KNM-LH1: a 23,000 year old human from Kenya

From the paper:

KNM-LH 1 and other Pleistocene African specimens, all of which are potentially sampling candidate populations for dispersals across and out of Africa during the Late Pleistocene (12–15, 50, 59), differ substantially not only from recent Africans but also from individuals drawn from Holocene LSA archaeological sites. KNM-LH 1 and other Pleistocene African specimens (found with MSA and LSA artifacts) are also distinct from most EUP individuals.

Things are looking good for my Afrasian-Palaeoafrican admixture hypothesis which postulates that modern Africans are a mixture of "Afrasians" (a group of humans that also spilled over into Eurasia and/or back-migrated to Africa) and various groups of very divergent "Palaeoafrican" populations. In the context of this hypothesis, greater African genetic diversity is understood not as the result of a bottleneck of epic proportions during Out-of-Africa, but rather as a result of admixture between the two groups.

PNAS doi: 10.1073/pnas.1417909112

Late Pleistocene age and archaeological context for the hominin calvaria from GvJm-22 (Lukenya Hill, Kenya)

Christian A. Tryon et al.

Kenya National Museums Lukenya Hill Hominid 1 (KNM-LH 1) is a Homo sapiens partial calvaria from site GvJm-22 at Lukenya Hill, Kenya, associated with Later Stone Age (LSA) archaeological deposits. KNM-LH 1 is securely dated to the Late Pleistocene, and samples a time and region important for understanding the origins of modern human diversity. A revised chronology based on 26 accelerator mass spectrometry radiocarbon dates on ostrich eggshells indicates an age range of 23,576–22,887 y B.P. for KNM-LH 1, confirming prior attribution to the Last Glacial Maximum. Additional dates extend the maximum age for archaeological deposits at GvJm-22 to >46,000 y B.P. (>46 kya). These dates are consistent with new analyses identifying both Middle Stone Age and LSA lithic technologies at the site, making GvJm-22 a rare eastern African record of major human behavioral shifts during the Late Pleistocene. Comparative morphometric analyses of the KNM-LH 1 cranium document the temporal and spatial complexity of early modern human morphological variability. Features of cranial shape distinguish KNM-LH 1 and other Middle and Late Pleistocene African fossils from crania of recent Africans and samples from Holocene LSA and European Upper Paleolithic sites.

Link

mtDNA from southeastern Kenyan Bantu

Am J Phys Anthropol DOI: 10.1002/ajpa.22227

Mitochondrial DNA Diversity in Two Ethnic Groups in Southeastern Kenya: Perspectives from the Northeastern Periphery of the Bantu Expansion

Ken Batai et al.

The Bantu languages are widely distributed throughout sub-Saharan Africa. Genetic research supports linguists and historians who argue that migration played an important role in the spread of this language family, but the genetic data also indicates a more complex process involving substantial gene flow with resident populations. In order to understand the Bantu expansion process in east Africa, mtDNA hypervariable region I variation in 352 individuals from the Taita and Mijikenda ethnic groups was analyzed, and we evaluated the interactions that took place between the Bantu- and non-Bantu-speaking populations in east Africa. The Taita and Mijikenda are Bantu-speaking agropastoralists from southeastern Kenya, at least some of whose ancestors probably migrated into the area as part of Bantu migrations that began around 3,000 BCE. Our analyses indicate that they show some distinctive differences that reflect their unique cultural histories. The Taita are genetically more diverse than the Mijikenda with larger estimates of genetic diversity. The Taita cluster with other east African groups, having high frequencies of haplogroups from that region, while the Mijikenda have high frequencies of central African haplogroups and cluster more closely with central African Bantu-speaking groups. The non-Bantu speakers who lived in southeastern Kenya before Bantu speaking groups arrived were at least partially incorporated into what are now Bantu-speaking Taita groups. In contrast, gene flow from non-Bantu speakers into the Mijikenda was more limited. These results suggest a more complex demographic history where the nature of Bantu and non-Bantu interactions varied throughout the area.

Link

"In Africa" project

The new 5-year "In Africa" project headed by Marta Mirazon Lahr has a wonderful website filled with information. From the Aims section:


"The project hopes to achieve five main goals:

1. to increase significantly the number of human and other mammalian fossils in East Africa dating to the last 250,000 years;
2. to map changes in human morphology, behaviour and occupation in different basins of East Africa in the period before and after the main modern human dispersals across and out of Africa;
3. to map the character and timing of the Middle to Later Stone Age transition in the Central Rift Valley;
4. to integrate the human prehistoric record with local palaeoenvironmental data to explore the role climate change and its expression in the African tropics may have played in our recent evolutionary history;
5. to increase the scientific and public awareness of how important it is to understand what happened in Africa in order to understand why Homo sapiens and its diversity evolved."

An example of the information that can be found in this site is this list of Middle Pleistocene Sub-Saharan African fossils (pdf). Please note that some of the given dates (such as that of Broken Hill/Kabwe) are controversial. The e-library is also full of a large number of  papers and is a very useful resource.

mtDNA variation in East Africa (Boattini et al. 2013)

From the paper:

Language diversity in EA fits well with its complicated genetic history. In Fleming words, ‘‘Ethiopia by itself has more languages than all of Europe, even counting all the so-called dialects of the Romance family’’ (Fleming, 2006). All African linguistic phyla are found in EA: Afro-Asiatic (AA), Nilo-Saharan, Niger-Congo and Khoisan (however, the genealogical unit of Khoisan is no longer generally accepted). Among them, AA is the most differentiated, being represented by three (Omotic, Cushitic, Semitic) of its six major clades (the others being Chadic, Berber and Egyptian). Omotic and Cushitic are considered the deepest clades of AA, and both are found almost exclusively in the Horn of Africa, along with the linguistic relict Ongota that is traditionally assigned to the Cushitic family but whose classification is still widely debated (Fleming, 2006). These observations are in agreement with a North-Eastern African origin of the AA languages, most probably in pre-Neolithic times (Ehret, 1979, 1995; Kitchen et al., 2009).

and:

