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Papers by Mark Thomas

There has been considerable debate on the geographic origin of the human Y chromosome Alu polymor... more There has been considerable debate on the geographic origin of the human Y chromosome Alu polymorphism (YAP). Here we report a new, very rare deep-rooting haplogroup within the YAP clade, together with data on other deep-rooting YAP clades. The new haplogroup, found so far in only five Nigerians, is the least-derived YAP haplogroup according to currently known binary markers. However, because the interior branching order of the Y chromosome genealogical tree remains unknown, it is impossible to impute the origin of the YAP clade with certainty. We discuss the problems presented by rare deep-rooting lineages for Y chromosome phylogeography.

Nature Ecology & Evolution

The roles of migration, admixture and acculturation in the European transition to farming have be... more The roles of migration, admixture and acculturation in the European transition to farming have been debated for over 100 years. Genome-wide ancient DNA studies indicate predominantly Aegean ancestry for continental Neolithic farmers, but also variable admixture with local Mesolithic hunter-gatherers. Neolithic cultures first appear in Britain ca. 4000 BCE, a millennium after they appear in adjacent areas of continental Europe. The pattern and process of this delayed British Neolithic transition remains unclear. We assembled genome-wide data from six Mesolithic and 67 Neolithic individuals found in Britain, dating from 8500-2500 BCE. Our analyses reveal persistent genetic affinities between Mesolithic British and Western European hunter-gatherers. We find overwhelming support for agriculture being introduced to Britain by incoming continental farmers, with small, geographically-structured levels of hunter-gatherer ancestry. Unlike other European Neolithic populations, we detect no resurgence of hunter-gatherer ancestry at any time during the Neolithic in Britain. Genetic affinities with Iberian Neolithic individuals indicate that British Neolithic people were mostly descended from Aegean farmers who followed the Mediterranean route of dispersal. We also infer considerable variation in pigmentation levels in Europe by ca. 6000 BCE.

Genealogy

Direct-to-consumer genetic ancestry testing is a new and growing industry that has gained widespr... more Direct-to-consumer genetic ancestry testing is a new and growing industry that has gained widespread media coverage and public interest. Its scientific base is in the fields of population and evolutionary genetics and it has benefitted considerably from recent advances in rapid and cost-effective DNA typing technologies. There is a considerable body of scientific literature on the use of genetic data to make inferences about human population history, although publications on inferring the ancestry of specific individuals are rarer. Population geneticists have questioned the scientific validity of some population history inference approaches, particularly those of a more interpretative nature. These controversies have spilled over into commercial genetic ancestry testing, with some companies making sensational claims about their products. One such company—BritainsDNA—made a number of dubious claims both directly to its customers and in the media. Here we outline our scientific concer...

Proceedings. Biological sciences, Jan 11, 2018

The high degree of endemism on Sulawesi has previously been suggested to have vicariant origins, ... more The high degree of endemism on Sulawesi has previously been suggested to have vicariant origins, dating back to 40 Ma. Recent studies, however, suggest that much of Sulawesi's fauna assembled over the last 15 Myr. Here, we test the hypothesis that more recent uplift of previously submerged portions of land on Sulawesi promoted diversification and that much of its faunal assemblage is much younger than the island itself. To do so, we combined palaeogeographical reconstructions with genetic and morphometric datasets derived from Sulawesi's three largest mammals: the babirusa, anoa and Sulawesi warty pig. Our results indicate that although these species most likely colonized the area that is now Sulawesi at different times (14 Ma to 2-3 Ma), they experienced an almost synchronous expansion from the central part of the island. Geological reconstructions indicate that this area was above sea level for most of the last 4 Myr, unlike most parts of the island. We conclude that emerg...

Hypertension (Dallas, Tex. : 1979), Feb 11, 2017

Liddle syndrome is considered a rare Mendelian hypertension. We have previously described 3 repor... more Liddle syndrome is considered a rare Mendelian hypertension. We have previously described 3 reportedly unrelated families, native of an Italian area around the Strait of Messina, carrying the same mutation (βP617L) of the epithelial sodium channel. The aims of our study were (1) to evaluate whether a close genomic relationship exists between the 3 families through the analysis of mitochondrial DNA and Y chromosome; and (2) to quantify the genomic relatedness between the patients with Liddle syndrome belonging to the 3 families and assess the hypothesis of a mutation shared through identity by descent. HVRI (the hypervariable region I) of the mitochondrial DNA genome and the Y chromosome short tandem repeats profiles were analyzed in individuals of the 3 families. Genotyping 542 585 genome-wide single nucleotide polymorphisms was performed in all the patients with Liddle syndrome of the 3 families and some of their relatives. A panel of 780 healthy Italian adult samples typed for the...

