April 29, 2005

Y chromosomes in Bosnia-Herzegovina

A very important new paper from a little-studied region of the world sheds some light on the genetic composition of Serbs, Croats and "Bosniacs" from Bosnia-Herzegovina. I will probably have more to say on this subject after this Easter season.

Annals of Human Genetics (OnlineEarly)

The Peopling of Modern Bosnia-Herzegovina: Y-chromosome Haplogroups in the Three Main Ethnic Groups

D. Marjanovic et al.


The variation at 28 Y-chromosome biallelic markers was analysed in 256 males (90 Croats, 81 Serbs and 85 Bosniacs) from Bosnia-Herzegovina. An important shared feature between the three ethnic groups is the high frequency of the "Palaeolithic" European-specific haplogroup (Hg) I, a likely signature of a Balkan population re-expansion after the Last Glacial Maximum. This haplogroup is almost completely represented by the sub-haplogroup I-P37 whose frequency is, however, higher in the Croats (~71%) than in Bosniacs (~44%) and Serbs (~31%). Other rather frequent haplogroups are E (~15%) and J (~7%), which are considered to have arrived from the Middle East in Neolithic and post-Neolithic times, and R-M17 (~14%), which probably marked several arrivals, at different times, from eastern Eurasia. Hg E, almost exclusively represented by its subclade E-M78, is more common in the Serbs (~20%) than in Bosniacs (~13%) and Croats (~9%), and Hg J, observed in only one Croat, encompasses ~9% of the Serbs and ~12% of the Bosniacs, where it shows its highest diversification. By contrast, Hg R-M17 displays similar frequencies in all three groups. On the whole, the three main groups of Bosnia-Herzegovina, in spite of some quantitative differences, share a large fraction of the same ancient gene pool distinctive for the Balkan area.


The impact of the Bantu in Africa

European Journal of Human Genetics (advance online publication)

Contrasting patterns of Y chromosome and mtDNA variation in Africa: evidence for sex-biased demographic processes

Elizabeth T Wood et al.

To investigate associations between genetic, linguistic, and geographic variation in Africa, we type 50 Y chromosome SNPs in 1122 individuals from 40 populations representing African geographic and linguistic diversity. We compare these patterns of variation with those that emerge from a similar analysis of published mtDNA HVS1 sequences from 1918 individuals from 39 African populations. For the Y chromosome, Mantel tests reveal a strong partial correlation between genetic and linguistic distances (r=0.33, P=0.001) and no correlation between genetic and geographic distances (r=-0.08, P>0.10). In contrast, mtDNA variation is weakly correlated with both language (r=0.16, P=0.046) and geography (r=0.17, P=0.035). AMOVA indicates that the amount of paternal among-group variation is much higher when populations are grouped by linguistics (ΦCT=0.21) than by geography (ΦCT=0.06). Levels of maternal genetic among-group variation are low for both linguistics and geography (ΦCT=0.03 and 0.04, respectively). When Bantu speakers are removed from these analyses, the correlation with linguistic variation disappears for the Y chromosome and strengthens for mtDNA. These data suggest that patterns of differentiation and gene flow in Africa have differed for men and women in the recent evolutionary past. We infer that sex-biased rates of admixture and/or language borrowing between expanding Bantu farmers and local hunter-gatherers played an important role in influencing patterns of genetic variation during the spread of African agriculture in the last 4000 years.


April 28, 2005

The evolution of altruistic punishment

Proc. Natl. Acad. Sci. USA, 10.1073/pnas.0500938102

Altruistic punishment and the origin of cooperation

James H. Fowler

How did human cooperation evolve? Recent evidence shows that many people are willing to engage in altruistic punishment, voluntarily paying a cost to punish noncooperators. Although this behavior helps to explain how cooperation can persist, it creates an important puzzle. If altruistic punishment provides benefits to nonpunishers and is costly to punishers, then how could it evolve? Drawing on recent insights from voluntary public goods games, I present a simple evolutionary model in which altruistic punishers can enter and will always come to dominate a population of contributors, defectors, and nonparticipants. The model suggests that the cycle of strategies in voluntary public goods games does not persist in the presence of punishment strategies. It also suggests that punishment can only enforce payoff-improving strategies, contrary to a widely cited "folk theorem" result that suggests that punishment can allow the evolution of any strategy.


Clicks and pygmies

Science reports on some exciting new findings from the 2005 Paleoanthropology meeting:
Human relations. Sarah Tishkoff and Floyd Reed of the University of Maryland, College Park, presented preliminary analyses of a massive data set on genetic variation in humans around the world, particularly Africans. Samples from more than 3000 people, including 2000 Africans, were processed at 1275 loci by a genotyping powerhouse, the Marshfield Clinic Research Foundation in Wisconsin. Tishkoff and Reed, who received the complete data set only 3 weeks ago, say it offers a powerful tool to uncover relationships among populations. For example, the data suggest that culturally distinct groups of Pygmies are more closely related to each other than to other Africans. The researchers also detected unique similarities in the peoples of Oceania and East Africa, lending support to the hypothesis of an early "southern route" of migration out of Africa, around the coast of India to Oceania and then Australia. Finally, they found ancient kinship among three groups of click speakers, supporting the idea that the click languages form a single, ancient language family
Addendum: Research page of Sarah Tishkoff.

April 27, 2005

How to eradicate drug production

International Journal of Drug Policy
Volume 16, Issue 2 , March 2005, Pages 81-91

Where have all the flowers gone?: evaluation of the Taliban crackdown against opium poppy cultivation in Afghanistan

Graham Farrell et al.


This study presents what we believe to be the first formal evaluation of the Taliban crackdown against opium poppy cultivation in Afghanistan. Afghanistan was the main source of the world's illicit heroin supply for most of the 1990s. From late 2000 and the year that followed, the Taliban enforced a ban on poppy farming via threats, forced eradication, and public punishment of transgressors. The result was a 99% reduction in the area of opium poppy farming in Taliban-controlled areas. The evaluation uses multiple comparison areas: the non-Taliban area of Afghanistan, neighbouring countries, the non-contiguous comparison area of Myanmar (Burma), and, the rest of the world. Alternative possible causes of the reduction such as drought, migration or changes in global opium markets are reviewed and excluded. It is concluded that the reduction in Afghan poppy cultivation was due to the enforcement action by the Taliban. Globally, the net result of the intervention produced an estimated 35% reduction in poppy cultivation and a 65% reduction in the potential illicit heroin supply from harvests in 2001. Though Afghan poppy growing returned to previous levels after the fall of the Taliban government, this may have been the most effective drug control action of modern times.


Muscular men and thin women

Body Image
Volume 2, Issue 1 , March 2005, Pages 81-86

Do representations of male muscularity differ in men's and women's magazines?

David A. Frederick et al.


Men overestimate the degree of muscularity that is attractive to women, and women overestimate the degree of thinness that is most attractive to men. Consistent with the thesis that sociocultural input influences such body type preferences and beliefs, we postulated that magazines aimed at a male audience would portray a more muscular male body ideal than would magazines aimed at a female audience. Systematic comparison of popular magazines (Cosmopolitan, Men's Health, Men's Fitness, and Muscle & Fitness) revealed that the ideal male body marketed to men is more muscular than the ideal male body marketed to women. We introduce the Physical Trait Overvaluation Hypothesis, which proposes that gender-specific media fuel emphasis on certain body parts in within-gender prestige competitions. The resulting competitive escalation creates a disconnect between the preferences of one gender and the personal aspirations of the other.


