April 30, 2008
See also: mtDNA of Chad Basin populations, Inferring the population of origin of DNA evidence within the UK by allele-specific hybridization of Y-SNPs
Am J Hum Biol. 2008 Apr 28 [Epub ahead of print]
Mitochondrial DNA and craniofacial covariability of Chad Basin females indicate past population events.
Hájek M, Cerný V, Brůžek J.
The Chad Basin lies in the middle of the Sudanic African belt between the Sahara and the tropical rain forests. Its present-day settlement is a result of Holocene climatic changes and human immigrations from different parts of Africa. This study presents a statistical analysis of the relationships of physical features (stature and five main craniofacial measurements) and mitochondrial (mtDNA) haplogroup classifications in a sample of 282 adult individuals belonging to seven populations of different ethno-linguistic groups living in the Chad Basin. Drawing on the analysis of variance, we identified a female-specific DNA association between mtDNA haplogroup assignment and facial height. More specifically, the mtDNA haplogroups of East-African origin occur more frequently in females with relatively longer faces and, conversely, the mtDNA of West-African origin are found more frequently in females with lower faces. Interestingly, this kind of association is not found in the males of the same populations. Our interpretation refers mainly to population history; we suggest that facial height and mtDNA haplogroup co-variance in Chad Basin females reflects a long-term east-west population distribution in the past that made the facial differentiation possible.
Am J Hum Biol. 2008 Apr 28 [Epub ahead of print]
The mtDNA ancestry of admixed Colombian populations.
Salas A, Acosta A, Alvarez-Iglesias V, Cerezo M, Phillips C, Lareu MV, Carracedo A.
A total of 185 individuals from Colombia were sequenced for the first hypervariable region (HVS-I) of the mitochondrial DNA (mtDNA) genome, and a subset of these individuals were additionally genotyped for the second hypervariable segment (HVS-II). These individuals were collected according to their "self-reported ethnicity" in Colombia, comprising "Mestizos," "Mulatos," and "Afro-Colombians." We used databases containing more than 4,300 Native American lineages, 6,800 Africans, and 15,600 Europeans for population comparisons and phylogeographic inferences. We observe that Mulatos and Afro-Colombians have a dominant African mtDNA component, whereas Mestizos carry predominantly Native American haplotypes. All the populations analyzed have high diversity indices and there are no signatures of dramatic genetic drift episodes. Central and South America are the main candidate source populations of the Colombian Native American lineages, whereas west-central, southwest, and southeast Africa are the main original mtDNA sources for the African Colombian mtDNAs. We found that our results differ from those obtained in other studies for the same "population groups" in terms of haplogroup frequencies. This observation leads us to conclude that (i) self-reported ancestry is not a reliable proxy to indicate an individual's "ethinicity" in Colombia, (ii) our results do not support the use of outmoded race descriptions (Mestizos, Mulatos, etc.) mainly because these labels do not correspond to any genetically homogeneous population group, and (iii) studies relying on these terms to describe the population group of the individual, which then treat them as genetically homogeneous, carry a high risk of type I error (false positives) in medical studies in this country and of misinterpretation of the frequency of observed variation in forensic casework.
A Genetic Signal of Central European Celtic Ancestry:Preliminary Research Concerning Y-Chromosome Marker S28 / U152
David K. Faux
"The goal of the present study is to use historical references (via the Greco – Roman Classical authors), plus linguistic and archaeological data, to link the Hallstatt and La Tene Celtic people of Central Europe to a Y-chromosome marker, S28 / U152. The hypothesis under consideration is that all who are S28 positive (thus placed in the phylogenetic haplogroup R1b1c10 / R1b1b2h) are living descendants of these ancient Celtic people who emerged from an Alpine European homeland; with the possible exception of distantly related folk who reside along the Mediterranean coast south to Sardinia."
April 29, 2008
The best estimate of the burial age of EYJR 2 is an age range that encompasses the uncertainty in the model EU-ESR ages of EYJR 2: 88–132 ka. We use this estimate to infer the age of the associated finds, including EH06.This ties in well with the idea of persistence of archaic features within African populations long after the appearance of more modern features, with the fully modern Omo coming before Homo sapiens idaltu from Herto, with its mix of archaic and modern traits, coming before more archaic EH06 from Lake Eyasi.
If the latter possibility is correct, EH06 shows an interesting continuation of the primitive features shown in Eyasi 1, in a period for which other areas have yielded, from a morphological standpoint, substantially more modern-looking specimens.
These modern-looking features are defined in broadly contemporary hominids by the expansion of the frontal area of the skull, with a more elevated and rounder slope of the frontal bone, together with a reduction of the supraorbital torus, supratoral area, and postorbital constriction. These are some of the features that morphologically differentiate Homo sapiens from earlier hominids. These features can be observed on the Omo and Herto crania (Ethiopia) and the Ngaloba (Tanzania), Jebel Irhoud (Morocco) and Florisbad (South Africa) crania, dated between 265,000 and 120,000 years ago ([Wolpoff, 1999], [White et al., 2003] and [McDougall et al., 2005]).
Journal of Human Evolution doi:10.1016/j.jhevol.2008.02.002
A new archaic Homo sapiens fossil from Lake Eyasi, Tanzania
M. Domínguez-Rodrigo et al.
April 27, 2008
April 26, 2008
Volume 59, Issue 1, 7 March 2008, Pages 1-26
Variability of the Upper Palaeolithic skulls from Předmostí near Přerov (Czech Republic): Craniometric comparison with recent human standards
J. Velemínská et al.
One of the largest skeletal series of the Upper Palaeolithic period from Předmostí was destroyed during the Second World War, but the study of this material continues up to the present. The discovery of Matiegka's original photographic documentation on glass plates [Velemínská et al., 2004. The use of recently re-discovered glass plate photo-documentation of those human fossil finds from Předmostí u Přerova destroyed during World War II. J. Nat. Mus. Nat. Hist. Ser. 173, 129–132] gives an opportunity to perform a new and detailed craniometric analysis of five adult skulls in their lateral projection.
The craniometric data were analysed using specialised Craniometrics software, and the analysis included morphological and dimensional comparisons with current Central European norms. The aim of the study was not only to monitor the skull shape as a whole, but predominantly, to evaluate the size and shape of various parts of the splanchnocranium.
The Upper Palaeolithic skulls are significantly longer, and male skulls are also higher than the current norms. The crania of anatomically modern humans are characterised by two general structural features: mid-lower facial retraction and neurocranial globularity. The height of the face of the Palaeolithic skulls corresponds to that of the current Central European population. The face has a markedly longer mandibular body (3–4 SD), while female mandibular rami are shorter. The skulls are further characterised by a smaller gonial angle, the increased steepness of the mandibular ramus, and the greater angle of the chin. These changes in the size and shape associated with anterior rotation of the face produce a strong protrusion of both jaws, but the sagittal inter-maxillary relationships remain unchanged. The observed facial morphology is similar to the Czech Upper Palaeolithic skulls from Dolní Věstonice.
This study confirms the main diachronic changes between skulls of Upper Palaeolithic and present-day human populations.
April 25, 2008
It is common to distinguish between Africans and non-Africans, with the former being much more genetically diverse than the latter. But, the real "gap" in human origins seems to be between the really old Africans ("Paleoafricans") and the rest ("Afrasians").Now, a new paper has come along that provides further support for the ancient split among humans in Africa, and its more recent "healing".
The Paleoafrican element is entirely confined to Africa, while the Afrasian one is found in both Africa and Eurasia. Indeed, modern humans can be entirely split into two groups: (i) a group of "pure" Afrasians which includes all non-Africans, and (ii) a group of Afrasian-Paleoafricans which includes all non-Caucasoid Africans. Human groups of entirely Paleoafrican origin, unhybridized with the younger Afrasians are no longer in existence.
The Afrasians are a recent branch of humankind, and one which was for a great length of time separated reproductively from the Paleoafricans. This accounts for the reduced genetic diversity of Eurasians who are descended entirely from the Afrasian branch; by contrast, Sub-Saharan Africans and East Africans are the result of the intermixture of the Afrasians with the Paleoafricans, and this accounts for the high genetic diversity and antiquity of these populations.
The BBC has a story on this.
