Phillip Endicott

• D.Phil. (Magdalen College Oxford)
• Muséum National d'Histoire Naturelle

Roman writers found the relative empowerment of Celtic women remarkable¹. In southern Britain, the Late Iron Age Durotriges tribe often buried women with substantial grave goods². Here we analyse 57 ancient genomes from Durotrigian burial sites and find an extended kin group centred around a single maternal lineage, with unrelated (presumably inwar...

West and South Asian populations profoundly influenced Eurasian genetic and cultural diversity. We investigate the genetic history of the Y chromosome haplogroup L1-M22, which, while prevalent in these regions, lacks in-depth study. Robust Bayesian analyses of 165 high-coverage Y chromosomes favor a West Asian origin for L1-M22 ∼20.6 thousand years...

Integrating datasets from different disciplines is hard because the data are often qualitatively different in meaning, scale and reliability. When two datasets describe the same entities, many scientific questions can be phrased around whether the (dis)similarities between entities are conserved across such different data. Our method, CLARITY, quan...

Multiple lines of evidence show that modern humans interbred with archaic Denisovans. Here, we report an account of shared demographic history between Australasians and Denisovans distinctively in Island Southeast Asia. Our analyses are based on ∼2.3 million genotypes from 118 ethnic groups of the Philippines, including 25 diverse self-identified N...

Integrating datasets from different disciplines is hard because the data are often qualitatively different in meaning, scale, and reliability. When two datasets describe the same entities, many scientific questions can be phrased around whether the similarities between entities are conserved. Our method, CLARITY, quantifies consistency across datas...

Kalmyks, the only Mongolic-speaking population in Europe, live in the southeast of the European Plain, in Russia. They adhere to Buddhism and speak a dialect of the Mongolian language. Historical and linguistic evidence, as well a shared clan names, suggests a common origin with Oirats of western Mongolia; yet, only a limited number of genetic stud...

Founder effects in modern populations The genomes of ancient humans can reveal patterns of early human migration (see the Perspective by Achilli et al. ). Iceland has a genetically distinct population, despite relatively recent settlement (∼1100 years ago). Ebenesersdóttir et al. examined the genomes of ancient Icelandic people, dating to near the...

Little is known regarding the first people to enter the Americas and their genetic legacy.Genomic analysis of the oldest human remains from the Americas showed a direct relationship between a Clovis-related ancestral population and all modern Central and South Americans as well as a deep split separating them from North Americans in Canada.We prese...

The debate concerning the origin of the Polynesian speaking peoples has been recently reinvigorated by genetic evidence for secondary migrations to western Polynesia from the New Guinea region during the 2nd millennium BP. Using genome-wide autosomal data from the Leeward Society Islands, the ancient cultural hub of eastern Polynesia, we find that...

Human mitochondrial DNA haplogroup U is among the initial maternal founders in Southwest Asia and Europe and one that best indicates matrilineal genetic continuity between late Pleistocene hunter-gatherer groups and present-day populations of Europe. While most haplogroup U subclades are older than 30 thousand years, the comparatively recent coales...

Medieval era encounters of nomadic groups of the Eurasian Steppe and largely sedentary East Europeans had a variety of demographic and cultural consequences. Amongst these outcomes was the emergence of the Lipka Tatars—a Slavic-speaking Sunni-Muslim minority residing in modern Belarus, Lithuania and Poland, whose ancestors arrived in these territor...

Significance This report is the first publication, to our knowledge, to report the complete mitochondrial genome of an ancient Aboriginal Australian. In addition, it also provides important evidence about the reliability of the only previous publication of this kind. The paper attained international significance, although its conclusions have remai...

The Slavic branch of the Balto-Slavic sub-family of Indo-European languages underwent rapid divergence as a result of the spatial expansion of its speakers from Central-East Europe, in early medieval times. This expansion-mainly to East Europe and the northern Balkans-resulted in the incorporation of genetic components from numerous autochthonous p...

Background Complete mitochondrial DNA (mtDNA) genome analyses have greatly improved the phylogeny and phylogeography of human mtDNA. Human mitochondrial DNA haplogroup U6 has been considered as a molecular signal of a Paleolithic return to North Africa of modern humans from southwestern Asia. Results Using 230 complete sequences we have refined...

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...

DefinitionHuman evolution (molecular clocks). The timescale of human evolution and migration can be estimated from genetic data that have been sampled from living, historical, and ancient humans. This can be done using statistical methods based on the molecular clock hypothesis.IntroductionThe timescale of human evolutionary origins and migration a...