This study confirms the central role of EA and the Horn of Africa in the genetic and linguistic history of a wide area spanning from Central and Northern Africa to the Levant. Our results confirm high mtDNA diversity and strong genetic structuring in EA. We were indeed able to identify three population clusters (A, B1, B2) that are related both to geography and linguistics, and signaling different population events in the history of the region. The Horn of Africa (cluster A), in accordance with its role as a major gateway between sub-Saharan Africa and the Levant, shows widespread contacts with populations from CA (AA-Chadic speakers), the Arabian peninsula and the Nile Valley. Southwards, Kenya, and Tanzania (clusters B1 and B2), despite being both heavily involved in Bantu and Nilo-Saharan pastoralist expansions, reveal traces of a more ancient genetic stratum associated with Cushitic-speaking groups (cluster B2). Conversely, Berber- and Semitic-speaking populations of NA and the Levant show only marginal traces of admixture with sub-Saharan groups, as well as a different mtDNA genetic background, making the hypothesis of a Levantine origin of AA unlikely. In conclusion, EA genetic structure configures itself as a complicated palimpsest in which more ancient strata (AA-Cushiticspeaking groups) are largely overridden by recent different migration events. Further explorations of AA-Cushitic- speaking populations – both in terms of sampled groups and typed genetic markers – will be of great importance for the reconstruction of the genetic history of EA and AA-speakers. 

The African origin of Afroasiatic would agree with its linguistic separateness from Eurasian languages, and the fact that a single branch of the family (Semitic) is likely to have originated in Asia, and fairly recently at that.

Related:

• Disentangling the histories of mtDNA haplogroups M1 and U6
• Ethiopian origins (Pagani et al. 2012)
• mtDNA and ethnic differentiation in East Africa

Am J Phys Anthropol DOI: 10.1002/ajpa.22212

mtDNA variation in East Africa unravels the history of afro-asiatic groups

Alessio Boattini et al.

East Africa (EA) has witnessed pivotal steps in the history of human evolution. Due to its high environmental and cultural variability, and to the long-term human presence there, the genetic structure of modern EA populations is one of the most complicated puzzles in human diversity worldwide. Similarly, the widespread Afro-Asiatic (AA) linguistic phylum reaches its highest levels of internal differentiation in EA. To disentangle this complex ethno-linguistic pattern, we studied mtDNA variability in 1,671 individuals (452 of which were newly typed) from 30 EA populations and compared our data with those from 40 populations (2970 individuals) from Central and Northern Africa and the Levant, affiliated to the AA phylum. The genetic structure of the studied populations—explored using spatial Principal Component Analysis and Model-based clustering—turned out to be composed of four clusters, each with different geographic distribution and/or linguistic affiliation, and signaling different population events in the history of the region. One cluster is widespread in Ethiopia, where it is associated with different AA-speaking populations, and shows shared ancestry with Semitic-speaking groups from Yemen and Egypt and AA-Chadic-speaking groups from Central Africa. Two clusters included populations from Southern Ethiopia, Kenya and Tanzania. Despite high and recent gene-flow (Bantu, Nilo-Saharan pastoralists), one of them is associated with a more ancient AA-Cushitic stratum. Most North-African and Levantine populations (AA-Berber, AA-Semitic) were grouped in a fourth and more differentiated cluster. We therefore conclude that EA genetic variability, although heavily influenced by migration processes, conserves traces of more ancient strata.

Link

Multiple species of early Homo

I will point you towards Hominid Hunting, the NY Times, and Nature for coverage of the paper. From the press release:

Found within a radius of just over 10 km from 1470's location, the three new fossils are dated between 1.78 million and 1.95 million years old. The face KNM-ER 62000, discovered by field crew member Elgite Lokorimudang in 2008, is very similar to that of 1470, showing that the latter is not a single "odd one out" individual. Moreover, the face's well-preserved upper jaw has almost all of its cheek teeth still in place, which for the first time makes it possible to infer the type of lower jaw that would have fitted 1470. A particularly good match can be found in the other two new fossils, the lower jaw KNM-ER 60000, found by Cyprian Nyete in 2009, and part of another lower jaw, KNM-ER 62003, found by Robert Moru in 2007. KNM-ER 60000 stands out as the most complete lower jaw of an early member of the genus Homo yet discovered.

I'm not competent enough to express an opinion, so I won't. Still, if there were two species living at that time, it would not be surprising; in the recent past where we do have more complete data, it seems that our Homo sapiens ancestors shared the planet with other quite divergent hominins. Perhaps this was the norm for the greater part of human prehistory, until evolution came up with us, and we came up with ideas (whether through love or war) to drive the rest of Homo to non-existence, leaving us as the only living twig of a quite bushy family tree.

Nature 488, 201–204 (09 August 2012) doi:10.1038/nature11322

New fossils from Koobi Fora in northern Kenya confirm taxonomic diversity in early Homo

Meave G. Leakey, Fred Spoor, M. Christopher Dean, Craig S. Feibel, Susan C. Antón, Christopher Kiarie & Louise N. Leakey

Since its discovery in 1972 (ref. 1), the cranium KNM-ER 1470 has been at the centre of the debate over the number of species of early Homo present in the early Pleistocene epoch2 of eastern Africa. KNM-ER 1470 stands out among other specimens attributed to early Homo because of its larger size, and its flat and subnasally orthognathic face with anteriorly placed maxillary zygomatic roots3. This singular morphology and the incomplete preservation of the fossil have led to different views as to whether KNM-ER 1470 can be accommodated within a single species of early Homo that is highly variable because of sexual, geographical and temporal factors4, 5, 6, 7, 8, 9, or whether it provides evidence of species diversity marked by differences in cranial size and facial or masticatory adaptation3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20. Here we report on three newly discovered fossils, aged between 1.78 and 1.95 million years (Myr) old, that clarify the anatomy and taxonomic status of KNM-ER 1470. KNM-ER 62000, a well-preserved face of a late juvenile hominin, closely resembles KNM-ER 1470 but is notably smaller. It preserves previously unknown morphology, including moderately sized, mesiodistally long postcanine teeth. The nearly complete mandible KNM-ER 60000 and mandibular fragment KNM-ER 62003 have a dental arcade that is short anteroposteriorly and flat across the front, with small incisors; these features are consistent with the arcade morphology of KNM-ER 1470 and KNM-ER 62000. The new fossils confirm the presence of two contemporary species of early Homo, in addition to Homo erectus, in the early Pleistocene of eastern Africa.