April 26, 2005

Somerled's Viking roots

DNA shows Celtic hero Somerled's Viking roots

A HISTORIC Celtic hero credited with driving the Vikings out of western Scotland was actually descended from a Norseman, according to research by a leading DNA expert.

According to traditional genealogies, Somerled, who is said to have died in 1164 after ousting the Vikings from Argyll, Kintyre and the Western Isles, was descended from an ancient royal line going back to when the Scots were living in Ireland.


Prof Sykes’ studies of three Scottish clans have also led to the conclusion that some 500,000 people alive today are descended from Somerled - a number only bettered by Genghis Khan, who, among historical figures studied to date, has an estimated 16 million living descendants.

The MacDonald, MacDougall and MacAllister clans all claim descent from Somerled and Prof Sykes found that between 25 and 45 per cent of them shared the same Y-chromosome, of a kind normally found in Norway but rare in Scotland and Ireland.

By analysing the rate of mutation in DNA samples from clan members, Prof Sykes was able to show that the Y-chromosome came from a common ancestor who lived roughly 1,000 years ago.

He then tested five chiefs from the clans and discovered they all shared the same chromosome, which convinced him that the common ancestor must be Somerled, Lord of the Isles, in keeping with clan histories.

Male/Female preferences for risk-taking

In a very interesting new study, researchers investigated the attitudes of men and women towards risk-takers. These were divided into "heroic" risk-takers, i.e., risk-takers with a practical purpose, of e.g., saving lives, vs. "non-heroic" risk-takers, e.g., playing dangerous sports. Furthermore, attitudes were assessed toward risk-taking potential mates compared to potential friends.

Both men and women liked heroic risk-takers as potential mates, and women did so more than men. Hence, heroes do get the girl. However, non-heroic risk-takers were avoided by both men and women as mates. Therefore, activities like playing dangerous sports are not generally seen as costly expressions of a strong individual, but rather as stupid.

For same sex friends, men preferred non-heroic risk takers, while women preferred non-heroic risk avoiders. Therefore, the tendency of men to take unnecessary risks may not be directed toward the opposite sex, but rather toward their own sex. However, men thought that women actually liked non-heroic risk takers, so it is quite possible that men take non-heroic risks to impress women - who are not, however, impressed.

Evolution and Human Behavior
Volume 26, Issue 2, March 2005, Pages 171-185

Attitudes toward heroic and nonheroic physical risk takers as mates and as friends

G. William Farthing


Several hypotheses about attitudes toward risk takers, derived from costly signaling theory (CST), were tested. Male and female participants evaluated the attractiveness of risk takers compared with risk avoiders as potential mates, and as potential same-sex friends, in 21 different scenarios. Both females and males preferred heroic physical risk takers as mates, with the preference being stronger for females. Contrary to predictions, for nonheroic physical risks (such as risky sports), both males and females preferred risk avoiders over risk takers as mates. However, for same-sex friends, males significantly preferred nonheroic physical risk takers, whereas females preferred risk avoiders. It was concluded that insofar as nonheroic risk taking by males is a costly signal, the signal is directed more toward fellow males than toward females. Preferences for risk takers were positively correlated with reported self risk-taking tendencies, but the correlation was significantly higher for friends than for mates for both heroic and nonheroic physical risks.

In a second study, both males and females accurately predicted the opposite sex's preferences for heroic risk takers as mates. However, males failed to predict females' preferences for nonheroic physical risk avoiders. Both males and females underestimated the opposite sex's preferences for drug risk avoiders.


April 25, 2005

Women don't know when they ovulate

This will be of particular interest to the proponents of "natural" contraception methods which depend on the woman's knowledge of when she is ovulating to avoid intercourse during the more fertile period of her menstrual cycle.

American Journal of Human Biology
Volume 17, Issue 3 , Pages 310 - 320

Validating signals of ovulation: Do women who think they know, really know?

Lynnette Leidy Sievert et al.


This study was carried out to test whether women who think they know when they ovulate, really know. Fifty-three women of age 18.7 to 46.1 (mean age 28.4 years) participated in initial interviews about ovulation. Criteria for recruitment included perceived ovulation, regular menstrual cycles, and not using hormonal contraception. Women collected and refrigerated urine samples from day 5 until they thought they ovulated. Samples collected within 48 h of the perceived signal were then tested for a pre-ovulatory LH surge. Of the 53 original participants, 36 women provided urine samples for 1-6 cycles, so that 87 cycles were tested. Subjective signals of ovulation varied between women and between cycles but included abdominal pain and changes in cervical discharge, libido, and mood. Of the 87 cycles tested, during which women identified one or multiple signals of ovulation, 37 of the 87 urine specimens tested positive for an LH surge for a concordance rate of 42.5%. Using the first tested cycle from the 36 women who provided urine specimens, 13 of those specimens demonstrated an LH surge, for a concordance rate of 36.1%. That rate dropped to 28% (7/25) when women who used basal body temperature as an ovulatory signal were excluded. Finally, the mean level of accuracy among the 15 women who contributed 3-6 urine specimens for testing was 48.9%. The results of this study demonstrate a low degree of concordance between LH surge and perceived ovulation among women who think they know when they ovulate. The most motivated study participants were right about half of the time. Although there is variation among women in their ability to know when they ovulate, this study suggests that, for most women, ovulation is concealed.


The rituals of the Krapina Neanderthals

Red Nova reports on rituals performed by Neanderthals from Krapina, Croatia. Ritual treatment of the dead is one of the differences which are believed to have differentiated Homo sapiens from Neanderthals, but these new findings indicate that Neanderthals performed elaborate, albeit gruesome, rituals for the dead.
After excavating a cache of Neandertal fossils about 100 years ago at Krapina Cave in what's now Croatia, researchers concluded that incisions on the ancient individuals' bones showed that they had been butchered and presumably eaten by their comrades. That claim has proved difficult to confirm. A new, high-tech analysis indicates that the Krapina Neandertals ritually dismembered corpses in ways that must have held symbolic meaning for the group-whether or not Neandertals ate those remains [...] Krapina 3 [DP: pictured below] and other skull remains exhibit marks made by slicing away the ears, removing the tongue, detaching the lower jaw, and skinning the head. Lower-body fossils contain incisions created by removing muscle from bones as well as abrasions caused by scrubbing fat and gristle off bones. Cuts on pelvic and leg bones indicate that bodies lay facedown during dismemberment.
The findings were announced in the 2005 meeting of the Palaeoanthropology Society. The program of the conference is available online as a pdf, and the presentation is titled "Cook, J. D. Frayer and J. Radovcic. New evidence for symbolic behavior by the Krapina Neandertals", although there is no abstract available on the site.

April 24, 2005

Spencer Wells responds (again)

Via an e-mail forwarded to the GENEALOGY-DNA-L list:
We will primarily be collecting males from the indigenous populations around the world, which will maximize the number of Y-chromosomes while providing mtDNA as well. It is also easier to study X-chromosome variation in men, since the X is only present in one copy and it is therefore easier to infer haplotypes.