Molecular ecology, Jan 22, 2017

Maladaptation to modern diets has been implicated in several chronic disorders. Given the higher ... more Maladaptation to modern diets has been implicated in several chronic disorders. Given the higher prevalence of disease such as dental caries and chronic gum diseases in industrialized societies, we sought to investigate the impact of different subsistence strategies on oral health and physiology, as documented by the oral microbiome. To control for confounding variables such as environment and host genetics, we sampled saliva from three pairs of populations of hunter-gatherers and traditional farmers living in close proximity in the Philippines. Deep shotgun sequencing of salivary DNA generated high-coverage microbiomes along with human genomes. Comparing these microbiomes with publicly available data from individuals living on a Western diet revealed that abundance ratios of core species were significantly correlated with subsistence strategy, with hunter-gatherers and Westerners occupying either end of a gradient of Neisseria against Haemophilus, and traditional farmers falling in...

Proceedings of the National Academy of Sciences of the United States of America, Aug 1, 2017

Precise estimation of age is essential in evolutionary anthropology, especially to infer populati... more Precise estimation of age is essential in evolutionary anthropology, especially to infer population age structures and understand the evolution of human life history diversity. However, in small-scale societies, such as hunter-gatherer populations, time is often not referred to in calendar years, and accurate age estimation remains a challenge. We address this issue by proposing a Bayesian approach that accounts for age uncertainty inherent to fieldwork data. We developed a Gibbs sampling Markov chain Monte Carlo algorithm that produces posterior distributions of ages for each individual, based on a ranking order of individuals from youngest to oldest and age ranges for each individual. We first validate our method on 65 Agta foragers from the Philippines with known ages, and show that our method generates age estimations that are superior to previously published regression-based approaches. We then use data on 587 Agta collected during recent fieldwork to demonstrate how multiple p...

European journal of endocrinology, Jan 20, 2017

Mutations in the aryl hydrocarbon receptor-interacting protein (AIP) gene are associated with pit... more Mutations in the aryl hydrocarbon receptor-interacting protein (AIP) gene are associated with pituitary adenoma, acromegaly and gigantism. Identical alleles in unrelated pedigrees could be inherited from a common ancestor or result from recurrent mutation events. Observational, inferential and experimental study, including: AIP mutation testing; reconstruction of 14 AIP-region (8.3 Mbp) haplotypes; coalescent-based approximate Bayesian estimation of the time to most recent common ancestor (tMRCA) of the derived allele; forward population simulations to estimate current number of allele carriers; proposal of mutation mechanism; protein structure predictions; co-immunoprecipitation and cycloheximide chase experiments. Nine European-origin, unrelated c.805_825dup-positive pedigrees (four familial, five sporadic from the UK, USA and France) included 16 affected (nine gigantism/four acromegaly/two non-functioning pituitary adenoma patients and one prospectively-diagnosed acromegaly patie...

Molecular biology and evolution, Aug 21, 2017

Ancient DNA provides an opportunity to infer the drivers of natural selection by linking allele f... more Ancient DNA provides an opportunity to infer the drivers of natural selection by linking allele frequency changes to temporal shifts in environment or cultural practices. However, analyses have often been hampered by uneven sampling and uncertainties in sample dating, as well as being confounded by demographic processes. Here we present a Bayesian statistical framework for quantifying the timing and strength of selection using ancient DNA that explicitly addresses these challenges. We applied this method to time series data for two loci: TSHR and BCDO2, both argued to have undergone strong and recent selection in domestic chickens. The derived variant in TSHR, associated with reduced aggression to conspecifics and faster onset of egg laying, shows strong selection beginning around 1,100 years ago, coincident with archaeological evidence for intensified chicken production and documented changes in egg and chicken consumption. To our knowledge, this is the first example of pre-industr...