Link

Clusters Galore analysis of East Africans

I have included the new data from Pagani et al. (2012) together with various other East African datasets available to me, including various East African Dodecad Project participants.

The first four PCA dimensions can be seen below:

Project participants can find their co-ordinates in the first four dimensions below:

I have also run MCLUST over the first 4 dimensions, which resulted in 12 clusters inferred:

All Project participants fall in the expected clusters, so there is no need to report any individual clustering results.

mtDNA haplogroup L0 in elite Kenyan distance runners

Med Sci Sports Exerc. 2008 Dec 11.

Mitochondrial Haplogroups Associated with Elite Kenyan Athlete Status.

Scott RA, Fuku N, Onywera VO, Boit M, Wilson RH, Tanaka M, H Goodwin W, Pitsiladis YP.

The maternal inheritance of mitochondrial DNA (mtDNA) has enabled construction of detailed phylogenies. Analysis of key polymorphisms from these phylogenies allows mtDNA to be assigned to haplogroups, which have been associated with elite endurance performance. PURPOSE:: To compare the frequencies of mtDNA haplogroups found in elite Kenyan athletes with those in the general Kenyan population. METHODS:: DNA samples were obtained from 221 national level Kenyan athletes (N), 70 international Kenyan athletes (I), and 85 members of the general Kenyan population (C). mtDNA haplogroups were classified by sequencing 340 bases of hypervariable section (HVS I) and by genotyping known restriction sites. Frequency differences between groups were assessed using exact tests of population differentiation. RESULTS:: The haplogroup distribution of national (P = 0.023) and international athletes (P less than 0.001) differed significantly from controls, with international athletes showing a greater proportion of L0 haplogroups (C = 15%, N = 18%, I = 30%) and lower proportion of L3* haplogroups (C = 48%, N = 36%, I = 26%). Although a high number of international athletes originated from the Rift Valley province relative to controls (C = 20%, N = 65%, I = 81%), subjects from this province did not differ in haplogroup distribution from other regions (P = 0.23). Nor did Bantu subjects differ from Nilotic (P = 0.12) despite an overrepresentation of Nilotic languages among the athletes. CONCLUSIONS:: International athletes differed in their mtDNA haplogroup distribution relative to the general Kenyan population. They displayed an excess of L0 haplogroups and a dearth of L3* haplogroups. These findings suggest that mtDNA haplogroups are influential in elite Kenyan distance running, although population stratification cannot be ruled out.

Link

ASHG 2008 abstracts

Just a sample of abstracts that I found interesting from the upcoming meeting of the American Society of Human Genetics.

Strong linkage disequilibrium for the frequent GJB2 35delG mutation in the Greek population.

Up to forty percent of autosomal recessive, congenital, severe to profound hearing impairment cases result from mutations in the GJB2 gene. The 35delG mutation accounts for the majority of mutations detected in Caucasian populations and represents one of the most frequent disease mutations identified so far. Some previous studies have assumed that the high frequency of the 35delG mutation reflects the presence of a mutational hot spot, whilst other studies support the theory of a common founder. Greece is amongst the countries presenting the highest frequency of the 35delG mutation (3.5%), and a recent study raised the hypothesis of the origin of this mutation in ancient Greece. We genotyped 60 Greek deafness patients homozygous for the 35delG mutation for six single nucleotide polymorphisms (SNPs) and two microsatellite markers, mapping within or flanking the GJB2 gene, as compared to 60 Greek hearing controls. A strong linkage disequilibrium was found between the 35delG mutation and the DNA markers at distances of 34 kb on the centromeric and 90 kb on the telomeric side of the gene, respectively. A comparison of the present findings with those of a previous study from Belgium, UK and USA, demonstrated a common haplotype reflecting the common founder. Our study supports the hypothesis of a founder effect and we further propose that ethnic groups of Greek ancestry could have propagated the 35delG mutation, as evidenced by historical data beginning from the 15th century BC.

Detection of population substructure among Jews and a north/south gradient within Ashkenazi Jews using 32 STR markers.

Understanding and detecting population substructure are critical issues. Using 32 autosomal STR markers and the program STRUCTURE we demonstrated differentiation between Ashkenazi (AJ) (N=135) and Sephardic (SJ) (N=226) Jewish populations in the form of Northern and Southern European genetic components (AJ north 73%, south 22%, SJ north 32%, south 61%) and a significant relationship between latitude of grandparental country of origin (GCO) and percent north/south genetic component in AJ. Notably, we revealed substructure among Jews (and among European Americans (EA)) using a small STR panel, only when additional samples representing major continental populations (African American, EA, Asian) were included in analyses. Further, negative RIS (-0.035) indicates recent admixture in individuals with both SJ and AJ parents (N=38). RIS is a measure of inbreeding adapted from FIS for STR markers. Negative RIS indicates allelic variation within individuals greater than expected under random mating, i.e., excess heterozygosity due to outbreeding. Although geographic patterns are seen in the average north/south percent assignment values between groups as defined by AJ or SJ, grandparental world region of origin, or GCO, within each group there is high variability among individual assignment values. Thus, even based on data from a small marker set, AJ is not a homogeneous population. The north/south gradient in AJ may be a reflection of the pre-existing north/south gradient in European host populations (recently shown in other studies using large numbers of SNPs) with which Jews admixed slowly. We also demonstrate the utility of including purported parental populations when attempting to detect population substructure within closely related populations.

Mutation meltdown of mitochondrial DNA and Neanderthal extinction.

There is emerging evidence that mitochondrial DNA (mtDNA) plays and integral role in the evolution of the human species. Although contentious, recent phylogenetic studies of modern humans implicate genetic variation of mitochondrial DNA (mtDNA) as a major factor underpinning the climatic adaptation of across the globe. Greater sequence diversity in the MTATP6 gene in arctic populations led to the idea that specific mtDNA polymorphisms cause subtle uncoupling of the respiratory chain, with the subsequent generation of additional heat being adaptive in northern climes. Our knowledge of mtDNA and its affect on adaptability may help us to understand how modern humans have survived their early ancestors. Here, we characterise the mtDNA of one of these extinct hominids. Neanderthals are the closest hominid relatives of modern humans, who up until 30,000 years ago coexisted in Europe and western Asia. Recently, over 1Mb of DNA was successfully extracted and characterised from the Vi-80 Neanderthal fossil. We reanalysed 2,705 base pairs of mtDNA in order to examine the hypothesis that mitochondrial dysfunction contributed to the Neanderthals demise. We identified thirty-two nucleotide differences from the modern human mtDNA reference sequence and by treating the Vi-80 as a diagnostic sample leads us to the conclusion that sequence variants that are highly likely to be artifacts, and a large proportion of the remaining mutations could be due to nuclear pseudogene amplification. We did identify a potentially deleterious variation; however more study may be needed to ascertain the effect of mitochondrial dysfunction on Neanderthal survival.