The populations will be chosen through a process of consultation with elders and the people themselves. I have been in Australia for the past few days getting this started, and am off to Singapore and India this week. We will sample both ‘ethnically defined’ (by language, customs, etc.) and ‘geographically defined’ (i.e. if a group, such as the Kazaks of Central Asia, are widespread then we will attempt to sample roughly on a grid) groups.

Sampling from indigenous groups will be through blood draws, which will yield hundreds of micrograms of DNA. This amount of DNA if far more than we need for typing Y and mtDNA, and it will allow us to apply new markers to the study of migratory patterns in the future. Particularly as the HapMap data becomes available, new autosomal haplotype systems should provide great resolution for questions that are unanswerable using Y and mtDNA (remember that these only assess a tiny fraction of your complete genomic ancestry). The DNA will be stored at the regional center that collected it, and will be available for study in the future by all members of the scientific community – effectively a virtual, global biobank. These studies will only take place as collaborations, and the proposed genotyping must follow the guidelines for the study – e.g. only markers that tell us about historical or anthropological information. Also, the actual laboratory work will take place at the regional center(s) – one of our project goals is to build scientific capacity in the less developed countries (Brazil, South Africa, India, etc.) where we have centers. No medical research will ever be conducted using these samples, for reasons having to do with informed consent and intellectual property. We will release all of the anonymous data into the public domain as we analyze it. We feel that this information is part of the ‘commons’ of our species – it belongs to everyone – and no attempt will be made to patent it.

We will be testing every indigenous sample collected for Y and mtDNA. In the case of the former, a multiplex PCR technique will be used to type AT LEAST the 12 STR markers typed by Family Tree DNA. We will probably be typing more – perhaps as many as 20 – in the initial screen. We will also sequence HVR-1 in each individual. Initially, we will also SNP type every Y-chromosome and mtDNA to confirm the haplogroup. Once we have a sufficient database, we will probably be able to predict haplogroup affiliation with a high degree of precision, allowing us to simply type the STRs for most individuals. Over time new markers will be discovered – some perhaps by us, to answer specific questions – but the key will always be having access to the indigenous DNA samples to type these markers. These are the most valuable asset of the project, and we don’t have to limit ourselves to any particular markers – we’ll choose the best ones to answer the questions we are investigating.

The maps shown on the website atlas at the moment demonstrate the routes followed by the markers that will be reported in the public component at the moment. Over time we will add more routes (= subhaplogroups) as the information on them improves. Remember that this is a GLOBAL project of enormous logistical complexity, and therefore that we may not show all of the details of a well-studied region like Europe at this time. We will be improving the level of detail over the coming years, and European users in particular should see their routes become much more detailed. Purchasing a participant’s kit is like purchasing a ‘subscription to your genome’, and you will be able to check back every few months to see what has been updated in your profile.

Finally, the data collected from the public part of the project will allow us to add an enormous number of genotypes to the database, giving us the power to answer some key questions. For instance, at the moment there is no evidence for interbreeding with Neanderthals as modern humans migrated into western Europe, but this is based on only 15-20,000 individuals who have been genotyped. Will we find a rare Neanderthal lineage in the 234,000th sample we type? Also, the public samples will allow us to assess patterns of genetic variation in admixed populations. There are some interesting studies we hope to do with the US census data, comparing Y and mtDNA patterns to that database. So these samples really are part of the project, not simply a way to raise funds - although that is a great aspect as well. Most people I've spoken to love the fact that all of the net proceeds from their kit - slightly more than 20% of the $99.95 price - get plowed back into the research and Legacy project.

Spencer Wells

See the earlier response as well.

Hydrogen sulfide, hibernating mice, and the sleep of Epimenides

Three unrelated bits of information which -if combined- would make quite a good story.


Epimenides was a Cretan seer who is said to have slept in a cave for fifty-seven years. According to Diogenes Laertius:
He was sent by his father to the countryside to look for a sheep, and around noon he went to sleep in a cave, and he slept for fifty-seven years. He awoke after fifty seven years and started looking for the sheep, imagining that he had slept only for a short while.

Bad Air

Naturally occurring gases found in caves are; carbon dioxide (CO2), hydrogen sulfide (H2S), methane (CH4), nitrogen (N2), nitrogen oxides (NO) (NO2), and radon, Rn @ wt (C12) 222 or (O16) 222 @ no 86. [...] Hydrogen sulfide, (H2S)-- -is colorless, heavier then air, toxic and smells like rotten eggs at low concentrations. At high concentrations the sense of smell is deadened, and serious problems will result. Hydrogen sulfide can form from ground water and sulfides. If the slightest smell of rotten eggs is detected, leave immediately.


Science, Vol 308, Issue 5721, 518 , 22 April 2005

H2S Induces a Suspended Animation–Like State in Mice

Eric Blackstone et al.

Mammals normally maintain their core body temperature (CBT) despite changes in environmental temperature. Exceptions to this norm include suspended animation–like states such as hibernation, torpor, and estivation. These states are all characterized by marked decreases in metabolic rate, followed by a loss of homeothermic control in which the animal's CBT approaches that of the environment. We report that hydrogen sulfide can induce a suspended animation-like state in a nonhibernating species, the house mouse (Mus musculus). This state is readily reversible and does not appear to harm the animal. This suggests the possibility of inducing suspended animation-like states for medical applications.


April 23, 2005

Earlier presence of man in Britain

News story on an announcement presented in From Earthly Bowels into Light: The History of Geological Speleology and Cave Finds conference.

Ancient jaw bone raises questions over early man
New research has revealed Britain's oldest fragment of modern human - a jaw bone unearthed in the Westcountry - is 6,000 years older than previously thought [...] Their findings indicate the piece actually dates back between 37,000 and 40,000 years. [...]

Barry Chandler, assistant curator at the museum, where the jaw bone is currently on display, said the new conclusions posed fresh questions. He said: "If the jaw is anatomically modern - from humans known as Cro-Magnons as Keith believed - then these people spread across Europe, reaching Britain far earlier than is currently thought.

"If, however, Keith was wrong and the jaw is from the human species known as the Neanderthals we will have the first direct evidence of Neanderthals on mainland Britain. We hope to resolve this problem by extracting ancient DNA from one of the teeth."

Attractiveness and sexual activity

Evolution and Human Behavior Volume 26, Issue 2 , March 2005, Pages 186-201

Attractiveness and sexual behavior: Does attractiveness enhance mating success?

Gillian Rhodes et al.