European journal of human genetics : EJHG, Feb 28, 2016

Recent ancient DNA studies on European Neolithic human populations have provided persuasive evide... more Recent ancient DNA studies on European Neolithic human populations have provided persuasive evidence of a major migration of farmers originating from the Aegean, accompanied by sporadic hunter-gatherer admixture into early Neolithic populations, but increasing toward the Late Neolithic. In this context, ancient mitochondrial DNA data collected from the Neolithic necropolis of Gurgy (Paris Basin, France), the largest mitochondrial DNA sample obtained from a single archeological site for the Early/Middle Neolithic period, indicate little differentiation from farmers associated to both the Danubian and Mediterranean Neolithic migration routes, as well as from Western European hunter-gatherers. To test whether this pattern of differentiation could arise in a single unstructured population by genetic drift alone, we used serial coalescent simulations. We explore female effective population size parameter combinations at the time of the colonization of Europe 45000 years ago and the most ...

Proceedings of the National Academy of Sciences of the United States of America, Nov 1, 2016

Nature, 2016

The human population history of Australia remains contentious, not least because of a lack of lar... more The human population history of Australia remains contentious, not least because of a lack of large extensive genomic data. We generated high-coverage genomes for 83 geographically diverse Aboriginal Australians (all speakers of Pama-Nyungan languages) and 25 Papuans from the New Guinea Highlands. We find that Papuan and Aboriginal Australian ancestors diversified from each other 25-40 thousand years ago (kya), suggesting early population structure in the ancient continent of Sahul (Australia, New Guinea and Tasmania). However, all contemporary Aboriginal Australian studied descend from a single founding population that differentiated around 10-32 kya. We find evidence for a population expansion in northeast Australia during the Holocene (past c.10 kya) associated with limited gene flow from this region to the rest of Australia. This is broadly consistent with the spread of the Pama-Nyungan languages and cultural changes taking place across the continent in the mid-Holocene. We find evidence for a single out of Africa dispersal for all contemporary humans and estimate that Aboriginal Australians and Papuans shared a common ancestor with other Eurasians 60-100 kya, with subsequent admixture with different archaic populations. Finally, we report evidence of selection in Aboriginal Australians potentially associated with living in the desert. During most of the last 100 ky, Australia, Tasmania and New Guinea formed a single continent, Sahul, which was separated from Sunda (the continental landmass including mainland and western island Southeast Asia) by a series of deep oceanic troughs never exposed by changes in sea level (the Wallacean region as defined by biogeographers). Colonisation of Sahul is thought to have required at least 8-10 separate sea crossings between islands 1 , potentially constraining the occupation of Australia and New Guinea by earlier hominins 2. The age of the first occupation of Australia has been disputed. There are several archaeological sites in Australia dating to 40-45 kya (Figure 1), long argued to represent the age of first occupation 3 despite a few sites dating to ≥ 50 kya. However, recent studies support the earlier dates, suggesting that Sahul was first settled by 47.5-55 kya 4-6. This is consistent with the earliest evidence for modern humans in Sunda at a similar time 7 (Figure 1). Moreover skeletal remains that share morphological similarities with the ancestors of Aboriginal Australians and Papuans are found in South East Asia up until about 3,5 kya 8 , suggesting that the ancestors of Aboriginal Australians and Papuans extended from Sahul to Sunda. Historically, the morphological diversity among Aboriginal Australians was interpreted by some as indicating multiple ancestral migrations 9-11 ,or descent from Javanese Homo erectus, with varying levels of gene flow from contemporaneous populations 12. However, statistical analyses indicate that Australian crania show no evidence of H. erectus admixture 13. Still, the distinctiveness of the Australian archaeological record has led to the suggestion that the ancestors of Aboriginal Australians and Papuans (hereafter referred to as Australo-Papuans), as well as a small number of other populations, left the African continent earlier than the ancestors of present-day Eurasians 14. Although such multiple dispersals from Africa are supported by some genetic studies 15,16 , others have found support for only one out of Africa (OoA) event, with one 17 or two 18 independent founding waves into Asia, of which the earlier contributed to Australo-Papuan ancestry 19,20. Recent genomic results have also shown that both Aboriginal Australian 20 and Papuan 21 ancestors likely admixed with Neanderthal and Denisovan archaic hominins after leaving Africa. Once in Sahul, contact among groups would have been affected by rising sea-levels that separated the Australian continent from New Guinea and Tasmania 7-14.5 kya through the formation of the Arafura Sea and Bass Strait 22,23 (Figure 1). These events still appear to be part of the oral tradition of several Aboriginal Australian communities 24. Similarly, environmental variation accentuated during the last glacial maximum (LGM) 19-26.5 kya, leading to greater desertification of Australia 25 and more challenging temperature gradients, appears to had an impact on the number and density of human populations 26,27. In the same context, morphological and physiological studies find that Aboriginal Australians living in the desert areas today have unique adaptations 28-30 , such as the absence of the increased metabolic rates observed in Europeans when exposed to the freezing night temperatures common in the desert 31,32. At the time of European contact, Aboriginal Australians spoke over 250 distinct languages 33 , two-thirds of which belong to the Pama-Nyungan family. The place of origin of this language family, which covers 90% of the Australian mainland, has been debated 34 , as has the effect of its extensive diffusion on its internal phylogenetic structure 33. The pronounced similarity among Pama-Nyungan languages, together with shared socio-cultural patterns, have been interpreted as the result of a recent, mid-Holocene, expansion 35. Other changes in the mid-late Holocene (~4 kya) include the efflorescence of backed blades (microliths 36) and the introduction of the dingo 37. The spatial distribution of microliths