Ancient humans started down the path of evolving into two separate species before merging back into a single population, a genetic study suggests.The American Journal of Human Genetics doi:10.1016/j.ajhg.2008.04.002
The genetic split in Africa resulted in distinct populations that lived in isolation for as much as 100,000 years, the scientists say....
"We don't know how long it takes for hominids to fission off into separate species, but clearly they were separated for a very long time," said Dr Spencer Wells, director of the Genographic Project.
"They came back together again during the Late Stone Age - driven by population expansion."...
Dr Wells told BBC News: "Once this population reached southern Africa, it was cut off from the eastern African population by these drought events which were on the route between them."
Modern humans are often presumed to have originated in East Africa and then spread out to populate other areas. But the data could equally support an origin in southern Africa followed by a migration to East and West Africa.
The genetic data show that populations came back together as a single, pan-African population about 40,000 years ago.
This renewed contact appears to coincide with the development of more advanced stone tool technology and may have been helped by more favourable environmental conditions.
"[The mixing] was two-way to a certain extent, but the majority of mitochondrial lineages seem to have come from north-eastern Africa down to the south," said Spencer Wells.
The Dawn of Human Matrilineal Diversity
Doron M. Behar et al.
The quest to explain demographic history during the early part of human evolution has been limited because of the scarce paleoanthropological record from the Middle Stone Age. To shed light on the structure of the mitochondrial DNA (mtDNA) phylogeny at the dawn of Homo sapiens, we constructed a matrilineal tree composed of 624 complete mtDNA genomes from sub-Saharan Hg L lineages. We paid particular attention to the Khoi and San (Khoisan) people of South Africa because they are considered to be a unique relic of hunter-gatherer lifestyle and to carry paternal and maternal lineages belonging to the deepest clades known among modern humans. Both the tree phylogeny and coalescence calculations suggest that Khoisan matrilineal ancestry diverged from the rest of the human mtDNA pool 90,000-150,000 years before present (ybp) and that at least five additional, currently extant maternal lineages existed during this period in parallel. Furthermore, we estimate that a minimum of 40 other evolutionarily successful lineages flourished in sub-Saharan Africa during the period of modern human dispersal out of Africa approximately 60,00070,000 ybp. Only much later, at the beginning of the Late Stone Age, about 40,000 ybp, did introgression of additional lineages occur into the Khoisan mtDNA pool. This process was further accelerated during the recent Bantu expansions. Our results suggest that the early settlement of humans in Africa was already matrilineally structured and involved small, separately evolving isolated populations.
April 24, 2008
The “warrior burials”, “burials with bronzes” and the single-chamber tombs (tombs of Mainland architecture) are not necessarily associated with Mainlanders. In fact, none of the examined individuals from these LMII–IIIA1 and LMIIIA2 tombs was non-local at Knossos that would be expected based upon the tested theory.Journal of Archaeological Science doi:10.1016/j.jas.2008.03.006
“Mycenaean” political domination of Knossos following the Late Minoan IB destructions on Crete: negative evidence from strontium isotope ratio analysis (87Sr/86Sr)
Strontium isotope ratio analysis of human dental enamel and bone is applied to investigate a highly debated question of population movement and cultural discontinuity in Prehistoric Aegean Archaeology. The Late Minoan IB (ca. 1490/1470 BC) destructions on Crete are succeeded by cultural upheaval. The novel cultural features that appear at Knossos (Crete) in this period have forerunners in the Mainland. In Cretan context, the Linear B writing system, the funerary architecture and burial practices of the Mainland style are interpreted as evidence of an actual “Mycenaean” long-term settlement and political domination of Knossos. Human skeletal material from tombs that are associated with non-locals from the Mainland based upon the material culture is analysed to measure 87Sr/86Sr. The results of the analysis show that all the examined individuals from the Knossos tombs were born locally.
April 23, 2008
Origin and evolution of two Yugur sub-clans in Northwest China: a case study in paternal genetic landscape.
Zhou R, Yang D, Zhang H, Yu W, An L, Wang X, Li H, Xu J, Xie X.
Background: Yugur is an ethnic group that was officially identified by the Chinese Government in 1953. Within the population there are two sub-clans distinctly identified as the Eastern Yugur and Western Yugur, partly because they have different local languages. Aim: A parentage comparison was conducted between the two sub-clans to investigate their genetic relationship. Subjects and methods: Male subjects were chosen from the two clans to investigate their paternal genetic landscape through typing 14 single nucleotide polymorphisms (SNP) and 12 short tandem repeats (STR) of the Y chromosome. Results: Significant differences were revealed between the sub-clans at the haplogroup level. Genetic divergence was also observed by analyses of multidimensional scaling (MDS) and principal components (PC). Genetically, the Eastern Yugur are closer to the Han Chinese and Mongolian people than the Western Yugur. The Uygur people, who share a common ancestor (ancient Huihu) with the Yugur, were genetically separate from both sub-clans of Yugur. Moreover, the constructed phylogenetic network for haplogroup O provided further evidence that the two Yugur sub-groups present an underlying genetic difference. Conclusion: Overall, the diffusion of Mongolians during the Mongol Period has affected the Eastern Yugur more than the Western Yugur. The genetic contribution of the Han people to the Eastern Yugur seems to be more pronounced than to the Western Yugur. Besides the two different contributions referred to above, small population size and genetic drift have resulted in the genetic differentiation of the current sub-clans of Yugur.
Ann Hum Biol. 2008 Mar-Apr;35(2):212-31.
Mitochondrial DNA variation in Jordanians and their genetic relationship to other Middle East populations.
González AM, Karadsheh N, Maca-Meyer N, Flores C, Cabrera VM, Larruga JM.
Background: The Levant is a crucial region in understanding human migrations between Africa and Eurasia. Although some mitochondrial DNA (mtDNA) studies have been carried out in this region, they have not included the Jordan area. This paper deals with the mtDNA composition of two Jordan populations. Aim: The main objectives of this article are: first, to report mtDNA sequences of an urban and an isolate sample from Jordan and, second, to compare them with each other and with other nearby populations. Subjects and methods: The analyses are based on HVSI and HVSII mtDNA sequences and diagnostic RFLPs to unequivocally classify into haplogroups 101 Amman and 44 Dead Sea unrelated individuals from Jordan. Results: Statistical analysis revealed that, whereas the sample from Amman did not significantly differ from their Levantine neighbours, the Dead Sea sample clearly behaved as a genetic outlier in the region. Its outstanding Eurasian haplogroup U3 frequency (39%) and its south-Saharan Africa lineages (19%) are the highest in the Middle East. On the contrary, the lack ((preHV)1) or comparatively low frequency (J and T) of Neolithic lineages is also striking. Although strong drift by geographic isolation could explain the anomalous mtDNA pool of the Dead Sea sample, the fact that its mtDNA lineage composition mirrors, in geographic origin and haplogroup frequencies, its Y-chromosome pool, points to founder effect as the main cause. Ancestral M1 lineages detected in Jordan that have affinities with those recently found in Northwest but not East Africa question the African origin of the M1 haplogroup. Conclusion: Results are in agreement with an old human settlement in the Jordan region. However, in spite of the attested migratory spreads, genetically divergent populations, such as that of the Dead Sea, still exist in the area.
Pattison reviewed existing archaeological and genetic evidence, and conducted a new analysis of British DNA. Then, starting in 2001 and working backwards to pre-Roman times, Pattison calculated for each generation the net population growth and the origins of immigrants.The home page of John Pattison.
He concludes that people with Germanic origins came to Britain well before and after the early Anglo-Saxon period, and this long period of immigration can explain a relatively strong Germanic genetic signal today.
He adds that about 60% of the current British population still has some native Briton DNA, arguing against the idea, put forward by Mark Thomas at University College London and colleagues that Saxon invaders ethnically purged the country.
The textual and archaeological evidence collected by Thomas's team is also controversial, says Pattison.
Pattison, J.E., Is it Necessary to Assume an Apartheid-like Social Structure in Early Anglo-Saxon England; in press, Proceedings of the Royal Society B, April 2008.
UPDATE (Apr 23): The paper is now online. I like this kind of paper which tries to capture some of the complexity of human movements. Quite often in genetics one sees simplistic explanations of population origins. A prime example of this is the Paleolithic/Neolithic theory of European origins, that has been done to death, as if Europe and Asia weren't connected for tens of thousands of years before the emergence of agriculture and ten thousand years after it, allowing the movements of people both ways; all this complexity is shoved under the rug and origins are sought in a simple admixture event at the onset of the Neolithic.