If attractiveness is an important cue for mate choice, as proposed by evolutionary psychologists, then attractive individuals should have greater mating success than their peers. We tested this hypothesis in a large sample of adults. Facial attractiveness correlated with the number of short-term, but not long-term, sexual partners, for males, and with the number of long-term, but not short-term, sexual partners and age of first sex, for females. Body attractiveness also correlated significantly with the number of short-term, but not long-term, sexual partners, for males, and attractive males became sexually active earlier than their peers. Body attractiveness did not correlate with any sexual behavior variable for females. To determine which aspects of attractiveness were important, we examined associations between sexual behaviors and three components of attractiveness: sexual dimorphism, averageness, and symmetry. Sexual dimorphism showed the clearest associations with sexual behaviors. Masculine males (bodies, similar trend for faces) had more short-term sexual partners, and feminine females (faces) had more long-term sexual partners than their peers. Feminine females (faces) also became sexually active earlier than their peers. Average males (faces and bodies) had more short-term sexual partners and more extra-pair copulations (EPC) than their peers. Symmetric women (faces) became sexually active earlier than their peers. Given that male reproductive success depends more on short-term mating opportunities than does female reproductive success, these findings suggest that individuals of high phenotypic quality have higher mating success than their lower quality counterparts.


April 22, 2005

PACAP and the evolution of human cognition

New research has identified a gene contributing to human cognition and was under strong positive selection. Until now, the FOXP2 gene had been known to differentiate humans from other primates, and to be related with the origin of language. [Update: See also John Hawks' post on the subject]

Genetics (Published Articles Ahead of Print)

Accelerated Evolution of the PACAP Precursor Gene During Human Origin

Yinqiu Wang et al.


Pituitary adenylate cyclase-activating polypeptide (PACAP) is a neuropeptide abundantly expressed in the central nervous system, and involved in regulating neurogenesis and neuronal signal transduction. The amino acid sequence of PACAP is extremely conserved across vertebrate species, indicating a strong functional constraint during the course of evolution. However, through comparative sequence analysis, we demonstrated that the PACAP precursor gene underwent an accelerated evolution in the human lineage since the divergence from chimpanzees, and the amino acid substitution rate in humans is at least seven times faster than in other mammal species resulting from strong Darwinian positive selection. Eleven human-specific amino acid changes were identified in the PACAP precursors which are conserved from murine to African apes. Protein structural analysis suggested that a putative novel neuropeptide might have originated during human evolution and functioned in the human brain. Our data suggested that the PACAP precursor gene underwent adaptive changes during human origin and may contribute to the formation of human cognition.


More authoritative info on the Oxyrhynchus Papyri

Some more authoritative information is posted in the CLASSICS-L list. An excerpt:
The London press got wind of this (the unrolled Herculaneum papyrus of Epicurus' Peri physeos in the British Library is being done this week) and reported enthusiastically, if selectively. No mention, for example, was made of the success on the Bodleian Herculaneum papyrus (P.Herc. 118), now thereby revealed to be a Peri Epikourou or at any rate a pre-Philodemean history of the school. The article certainly should not have said (if it did) that all the papyri had been discovered yesterday, only that we made significant (and sufficiently exciting) advances in reading and confirmation of identifications with some, the same with some other pieces, while still others were identified for the first time, some standard classical authors, as usual, while others remain complete mysteries. Readings from some identified from earlier multi-spectral trials since 2002 were refined. The Oxyrhynchus texts will be published in The Oxyrhynchus Papyri, beginning with the next volume (LXIX), still scheduled for publication next month. An article on the technical aspects is planned for Scientific American.

The origin of domestic animals

Keats' Telescope posts a link to a study on the origin of domestic animals. The low level of mtDNA diversity in many domestic animals indicates that these are descended from only a few domestication events. However, modern domestic animals seem to also possess some evidence of genes of "wild" origin, indicating that after they were domesticated they did not become isolated genetically, but continued to be crossed with wild animals, either intentionally (by humans), or by accident.

Trends in Genetics
Volume 21, Issue 4 , April 2005, Pages 214-218

Genes of domestic mammals augmented by backcrossing with wild ancestors

Carles Vilà et al.

Both archaeological data and the presence of few mitochondrial DNA lineages suggest that most widespread domestic mammals (cattle, sheep, goats, pigs and dogs) derive from only a handful of domestication events. However, each of these species shows a high level of diversity at the nuclear genes of the major histocompatibility complex (MHC). Through simulations incorporating various degrees of population subdivision, growth rate and selection, we demonstrate that the numerous MHC DRB alleles that are present in modern domestic mammals implies that substantial backcrossing with wild ancestors, either accidental or intentional, has been important in shaping the genetic diversity of our domesticates. These results support the view that, contrary to common assumption, domestic and wild lineages might not have been clearly separated throughout their history.


Predynastic necropolis found in Egypt

Ancient necropolis found in Egypt
Archaeologists say they have found the largest funerary complex yet dating from the earliest era of ancient Egypt, more than 5,000 years ago.

The necropolis was discovered by a joint US and Egyptian team in the Kom al-Ahmar region, around 600 km (370 miles) south of the capital, Cairo.

Inside the tombs, the archaeologists found a cow's head carved from flint and the remains of seven people.

They believe four of them were buried alive as human sacrifices.

The remains survived despite the fact that the tombs were plundered in ancient times.

Egypt's chief archaeologist, Zahi Hawass, said the discovery would add greatly to knowledge of the elusive pre-dynastic period, when Egypt was first becoming a nation.

The complex is thought to belong to a ruler of the ancient city of Hierakonpolis in around 3600 BC, when it was the largest urban centre on the Nile river.

Egyptologists say the city probably extended its influence northwards defeating rival entities. The unification of Upper and Lower Egypt eventually led to the establishment of rule by the Pharaohs.

Excavations at the site started in 2000 under the leadership of Egyptologist Barbara Adams, who died in 2002.

The site contains some of the earliest examples of mummification found in Egypt.

April 21, 2005

Neolithic vs. Paleolithic effect on Europeans

Proceedings: Biological Sciences
ISSN: 0962-8452 (Paper) 1471-2954 (Online)

The effect of the Neolithic expansion on European molecular diversity

Mathias Currat and Laurent Excoffier


We performed extensive and realistic simulations of the colonization process of Europe by Neolithic farmers, as well as their potential admixture and competition with local Palaeolithic hunter–gatherers. We find that minute amounts of gene flow between Palaeolithic and Neolithic populations should lead to a massive Palaeolithic contribution to the current gene pool of Europeans. This large Palaeolithic contribution is not expected under the demic diffusion (DD) model, which postulates that agriculture diffused over Europe by a massive migration of individuals from the Near East. However, genetic evidence in favour of this model mainly consisted in the observation of allele frequency clines over Europe, which are shown here to be equally probable under a pure DD or a pure acculturation model. The examination of the consequence of range expansions on single nucleotide polymorphism (SNP) diversity reveals that an ascertainment bias consisting of selecting SNPs with high frequencies will promote the observation of genetic clines (which are not expected for random SNPs) and will lead to multimodal mismatch distributions. We conclude that the different patterns of molecular diversity observed for Y chromosome and mitochondrial DNA can be at least partly owing to an ascertainment bias when selecting Y chromosome SNPs for studying European populations.


The dating of Liujiang

Liujiang (pictured below, from Peter Brown's page) is the earliest anatomically modern human from East Asia.

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Journal of Human Evolution
Volume 43, Issue 6 , December 2002, Pages 817-829

U-Series dating of Liujiang hominid site in Guangxi, Southern China

Guanjun Shen et al.