Early Siberian Maternal Lineages in the Tubalar of Northeastern Altai Inferred from High-Resolution Mitochondrial DNA Analysis

At the hight of the last glaciation (~18 kya) Siberians were confined to the southern strongholds, which were areas of continuous occupation, and where immediate ancestors of the Uralic, Kettic and Altaian language groups differentiated. To better understand the evolutionary relationships between the earlier and contemporary Siberians, we focused on the northern Altaic prehistory preserved in the mtDNA diversity of the Tubalar, until recently representing a typical hunting-gathering population. The present study includes 139 Tubalar. All mtDNAs were subjected to high-resolution SNP analysis, followed by complete sequencing of selected mtDNA samples. We showed that the core of the Tubalar genetic makeup proved to be a mixture of west (H8, U4b, U5a1, and X2e) and east Eurasian (A and B1) haplogroups derived from macrohaplogroup N, and Siberian derivatives of the macrohaplogroup M identifiable by subhaplogroup-specific mutations. For example, among the 36 Tubalar mtDNA samples that belong to haplogroup D, 10 (28%) harbored diagnostic markers of the subhaplogroup D3a2a shared with the Chukchi and Eskimos. This finding verified at the complete sequence level we attributed to ancient link between early Siberians, who underwent pronounced differentiation in the Altai-Sayan region, and some of the Eskimo tribes. A comparison of the mtDNA data generated through the course of this study with published complete sequences has contributed essentially to parsimonious phylogenetic structure of mtDNA evolution in west Siberia. Specifically, northeastern Altai appears to be a good candidate for the ancestral homeland of the haplogroup U4b, which is apparently ancient European. For some haplogroups, such as X2e, the relatively recent arrival to the Altai region is more likely.

Sex-specific gene flow between Pygmy and non-Pygmy populations

Cultural traditions and preferences may drive sex-specific gene flow among human populations. We have examined sex-specific gene flow between Mbuti Pygmies, a hunter-gather population, and surrounding agriculturist groups, the Alur, Hema, and Nande, which all reside in Central Africa. We used 18 lineage-defining Y chromosome SNPs and HVS1 mitochondrial DNA sequence information to examine patterns of gene flow among these groups. Mbuti Pygmy males have more diverse Y chromosome lineages (Mbuti Pygmy [n = 28]: = 0.229; Alur [n = 10]: 0.193; Hema [n = 18]: 0.178; Nande [n = 15]: 0.090) and slightly less mtDNA diversity than neighboring groups (0.020, 0.023, 0.025, 0.022 in Mbuti Pygmy, Alur, Hema, and Nande groups, respectively). The majority of Mbuti Pygmy males have a Y haplotype characteristic of Mbuti Pygmies (B2b); however, more than 30% of Pygmy males exhibit Y haplotypes associated with Bantu-speaking agricultural populations (E3a lineage). Conversely, no agriculturist males exhibit Y haplogroups associated with Mbuti Pygmy populations but instead have derived Y haplogroups characteristic of Bantu agriculturalists (E2, E3a). Pairwise FST was calculated among all populations using Y haplogroup frequency and HVS1 mtDNA sequence data. YDNA and mtDNA FST values between Mbuti Pygmy and non-Pygmy groups (Alur, Hema, and Nande) were 0.278, 0.355, and 0.217 (for YDNA) and 0.088, 0.239 and 0.217 (for mtDNA), respectively. A Mantel test between pairwise FST matrices showed no significant correlation ((r = 0.27; p 0.35), which indicates that patterns of genetic differentiation differ between Y chromosome SNPs and mtDNA sequence patterns. These results also suggest no emigration of Mbuti Pygmy Y chromosomes into surrounding groups but immigration of non-Mbuti Pygmy Y chromosomes into the Mbuti Pygmy population.

Population Structure in Mongolia from a Mitochondrial DNA Perspective.

Mongolia has experienced a complex series of demographic movements over the past 10-20 millennia that have shaped the patterns of its modern human genetic variation. However, modern populations in Mongolia have not been extensively studied for DNA diversity, nor has the genetic contribution of Mongolians to the gene pools of contemporary populations in Southeast Asia and Oceania been fully resolved. Archaeological evidence from as early as the late Neolithic suggests the presence of both West and East Eurasian cultures in this region. Later demographic movements involving the emergence of the Mongolian and later Manchu Empires have further convoluted Mongolias population structure. To clarify the complex population history of Mongolia, we analyzed variation in the mtDNAs of 190 individuals from several Mongolian ethnic groups, including the Uriankhai, Zakhchin, Derbet, Khoton and Khalkha. We screened all samples for phylogenetically informative coding region SNPs and sequenced HVSI to assess control region variation in them. Our data suggest that the mtDNA diversity present in our population is consistent with the general pattern of variation observed in East Asia, with the most frequent haplogroups being C, D and G. Haplogroup variation in Mongolian ethnic groups reveals considerable maternal diversity with a predominance of basal M types. Interestingly, the Mongolians also possessed West Eurasian haplogroups, such as H, J and K, which are not commonly observed in East Asia, even at low frequencies. The main ethnic group in Mongolia, the Khalkha, was highly variable with respect to mtDNA haplotypes in comparison with the other ethnic groups, and clearly distinct from the Khoton and Zakhchin, as evidenced by distance measures. Overall, these data provide insights into the origins and affinities of these populations, their relationships with East Asian groups and neighboring Turkic speaking groups, including indigenous Altaians, and their possible role in the peopling of the Americas.

Allocation of YSTR Microvariant Alleles to Y-Chromosome Binary Haplogroups.