The population history of Aboriginal Australians remains largely uncharacterized. Here we generat... more The population history of Aboriginal Australians remains largely uncharacterized. Here we generate high-coverage genomes for 83 Aboriginal Australians (speakers of Pama–Nyungan languages) and 25 Papuans from the New Guinea Highlands. We find that Papuan and Aboriginal Australian ancestors diversified 25–40 thousand years ago (kya), suggesting pre-Holocene population structure in the ancient continent of Sahul (Australia, New Guinea and Tasmania). However, all of the studied Aboriginal Australians descend from a single founding population that differentiated ~10–32 kya. We infer a population expansion in northeast Australia during the Holocene epoch (past 10,000 years) associated with limited gene flow from this region to the rest of Australia, consistent with the spread of the Pama–Nyungan languages. We estimate that Aboriginal Australians and Papuans diverged from Eurasians 51–72 kya, following a single out-of-Africa dispersal, and subsequently admixed with archaic populations. Fin...

Proceedings of the Royal Society B: Biological Sciences, 2016

The Palenque, a black community in rural Colombia, have an oral history of fugitive African slave... more The Palenque, a black community in rural Colombia, have an oral history of fugitive African slaves founding a free village near Cartagena in the 17 th Century. Recently linguists have identified some 200 words in regular use that originate in a Kikongo language, with Yombe, mainly spoken in the Congo region, being the most likely source. The non-recombining portion of the Y chromosome (NRY) and mitochondrial DNA were analysed to establish whether there was greater similarity between present day members of the Palenque and Yombe than between the Palenque and 42 other African groups (for all individuals, n=2,799) from which forced slaves might have been taken. NRY data are consistent with the linguistic evidence that Yombe is the most likely group from which the original male settlers of Palenque came. Mitochondrial DNA data suggested substantial maternal sub-Saharan African ancestry and a strong founder effect but did not associate Palenque with any particular African group. In addition, based on cultural data including inhabitants' claims of linguistic differences, it has been hypothesized that the two districts of the village (Abajo and Arriba) have different origins, with Arriba founded by men originating in Congo and Abajo by those born in Colombia. Although significant genetic structuring distinguished the two from each other, no supporting evidence for this hypothesis was found.

Proceedings of the National Academy of Sciences of the United States of America, Jan 17, 2015

Theories for the origins of agriculture are still debated, with a range of different explanations... more Theories for the origins of agriculture are still debated, with a range of different explanations offered. Computational models can be used to test these theories and explore new hypotheses; Bowles and Choi [Bowles S, Choi J-K (2013) Proc Natl Acad Sci USA 110(22):8830-8835] have developed one such model. Their model shows the coevolution of farming and farming-friendly property rights, and by including climate variability, replicates the timings for the emergence of these events seen in the archaeological record. Because the processes modeled occurred a long time ago, it can be difficult to justify exact parameter values; hence, we propose a fitting to idealized outcomes (FIO) method to explore the model's parameter space in more detail. We have replicated the model of Bowles and Choi, and used the FIO method to identify complexities and interactions of the model previously unidentified. Our results indicate that the key parameters for the emergence of farming are group structu...