It has been established that modern humans were living in the Levant and Africa ca. 100 ka ago. Hitherto, this has contrasted with the situation in China where no unequivocal specimens of this species have been securely dated to more than 30 ka. Here we present the results of stratigraphic studies and U-series dating of the Tongtianyan Cave, the discovery site of the Liujiang hominid, which represents one of the few well-preserved fossils of modern Homo sapiens in China. The human fossils are inferred to come from either a refilling breccia or a primarily deposited gravel-bearing sandy clay layer. In the former case, which is better supported, the fossils would date to at least ~68 ka, but more likely to ~111–139 ka. Alternatively, they would be older than ~153 ka. Both scenarios would make the Liujiang hominid one of the earliest modern humans in East Asia, possibly contemporaneous with the earliest known representatives from the Levant and Africa. Parallel studies on other Chinese localities have provided supporting evidence for the redating of Liujiang, which may have important implications for the origin of modern humans.


Y-chromosome Lineages from Portugal, Madeira and Açores

A very interesting new paper on Portuguese Y-chromosomes. Three important conclusions are derived from the study of Sub-Saharan African, E3b, and J1 lineages in Portugal. The Sub-Saharan component seems to be small (0.7%) unlike the corresponding mtDNA component. The E3b lineages are highly heterogeneous, and include various sub-types, including the Aegean E-M78 cluster α as well as North African E3b2 and Middle Eastern E3b3. Interestingly, the North African component seems to be primarily of earlier Berber rather than historical Moorish origin:
North African component at least for mtDNA, is mainly concentrated in the North of Portugal. The mtDNA and Y data indicate that the Berber presence in that region dates prior to the Moorish expansion in 711 AD. Our Y chromosome results are also consistent with a continuous and regular assimilation of Berbers in North of Portugal. This argues against previous interpretations of Moorish mediated contributions, based on Y chromosome data (Bosch et al. 2001; Pereira et al. 2000b; Cruciani et al. 2004) and provides an alternative view of an earlier Berber presence in the North of Portugal.

Finally, the J lineages in Portugal are mainly in the J2 clade, but there is a substantial presence of the J1 clade as well, which is found in Arabs and Jews and not as often in European populations. The Portuguese J1 chromosomes cluster around the Cohen Modal Haplotype, rather than the known modal haplotypes of the Arabs. Therefore, it seems probable that these were introduced by Sephardic Jews, rather than Arabs.

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Annals of Human Genetics (OnlineEarly)

Y-chromosome Lineages from Portugal, Madeira and Açores Record Elements of Sephardim and Berber Ancestry

Rita Gonçalves et al.


A total of 553 Y-chromosomes were analyzed from mainland Portugal and the North Atlantic Archipelagos of Açores and Madeira, in order to characterize the genetic composition of their male gene pool. A large majority (78-83% of each population) of the male lineages could be classified as belonging to three basic Y chromosomal haplogroups, R1b, J, and E3b. While R1b, accounting for more than half of the lineages in any of the Portuguese sub-populations, is a characteristic marker of many different West European populations, haplogroups J and E3b consist of lineages that are typical of the circum-Mediterranean region or even East Africa. The highly diverse haplogroup E3b in Portuguese likely combines sub-clades of distinct origins. The present composition of the Y chromosomes in Portugal in this haplogroup likely reflects a pre-Arab component shared with North African populations or testifies, at least in part, to the influence of Sephardic Jews. In contrast to the marginally low sub-Saharan African Y chromosome component in Portuguese, such lineages have been detected at a moderately high frequency in our previous survey of mtDNA from the same samples, indicating the presence of sex-related gene flow, most likely mediated by the Atlantic slave trade.


More on Oxyrhynchus Papyri

The "classical holy grail" or unholy hype?
With all of these questions about the article, I decided to wait until after my seminar today to write it up. I'm glad I did, because Martinez seemed fairly surprised and a bit skeptical about the news. Some of the papyrologists on the "PAPY list," the listserv where many papyrologists from around the world make announcements, ask questions, etc., were openly derisive of the article. Most of the criticisms that I've raised above were raised on the list, and none of the postings (there were only a handful so far, but by non-lightweights) were inclined to take the article's hyperbolic claims at face value.

Furthermore, the page that appears to describe the project referenced in the article looks more like a digital archiving project than a new imaging project, and it contains nothing that would support the claims made in the article. But maybe I've got the wrong page. I couldn't find anything by googling BYU, which is supposed to be involved in this.

So as of right now, the rest of the papyrological community is waiting to hear Dirk Obbink at Oxford either back up for disavow the claims made in the article. At the very best, the Independent's reporters are covering some kind of new imaging breakthrough in an extremely hyperbolic fashion. And at the worst, they're trying to make a major story out of 20-year-old news.

mtDNA of an early Danish sample

Sample assignments and nucleotide substitutions:

Free Image Hosting at www.ImageShack.us

Am J Phys Anthropol.
[Epub ahead of print]

mtDNA analysis of human remains from an early Danish Christian cemetery.

Rudbeck L et al.

One of Denmark's earliest Christian cemeteries is Kongemarken, dating to around AD 1000-1250. A feature of early Scandinavian Christian cemeteries is sex segregation, with females buried on the northern sides and males on the southern sides. However, such separation was never complete; in the few early Christian cemeteries excavated in Scandinavia, there were always a few males placed on the north side, and some females on the south side. At Kongemarken, several males with juxtaposed females were found on the north side of the cemetery. Thus, to evaluate possible kinship relationships, and more general questions of population affinity, we analyzed mitochondrial DNA extracted from nine individuals excavated in two different areas within the cemetery: one male and four females from Area 1, and one male and three females from Area 2. Using stringent laboratory protocols, each individual was unequivocally assigned to a mitochondrial haplogroup. A surprising amount of haplogroup diversity was observed (Area 1: 1 U7 (male), 1 H, 1 I, 1 J, and 1 T2; Area 2: 2 H, 1 I, and 1 T, with one H being male); even the three subjects of haplogroup H were of different subtypes. This indicates that no subjects within each area were maternally related. The observed haplogroup, U7, while common in India and in western Siberian tribes, was not previously observed among present-day ethnic Scandinavians, and haplogroup I is rare (2%) in Scandinavia. These observations suggest that the individuals living in the Roskilde region 1,000 years ago were not all members of a tightly knit local population and comprised individuals with genetic links with populations that were from much farther away.


April 19, 2005

DNA testing of Xinjiang mummies

Genetic testing reveals awkward truth about Xinjiang’s famous mummies
“I spent six months in Sweden last year doing nothing but genetic research,” Mair said from his home in the United States where he teaches at the University of Pennsylvania.

“My research has shown that in the second millennium BC, the oldest mummies, like the Loulan Beauty, were the earliest settlers in the Tarim Basin.

“From the evidence available, we have found that during the first 1,000 years after the Loulan Beauty, the only settlers in the Tarim Basin were Caucasoid.”

East Asian peoples only began showing up in the eastern portions of the Tarim Basin about 3,000 years ago, Mair said, while the Uighur peoples arrived after the collapse of the Orkon Uighur Kingdom, largely based in modern day Mongolia, around the year 842.

“Modern DNA and ancient DNA show that Uighurs, Kazaks, Krygyzs, the peoples of Central Asia are all mixed Caucasian and East Asian. The modern and ancient DNA tell the same story,” he said.

