the G-13915 alleles in Ethiopia. In addition, we detected a strong association between LP and genomic regions on several chromosomes in the Maasai pastoralists based on Fisher's Exact Test, suggesting candidate regions that might contribute to LP in this population. Overall, this genome-wide study offers new insights into the genetic basis and evolutionary history of LP in Africa.

Xyyman comment: - More and more is being revealed about LCT in Africa and it’s immense diversity

[djoser-xyyman]

Paleo-population genetics: Illuminating the role of selection in shaping human diversity
Yassine Souilmi1, Raymond Tobler1, Fernando Racimo2, Christian Huber1, Angad Johar1, Iain Mathieson3, Murray Cox5, Graham Gower1, Matthew Williams1, Matthew Robinson4, Joao Teixeira1, Alan Cooper1
1University of Adelaide (Australia), 2University of Copenhagen (Denmark), 3University of Pennsylvania (United States), 4University of Lausanne (Switzerland), 5Massey University (New Zealand)
Ancient human DNA studies have primarily focused on the questions surrounding ancestral migrations, admixture, phylogeography, and demography. To date, however, these studies have not fully explored the role of adaptation in shaping modern human diversity. With the number of publicly available ancient human genomes surpassing 1000 in 2018, it is now possible to utilise a range of population genetic approaches to elucidate the genetic history of multiple human phenotypes. Using a comprehensive aDNA database, the Online Ancient Genome Repository (OAGR; oagr.org.au), we utilised ~300 ancient Eurasian genomes to explore human phenotypic evolution from the late Pleistocene to the present, a period covering the major socio-cultural transitions in human history. We performed a series of selection screens on Mendelian and polygenic traits, building a comprehensive spatiotemporal map of human adaptation over our recent history. Our research provides a unique window into the factors that have shaped modern human diversity and pathology.

Identifying natural selection by constructing genome-wide genealogies
Leo Speidel1, Simon Myers1
1University of Oxford (United Kingdom)
All observed genetic variation can be traced back to a genealogy, which records historical recombination and coalescence events. However, the reconstruction of genealogies has been very difficult due to the enormous number of possibilities and weak information for the correct genealogy. As a consequence, existing methods usually scale to no more than tens of samples. We have developed a method for estimating genome-wide genealogies for thousands of samples, and applied it to 2478 present-day humans from 26 populations in the 1000 Genomes Project. We estimated historical population sizes and identified split times between all pairs of populations. In agreement with previous studies, we have identified evidence of Neanderthal introgression in samples from Eurasia, as well as historical mutation rate fluctuations consistent with population structure. In this talk, we will focus on detecting signals of positive selection in the estimated genealogy, which can appear as bursts of coalescent events following an advantageous mutation. We define a p-value for selection evidence that quantifies how quickly a mutation has spread. We obtain a p-value for almost all biallelic SNPs in the 1000 Genomes Project dataset. We confirm evidence of strong positive selection in well-known targets, such as the Lactase region in Europeans and the EDAR region in East Asians. In addition, we find an enrichment of GWAS hits among SNPs with low selection p-value, suggesting a wide-reaching effect of positive selection in functional parts of the human genome. Finally, we identify multi-allelic traits likely to be under positive selection in different groups.


A 2,200 year old Mycobacterium leprae genome from an Egyptian mummy
Judith Neukamm1, 2, 3, Saskia Pfrengle1, Martyna Molak4, Michael Francken1, 5, Beatrix Welte1, Katerina Harvati1, 5, 6, Kay Nieselt2, Johannes Krause7, 1, 5, Verena J. Schuenemann1, 3, 5
1University of Tuebingen (Germany), 2University of Tuebingen (Germany), 3University of Zurich (Switzerland), 4Polish Academy of Sciences (Poland), 5University of Tuebingen (Germany), 6University of Tuebingen (Germany), 7Max Planck Institute for the Science of Human History (Germany)
Analyzing ancient DNA opens the possibility to study the evolutionary history of pathogens, such as Mycobacterium leprae, one of the oldest recorded diseases in human history. M. leprae is the main causative agent of leprosy, which was a common disease in Europe until the 16th century, but is still endemic in many parts of the world. Recent studies on ancient and modern M .leprae genomes resulted in a phylogeny that separates five main lineages. Until now, ancient M. leprae genomes were recovered from skeletal remains, mostly teeth and bones, of infected individuals with characteristic lesions, while other sources have not been used. Advanced sequencing technologies and improved analysis methods allowed us recently to establish Egyptian mummies as a genetic source to study ancient human history. Here we present a metagenomic study of various soft tissue and skeletal samples from 93 mummified individuals from Egypt with a focus on the general bacterial composition. For one individual we were able to reconstruct a complete M. lepraegenome from the Ptolemaic period dated to cal BC 342-117. The so far oldest M. leprae genome clusters with modern strains from West Africa and Brazil and is located close to the node of lineage 4. Our results demonstrate the possibility to use Egyptian mummies as a source for metagenomic analysis. Furthermore, for one particular pathogen, M. leprae, our data allow us to refine the current phylogeographic models of leprosy's** past distribution** and spread.