In some cases, the nature of the migration makes a "repeat performance" unlikely, as in e.g., the arrival of the ancestors of Native Americans to the New World at a time when there was a land passage to it.
Quite often, the more dramatic events in a land's migration history tend to overshadow the more quiet and long-standing ones. The sudden arrival of a people in a short period of time, be them Anglo-Saxons in Great Britain, or European colonists in the New World, leaves a lasting impression, and is likely to be remembered well into the future, whereas the more limited and occasional movements of people from the same source areas but over longer periods of time do no attract attention: e.g., one tends to remember the Mayflower, the Puritans, etc. in the history of the colonization of North America, but the flow of British immigrants did not really cease for any substantial time ever since.
Pattison's paper makes two unrelated arguments against the thesis of Thomas et al. (2006). The first one is that the disadvantages suffered by indigenous Britons were a kind of incentive for them to adopt a Germanic identity; the second, that pre- and post- Anglo-Saxon migration can account for the Germanic Y-DNA in England, so the effects of the social situation during the time of the Anglo-Saxon migration need not have been so dramatic or even at all present.
The first claim:
A similar strategy was employed by the Moorish Caliphate in Medieval Spain: Jews and Christians were subject to a special tax—the jizya, which Muslims did not pay—in an endeavour to encourage non-Muslims to convert to Islam. According to the Qur’an (1990), non-Muslims who refused to pay the tax, were required to either convert to Islam or face the death penalty. The ethnicities of the people involved were of no concern.This does establish the essential difference between the regime of apartheid and the proposed situation in England at the time. In a South-African-style apartheid regime it was impossible for a member of the disadvantaged group (blacks) to become part of the advantaged one. In the Muslim case, it was possible for non-Muslims to become Muslims. Thus, in both cases there was discrimination, but in one case there were rigid boundaries between groups, while in the other there was not - at least not in the direction of Christian->Muslim conversion.
It should be noted, however, that while wherever Muslims and Christians co-existed, there was a steady discrimination against Christians, resulting in conversions, emigration, or massacres, all of which would have diminished the Christian element, at the same time, the Christians were a source of economic revenue for the regime, and the policy of the Muslim political authorities, e.g., the Sultan in the Ottoman Empire was not so much to eradicate the non-Muslim population, but rather to maintain it with enough freedom for it to be productive, but also with enough fear to be subservient to the dominant group.
The second issue is the real substance of the paper: was the social situation (whether one calls it apartheid or not) in early Anglo-Saxon England the cause of the significant Germanic element in modern Englishmen or not? That is an empirical question relying on the prevalence and arrival of Germanic elements in pre-Anglo-Saxon England and their subsequent arrival over the centuries. The paper does succeed in weakening the case for a substantial contribution of Anglo-Saxon/Briton social tensions in favor of the former's genetic success.
Is it necessary to assume an apartheid-like social structure in Early Anglo-Saxon England?
John E. Pattison
It has recently been argued that there was an apartheid-like social structure operating in Early Anglo-Saxon England. This was proposed in order to explain the relatively high degree of similarity between Germanic-speaking areas of northwest Europe and England. Opinions vary as to whether there was a substantial Germanic invasion or only a relatively small number arrived in Britain during this period. Contrary to the assumption of limited intermarriage made in the apartheid simulation, there is evidence that significant mixing of the British and Germanic peoples occurred, and that the early law codes, such as that of King Ine of Wessex, could have deliberately encouraged such mixing. More importantly, the simulation did not take into account any northwest European immigration that arrived both before and after the Early Anglo-Saxon period. In view of the uncertainty of the places of origin of the various Germanic peoples, and their numbers and dates of arrival, the present study adopts an alternative approach to estimate the percentage of indigenous Britons in the current British population. It was found unnecessary to introduce any special social structure among the diverse Anglo-Saxon people in order to account for the estimates of northwest European intrusion into the British population.
April 22, 2008
R1b: +0.80 with J2, -0.73 with I, -0.50 with R1a1
R1a1: -0.72 with J2, -0.50 with R1b
I: -0.73 with R1b
J2: +0.80 with R1b, -0.72 with R1a1
The main points of interest are:
- R1b and J2, vs. R1a1
- I vs. R1b
Next, I tried to find spatial patterns of variation, by correlating haplogroup frequencies with longitude and latitude.
Longitude (west-to-east): J2 (-0.82), R1b (-0.59), R1a1 (+0.72)
Latitude (south-to-north): R1b (-0.56), R1a1 (+0.53)
The southwestern association of R1b is consistent with Iberian or Italian origins; the northeastern association of R1a1, in the direction of Poland and the Baltic states also makes sense.
The strong western (-0.82) but weak southern (-0.37) orientation of J2 is unexpected if J2 came to Germany from the Balkans, but is consistent with a maritime mode of propagation of this haplogroup.
Interestingly, the J2 frequencies in French (5-17.3%), Dutch (6.2%) and Belgian (5.0%) samples (Table 17) all exceed the German average (4.0%), so they are probably consistent with this interpretation.
We really need to differentiate between J2a and J2b clades in this area, since J2a may hold the promise of reflecting maritime colonization (as its high frequency in coastal and island southern Europe suggests) or Roman descendants, while J2b may hold the signal of an expansion out of the Balkan area (See also Some aspects of J2 distribution). In terms of the latter, it is interesting to note that haplogroup E3b, which includes the common Balkan subclade E-V13 has a south-to-north spatial correlation in Germany (-0.41), but no detectable association with longitude
- p. 67: points (1) and (2) both refer to a north-south gradient of haplogroup R1b in the Balkans; one of them probably should refer to a different haplogroup (R1a?).
- Table 12 gives the frequency of haplogroups in Macedonians, identified in Maps 64-65 by the former Yugoslav Republic of Macedonia (fYROM). However, the ultimate source of the data is Semino et al. "The Genetic Legacy of Paleolithic Homo sapiens sapiens in Extant Europeans: A Y Chromosome Perspective", SCIENCE VOL 290 10 NOVEMBER 2000 where the sample is described as "20 Macedonians from northern Greece". Thus, the identification of the sample as Slavic and representing the fYROM is incorrect (cf. Pericic et al. Mol. Biol. Evol. 22(10):1964–1975.) where the "Macedonians" of Semino et al. (2000) are clearly listed as "Macedonian (Greek)" and their language is listed as "IE (Greek)".
A source of data from the fYROM is: Bosch et al. "Paternal and maternal lineages in the Balkans show a homogeneous landscape over linguistic barriers, except for the isolated Aromuns", Ann Hum Genet. 2006 Jul;70(Pt 4):459-87.
- Map 1 shows the expansion of N3 into Europe as taking place 12,000 years ago. According to Derenko et al. (J Hum Genet (2007) 52:763–770) there is substructure within N3, and the oldest N3 cluster expanded 8kya into Europe.
- The Subclades of mtDNA Haplogroup J and Proposed Motifs for Assigning Control-Region Sequences into these Clades
- A New Subclade of Y Haplogroup J2b
- Where Did European Men Come From (18MB pdf)
I recommend, in particular, the last article by Finnish scholar Kalevi Wiik, for its maps and tables of data if nothing else. I will probably comment on Wiik's attempt at synthesis of European origins based on Y-chromosome data.
April 19, 2008
This study finally shows that there are widespread regions of the genome where the genealogies relating our closest living relatives are not the same as the species relationships. At these loci, chimpanzees and bonobos trace their ancestry independently to the time before speciation from humans. These regions are interesting because they may provide information about the period 5–7 million years ago when human and chimpanzee ancestors separated.PLoS Genet 4(4): e1000057. doi:10.1371/journal.pgen.1000057
Analysis of Chimpanzee History Based on Genome Sequence Alignments
Jennifer L. Caswell et al.