Mair hopes to publish his new findings in the coming months.

China has only allowed the genetic studies in the last few years, with a 2004 study carried out by Jilin University also finding that the mummies’ DNA had Europoid genes, further proving that the earliest settlers of Western China were not East Asians.
See also this 2004 study on ancient Central Asians from Kazakhstan which essentially agrees with the content of this story, and a paper on a modern Caucasoid-Mongoloid population from Xinjiang.

Habent Papam

Here is the fan club of the new Pope Benedict XVI where you can read some writings and other information of the man that will lead the Roman church. [At the moment: "The server is temporarily unable to service your request due to maintenance downtime or capacity problems."]

Three phylogeographic anomalies

In the last few years, the phylogeography of many clades of the human mtDNA and Y-chromosome systems has been adequately resolved, but there still exist several big remaining puzzles.

The first one is that of mtDNA haplogroup X, which has been addressed in a recent paper. This is a very ancient clade, which is found at low frequencies almost everywhere, and is divided into two subclades: X1 is found mainly in eastern and northern Africa, whereas X2 is found in northern Africa and everywhere else, including Native Americans. It is interesting that the X2 seems to have spread after the Last Glacial Maximum, and the Native American clade, X2a was an "early split": today's Siberian X2 seem to be recently derived from Western Eurasia than those of the ancient trek which brought X2 into the New World. It is fascinating that X2 was brought into the New World by some ancient expansion that did not leave any traces in the genes of modern inhabitants of the likely routes.

The second great puzzle is mtDNA haplogroup M1 which occurs in East and North Africa, West Asia and Southern Europe, but not apparently anywhere else. M1 is a branch of the mainly Asian macrohaplogroup M, which is of great antiquity in Asia and likely originated there. According to a recent abstract, Holden et al. indicate that M1 is found at high frequencies in East and Northern Africa but not in Sub-Saharan Africa, and hint that it may be linked to the Afro-Asiatic language family. This suggestion is reasonable, and in my opinion the correspondence between M1 and Y-chromosome haplogroup E3b is quite remarkable throughout the broad peri-Mediterranean region, with E3b also reaching high frequencies in Afro-Asiatic speakers.

The third puzzle is that of Y-chromosome haplogroup DE defined by the YAP mutation. The E clade of YAP encompasses the great majority of African Y-chromosomes, and is clearly split into a subclade, E3b which has a peri-Mediterranean distribution similar to that of the aforementioned M1, and all the rest, almost exclusively limited to Sub-Saharan Africa. The "brother" of E, is haplogroup D, which is found in such peoples as the Andamanese, the Tibetans, and the Ainu. At present it seems reasonable that E originated somewhere in Africa, but the origin of D is far from certain, as it is now found in certain "fringe" populations, but also in low frequencies among many Asians. Perhaps, D had a much more prevalent distribution in the past, but the expansion of later successful lineages, such as O, the main haplogroup found in East Asians today overwhelmed those earlier Asian populations. What about YAP itself? Dit it originate in Asia, where its D descendants are located, or in Africa, where its E descendants are? As late as 2003, we don't know, and no new research has appeared to shed light on this problem.

mtDNA of Lokomotiv Siberians from Lake Baikal

According to this paper:
authentic SNP data identifying the East Eurasian haplogroups A, C, D, F and G2a have been characterised for 28 of 37 (76%) Lokomotiv burials. Of these 28 individuals, subsequent mtDNA HVI sequencing identified five unique HVI lineages for eight of them. Another three individuals produced SNP profiles characteristic of macrohaplogroup N (i.e., -DdeI 10394 and -AluI 10397) and two of them were subsequently assigned to haplogroup U5a (16256, 16270) based on HVI sequence variants [...] The other N individual is also likely to be U5a but awaits confirmatory sequencing. The remaining six individuals were found to produce contaminant mtDNA variants and thus, were not included in this dataset.
Journal of Archaeological Science Volume 32, Issue 4, April 2005, Pages 619-634

Matrilineal affinities and prehistoric Siberian mortuary practices: a case study from Neolithic Lake Baikal

K.P. Mooder et al.


The ‘Lokomotiv’ cemetery in the Lake Baikal region of Siberia is considered to be the largest Neolithic cemetery in North Asia. A large degree of mortuary variability has been documented at Lokomotiv including striking differences in grave architecture, body treatment and grave good assemblages. The purpose of this study is to understand whether observed mortuary variability at Lokomotiv was used to indicate differential biological affinity for those buried in this cemetery. To answer this, we compared the distribution of matrilineally-inherited mitochondrial DNA (mtDNA) markers retrieved from Lokomotiv skeletal remains against various lines of archaeological evidence. Using a combined strategy of coding-region SNP and HVI sequence detection, we were able to produce mtDNA profiles for 31 of 37 Lokomotiv individuals. Our results to date suggest that while matrilineal affinities did not overtly shape the spatial organisation of Lokomotiv, they may have influenced the type of grave one was interred in and in certain cases, the type of mortuary treatment given to an individual. The most compelling differences in matrilineal affinity were found between group grave and single grave burials in one cluster of the cemetery and evoke a notion of intra-community power structure shaped by matrilineally-ascribed group membership. The findings from this study will be further explored with future enhancements to the archaeological and biological datasets for Lokomotiv as well as a contemporaneous Baikal region cemetery known as Shamanka II. In doing so, we hope to further illuminate the social complexities governing these prehistoric Siberian communities.


E-mail address change

Note the e-mail address change:

April 18, 2005

BBC on Oxyrhynchus Papyri

Via Rogue Classicism, a link to OXYRHYNCHUS - CITY OF THE SHARP NOSED FISH

More info on pre-sapiens ancestry in modern humans

Recently, I speculated about the possibility of finding that some humans may have ancestry older than that from recent African Homo sapiens, and soon after I read several new abstracts from AAPA which dealt with exactly the same topic, hinting that such ancestry is a fact. John Hawks, having attended the conference, also posts on this topic.
The study is a powerful blow against the case for a recent, exclusively African origin of modern humans. It doesn't demolish the case, since the arguments for a recent African origin extend to other aspects of the genetic record, but it is damaging and suggests that a lot of work should be reevaluated.
It does seem like the pendulum has begun to swing away from the pure Out-of-Africa theory, and towards two intriguing possibilities: that the case for Out-of-Africa may in fact have been overstated and modern humans originated somewhere else, or that some modern humans may in fact have deep pre-sapiens ancestry, in addition to their recent common ancestry.

ESHG Conference 2005

The European Society of Human Genetics conference (ESHG 2005) will take place next month, and several interesting presentations will take place. I am sure that many of these pieces of research will be published in the next year or so. I am personally looking forward to the new research from Fulvio Cruciani on haplogroups A, E, and R1b. Dr. Cruciani was the author of a very informative recent study on Y haplogroup E3b.