Archaic introgression and gene regulation: a disproportionate degree of Neanderthal ancestry in T-cells enhancers
Martin Silvert1, 2, 4, Maxime Rotival1, 2, 3, Lluis Quintana-Murci1, 2, 3
1Institut Pasteur (France), 2Institut Pasteur (France), 3CNRS (France), 4Universite Pierre et Marie Curie (France)
There is increasing evidence to suggest that admixture with ancient hominins has been a non-negligible source of genetic diversity in non-African populations, with Neanderthal haplotypes covering 1-3% of the genome of modern Eurasians. Recent work has shown that this archaic introgression contributed to phenotypic diversity, mostly through the modulation of gene expression. However, the mechanisms through which Neanderthal variants alter gene expression, and the forces driving the introgression landscape at regulatory regions remain elusive. To answer these questions, we analyzed the Epigenomic Roadmap and 1,000G datasets to study the distribution and frequency of introgressed Neanderthal variants (archaic SNPs, or aSNPs), in Eurasian populations, across functional elements from 127 tissues. We found that enhancers and promoters are enriched in high frequency aSNPs (>5%). However, while the impact of aSNPs on promoters is stable across tissues, the excess of aSNPs in enhancers is primarily driven by enhancers that are active in T-cells. Interestingly, we show that the enrichment in aSNPs in T-cell enhancers is maintained despite the strong degree of background selection targeting Neanderthal haplotypes in these regions. Furthermore, aSNPs in T-cell enhancers display both high frequencies and high levels of population differentiation (FST) between European and East-Asian populations, suggesting that introgressed variants in T-cell enhancers were adaptive. Overall, our study sheds new light onto how admixture with Neanderthals introduced advantageous regulatory variation related to immune responses into Eurasian genomes, targeting in particular phenotypes related to acquired immunity.

[djoser-xyyman]

Database of ancient genome...


www.oagr.org.au/source/

[zarahan]

Excellent roundup! Keep it coming!

quick ques:
Here we present a metagenomic study of various soft tissue and skeletal samples from 93 mummified individuals from Egypt with a focus on the general bacterial composition. For one individual we were able to reconstruct a complete M. lepraegenome from the Ptolemaic period dated to cal BC 342-117. The so far oldest M. leprae genome clusters with modern strains from West Africa and Brazil and is located close to the node of lineage 4. Our results demonstrate the possibility to use Egyptian mummies as a source for metagenomic analysis. Furthermore, for one particular pathogen, M. leprae, our data allow us to refine the current phylogeographic models of leprosy's** past distribution** and spread.

^So basically they are saying that this gene element associated with leprosy in the
Egyptian mummies has its closest link to a common West African strain of the disease?

[djoser-xyyman]

These are Abstract for the upcoming symposium....that I pulled and may have compelling information. The full study hasn't been publish. Yes, this is what they are saying but we have to wait until the data packet is released. The distribution pattern will be revealed and it looks like it may be similar to Sickle Cell distribution pattern which shows a RECENT(Holocene) African origin for all sickle cell strains....even in Eurasia.

[zarahan]

Can you post that sickle cell data again?

[djoser-xyyman]

Jul 12, 2018 15:45:04 GMT -5 zarahan said:

Can you post that sickle cell data again?

www.egyptsearch.com/forums/ultimatebb.cgi?ubb=get_topic;f=8;t=009902;p=1

www.egyptsearch.com/forums/ultimatebb.cgi?ubb=get_topic;f=8;t=009902;p=1

[zarahan]

Good work. DOn;t have access to the full PDFs or as much time these days to dig
into it, but I remember you had something posted a while back on the presence of
Sickle Cell in Greece. Can you link to it, or recap, er quick queries below- to wit:

Quick questions:
1) OK so we know there are different variants of sickle cell, but your
study link shows that the origin of ALL of them is Africa?


2) Doesn't the African variant of sickle cell appear in Greece, and/or
various areas of the Balkans? And if so, is this evidence of various African
migrations to Greece and/or the Balkan zone, BEFORE the historic era of Alexander
the Great, Rome etc etc..?