"The "negrito" hypothesis predicts that a shared phenotype among various contemporary groups of hunter-gatherers in Southeast Asia-dark skin, short stature, tight curly hair-is due to common descent from a region-wide, pre-Neolithic substrate of humanity. The alternative is that their distinctive phenotype results from convergent evolution. The cor...

The indigenous inhabitants of the Andaman Islands were considered by many early anthropologists to be pristine examples of a "negrito" substrate of humanity that existed throughout Southeast Asia. Despite over 150 years of research and study, questions over the extent of shared ancestry between Andaman Islanders and other small-bodied, gracile, dar...

Dear Dr. Padilla, This paper has some excellent content on the history of negrito populations as well as providing a much-needed GIS approach to the their geographical location in the Philippine through time. The impact of the manuscript would benefit from a slight re organisation of the content and additional emphasis on the important contribution...

A better understanding of the evolutionary relationship between modern humans and Neanderthals is essential for improving the resolution of hominin phylogenetic hypotheses. Currently, four distinct chronologies for the timing of population divergence are available, ranging from the late Middle Pleistocene to the late Early Pleistocene, each based o...

The analysis of targeted genetic loci from ancient, forensic and clinical samples is usually built upon polymerase chain reaction (PCR)-generated sequence data. However, many studies have shown that PCR amplification from poor-quality DNA templates can create sequence artefacts at significant levels. With hominin (human and other hominid) samples,...

Different methodologies and modes of calibration have produced disparate, sometimes irreconcilable, reconstructions of the evolutionary and demographic history of our species. We discuss how date estimates are affected by the choice of molecular data and methodology, and evaluate various mitochondrial estimates of the timescale of human evolution i...

Background Progress in the field of human ancient DNA studies has been severely restricted due to the myriad sources of potential contamination, and because of the pronounced difficulty in identifying authentic results. Improving the robustness of human aDNA results is a necessary pre-requisite to vigorously testing hypotheses about human evolution...

qPCR results for the Iceman (extract HB50). The blue diamonds are the various dilutions of the reference standard, and the red ones represent the Iceman extract. This gives the estimated starting copy number per microlitre of extract (~18 k).

K1 multiplex SBE primers. The name of the Single-Base-Extension primer indicates the site being tested and the strand orientation, whilst the last column gives the possible ancestral and derived alleles.

Cloned HVS1 sequences from the Iceman. HVR1 sequences covering diagnostic SNPs at nps 16311 and 16362, obtained from three extracts of the Iceman's DNA (BPE1, HB49, HB50).

K1 multiplex PCR primers. The fourth and the sixth columns give the 5' ends of the forward and reverse primers, respectively, whilst the second column indicates the position of the site being targeted in the SBE reaction.

Table of mtDNA haplotypes. List of mtDNA haplotypes of all results from aDNA extracts an negative controls (NC) with putative European human mtDNA prepared in the ABC isolation facility in Oxford. rCRS means that there were no mutations observed relative to the revised Cambridge Reference Sequence.

Table of Singleplex PCR primers used in this study. The first and fourth columns give the 5' ends of the forward and reverse primers, respectively.

Quantitative PCR primers and synthetic standards. The name of the primer indicates the position immediately 3' of the primer sequence.

This paper recalls the early life of Dr Arthur Conan Doyle when his writing centred briefly on India. The significance of a young female skeleton given to the museum of the Royal College of Surgeons of Edinburgh in 1879 is reviewed. Morphometric and genetic evidence is provided to show that the skeleton originated in the Andaman Islands. It is sugg...

High levels of non-authentic sequence data can be generated by traditional PCR-based methodologies when DNA is damaged, template numbers are small and/or the target amplification size too large. We therefore present an alternate methodology based on single primer extension (SPEX) amplification; that places no pre-defined size constraints on amplifi...

To the editor: In a recent study of Native American mitochondrial genomes, Fagundes et al.1 claimed to have found molecular evidence that the colonization of the New World occurred well before the appearance of the Clovis cultural horizon (c. 12.6–13.2 thousand years [kyr] ago2). To support this claim, the authors performed a variety of phylogeneti...

Accurate estimates of mitochondrial substitution rates are central to molecular studies of human evolution, but meaningful comparisons of published studies are problematic because of the wide range of methodologies and data sets employed. These differences are nowhere more pronounced than among rates estimated from phylogenies, genealogies, and ped...

The population genetics of the Indian subcontinent is central to understanding early human prehistory due to its strategic location on the proposed corridor of human movement from Africa to Australia during the late Pleistocene. Previous genetic research using mtDNA has emphasized the relative isolation of the late Pleistocene colonizers, and the p...