Population geneticists often study small numbers of carefully chosen loci, but it has become possible to obtain orders of magnitude for more data from overlaps of genome sequences. Here, we generate tens of millions of base pairs of multiple sequence alignments from combinations of three western chimpanzees, three central chimpanzees, an eastern chimpanzee, a bonobo, a human, an orangutan, and a macaque. Analysis provides a more precise understanding of demographic history than was previously available. We show that bonobos and common chimpanzees were separated ~1,290,000 years ago, western and other common chimpanzees ~510,000 years ago, and eastern and central chimpanzees at least 50,000 years ago. We infer that the central chimpanzee population size increased by at least a factor of 4 since its separation from western chimpanzees, while the western chimpanzee effective population size decreased. Surprisingly, in about one percent of the genome, the genetic relationships between humans, chimpanzees, and bonobos appear to be different from the species relationships. We used PCR-based resequencing to confirm 11 regions where chimpanzees and bonobos are not most closely related. Study of such loci should provide information about the period of time 5–7 million years ago when the ancestors of humans separated from those of the chimpanzees.
April 17, 2008
Bayesian Inference of Errors in Ancient DNA Caused by Post Mortem Degradation
Ligia M. Mateiu and Bruce Rannala
Methods for extracting and amplifying sequences using ancient DNA (aDNA) can be prone to errors caused by post mortem modifications of the DNA strand. A new statistical method is developed for predicting errors in aDNA sequences caused by such processes. In addition to the canonical DNA substitution model parameters, a discrete Markov chain is used to describe nucleotide substitutions occurring via post mortem degradation of the aDNA sequences. A computer program, BYPASSR-degr, was developed implementing the method and was used in subsequent analyses of simulated datasets under the new model. Simulation studies show that the new method can be powerful and accurate in identifying damaged sites. The method is applied to analyze aDNA sequences of Etruscans, Adélie penguins and horses. No significant signals of degradation were observed at any sites of the aDNA sequences we analyzed.
April 16, 2008
Researchers have disagreed for decades about an issue that is only skin-deep: How quickly did the first modern humans who swept into Europe acquire pale skin? Now a new report on the evolution of a gene for skin color suggests that Europeans lightened up quite recently, perhaps only 6000 to 12,000 years ago. This contradicts a long-standing hypothesis that modern humans in Europe grew paler about 40,000 years ago, as soon as they migrated into northern latitudes. Under darker skies, pale skin absorbs more sunlight than dark skin, allowing ultraviolet rays to produce more vitamin D for bone growth and calcium absorption. "The [evolution of] light skin occurred long after the arrival of modern humans in Europe," molecular anthropologist Heather Norton of the University of Arizona, Tucson, said in her talk.This seems to be in agreement with accelerating recent selection in the human genome. The Science story is referring to the AAPA 2007 meeting. More from the Science story regarding the SLC24A5 gene:
The genetic origin of the spectrum of human skin colors has been one of the big puzzles of biology. Researchers made a major breakthrough in 2005 by discovering a gene, SLC24A5, that apparently causes pale skin in many Europeans, but not in Asians. A team led by geneticist Keith Cheng of Pennsylvania State University (PSU) College of Medicine in Hershey found two variants of the gene that differed by just one amino acid. Nearly all Africans and East Asians had one allele, whereas 98% of the 120 Europeans they studied had the other (Science, 28 October 2005, p. 601).This is a wonderful confirmation of Cavalli-Sforza's prediction about recent selection for skin color:
Either way, the implication is that our European ancestors were brown-skinned for tens of thousands of years--a suggestion made 30 years ago by Stanford University geneticist L. Luca Cavalli-Sforza. He argued that the early immigrants to Europe, who were hunter-gatherers, herders, and fishers, survived on ready-made sources of vitamin D in their diet. But when farming spread in the past 6000 years, he argued, Europeans had fewer sources of vitamin D in their food and needed to absorb more sunlight to produce the vitamin in their skin. Cultural factors such as heavier clothing might also have favored increased absorption of sunlight on the few exposed areas of skin, such as hands and faces, says paleoanthropologist Nina Jablonski of PSU in State College.Perhaps it was the larger population sizes made possible by farming that made it possible for the adaptive mutation to arise in one individual, or the mutation pre-existed in early agriculturalists.
I was looking through the book of abstracts (pdf) of this year's AAPA 2008, and another skin color-related abstract caught my attention:
Social classification, skin color, and genetic ancestry: a bio-cultural analysis of health disparities.
A.L. Non, C.C. Gravlee, C.J. Mulligan. Dept. of Anthropology, University of Florida.
Consistent disparities in health are well documented across racially defined groups for many complex diseases. Researchers have proposed both genetic and socio-cultural hypotheses to explain these disparities, but few studies combine both genetic and sociocultural data to test competing hypotheses directly. Here we address this problem in the context of debate about hypertension in populations of African descent. Some researchers suggest that people of greater African ancestry are genetically predisposed to develop high blood pressure. In support of this hypothesis, some researchers point to preliminary evidence of a modest association between blood pressure and genetic estimates of African ancestry. However, the association between ancestry and disease phenotypes may be due to residual confounding with environmental stressors such as discrimination and poverty. Our study, based on fieldwork in southeastern Puerto Rico, is the first to test these alternatives. We incorporate genetic measures of ancestry, genotyping of candidate genes, and an ethnographically derived measure of social classification that estimates how individuals’ color is perceived in everyday social interactions. We find that social classification of color, but not genetic ancestry, is associated with both systolic and diastolic blood pressure through an interaction with socioeconomic status. These findings emphasize the importance of gathering bociocultural data in studies on health and disease, rather than relying on skin color or genetic ancestry as a proxy for potential disease status.
Remember that while skin color is correlated with ancestry, the correlation is not perfect, i.e., a person with more Caucasoid than Negroid ancestry could in fact be darker than a person with more Negroid than Caucasoid ancestry (*). On top of that, the social perception of skin color may blur the picture even more, since skin color is not value-neutral in most multiracial societies. Thus, "social skin color" is two levels removed from "ancestry". What this abstract suggests is that "social skin color", rather than "ancestry" is the culprit for the disease discrepancies. Hopefully a paper on this will follow.
(*) "More" within reason, e.g., a 100% Caucasoid will be almost always lighter than a 100% Negroid.
Molecular Biology and Evolution, doi:10.1093/molbev/msn091
The Timing of Selection at the Human FOXP2 Gene
Graham Coop et al.
Krause et al. (2007) recently examined patterns of genetic variation at FOXP2 in two Neandertals. This gene is of particular interest because it is involved in speech and language and was previously shown to harbor the signature of recent positive selection. The authors found the same two amino-acid substitutions in Neandertals as in modern humans. Assuming that these sites were the targets of selection and no interbreeding between the two groups, they concluded that selection at FOXP2 occurred before the populations split, over 300Kya. Here, we show that the data are unlikely under this scenario but may instead be consistent with low rates of gene flow between modern humans and Neandertals. We also collect additional data and introduce a modeling framework to estimate levels of modern human contamination of the Neandertal samples. We find that, depending on the assumptions, additional control experiments may be needed to rule out contamination at FOXP2.
April 15, 2008
First, I looked at the correlation between the frequencies of occurrence of different haplogroups, limiting myself to haplogroups E3b1, I1a, I1b, J2, N2, N3, R1a, R1b3. For each haplogroup, I report the correlations which are at least 0.5 in absolute value (either positive or negative).
I1a: -0.56 with R1a
I1b: -0.76 with N3, -0.66 with N2
N2: -0.66 with I1b
N3: -0.76 with I1b, -0.66 with R1a
R1a: -0.66 with N3, -0.54 with I1a
The main points of interest are:
- I1a vs. R1a
- I1b vs. N3/N2
- R1a vs. N3
Longitude (west-to-east): R1a (-0.51), N2 (+0.56)
Latitude (south-to-north): I1b (-0.87), R1a (-0.57), N2 (+0.61), N3 (+0.79)
These observations suggest that the most striking features of the Russian Y-DNA landscape are the contrast between southern haplogroup I1b, and southwestern haplogroup R1a on the one hand, and northern haplogroup N3, and northeastern haplogroup N2 on the other. Thus, as a first-order approximation, the title of the paper, "Two Sources of the Russian Patrilineal Heritage in Their Eurasian Context" is justified, the two sources being R1a/I1b dominated SW/S group, and the other being N2/N3 dominated NE/N group.
Within the SW/S group, there is some concordance between the frequencies of haplogroups R1a and I1b, with a correlation of +0.40. Similarly, for the NE/N group, the correlation between N3 and N2 is +0.47. This suggests the pre-existence of these two combinations, while leaving open the possibility that a two-source solution is not the whole story.