3) In what way does the pre-dating of the sickle cell variant BEFORE the Bantu expansion
cast doubt on said Bantu expansion? Couldn't the mutation have developed, after which
the Bantu expansion happened anyway? How aer the 2 linked in other words?

---------------------------------------------------------------------------------------------

quote:

Whole-Genome-Sequence-Based Haplotypes Reveal Single Origin of the Sickle Allele during the Holocene Wet Phase

Daniel Shriner, Charles N. Rotimi

Published Online: March 08, 2018

Five classical designations of sickle haplotypes are made on the basis of the presence or absence of restriction sites and are named after the ethno-linguistic groups or geographic regions from which the individuals with sickle cell anemia originated. Each haplotype is thought to represent an independent occurrence of the sickle mutation rs334 (c.20A>T [p.Glu7Val] in HBB). We investigated the origins of the sickle mutation by using whole-genome-sequence data. We identified 156 carriers from the 1000 Genomes Project, the African Genome Variation Project, and Qatar. We classified haplotypes by using 27 polymorphisms in linkage disequilibrium with rs334. Network analysis revealed a common haplotype that differed from the ancestral haplotype only by the derived sickle mutation at rs334 and correlated collectively with the Central African Republic (CAR), Cameroon, and Arabian/Indian haplotypes. Other haplotypes were derived from this haplotype and fell into two clusters, one composed of Senegal haplotypes and the other composed of Benin and Senegal haplotypes. The near-exclusive presence of the original sickle haplotype in the CAR, Kenya, Uganda, and South Africa is consistent with this haplotype predating the Bantu expansions. Modeling of balancing selection indicated that the heterozygote advantage was 15.2%, an equilibrium frequency of 12.0% was reached after 87 generations, and the selective environment predated the mutation. The posterior distribution of the ancestral recombination graph yielded a sickle mutation age of 259 generations, corresponding to 7,300 years ago during the Holocene Wet Phase. These results clarify the origin of the sickle allele and improve and simplify the classification of sickle haplotypes.



Quote:
"Classical haplotypes in eastern Arabia tend to have the Arabian/Indian designation, whereas those in western
Arabia tend to have the Benin designation.18,21 The Arabian/Indian haplotype has been hypothesized to have
originated in either east Saudi Arabia or India.5 Although our samples include only one predicted instance of the
Arabian/Indian haplotype, the occurrence of this haplotype in the Luhya in Kenya and its clustering with the predominant
haplotype found in Kenya and Uganda are consistent with the hypothesis that the Arabian/Indian
haplotype originated in Africa and had an overseas migration route from eastern Africa to eastern Arabia and
India.13,19 In contrast, the absence of the Benin haplotype in the Luhya in Kenya and the Baganda in Uganda provides
evidence against an overseas migration route from eastern Africa to western Arabia. Instead, the presence of
the Benin haplotype in western Arabia is consistent with an African origin and an overland migration route through
northeast Africa"

[djoser-xyyman]

Modern human cranial diversity in the Late Pleistocene of Africa and Eurasia: evidence from Nazlet Khater, Peştera cu Oase, and Hofmeyr.
Crevecoeur I1

I. Crevecoeur, et al.
Late Stone Age human remains from Ishango (Democratic Republic of Congo): new insights on Late Pleistocene modern human diversity in Africa


K. Harvati, et al.
The Later Stone Age Calvaria from Iwo Eleru, Nigeria: morphology and chronology



P. Gunz, et al.
Early modern human diversity suggests subdivided population structure and a complex out-of-Africa scenario

J.T. Stock
The skeletal phenotype of ‘Negritos’ from the Andaman Islands and Philippines relative to global variation among hunter-gatherers


E.M.L. Scerri
The West African Stone Age


E.M.L. Scerri
The North African Middle Stone Age and its place in recent human evolution

E.M.L. Scerri, et al.
Persistence of Middle Stone Age technology to the Pleistocene/Holocene transition supports a complex hominin evolutionary scenario in West Africa

S.J. Shennan, et al.
Isolation-by-distance, homophily and ‘core’ vs. ‘package’ cultural evolution models in Neolithic Europe

S. Mallick, et al.
The Simons Genome Diversity Project: 300 genomes from 142 diverse populations

F. Broushaki, et al.
Early Neolithic genomes from the eastern Fertile Crescent


D. Xu, et al.
Archaic hominin introgression in Africa contributes to functional salivary MUC7 genetic variation

N.A. Drake, et al.
Ancient watercourses and biogeography of the Sahara explain the peopling of the desert

F. Montinaro, et al.
Complex ancient genetic structure and cultural transitions in southern African populations