The Quarterly Review of Biology, 2015

We propose that plant foods containing high quantities of starch were essential for the evolution... more We propose that plant foods containing high quantities of starch were essential for the evolution of the human phenotype during the Pleistocene. Although previous studies have highlighted a stone tool-mediated shift from primarily plant-based to primarily meat-based diets as critical in the development of the brain and other human traits, we argue that digestible carbohydrates were also necessary to accommodate the increased metabolic demands of a growing brain. Furthermore, we acknowledge the adaptive role cooking played in improving the digestibility and palatability of key carbohydrates. We provide evidence that cooked starch, a source of preformed glucose, greatly increased energy availability to human tissues with high glucose demands, such as the brain, red blood cells, and the developing fetus. We also highlight the auxiliary role copy number variation in the salivary amylase genes may have played in increasing the importance of starch in human evolution following the origins of cooking. Salivary amylases are largely ineffective on raw crystalline starch, but cooking substantially increases both their energy-yielding potential and glycemia. Although uncertainties remain regarding the antiquity of cooking and the origins of salivary amylase gene copy number variation, the hypothesis we present makes a testable prediction that these events are correlated.

PLoS genetics, 2015

The Ari peoples of Ethiopia are comprised of different occupational groups that can be distinguis... more The Ari peoples of Ethiopia are comprised of different occupational groups that can be distinguished genetically, with Ari Cultivators and the socially marginalised Ari Blacksmiths recently shown to have a similar level of genetic differentiation between them (FST ≈ 0.023 - 0.04) as that observed among multiple ethnic groups sampled throughout Ethiopia. Anthropologists have proposed two competing theories to explain the origins of the Ari Blacksmiths as (i) remnants of a population that inhabited Ethiopia prior to the arrival of agriculturists (e.g. Cultivators), or (ii) relatively recently related to the Cultivators but presently marginalized in the community due to their trade. Two recent studies by different groups analysed genome-wide DNA from samples of Ari Blacksmiths and Cultivators and suggested that genetic patterns between the two groups were more consistent with model (i) and subsequent assimilation of the indigenous peoples into the expanding agriculturalist community. W...

Human molecular genetics, Jan 18, 2015

The human salivary amylase genes display extensive copy number variation (CNV), and recent work h... more The human salivary amylase genes display extensive copy number variation (CNV), and recent work has implicated this variation in adaptation to starch-rich diets, and in association with body mass index. In this work, we use paralogue ratio tests, microsatellite analysis, read depth and fibre-FISH to demonstrate that human amylase CNV is not a smooth continuum, but is instead partitioned into distinct haplotype classes. There is a fundamental structural distinction between haplotypes containing odd or even numbers of AMY1 gene units, in turn coupled to CNV in pancreatic amylase genes AMY2A and AMY2B. Most haplotypes have one copy each of AMY2A and AMY2B and contain an odd number of copies of AMY1; consequently, most individuals have an even total number of AMY1. In contrast, haplotypes carrying an even number of AMY1 genes have rearrangements leading to CNVs of AMY2A/AMY2B. Read-depth and experimental data show that different populations harbour different proportions of these basic h...

Genome Research, 2015

It is commonly thought that human genetic diversity in non-African populations was shaped primari... more It is commonly thought that human genetic diversity in non-African populations was shaped primarily by an out-of-Africa dispersal 50–100 thousand yr ago (kya). Here, we present a study of 456 geographically diverse high-coverage Y chromosome sequences, including 299 newly reported samples. Applying ancient DNA calibration, we date the Y-chromosomal most recent common ancestor (MRCA) in Africa at 254 (95% CI 192–307) kya and detect a cluster of major non-African founder haplogroups in a narrow time interval at 47–52 kya, consistent with a rapid initial colonization model of Eurasia and Oceania after the out-of-Africa bottleneck. In contrast to demographic reconstructions based on mtDNA, we infer a second strong bottleneck in Y-chromosome lineages dating to the last 10 ky. We hypothesize that this bottleneck is caused by cultural changes affecting variance of reproductive success among males.