Y-chromosome short tandem repeat (YSTR) loci are used extensively in studies of population substructure, temporality of population dynamics, and forensic identification. The occurrence of non-consensus YSTR alleles, such as unusually short alleles or partial insertion/deletion events (microvariants), have been used successfully as indicators of common ancestry among YSTR haplotypes, exposing further levels of phylogenetic substructure with restricted geographic distributions. However, the high variability of STR loci can potentially lead to false associations due to homoplasy (ie, recurrent mutation). Thus, YSTR haplotypes are best interpreted within the context of the binary marker defined Y-chromosome phylogeny. To identify YSTR microvariant alleles potentially useful for elucidating further phylogenetic substructure within binary haplogroups, we have assessed the haplogroup affiliation of microvariant alleles found at informative frequencies in public YSTR databases for the following YSTR loci: DYS385, DYS392, DYS441, DYS446, DYS447, DYS449 and DYS464. We report haplogroup affiliations for each variant allele and geographic origins of representative samples.

L1c2a, the (African) Haplogroup With The Longest Mitochondrial Genome!

Haplotypes derived from the maternally-inherited mitochondrial DNA (mtDNA) control region are often employed as a first step in determining phylogenetic-relevant samples that could be selected for additional coding region testing. Using the currently defined world mtDNA haplogroup tree, researchers can assign these haplotypes to specific branches, paying particular attention to novel mutations that could assist in identifying new subclades. During a recent survey of the nearly 58000 mtDNA control region haplotypes currently present in the publicly accessible Sorenson Molecular Genealogy Foundation database, we observed a small number of mtDNAs (n=16) characterized by the presence of unusually long insertions of up to 200 bases. A small subset of these particularly long mtDNA haplotypes shared an identical insertion of 15 bases. Genealogical analysis combined with haplogroup prediction confirmed that these haplotypes shared a common African origin. Additionally, based on the pedigree data gathered, we determine the donors were not closely related. Moreover, through the analysis of complete mtDNA sequences, we conclude that the newly defined haplogroup is most likely of recent origin. As reported in this study, insertions of more than 10 bps are quite rare in the general population and in the published literature, thus providing an interesting case work in population and possibly future disease studies.

Mitochondrial DNA footprints in modern Mongolia.

Although Mongolia is one of the most sparsely populated countries in the world, it is located at a pivotal crossroad between the four corners of Asia (including the well-known Silk Road) and has been characterized throughout history by events that greatly added to its current cultural and ethnic diversity. Among these, perhaps one of the most significant happening was the ambitious expansion strategy employed by Mongolias most prominent personality, Genghis Khan, whose empire eventually stretched across all of modern-day China, a portion of modern Russia, Southern Asia, Eastern Europe and the Middle East. In 2007, through a well-planned collection effort, researchers at the Sorenson Molecular Genealogy Foundation and the National University of Mongolia were able to gather over 3,000 DNA samples, informed consents, and genealogical data throughout the country of Mongolia, including samples from 21 distinct tribal or ethnic populations. All the samples were sequenced for the three hypervariable segments of the mitochondrial DNA (mtDNA) control region to assess the genetic composition of modern Mongolia. The most common mtDNA haplotypes are typical of haplogroup C, which is frequent throughout Eastern Asia. However, nearly 40% of the observed mtDNA lineages are of Western Eurasian origin, including a significant frequency (~7%) of haplogroup H - the most common in Europe. The high prevalence of Western Eurasian lineages could be a remnant from Genghis Khans conquering efforts, trade and cultural exchanges along the Silk Route. To assess the extent of recent gene flow that could account for the elevated levels of Eurasian haplogroups within Mongolian populations, we have examined genealogical data of samples representative of Western Eurasian haplogroups.

Y chromosome microsatellite haplotypes in the Hutterite founders.

The current population of >12,000 Schmiedeleut Hutterites are descendants of 38 male founders who were born between 1700 and 1830 in Europe. Only 12 of these founders, each with a unique surname, have living male descendants related through male-only lineages. DNA samples were available in our laboratory for 75 male descendants of 11 of the 12 founders, accounting for 673 independent paternal meioses. We genotyped 9 microsatellite loci, which included a mean of 6.8 (range 2-23) males per lineage to evaluate potential relationships between the founders. Fourteen different haplotypes were identified, with an average of 3.5 (range 1-8) pairwise differences between haplotypes. All descendants within each of 9 lineages had identical Y haplotypes. Descendents of two of these lineages, 2 and 10, had the same haplotype despite different surnames, suggesting possible relatedness between the founders of these two lineages. Descendants of two lineages, 6 and 11, each carried three distinct haplotypes. Within each of these lineages the haplotypes differed from the ancestral haplotype by one repeat size at two loci. Additional male descendants in lineages 6 and 11 were then genotyped for the discrepant microsatellites, confirming the presence of three Y haplotypes each in lineages 6 and 11. The one mutation arose at each of four loci: DYS388, DYS389II, DYS390, DYS393. Three mutations were gains of one repeat; it was not possible to determine if the fourth mutation was a gain or loss of one repeat. The ancestral haplotypes in these two lineages are identical at four microsatellite loci; the alleles at the other five loci differ by one repeat size. The average mutation rate at these 9 loci was 0.00066 (95% CI 0.00015-0.0013), similar to other estimates. These data suggest that the founders of lineages 2 and 10 may have been related through paternal lines and that surnames do not strictly correspond to unique Y chromosomes. Moreover, certain ancestral haplotypes (i.e., those in lineages 6 and 11) may be more prone to mutation. Supported by NIH grants HD21244 and HL085197.

Genetic History of human populations of East African inferred from mtDNA and Y chromosome analyses.