Damir /. Marjanovic -- P1186. Y-chromosome bi-allelic and STR markers in the three main ethnic groups of modern Bosnia-Herzegovina

Sanghamitra Sengupta -- P1216. Genescape of India, as Reconstructed from Polymorphic DNA Variation in the Y chromosome

Andrea Novelletto -- P1222. Y chromosomal variation in the Czech Republic

Fulvio Cruciani -- P1230. Molecular dissection of the Y chromosome haplogroups A, E and R1b

Andrey V. Khrunin -- P1232. Y-microsatellite polymorphism in Russian populations from nothern and southern regions of European part of Russia

Rita Khusainova -- P1241. Genetic structure of Eurasian populations based on Alu insertion data

Ildus Kutuev -- C78. Phylogeographic analysis of mtDNA and Y chromosome lineages in Caucasus populations

Modern technology and the Oxyrhynchus Papyri

Oxford scientists have made some incredibly exciting new discoveries in the Oxyrhynchus Papyri.
Decoded at last: the 'classical holy grail' that may rewrite the history of the world

For more than a century, it has caused excitement and frustration in equal measure - a collection of Greek and Roman writings so vast it could redraw the map of classical civilisation. If only it was legible.

Now, in a breakthrough described as the classical equivalent of finding the holy grail, Oxford University scientists have employed infra-red technology to open up the hoard, known as the Oxyrhynchus Papyri, and with it the prospect that hundreds of lost Greek comedies, tragedies and epic poems will soon be revealed.

In the past four days alone, Oxford's classicists have used it to make a series of astonishing discoveries, including writing by Sophocles, Euripides, Hesiod and other literary giants of the ancient world, lost for millennia. They even believe they are likely to find lost Christian gospels, the originals of which were written around the time of the earliest books of the New Testament.


Christopher Pelling, Regius Professor of Greek at the University of Oxford, described the new works as "central texts which scholars have been speculating about for centuries".

Professor Richard Janko, a leading British scholar, formerly of University College London, now head of classics at the University of Michigan, said: "Normally we are lucky to get one such find per decade." One discovery in particular, a 30-line passage from the poet Archilocos, of whom only 500 lines survive in total, is described as "invaluable" by Dr Peter Jones, author and co-founder of the Friends of Classics campaign.


The previously unknown texts, read for the first time last week, include parts of a long-lost tragedy - the Epigonoi ("Progeny") by the 5th-century BC Greek playwright Sophocles; part of a lost novel by the 2nd-century Greek writer Lucian; unknown material by Euripides; mythological poetry by the 1st-century BC Greek poet Parthenios; work by the 7th-century BC poet Hesiod; and an epic poem by Archilochos, a 7th-century successor of Homer, describing events leading up to the Trojan War. Additional material from Hesiod, Euripides and Sophocles almost certainly await discovery.

Oxford academics have been working alongside infra-red specialists from Brigham Young University, Utah. Their operation is likely to increase the number of great literary works fully or partially surviving from the ancient Greek world by up to a fifth. It could easily double the surviving body of lesser work - the pulp fiction and sitcoms of the day.

See also a different article on the same topic, and an older post on a different potential source of ancient writings, that of Herculaneum.

Non-Caucasoid admixture in Turks (corrected)

Note: I had previously stated that the Anatolian Y-chromosome sample was composed of 513 individuals. In fact, it was composed of 523, which alters the percentages somewhat.

An article on the origin of the Nogays from the Caucasus (Phylogeographic Analysis of Mitochondrial DNA in the Nogays: A Strong Mixture of Maternal Lineages from Eastern and Western Eurasia, pdf) a convenient characterization of the mtDNA of a sample of 218 Turks, taken from Richards 2000 (pdf).

In this sample, the following non-Caucasoid haplogroups were detected:
  • 2.78% of L (Negroid)
  • 0.46% of A (Mongoloid)
  • 0.46% of A (Mongoloid)
  • 1.39% of C (Mongoloid)
  • 1.85% of D (Mongoloid)
  • 0.46% of F (Mongoloid)
  • 0.46% of Y (Mongoloid)
Therefore, 2.78% of Negroid admixture and 5.08% of Mongoloid admixture, for a total of 7.86% non-Caucasoid admixture. There is an additional occurrence of 1.5% of lineages of Indian origin, which however should not be labeled as non-Caucasoid.

We can also examine the non-Caucasoid admixture in Turkish patrilineages, using the large sample of 513 Anatolian Turks published by Cinnioglu (pdf), and which I previously analyzed for a different purpose here.
  • 0.38% of A (Negroid)
  • 0.19% of E3a (Negroid)
  • 0.38% of E3* (Negroid)
  • 0.38% of C*(xC3) (Mongoloid)
  • 0.96% of C3 (Mongoloid)
  • 0.19% of O3 (Mongoloid)
  • 2.87% of N*(xN3a) (Mongoloid)
  • 0.96% of N3a (Mongoloid
  • 0.19% of Q2 (Mongoloid)
  • 1.72% of Q*(xQ2) (Mongoloid)
There is thus 0.95% of Negroid admixture and 7.27% of Mongoloid admixture, for a total of 8.22% non-Caucasoid admixture.

Based on these numbers, the non-Caucasoid admixture in Turks can be quantified as 1.87% Negroid, and 6.18% Mongoloid, total 8.05%.

April 17, 2005

IBM - The Genographic Project Video

Can be found here. See another video and some of my comments here.

Also listen to a 51' audio presentation by Spencer Wells from October 2004 here. (not very interesting unless you know nothing about the area).

Also a 6' recent interview for Australian ABC (in Real Audio) here.

Abstracts from 74th Meeting of AAPA

They can be found here. Some interesting abstracts that caught my attention.

  • Inter- and intraspecific variation in Pan tooth crown morphology: implications for Neandertal taxonomy. [Nenaderthals are distinct from Europeans and a separate species]
  • Longevity in the Middle Paleolithic: Did modern humans live longer than Neandertals? [Increased longevity was not associated with anatomically modern humans but with the Upper Paleolithic]
  • Sequence data from the autosomes and X chromosome: Evidence for ancient admixture in the history of H. sapiens? [East Asians have 2million BP polymorphism]
  • MtDNA variation in North, East, and Central African populations gives clues to a possible back-migration from the Middle East. [M1 sharply differentiates North and East Africans from Sub-Saharans and may have originated outside Africa]
  • Rejection of isolation by distance for human gene geography and suggested alternatives. [Human genetic diversity is structured and is not well-described by isolation by distance]
  • Population structure in sub-Saharan Africans based on mitochondrial, Y chromosomal and X chromosomal DNA sequences. [Genetic diversity in Africa is explained by the fact that African populations were widely scattered and experienced gene flow between them]
  • Using measures of locus-specific differentiation to find genes underlying traits subject to recent genetic adaptation: a test case using skin pigmentation. [Europeans and Asians are light due to selection on different genes]
  • Demographic and selective history of African populations inferred from genome wide genetic markers. [Large multi-locus study finds significant substructure in Africa]
  • The distribution of ancestral alleles among populations. [The fact that Africans have more ancestral alleles than other humans does not mean that humanity originated in Africa]
  • History of modern human population structure inferred from the worldwide survey on Xp11.22 sequences. [1.1 million year old ancestry in North Africa and the Middle East]
  • Demographic history of African populations inferred from mtDNA analysis. [Mankind originated in Tanzania, and Khoisan speakers originated in East Africa]

Midfacial variation in recent human, Zhoukoudian Upper Cave, and Paleoindian crania.

J.C.M. Ahern et al.