Results showed that clothing preferences in adolescence appeared to influence future mental health, with different effects apparent by gender. Bangladeshi girls for example were most likely to benefit from traditional clothing choices, and White British girls benefited from integrated clothing choices. In contrast to Bangladeshi girls, White British girls with traditional clothing preferences had a higher risk of ill mental health, and White British girls who preferred clothing from other cultural groups (assimilated) were at an even higher risk. Bangladeshi boys who entirely preferred wearing western clothing had a lower risk of mental health problems, and White British boys with integrated clothing choices had the lowest risk of mental health problems at follow up, with the highest risk being those with marginalised clothing choices. These findings were sustained even after further adjustment for place of birth, religious groups and number of years resident in the UK.So, the best choices seem to be: White British boy/girl: integrated clothing; Bangladeshi girl: traditional; Bangladeshi boy: western.
The worst choices are: White British boy: marginalised; White British girl: assimilated.
Feel free to add your €.02 about what all these terms actually mean. There is also a 2005 article on a similar subject by the same author: Kamaldeep Bhui et al. "Cultural identity, acculturation, and mental health among adolescents in east London’s multiethnic community." Journal of Epidemiology and Community Health 2005;59:296-302
April 13, 2008
Victor Villarreal, Robert Tarin, Vincent Vizachero, Scandanavian DNA Project, John Simpson".
Speaking of myself, the predictor was not as accurate as Whit Athey's Haplogroup Predictor, but of course this would depend on the algorithm used, and the Y-STR collection used, so you might have different results.
April 12, 2008
I don't have the paper (send it to me if you do!), but a question is: does increasing attractiveness result from more averaging, or from the selection pressure imposed by raters? We do know that facial averaging has a beautifying effect: really attractive faces are not average, but average faces tend to be attractive. One could determine the effect of the selection pressure -above and beyond that of averaging- by comparing faces evolved under pressure with randomly bred faces.
Laryngoscope. 2008 Apr 7 [Epub ahead of print]
Evolving Attractive Faces Using Morphing Technology and a Genetic Algorithm: A New Approach to Determining Ideal Facial Aesthetics.
Wong BJ, Karimi K, Devcic Z, McLaren CE, Chen WP.
OBJECTIVES:: The objectives of this study were to: 1) determine if a genetic algorithm in combination with morphing software can be used to evolve more attractive faces; and 2) evaluate whether this approach can be used as a tool to define or identify the attributes of the ideal attractive face. STUDY DESIGN:: Basic research study incorporating focus group evaluations. METHODS:: Digital images were acquired of 250 female volunteers (18-25 y). Randomly selected images were used to produce a parent generation (P) of 30 synthetic faces using morphing software. Then, a focus group of 17 trained volunteers (18-25 y) scored each face on an attractiveness scale ranging from 1 (unattractive) to 10 (attractive). A genetic algorithm was used to select 30 new pairs from the parent generation, and these were morphed using software to produce a new first generation (F1) of faces. The F1 faces were scored by the focus group, and the process was repeated for a total of four iterations of the algorithm. The algorithm mimics natural selection by using the attractiveness score as the selection pressure; the more attractive faces are more likely to morph. All five generations (P-F4) were then scored by three focus groups: a) surgeons (n = 12), b) cosmetology students (n = 44), and c) undergraduate students (n = 44). Morphometric measurements were made of 33 specific features on each of the 150 synthetic faces, and correlated with attractiveness scores using univariate and multivariate analysis. RESULTS:: The average facial attractiveness scores increased with each generation and were 3.66 (+0.60), 4.59 (+/-0.73), 5.50 (+/-0.62), 6.23 (+/-0.31), and 6.39 (+/-0.24) for P and F1-F4 generations, respectively. Histograms of attractiveness score distributions show a significant shift in the skew of each curve toward more attractive faces with each generation. Univariate analysis identified nasal width, eyebrow arch height, and lip thickness as being significantly correlated with attractiveness scores. Multivariate analysis identified a similar collection of morphometric measures. No correlation with more commonly accepted measures such as the length facial thirds or fifths were identified. When images are examined as a montage (by generation), clear distinct trends are identified: oval shaped faces, distinct arched eyebrows, and full lips predominate. Faces evolve to approximate the guidelines suggested by classical canons. F3 and F4 generation faces look profoundly similar. The statistical and qualitative analysis indicates that the algorithm and methodology succeeds in generating successively more attractive faces. CONCLUSIONS:: The use of genetic algorithms in combination with a morphing software and traditional focus-group derived attractiveness scores can be used to evolve attractive synthetic faces. We have demonstrated that the evolution of attractive faces can be mimicked in software. Genetic algorithms and morphing provide a robust alternative to traditional approaches rooted in comparing attractiveness scores with a series of morphometric measurements in human subjects.
Computational models of facial attractiveness judgments.
Bronstad PM, Langlois JH, Russell R.
We designed two computational models to replicate human facial attractiveness ratings. The primary model used partial least squares (PLS) to identify image factors associated with facial attractiveness from facial images and attractiveness ratings of those images. For comparison we also made a model similar to previous models of facial attractiveness, in that it used manually derived measurements between features as inputs, though we took the additional step of dimensionality reduction via principal component analysis (PCA) and weighting of PCA dimensions via a perceptron. Strikingly, both models produced estimates of facial attractiveness that were indistinguishable from human ratings. Because PLS extracts a small number of image factors from the facial images that covary with attractiveness ratings of the images, it is possible to determine the information used by the model. The image factors that the model discovered correspond to two of the main contemporary hypotheses of averageness judgments: facial attractiveness and sexual dimorphism. In contrast, facial symmetry was not important to the model, and an explicit feature-based measurement of symmetry was not correlated with human judgments of facial attractiveness. This provides novel evidence for the importance of averageness and sexual dimorphism, but not symmetry, in human judgments of facial attractiveness.
April 11, 2008
Transformation of body and head shape in Moscow schoolchildren: secular aspects
Based on the results of several successive cross-sectional studies of Moscow schoolchildren, secular changes in body and head dimensions have been investigated.Data on children from 8 to 17 measured in the 1970’s, 1980’s and 1990’s (all in all about 10,000 individuals) have been compared. Some historical data on growth and development of children from the 1940’s and 1960’s have also been used for comparative purposes. [...] Possible causes of debrachicephalization are discussed. The argument is that this is a part of astenization and leptosomization processes, which go along with secular changes. This trend is revealed not only by recent data but also in the course of human evolution (Khrissanfova, 2002). Distribution of somatotypes (evaluated by Shtefko-Ostrovsky method) show the increasing frequencies of the so-called “astenoid”(ectomorph) type in the latest series (particularly in the 1990’s). The analysis of intra-group variability has shown that among somatotypes the most pronounced secular changes are typical for children of the astenoid type. They have the highest values of canonic correlation coefficients between head and face, and body measurements. This may suggest a “resonance” response of this particular type to secular changes.
European Journal of Human Genetics advance online publication 9 April 2008; doi: 10.1038/ejhg.2008.70
Reconstructing the phylogeny of African mitochondrial DNA lineages in Slavs.
Malyarchuk BA, Derenko M, Perkova M, Grzybowski T, Vanecek T, Lazur J.
To elucidate the origin of African-specific mtDNA lineages, revealed previously in Slavonic populations (at frequency of about 0.4%), we completely sequenced eight African genomes belonging to haplogroups L1b, L2a, L3b, L3d and M1 gathered from Russians, Czechs, Slovaks and Poles. Results of phylogeographic analysis suggest that at least part of the African mtDNA lineages found in Slavs (such as L1b, L3b1, L3d) appears to be of West African origin, testifying to an opportunity of their occurrence as a result of migrations to Eastern Europe through Iberia. However, a prehistoric introgression of African mtDNA lineages into Eastern Europe (approximately 10 000 years ago) seems to be probable only for European-specific subclade L2a1a, defined by coding region mutations at positions 6722 and 12903 and detected in Czechs and Slovaks. Further studies of the nature of African admixture in gene pools of Europeans require the essential enlargement of databases of African complete mitochondrial genomes.
Evaluation of HapMap data in six populations of European descent
Per E Lundmark et al.