Evidence from genetic, paleobiological, and archaeological studies suggest that Africa, especially East Africa, is most likely to be the cradle of the modern human species. Despite this fact, very little is currently known about genetic diversity in African populations in general, and East African populations in particular. Genetic data demonstrate that the patterns of genetic variation in East African populations are complex. All four major language families spoken in Africa (Afro-Asiatic, Nilo-Saharan, Niger-Kordofanian, and Khoisan) are found in the region. As part of a large study of population genetic diversity of East and Northeast Africa, we examined Y chromosome genetic diversity (to ascertain paternal lineages) as well as mitochondrial genetic diversity (to ascertain maternal lineages) in 1200 - 1500 individuals from ~ 40 Tanzanian, Sudanese, and Kenyan populations. For the Y chromosome analysis, we genotyped 60 UEPs (analyzed in a hierarchical manner to construct haplotypes) in a total of ~1500 male individuals. In order to infer ages of lineages and migration patterns, we further genotyped the individuals for 16 Y chromosome microsatellites. For the mtDNA analysis, we sequenced the mitochondrial D-loop in a total of 1200 individuals from the same populations, and for 200 individuals, we did complete mitochondrial genome sequencing. We compare our results with published results of studies from other parts of Africa and the Middle East. Our results indicate that East African populations have some of the most ancestral Y chromosome and mtDNA lineages in Africa, suggesting that they may have been an ancient source of dispersion throughout Africa. Additionally, we find evidence for ancient geneflow between East Africa and the Middle East. We also ascertained the effect of the Bantu-expansion and signature of recent migration of Cushitic-speaking groups originating from Ethiopia on peopling of East Africa.

Analysis of mtDNA and Y-chromosome haplogroups in Mexican Mestizos and Amerindian groups.

The Mexican population is mainly conformed by Mestizos, individuals with a genetic background consisting of Amerindian, European and African contributions. Genetic heterogeneity in Mexicans results from a complex demographic history that started with the peopling of North and Central America about 15,000 yrs ago, including the settlement of at least 60 different indigenous groups in Mexico, regional differences in admixture dynamics after colonization by Spaniards in the XVI century, epidemics and migration. Y chromosome-specific and mitcohondrial (mt) DNA polymorphisms are useful to help understand the genetic structure and history of human populations, due to their uniparental inheritance and lack of recombination. In order to refine the portrait of genetic variability derived from the Mexican Genome Diversity Project, we are characterizing maternal and paternal lineages participating in admixture. For this we included genotypic data from 163 mt SNPs and 123 Y chromosome SNPs present in the Illumina Human1M chip of 450 individuals, 300 mestizos from six states located in different regions: Northern, Central and Southern; and 150 individuals from different Amerindian groups (Tepehuanes, Zapotecos and Mayas). With this information, we are measuring genetic diversity using Fst and AMOVA analysis. Admixture analysis includes average and individual ancestral contribution estimates using autosomal SNPs. Initial results show that in our Mestizo sample, 88% of the mt haplogroups are Amerindian (A, B, C or D), and the rest includes European and African lineages. We have identified differences in proportions of each haplogroup in both Mestizos and Amerindians. Knowledege about the distribution of mt and Y-chromosome haplogroups in Mexican Mestizos and Amerindian groups, will generate valuable information to better understand genetic relationships between Mexicans and other Latin American populations. In addition, it may contribute to strengthen analysis in association studies of common complex diseases.

The origin of Native Americans from a mitochondrial DNA viewpoint.

America, the last continent to be colonized by modern humans, is characterized by an extraordinary linguistic and cultural diversity. Until recently, it was generally believed that starting around 13,500 years ago, the first Paleo-Indians arrived from Beringia, passing through an interior ice-free corridor in western North America, and spread rapidly all the way to Tierra del Fuego. Today, we realize that the peopling of the Americas involved a much more complex process. As for the maternally transmitted mitochondrial DNA (mtDNA), it has been clear since the early nineties that Native Americans could be traced back to four major maternal lineages (haplogroups) of Asian affinity. These were initially named A, B, C and D, and are now termed A2, B2, C1 and D1. More than 95% of living Native Americans belong to these four haplogroups, which can be considered pan-American, because they are shared by North, Central and South American populations. Later, five additional maternal lineages were discovered and named X2a, D2, D3, C4c, and D4h3. These less common or rare haplogroups are restricted only to some Native American populations or geographic areas and bring the overall number of Native American mtDNA lineages to nine. Our comprehensive overview of the four pan-American branches of the mtDNA tree suggests a scenario with a human entry and spread into the Americas from Beringia about 20,000 years ago, and preliminary data raise the possibility that the uncommon five Native American haplogroups might have marked additional migratory events from Asia or Beringia. Overall, through a combined analysis of modern and ancient Native American mtDNA, we are making an effort for reconstructing the complex pre-Columbian history at both macro- and micro-geographic levels.

Identifying genes affecting normal variation in human facial features using admixed populations.

Seven selection-nominated candidate genes (COL11A1, LMNA, FGFR1, FGFR2, TRPS, BRAF, FLNA) known to be involved in Mendelian craniofacial dysmorphologies and to have high allele frequency differences between West African and European populations were tested for admixture linkage to normal facial feature traits. The sample consists of 254 subjects (n=131 African Americans, n=123 Brazilians) of West African and European genetic ancestry. Each individual was genotyped at 176 ancestry informative markers (AIMs), which allowed for proportional estimation of genetic ancestry from four parental populations and adjustments for admixture stratification.
3D images of faces were acquired using the 3dMDface imaging system. 3D coordinate data were collected from 22 landmarks placed on each image using the 3dMDPatient software. The 231 possible pairwise landmark distances were scaled to the geometric mean and then analyzed using Euclidean Distance Matrix Analysis.
We used both ANOVA and ADMIXMAP to control for admixture stratification and to test for associations between the 231 pairwise landmark distances and 183 AIMs, using sex, height and BMI as covariates. We used a four-population model (West African, European, East Asian, and Native American).
There is a strong concordance between the ANOVA and ADMIXMAP results. Many landmark distances, particularly on the mouth and nose, were significantly associated with genetic ancestry. Additionally, three of the candidate genes show no effects on pairwise landmark distances while four show distinct patterns of association. For example, FGFR2 is associated primarily with the length of the face. These results represent the first identification of the first genes affecting normal variation in facial features.

Ethnicity-Confirmed Genetic Structure in New Hampshire.