Published and new samples of Aboriginal Australians and Melanesians were analyzed for mtDNA (n = 172) and Y variation (n = 522), and the resulting profiles were compared with the branches known so far within the global mtDNA and the Y chromosome tree. (i) All Australian lineages are confirmed to fall within the mitochondrial founder branches M and...

Ancient DNA (aDNA) research has long depended on the power of PCR to amplify trace amounts of surviving genetic material from preserved specimens. While PCR permits specific loci to be targeted and amplified, in many ways it can be intrinsically unsuited to damaged and degraded aDNA templates. PCR amplification of aDNA can produce highly-skewed dis...

Details of M31_M32 SBE primers (2.25 MB EPS)

Details of control regions polymorphisms detected in each sample. (1.72 MB EPS)

Details of M31_M32 multiplex PCR primers and target SNPs (0.41 MB EPS)

Details of PCR primers for control region sequencing (0.33 MB EPS)

This protocol describes a single nucleotide polymorphism (SNP) genotyping strategy for highly degraded DNA, using a two-stage multiplex whereby multiple fragments are first amplified in a single exponential reaction and the products of this PCR are added to a linear single-base-extension reaction. It utilizes the analytical power of a capillary ele...

The issue of errors in genetic data sets is of growing concern, particularly in population genetics where whole genome mtDNA sequence data is coming under increased scrutiny. Multiplexed PCR reactions, combined with SNP typing, are currently under-exploited in this context, but have the potential to genotype whole populations rapidly and accurately...

Understanding the genetic origins and demographic history of Indian populations is important both for questions concerning the early settlement of Eurasia and more recent events, including the appearance of Indo-Aryan languages and settled agriculture in the subcontinent. Although there is general agreement that Indian caste and tribal populations...

The First Americans: The Pleistocene Colonization of the New World. Edited by Nina G. Jablonski. Pp. 343. (University of California Press, Berkeley, 2002.) £24.95, ISBN 0–940228–50–5, paperback. - - Volume 37 Issue 1 - Phillip Endicott

Recent advances in the understanding of the maternal and paternal heritage of south and southwest Asian populations have highlighted their role in the colonization of Eurasia by anatomically modern humans. Further understanding requires a deeper insight into the topology of the branches of the Indian mtDNA phylogenetic tree, which should be context...

Table 8. Excel spreadsheet. MtDNA haplogroup frequencies among tribal populations. Frequencies of mtDNA haplogroups amongst the tribal populations of India, China and Thailand as averaged over states of India and provinces in China and Thailand.

Table 11. Excel spreadsheet. Frequencies of mtDNA haplogroups amongst the Indian caste populations as averaged over states of India.

Table 13. Excel spreadsheet. Frequencies of mtDNA haplogroups amongst different linguistic groupings of Indian populations.

Table 12. Excel spreadsheet. Comparison of the mtDNA haplogroup frequencies amongst the Indian caste and tribal populations.

Table 10. Excel spreadsheet. Frequencies of mtDNA haplogroups amongst the Indian populations.

Table 6. Excel spreadsheet. The list of studied populations. List and details of the populations whose mtDNA were used in the study. This includes both newly obtained datasets and previously published datasets

Table 7. Excel spreadsheet. MtDNA variation in the studied populations (raw data). MtDNA control and coding region variation in the populations that were used in the study. The database includes both the newly obtained datasets and the previously published datasets. The latter were in many cases reanalyzed both in silico and by typing for additiona...

Table 9. Excel spreadsheet. MtDNA haplogroup frequencies in India and Iran.

Figure 12. Image file in PNG format. Network of HVS-I haplotypes belonging to haplogroup R5. Circle areas are proportional to haplotype frequencies. Variant bases of the HVS-I are numbered as in (Anderson et al. 1981) minus 16,000 and shown along links between haplotypes. The diagnostic R5 coding region marker 8594 is shown in bold and numbered as...

BACKGROUND: Recent advances in the understanding of the maternal and paternal heritage of south and southwest Asian populations have highlighted their role in the colonization of Eurasia by anatomically modern humans. Further understanding requires a deeper insight into the topology of the branches of the Indian mtDNA phylogenetic tree, which shoul...

Mitochondrial sequences were retrieved from museum specimens of the enigmatic Andaman Islanders to analyze their evolutionary history. D-loop and protein-coding data reveal that phenotypic similarities with African pygmoid groups are convergent. Genetic and epigenetic data are interpreted as favoring the long-term isolation of the Andamanese, exten...