We studied how well the European CEU samples used in the Haplotype Mapping Project (HapMap) represent five European populations by analyzing nuclear family samples from the Swedish, Finnish, Dutch, British and Australian (European ancestry) populations. The number of samples from each population (about 30 parent-offspring trios) was similar to that in the HapMap sample sets. A panel of 186 single nucleotide polymorphisms (SNPs) distributed over the 1.5 Mb region of the GRID2 gene on chromosome 4 was genotyped. The genotype data were compared pair-wise between the HapMap sample and the other population samples. Principal component analysis (PCA) was used to cluster the data from different populations with respect to allele frequencies and to define the markers responsible for observed variance. The only sample with detectable differences in allele frequencies was that from Kuusamo, Finland. This sample also separated from the others, including the other Finnish sample, in the PCA analysis. A set of tagSNPs was defined based on the HapMap data and applied to the samples. The tagSNPs were found to capture the genetic variation in the analyzed region at r2>0.8 at levels ranging from 95% in the Kuusamo sample to 87% in the Australian sample. To capture the maximal genetic variation in the region, the Kuusamo, HapMap and Australian samples required 58, 63 and 73 native tagSNPs, respectively. The HapMap CEU sample represents the European samples well for tagSNP selection, with some caution regarding estimation of allele frequencies in the Finnish Kuusamo sample, and a slight reduction in tagging efficiency in the Australian sample.
April 10, 2008
Evolution and Human Behavior doi:10.1016/j.evolhumbehav.2007.12.009
Facial correlates of sociosexuality
Lynda G. Boothroyd et al.
Previous studies have documented variation in sexual behaviour between individuals leading to the notion of ‘restricted’ individuals (i.e., people who prefer long-term relationships) and ‘unrestricted’ individuals (i.e., people who are open to short-term relationships). This distinction is often referred to as sociosexual orientation. Observers have been previously found to distinguish sociosexuality from video footage of individuals, although the specific cues used have not been identified. Here we assessed the ability of observers to judge sexual strategy based specifically on cues in both facial composites and real faces. We also assessed how observers' perceptions of the masculinity/femininity and attractiveness of faces relate to the sociosexual orientation of the pictured individuals. Observers were generally able to identify restricted vs. unrestricted individuals from cues in both composites and real faces. Unrestricted sociosexuality was generally associated with greater attractiveness in female composites and real female faces and greater masculinity in male composites. Although male observers did not generally associate sociosexuality with male attractiveness, female observers generally preferred more restricted males' faces (i.e., those with relatively strong preferences for long-term relationships). Collectively, our results support previous findings that androgenisation in men is related to less restricted sexual behaviour and suggest that women are averse to unrestricted men.
April 09, 2008
From the paper:
The overwhelming majority of mtDNA clusters, identified in Czechs, were of the western-Eurasian origin. The frequency of eastern-Eurasian (Mongoloid) mtDNA lineages in this population constituted 1.8% (haplogroups A, N9a, and M). African lineage (with the frequency of 0.4%) belonging to haplogroup L2a and marked by the +13803HaeIII variant was also detected.
Low frequency of Mongoloid mtDNA variant in Letts and Lithuanians suggests that Mongoloid component was probably not typical of Balto-Slavic protogene pool. Thus, it seems reasonable that accumulation of Mongoloid mtDNA lineages in Slavs and their ancestors was intensified only in the last 4000 years.
The highest frequencies of the Mongoloid component are typical of the Russian populations from Russian Pomor’e and Northwestern region. These populations, however, differ in the mtDNA haplogroup composition. It was established that assimilation of the indigenous pre-Slavic population of Eastern Europe by true Slavs was of great importance to the process of the development of Russian population.
It is suggested that after the decay of Avar Khaganate the populations included into it were assimilated by Slavic tribes . It is thereby suggested that rather high frequencies of eastern-Eurasian mtDNA lineages observed in the gene pools of some populations of Western and Southern Slavs (especially on the territoryof former Avar Khaganate) can be considered as a consequence of the process described.
Concerning the population of Eastern Europe, it should be noted that the forest zone of Eastern Europe was the area of intense population admixture . It seems likely, that formation of the complex of Mongoloid traits happened not later than in Upper Paleolithic. For this reason, it is suggested that East Siberian populations could have much time for migration to Eastern Europe . The number of such migrations still remains unclear, since in the northwest of Eastern Europe Mongoloid component is detected 10 000–8000 years ago; in Dnepr–Donetsk tribes, 7000–6000 years ago, and on the territory of Ivanovo oblast (Sakhtysh), 6000–5000 years ago [35, 36]. The data on mtDNA variation in Russian populations are consistent with anthropological data, since they point to the substantial differences in the frequencies of Mongoloid mtDNA lineages between the Russian populations of the Russian North, Northwest, and the central/southern regions of the European part of Russia (Table 3). We hope that future investigations would provide
the possibility of analyzing the chronology of the development of the Mongoloid component diversity in the gene pools of Russians and other Slavic populations.
Russian Journal of Genetics, 10.1007/s11177-008-3016-9
On the origin of Mongoloid component in the mitochondrial gene pool of Slavs
B. A. Malyarchuk, M. A. Perkova and M. V. Derenko
Abstract The data on mitochondrial DNA (mtDNA) restriction polymorphism in Czech population (n = 279) are presented. It was demonstrated that in terms of their structure, mitochondrial gene pools of Czechs and other Slavic populations (Russians, Poles, Slovenians, and Bosnians) were practically indistinguishable. In Czechs, the frequency of eastern-Eurasian (Mongoloid) mtDNA lineages constituted 1.8%. The spread of eastern-Eurasian mtDNA lineages belonging to different ethnolinguistic groups in the populations of Europe was examined. Frequency variations of these DNA lineages in different Slavic groups was observed, with the range from 1.2 and 1.6% in Southern and Western Slavs, respectively, to 1.3 to 5.2% in Eastern Slavs, the Russian population of Eastern Europe. The highest frequency of Mongoloid component was detected in the mitochondrial gene pools of Russian populations from the Russian North and the Northwestern region of Russia. This finding can be explained in terms of assimilation of northern-European Finno-Ugric populations during the formation of the Russian population of these regions. The origin of Mongoloid component in the gene pools of different groups of Slavs is discussed.
April 08, 2008
John H. Relethford
Abstract A variety of methods have been used to make evolutionary inferences based on the spatial distribution of biological data, including reconstructing population history and detection of the geographic pattern of natural selection. This article provides an examination of geostatistical analysis, a method used widely in geology but which has not often been applied in biological anthropology. Geostatistical analysis begins with the examination of a variogram, a plot showing the relationship between a biological distance measure and the geographic distance between data points and which provides information on the extent and pattern of spatial correlation. The results of variogram analysis are used for interpolating values of unknown data points in order to construct a contour map, a process known as kriging. The methods of geostatistical analysis and discussion of potential problems are applied to a large data set of anthropometric measures for 197 populations in Ireland. The geostatistical analysis reveals two major sources of spatial variation. One pattern, seen for overall body and craniofacial size, shows an east-west cline most likely reflecting the combined effects of past population dispersal and settlement. The second pattern is seen for craniofacial height and shows an isolation by distance pattern reflecting rapid spatial changes in the midlands region of Ireland, perhaps attributable to the genetic impact of the Vikings. The correspondence of these results with other analyses of these data and the additional insights generated from variogram analysis and kriging illustrate the potential utility of geostatistical analysis in biological anthropology.
"With very high accuracy, even for 20 generations, we can trace the populations of those individuals who are indeed represented in your genome," says Stanford computer science Assistant Professor Serafim Batzoglou, who led a team of graduate students to create HAPAA. They include co-lead authors Andreas Sundquist and Eugene Fratkin, as well as Chuong B. Do.Genome Research, DOI: 10.1101/gr.072850.107
Batzoglou points out that because the HapMap database, a genetic record of 270 individuals of Western European, West African and East Asian ancestry, is very small, HAPAA now can only generate an ethnic profile in terms of these populations.
Fratkin himself was able to verify that he is of European ancestry, but not that he is 1/64th Polish. But more genomics data will become available, the researchers said, which will further expand the software's ability to help people discern their roots.
For now the HAPAA software provides proof of this concept but limited utility given the small size of the HapMap database. In the future the software will benefit not only from having more individuals available for comparison, Batzoglou said, but also more detailed data about each individual. Today's genome samples track about 500,000 markers, or common genetic differences, but there are about 10 million candidates. Most individuals have about 3 million such specific differences. As genomics technology improves, he says, so will HAPAA's ability to infer ancestry from the data.