Genetic population structure is known to result from shared ancestry. Though there have been several studies of genetic structure within and among different geographic regions and ethnic groups, little is known of the genetic structure of highly admixed US populations or whether the structure is concordant with self-reported ancestry. In this study, 1529 single nucleotide polymorphisms (SNPs) from 864 healthy control individuals from New Hampshire were measured as part of a bladder cancer epidemiology study. The SNPs were from approximately 500 cancer susceptibility genes scattered throughout the genome. Of these, 960 Tag SNPs were used to cluster individuals using the Structure algorithm for between 2 and 5 subpopulations. Subtle genetic structure was found, suggesting the appropriate number of subpopulations to be either 4 or 5 (FSTs 4 populations: 0.0377, 0.0399, 0.0363, 0.0340; 5 populations: 0.0452, 0.0536, 0.0585, 0.0534, 0.0521). We coded the individuals self-reported ancestries in a genotype fashion (i.e. 0= not reporting that ancestry, 1= reporting part that ancestry, 2= reporting only that ancestry) and conducted a Spearmans rank correlation between each ancestry and the structure q value, which represents the proportion of an individual that originated from a certain genetic subpopulation. Those of Russian, Polish and Lithuanian ancestry most consistently clustered together. The ancestry results support either 4 or 5 subpopulations. In order to investigate linkage disequilibrium (LD), the complete set of SNPs from the 7 most densely genotyped genes were used to make haploview plots between the different groups. The results vary by gene, though for one gene in particular, GHR, the results are very different for 4 subpopulations. These results suggest that despite New Hampshires admixture and presumed homogeneity, there are 4 or 5 distinct genetic subgroups within the population that can be linked to self-reported ancestry and display differences in patterns of LD.

Inference of human demographic parameters using haplotype patterns from genome-wide SNP data.

Accurate inference of human demographic history from genetic data is essential for identification of single nucleotide polymorphism (SNP) association with disease and for inference of natural selection. Haplotype diversity and haplotype sharing carry additional demographic information to that obtainable from SNP frequency spectra, and so we propose a novel method using haplotype summary statistics to fit demographic models to genome-wide SNP data. We divide the genome into 0.25 cM windows and for each we tabulate the number of distinct haplotypes and the frequency of the most common haplotype. We summarize the data by the genome-wide joint distribution of these two statistics. Coalescent simulations are then used to evaluate whether different demographic models are compatible with the observed data. Application of our method to simulated data shows that our method can reliably infer parameters from complex demographic models (such as bottlenecks) and is relatively robust to the levels of SNP ascertainment bias found in many genome-wide datasets. We have applied our method to data collected by the International HapMap Consortium and find that a bottleneck model best fits the CEU population. We have also analyzed a large dataset consisting of Affymetrix 500k data from ~2,900 individuals with ancestry from Taiwan, Japan, India, Mexico and many European countries. Since this dataset includes ~2,300 European individuals, we are able to study haplotype patterns at a fine scale within Europe. Interestingly, we find that within Europe there is a south-to-north gradient with decreasing levels of haplotype diversity moving north, consistent with south to north migrations. We also find that the southwestern European sample has higher haplotype diversity than the southeastern European sample. Additionally, a higher proportion of haplotypes are shared between the southwestern European sample and the Yoruba sample than between southeastern European sample and the Yoruba sample. These two patterns are consistent with recent admixture across the Mediterranean from Northern Africa.

Genome wide analysis and heritability estimation of intelligence in the International Multi-centre ADHD Genetics (IMAGE) study.

Attention-Deficit/Hyperactivity Disorder (ADHD) is a neurodevelopmental disorder characterised by symptoms of inattention, hyperactivity and impulsivity. There is growing evidence of heterogeneity in its etiology, pathophysiology and clinical expression. One approach to resolving heterogeneity involves the identification of endophenotypes, intervening variables that might mediate pathways between specific genes and clinical phenotype. IQ is a candidate endophenotype for ADHD. Genome-wide linkage analyses of full scale IQ and IQ subscales were performed in the International Multi-centre ADHD Genetics (IMAGE) study including 1094 families with 1094 DSM-IV combined type ADHD probands and their 1441 siblings (unselected for ADHD status). IQ was measured using five subscales of the WISC-IIIR scale. The full scale prorated IQ score and the five subscales were used as quantitative traits for linkage analysis. 5,407 autosomal SNPs were used to run multipoint regression-based linkage analyses using MERLIN. The h2 estimates from the IQ subscales and the full IQ score ranged from 31% to 100%. Three suggestive linkage signals were found (LOD scores 2, p values 0.001) on chromosomes 7, 9 and 14 for three different subscales. Previously, two regions on chromosomes 7 and 14 were reported as being associated or linked to IQ. Our results, though only suggestive, suggest the presence of additional genetic variants contributing to the variance of IQ in ADHD.

More positive selection in recent humans: CASP12

It seems that positive selection studies are coming out in droves; you can use the search function ("positive selection") to find a bunch of them reported on this blog.

The newest study appears as a preprint in the American Journal of Human Genetics and is about a gene called human caspase-12 (CASP12) which has two variants: the active one is the original form, but the inactive one seems to have undergone positive selection beginning 60-100ky ago.

It is suggested that the inactive form confers some advantage against sepsis, which was also implicated in a frequent mtDNA haplogroup recently.

The distribution of the two versions of the gene...



... shows that the active version is largely confined to Sub-Saharan Africa. This parallels the situation in Microcephalin and ASPM.

The highest frequencies of the active version are in the Mbuti (0.60) and the San (0.57). These populations have a high frequency of non-M168 related Y-chromosomes and non-L3 related mtDNA and are thus descended from the most ancient African populations (which I have called "Paleoafricans"), rather than the more recent emergence of an population in east Africa ("Afrasians") which spawned the Eurasians and assimilated most Paleoafricans during its spread within Africa. In this regard, it is interesting that an east African population from Kenya shows the minimum (0.04) frequency of the active gene of CASP12.

American Journal of Human Genetics (in press)

Spread of an inactive form of caspase-12 in humans due to recent
positive selection

Yali Xue et al.

Abstract

The human caspase-12 gene is polymorphic for the presence or absence of a stop codon, resulting in the occurrence of both active (ancestral) and inactive (derived) forms of the gene in the population. It has previously been shown that carriers of the inactive gene are more resistant to severe sepsis. We have now investigated whether the inactive form has spread because of neutral drift or positive selection. We determined its distribution in a worldwide sample of 52 populations and re-sequenced the gene in 77 individuals from the HapMap Yoruba, Han Chinese and European populations. There is strong evidence for positive selection from low diversity, skewed allele frequency spectra and the predominance of a single haplotype. We suggest that the inactive form of the gene arose in Africa ~100-500 thousand years ago (KYA) and was initially neutral or almost neutral, but that positive selection beginning ~60-100 KYA drove it to near-fixation. We further propose that its selective advantage was sepsis resistance in populations that experienced more infectious diseases as population sizes and densities increased.