Effect of genetic divergence in identifying ancestral origin using HAPAA
Andreas Sundquist1, Eugene Fratkin1, Chuong B. Do, and Serafim Batzoglou
The genome of an admixed individual with ancestors from isolated populations is a mosaic of chromosomal blocks, each following the statistical properties of variation seen in those populations. By analyzing polymorphisms in the admixed individual against those seen in representatives from the populations, we can infer the ancestral source of the individual’s haploblocks. In this paper we describe a novel approach for ancestry inference, HAPAA (HMM-based analysis of polymorphisms in admixed ancestries), that models the allelic and haplotypic variation in the populations and captures the signal of correlation due to linkage disequilibrium, resulting in greatly improved accuracy. We also introduce a methodology for evaluating the effect of genetic divergence between ancestral populations and time-to-admixture on inference accuracy. Using HAPAA, we explore the limits of ancestry inference in closely related populations.
April 07, 2008
"Now that we have found that the program works well, we hope to implement it on a much larger scale, using hundreds of thousands of SNPs and thousands of individuals," said Drineas, who was funded by an NSF CAREER award. "The program will be a valuable tool for understanding our genetic ancestry and targeting drugs and other medical treatments because it might be possible that these can affect people of different ancestry in very different ways."PLoS Genet 3(9): e160. doi:10.1371/journal.pgen.0030160
Understanding our unique genetic makeup is a crucial step to unraveling the genetic basis for complex diseases. Although the human genome is 99 percent the same from human to human, it is that 1 percent that can have a major impact on our response to diseases, viruses, medications, and toxins. If researchers can uncover the minute genetic details that set each of us apart, biomedical research and treatments can be better customized for each individual, Drineas said.
This program will help people understand their unique backgrounds and aid historians and anthropologists in their study of where different populations originated and how humans became such a hugely diverse, global society.
The program was more than 99 percent accurate in trials and correctly identified the ancestry of hundreds of individuals. This included people from genetically similar populations (such as Chinese and Japanese) and complex genetic populations like Puerto Ricans who can come from a variety of backgrounds including Native American, European, and African ancestries.
"When we compared our findings to the existing datasets, only one individual was incorrectly identified and his background was almost equally close between Chinese and Japanese," Drineas said. Drineas explains that the results are preliminary, but extremely promising. The team is now working to test their program on a much larger data set.
PCA-Correlated SNPs for Structure Identification in Worldwide Human Populations
Peristera Paschou1*, Elad Ziv2,3,4, Esteban G. Burchard5,6, Shweta Choudhry7, William Rodriguez-Cintron8, Michael W. Mahoney9, Petros Drineas10
Existing methods to ascertain small sets of markers for the identification of human population structure require prior knowledge of individual ancestry. Based on Principal Components Analysis (PCA), and recent results in theoretical computer science, we present a novel algorithm that, applied on genomewide data, selects small subsets of SNPs (PCA-correlated SNPs) to reproduce the structure found by PCA on the complete dataset, without use of ancestry information. Evaluating our method on a previously described dataset (10,805 SNPs, 11 populations), we demonstrate that a very small set of PCA-correlated SNPs can be effectively employed to assign individuals to particular continents or populations, using a simple clustering algorithm. We validate our methods on the HapMap populations and achieve perfect intercontinental differentiation with 14 PCA-correlated SNPs. The Chinese and Japanese populations can be easily differentiated using less than 100 PCA-correlated SNPs ascertained after evaluating 1.7 million SNPs from HapMap. We show that, in general, structure informative SNPs are not portable across geographic regions. However, we manage to identify a general set of 50 PCA-correlated SNPs that effectively assigns individuals to one of nine different populations. Compared to analysis with the measure of informativeness, our methods, although unsupervised, achieved similar results. We proceed to demonstrate that our algorithm can be effectively used for the analysis of admixed populations without having to trace the origin of individuals. Analyzing a Puerto Rican dataset (192 individuals, 7,257 SNPs), we show that PCA-correlated SNPs can be used to successfully predict structure and ancestry proportions. We subsequently validate these SNPs for structure identification in an independent Puerto Rican dataset. The algorithm that we introduce runs in seconds and can be easily applied on large genome-wide datasets, facilitating the identification of population substructure, stratification assessment in multi-stage whole-genome association studies, and the study of demographic history in human populations.
Volume 29, Issue 2, March 2008, Pages 133-139
Height predicts jealousy differently for men and women
Abraham P. Buunk et al.
Because male height is associated with attractiveness, dominance, and reproductive success, taller men may be less jealous. And because female height has a curvilinear relationship with health and reproductive success (with average-height females having the advantages), female height may have a curvilinear relationship with jealousy. In Study 1, male height was found to be negatively correlated with self-reported global jealousy, whereas female height was curvilinearly related to jealousy, with average-height women reporting the lowest levels of jealousy. In Study 2, male height was found to be negatively correlated with jealousy in response to socially influential, physically dominant, and physically attractive rivals. Female height was negatively correlated with jealousy in response to physically attractive, physically dominant, and high-social-status rivals; in addition, quadratic effects revealed that approximately average-height women tend to be less jealous of physically attractive rivals but more jealous of rivals with “masculine” characteristics of physical dominance and social status.
April 06, 2008
Volume 29, Issue 2, March 2008, Pages 86-91
Adaptive preferences for leg length in a potential partner
Piotr Sorokowskia, and Boguslaw Pawlowski
It has been shown that height is one of the morphological traits that influence a person's attractiveness.next term To date, few studies have addressed the relationship between different components of height and physical previous termattractiveness.next term Here, we study how leg length influences previous termattractivenessnext term in men and women. Stimuli consisted of seven different pictures of a man and seven pictures of a woman in which the ratio between leg length and height was varied from the average phenotype by elongating and shortening the legs. One hundred men and 118 women were asked to assess the previous termattractivenessnext term of the silhouettes using a seven-point scale. We found that male and female pictures with shorter than average legs were perceived as less attractive by both sexes. Although longer legs appeared to be more attractive, this was true only for the slight (5%) leg length increase; excessively long legs decreased body previous termattractivenessnext term for both sexes. Because leg length conveys biological quality, we hypothesize that such preferences reflect the workings of evolved mate-selection mechanisms. Short and/or excessively long legs might indicate maladaptive biological conditions such as genetic diseases, health problems, or weak immune responses to adverse environmental factors acting during childhood and adolescence.
In the first step of the study, 30 men and women were presented with 100 different faces of Caucasian women, roughly of the same age, and were asked to judge the beauty of each face. The subjects rated the images on a scale of 1 through 7 and did not explain why they chose certain scores. Kagian and his colleagues then went to the computer and processed and mapped the geometric shape of facial features mathematically.Vision Research http://dx.doi.org/10.1016/j.visres.2007.11.007
Additional features such as face symmetry, smoothness of the skin and hair color were fed into the analysis as well. Based on human preferences, the machine "learned" the relation between facial features and attractiveness scores and was then put to the test on a fresh set of faces.
Says Kagian, "The computer produced impressive results -- its rankings were very similar to the rankings people gave." This is considered a remarkable achievement, believes Kagian, because it's as though the computer "learned" implicitly how to interpret beauty through processing previous data it had received.
A machine learning predictor of facial attractiveness revealing human-like psychophysical biases
Amit Kagian et al.
Recent psychological studies have strongly suggested that humans share common visual preferences for facial attractiveness. Here, we present a learning model that automatically extracts measurements of facial features from raw images and obtains human-level performance in predicting facial attractiveness ratings. The machine’s ratings are highly correlated with mean human ratings, markedly improving on recent machine learning studies of this task. Simulated psychophysical experiments with virtually manipulated images reveal preferences in the machine’s judgments that are remarkably similar to those of humans. Thus, a model trained explicitly to capture a specific operational performance criteria, implicitly captures basic human psychophysical characteristics.
April 05, 2008
The impact of the Austronesian expansion: evidence from mtDNA and Y-chromosome diversity in the Admiralty Islands of Melanesia
Manfred Kayser et al.
The genetic ancestry of Polynesians can be traced to both Asia and Melanesia, which presumably reflects admixture occurring between incoming Austronesians and resident non-Austronesians in Melanesia before the subsequent occupation of the greater Pacific; however, the genetic impact of the Austronesian expansion to Melanesia remains largely unknown. We therefore studied the diversity of non-recombining Y-chromosomal (NRY) and mitochondrial (mt) DNA in the Admiralty Islands, located north of mainland Papua New Guinea, and updated our previous data from Asia, Melanesia and Polynesia with new NRY markers. The Admiralties are occupied today solely by Austronesian-speaking groups, but their human settlement history goes back 20,000 years prior to the arrival of Austronesians about 3,400 years ago. On the Admiralties we found substantial mtDNA and NRY variation of both Austronesian and non-Austronesian origin, with higher frequencies of Asian mtDNA and Melanesian NRY haplogroups, similar to previous findings in Polynesia, and perhaps as consequence of Austronesian matrilocality. Thus, the Austronesian language replacement on the Admiralties (and elsewhere in Island Melanesia and coastal New Guinea) was accompanied by an incomplete genetic replacement that is more associated with mtDNA than with NRY diversity. These results provide further support for the "Slow Boat" model of Polynesian origins, according to which Polynesian ancestors originated from East Asia but genetically mixed with Melanesians before colonizing the Pacific. We also observed that non-Austronesian groups of coastal New Guinea and Island Melanesia had significantly higher frequencies of Asian mtDNA haplogroups than of Asian NRY haplogroups, suggesting sex-biased admixture perhaps as a consequence of non-Austronesian patrilocality. We additionally found that the predominant NRY haplogroup of Asian origin in the Admiralties (O-M110) likely originated in Taiwan, thus providing the first direct Y-chromosome evidence for a Taiwanese origin of the Austronesian expansion. Furthermore, we identified a NRY haplogroup (K-P79, also found on the Admiralties) in Polynesians that most likely arose in the Bismarck Archipelago, providing the first direct link between northern Island Melanesia and Polynesia. These results significantly advance our understanding of the impact of the Austronesian expansion and of human history in the Pacific region.
April 04, 2008
Using ancient mtDNA to reconstruct the population history of northeastern North America
Beth Alison Schultz Shook et al.
Mitochondrial DNA (mtDNA) was extracted and analyzed from the skeletal remains of 44 individuals, representing four prehistoric populations, and compared to that from two other prehistoric and several contemporary Native American populations to investigate biological relationships and demographic history in northeastern North America. The mtDNA haplogroup frequencies of ancient human remains from the Morse (Red Ocher tradition, 2,700 BP) and Orendorf (Mississippian tradition, 800 BP) sites from the Central Illinois River Valley, and the Great Western Park (Western Basin tradition, 800 BP) and Glacial Kame (2,900 BP) populations from southwestern Ontario, change over time while maintaining a regional continuity between localities. Haplotype patterns suggest that some ancestors of present day Native Americans in northeastern North America have been in that region for at least 3,000 years but have experienced extensive gene flow throughout time, resulting, at least in part, from a demic expansion of ancestors of modern Algonquian-speaking people. However, genetic drift has also been a significant force, and together with a major population crash after European contact, has altered haplogroup frequencies and caused the loss of many haplotypes.
April 03, 2008
Researchers, led by UO archaeologist, find pre-Clovis human DNA:
DNA from dried human excrement recovered from Oregon's Paisley Caves is the oldest found yet in the New World -- dating to 14,300 years ago, some 1,200 years before Clovis culture -- and provides apparent genetic ties to Siberia or Asia, according to an international team of 13 scientists.
The team’s extensively documented analyses on mitochondrial DNA -- genetic material passed on maternally -- removed from long-dried feces, known as coprolites, were published online April 3 in Science Express ahead of regular publication in the journal Science.
The DNA testing indicated that the feces belonged to Native Americans in haplogroups A2 and B2, haplogroups common in Siberia and east Asia.
Science DOI: 10.1126/science.1154116
DNA from Pre-Clovis Human Coprolites in Oregon, North America
M. Thomas P. Gilbert et al.
The timing of the first human migration into the Americas and its relation to the appearance of the Clovis technological complex in North America ca. 11-10.8 thousand radiocarbon years before present (14C ka B.P.) remains contentious. We establish that humans were present at Paisley 5 Mile Point Caves, south-central Oregon, by 12,300 14C yr. B.P., through recovery of human mtDNA from coprolites, directly dated by accelerator mass spectrometry. The mtDNA corresponds to Native American founding haplogroups A2 and B2. The dates of the coprolites are >1000 14C years earlier than currently accepted dates for the Clovis-complex.
POLITICAL STUDIES: 2008 VOL 56, 33–56
Immigration and the Imagined Community in Europe and the United States
Jack Citrin John Sides
Both Europe and the United States are confronting the challenges of economic and cultural integration posed by immigration. This article uses the ESS and CID surveys to compare transatlantic public opinion about immigrants and immigration.We find more tolerance for cultural diversity in the United States, but we also find that Americans, like Europeans, tend to overestimate the number of immigrants in their countries and tend to favor lower levels of immigration. The underpinnings of individual attitudes are similar in all countries and immigration attitudes are surprisingly unrelated to country-level differences in GDP, unemployment and the number and composition of the foreign born.An implication of these findings is that acceptance of higher levels of immigration, deemed by many to be an economic need, will require both more selective immigration policies and an emphasis on the cultural assimilation of newcomers.
April 02, 2008
The report is now online. Unfortunately, the supplementary information is not yet online.
I think that the Genographic Project has a lot of rewriting to do in their Atlas of the Human Journey given the proposed dates for the major haplogroups. For example, the oft-repeated claim that R1b has something to do with the Cro-Magnons is no longer tenable.
The supplementary material can be found here (pdf).
Genome Research DOI: 10.1101/gr.7172008
New binary polymorphisms reshape and increase resolution of the human Y chromosomal haplogroup tree
Tatiana M. Karafet et al.
Markers on the non-recombining portion of the human Y chromosome continue to have applications in many fields including evolutionary biology, forensics, medical genetics, and genealogical reconstruction. In 2002, the Y Chromosome Consortium published a single parsimony tree showing the relationships among 153 haplogroups based on 243 binary markers and devised a standardized nomenclature system to name lineages nested within this tree. Here we present an extensively revised Y chromosome tree containing 311 distinct haplogroups, including two new major haplogroups (S and T), and incorporating approximately 600 binary markers. We describe major changes in the topology of the parsimony tree and provide names for new and rearranged lineages within the tree following the rules presented by the Y Chromosome Consortium in 2002. Several changes in the tree topology have important implications for studies of human ancestry. We also present demography-independent age estimates for 11 of the major clades in the new Y chromosome tree.
A new Y-chromosome haplogroup tree will be published in Genome Research. Here is the public release:
The Y chromosome retains a remarkable record of human ancestry, since it is passed directly from father to son. In an article published online today in Genome Research (www.genome.org), scientists have utilized recently described genetic variations on the part of the Y chromosome that does not undergo recombination to significantly update and refine the Y chromosome haplogroup tree. The print version of this work will appear in the May issue of Genome Research, accompanied by a special poster of the new tree.
Hammer’s group integrated more than 300 new markers into the tree, which allowed the resolution of many features that were not yet discernable, as well as the revision of previous arrangements. “The major lineages within the most common African haplogroup, E, are now all sorted out, with the topology providing new interpretations on the geographical origin of ancient sub-clades,” describes Hammer. “When one polymorphism formerly described as unique, but recently shown to have reversed was replaced by recently reported markers, a sub-haplogroup of haplogroup O, the most common in China, was considerably rearranged,” explains Fernando Mendez, a co-author of the study.
In addition to improving the resolution of branches, the latest reconstruction of the tree allows estimates of time to the most recent common ancestor of several haplogroups. “The age of [haplogroup] DE is about 65,000 years, just a bit younger than the other major lineage to leave Africa, which is assumed to be about 70,000 years old,” says Hammer, describing an example of the fine resolution of age that is now possible. “Haplogroup E is older than previously estimated, originating approximately 50,000 years ago.”
Furthermore, Hammer explains that this work has resulted in the addition of two new major haplogroups, S and T, with novel insights into the ancestry of both. “Haplogroup T, the clade that Thomas Jefferson’s Y chromosome belongs to, has a Middle Eastern affinity, while haplogroup S is found in Indonesia and Oceania.”