Link (pdf)

Y haplogroup E3b1 in Somali males

A new study quantifies the extent of Eurasian (15%) and Sub-Saharan African (5%) paternal admixture in Somalis, a population which appears to be predominantly East African paternally. The authors also explain why the Somalis have low Sub-Saharan African admixture:

The time of the eastbound Bantu expansion was estimated to be 3400±1100 years ago.24 Bantu populations have high frequencies of E3a haplogroups.4 We have observed only a few individuals with the E3a haplogroup in our Somali population, thus, supporting the view that the Bantu migration did not reach Somalia.42 It has been suggested that a barrier against gene flow exist in the region.43 The barrier seems to be the Cushitic languages and cultures to which Somalis belongs. The Cushitic languages belong to the Afro-Asiatic languages that are spoken in Northern and Eastern Africa. The Cushitic languages and cultures are mainly found in the Somalis and the Oromos, one of the two main groups inhabiting Ethiopia.44, 45, 46. The Somali and Oromo languages have a high degree of similarity and the two populations share many cultural characteristics. The Somali and Oromo people live in clans with special patterns of marriage and the Somali and Oromo people have complex, interwoven pedigrees.44, 45

European Journal of Human Genetics (advance online publication)

High frequencies of Y chromosome lineages characterized by E3b1, DYS19-11, DYS392-12 in Somali males

Juan J Sanchez et al.

We genotyped 45 biallelic markers and 11 STR systems on the Y chromosome in 201 male Somalis. In addition, 65 sub-Saharan Western Africans, 59 Turks and 64 Iraqis were typed for the biallelic Y chromosome markers. In Somalis, 14 Y chromosome haplogroups were identified including E3b1 (77.6%) and K2 (10.4%). The haplogroup E3b1 with the rare DYS19-11 allele (also called the E3b1 cluster γ) was found in 75.1% of male Somalis, and 70.6% of Somali Y chromosomes were E3b1, DYS19-11, DYS392-12, DYS437-14, DYS438-11 and DYS393-13. The haplotype diversity of eight Y-STRs ('minimal haplotype') was 0.9575 compared to an average of 0.9974 and 0.9996 in European and Asian populations. In sub-Saharan Western Africans, only four haplogroups were identified. The West African clade E3a was found in 89.2% of the samples and the haplogroup E3b1 was not observed. In Turks, 12 haplogroups were found including J2*(xJ2f2) (27.1%), R1b3*(xR1b3d, R1b3f) (20.3%), E3b3 and R1a1*(xR1a1b) (both 11.9%). In Iraqis, 12 haplogroups were identified including J2*(xJ2f2) (29.7%) and J*(xJ2) (26.6%). The data suggest that the male Somali population is a branch of the East African population - closely related to the Oromos in Ethiopia and North Kenya - with predominant E3b1 cluster γ lineages that were introduced into the Somali population 4000-5000 years ago, and that the Somali male population has approximately 15% Y chromosomes from Eurasia and approximately 5% from sub-Saharan Africa.

Link

Racial Affinities of Prehistoric East Africans

Afrocentrists and Nordicists alike tend to assert that early East Africans were "Negroid". Since East Africa was the source of multiple migrations of early humans out of Africa, this allows the former to assert a "Negroid" stage in the evolution of Eurasians, or to postulate a later (mythological) stage of "Negroid" East African culture-bearers. Nordicists of the other hand, dissatisfied with the paucity to non-existence of genuine Sub-Saharan African genetic markers in Southeastern Europe have insinuated that Y-haplogroup E3b which originated in East Africa 26ky ago is "Negroid" or that mtDNA haplogroup M1 which according to some also originated in East Africa in Paleolithic times is also "Negroid".

W.W. Howells' study of world craniometric variation is especially relevant to the racial affinity of East Africans before the expansion of Negroids into the region. Howells studied some 2,500+ skulls from 28 populations of recent Homo sapiens based on 57 metric variables [1], including skulls from the Teita tribe of East Africa. These recent Teita tribesmen (and women) clustered with other Sub-Saharan Africans, indicating that (as is obvious) recent Kenyans belong primarily to the Negroid race.

Howells then studied prehistoric East Africans and other humans from around the world to determine whether or not they show any affinities with living races [2]. He did this to examine whether the morphological complexes of modern races can be discerned in remote times. Using the same multivariate approach he studied the Elmenteita, Nakuru and Willey's Kopje skulls from Kenya. His conclusion was that there is no racial continuity between recent Negroid East African skulls and these prehistoric remains, as the following passage illustrates ([2, p. 41]:

(...) The DISPOP [Dienekes: DISPOP is Howells' program] results here are not indicative of anything, except a general non-African nature for all these skulls. Display of POPKIN distances (infra) reinforces this and seems to find nearer neighbors among such more generalized populations as Peru, Guam, or Ainu, but also Europeans or even Easter Island.

Remembering that the Teita series (Bantu speakers of southeastern Kenya), and the recent East African skulls in table 4 above, do clearly exhibit African affiliations, it is fair to say, contra Rightmire, that there seems to be no clear continuity here in late prehistory. On the broad scale, looking at an "Out-of-Africa" scenario, one would expect that, in some region between southern and northeastern Africa, some differentiation would have been taking place within a Homo sapiens stock, evolving into something beginning to approximate later Sub-Saharan peoples on the one hand, and evolving in another direction on the other hand. East Africa would be a likely locale for appearance of the latter. So anyone is welcome to argue that this is what Elmenteita et al. are manifesting. The ensuing picture for East Africa, that is to say, would later have beeen changed through replacement by the expansion of Bantu or other "Negroid" tribes.

[1] Howells WW (1989) Skull shapes and the map: craniometric analyses in the dispersion of modern Homo. Peabody Museum Papers 79:1-189.
[2] Howells WW (1995) Who's Who in skulls: ethnic identification of crania from measurements. Peabody Museum Papers 82:1-108.