This study tests the hypothesis that the midfaces of select Late Pleistocene Asians and Paleoindians cannot be distinguished from recent Amerindians. Recent interpretations of Paleoindian remains have highlighted their variability and affinities to a variety of living non-Amerindian human populations. Although midfacial anatomy has been touched upon in some of these analyses, metric treatment of upper and lower midfacial anatomy has not been thoroughly examined. Given that midfacial anatomy is useful for determining population affinities among recent people, it may also prove effective at assessing past prehistoric population affinities.
Measurements of the upper and lower midface were collected on samples of three extant human populations: Amerindians (n=46), African Americans (n=58), and Euroamericans (n=62). Measurements were also collected on casts of the three crania from Zhoukoudian Upper Cave and the Spirit Cave and Wizards Beach Paleoindian specimens. The Upper Cave crania were chosen since they may represent a population ancestral to the first people to colonize the Americas. Spirit Cave and Wizards Beach were chosen since their differences epitomize the degree of variation and contrasting population affinities of North American Paleoindians. Using discriminant function analysis, Spirit Cave fell in the area of overlap between Amerindians and African Americans, while the other fossil crania had a higher probability Amerindian classification. Unlike some previous analyses, none of the fossil crania showed affinities with Europeans. Our results further indicate that the pattern of relationships and variation among Late Pleistocene Asians and Paleoindians was complex.

Inter- and intraspecific variation in Pan tooth crown morphology: implications for Neandertal taxonomy.

S.E. Bailey

Measures of divergence based on dental morphology are known to reflect biological distance in contemporary modern humans. Previous studies of Neandertal tooth crown morphology have shown that they possess a pattern of trait frequencies that differs significantly from that of contemporary and fossil anatomically modern humans. However, there is no taxonomic ‘yard stick’ against which to interpret the degree of dental divergence observed. The goal of this study was to test whether the dental morphological differences between Neandertals and anatomically modern humans were typical of subspecific (Pan troglodytes troglodytes:Pan troglodytes schweinfurthi) or closely related specific (Pan troglodytes:Pan paniscus) taxa. Eighteen dental crown traits were used to assess inter- and intraspecific variation. A Mean Measure of Divergence statistic was used to calculate morphological distance. The hominin sample included 33 Neandertals, 7 early modern humans, 19 Upper Paleolithic Europeans, and 179 contemporary humans from seven geographic regions. The Pan sample included 37 P.t. troglodytes, 44 P.t. schweinfurthi and 33 P. paniscus specimens. Measures of divergence based on pair-wise comparisons of Neandertals and anatomically modern humans were found to be higher than those derived from both subspecific and specific pair-wise comparisons of Pan. Moreover, Neandertals show no morphological affinity to either Upper Paleolithic or contemporary Europeans and are more than twice as divergent from all contemporary human samples as these samples are from each other. In as much as Pan represents an appropriate model for interpreting dental morphological divergence in Homo, these results are broadly supportive of the specific status of Neandertals.

Natural selection in the Tibet Autonomous Region.

C.M. Beall et al.

Indigenous high-altitude populations have been exposed to the opportunity for natural selection. The ability detect natural has been hampered because the genetic bases of the quantitative traits that appear to be adaptive are often unknown. However, Tibetan populations have a major gene for oxygen saturation of hemoglobin. One allele at the inferred locus is associated with 6-10% higher levels and less hypoxemia. We reported that Tibetan women residing at 4000m altitude with a high likelihood of having one or two alleles for high oxygen saturation had more living children because fewer of their live births died during infancy. Those findings suggested that high-altitude hypoxia is acting as an agent of natural selection on the locus for oxygen saturation of hemoglobin. Here, we consider the implications for understanding the evolution of adaptations to the environment. The relative fitness of the low saturation genotype as compared with the two high saturation genotypes was 0.44 based on the ratio of the number of living children. This relative fitness was lower than reported for comparisons of Hb AA and AS genotypes in malarial areas (0.66 – 0.88). Hypoxic stress differs qualitatively from malaria stress: hypoxia is constant whereas malaria parasitemia level fluctuates. Thus, the selective advantage of the high saturation allele is probably constant whereas the selective advantage of an antimalarial genotype may be intermittent. Large fitness differences among genotypes indicate the potential for rapid change in allele frequency. Human genetic adaptation may be rapid and may depend upon the nature of the environmental stress.

MtDNA diversity in six West Indian Islands throughout the Anglophone Caribbean.

J. Benn Torres et al.

The Caribbean is an example of a convergence of people and cultures from several continents. Few researchers have investigated how this phenomenon affected immigrants and their subsequent communities, even fewer have attempted to examine this convergence using anthropological genetics. In this analysis, mtDNA hypervariable region I (HVI) and haplogroup diagnostic RFLPs are examined in 318 individuals from six Afro-Caribbean communities in Dominica, St. Lucia, St. Kitts, St. Vincent, Grenada, and Trinidad. Genetic diversity and maternal genetic contributions to contemporary Caribbean populations are examined and comparisons are made between these data and those published from other African and African-derived populations.

All samples were collected from buccal swabs, extracted, and amplified using standard methods. The HVI was sequenced and 14 RFLPs were typed to determine the haplogroup. The Caribbean sequence summary statistics (pi, theta, gene diversity, average number of nucleotide differences, and Tajima’s D) are all similar to each other and similar to published African data. MtDNA haplogroup L is detected in 93% of the total sample, while the remaining 7% consists of haplogroups A, C, F, J, N1c, U6, and U7. The presence of non-L types is indicative of non- Sub-Saharan African female gene flow into these communities and for the most part, is likely due to recent immigration. Different ethnic groups make up the African Diaspora, such as African-Americans, West Indians/Afro-Caribbeans, and Afro-Latinos, this study examines the origins of a little studied group within this Diaspora.

Searching for signatures of natural selection in high altitude populations.

A.W. Bigham et al.

Hypoxia, caused by lowered barometric pressure at high altitude (defined as >2500 m above sea level), results in severe physiological stress to the human body. Although the suite of human physiological responses to this environmental condition has been well documented, the genetic bases for these adaptations remain unknown. To search for genes possibly involved in adaptation to high altitude, we used FST and other measures of allele frequency differentiation. Local natural selection especially positive selection can lead to elevated allele frequency differences measured as high FST and locus specific branch length (LSBL). Although demographic factors as well as genetic drift can also affect differences between populations, identifying high LSBL and high FST on genome-wide SNP datasets can be a powerful tool to rank candidate genes. Next, by comparing a high altitude, Indigenous American population (Quechua) to a low altitude, Indigenous American population (Nahua) using these statistics, a list of 451 SNPs (threshold FST >0.20) and 636 genes within 40kb region of those markers was generated. Based on this dataset, candidate genes that may have undergone natural selection in the Quechua population were revealed. Among these are nitric oxide synthase 2A (NOS2A) and endothelin 1 (Edn1).

Body orientations, sleep positions, and breast feeding behavior amongst solitary and co-sleeping (bedsharing) human mother-infant pairs: mutual physiological regulatory effects.

T. Brown et al.

Since the “back-to-sleep” campaign initiated in 1992, the rate per 1000 live births of American infants dying from SIDS has been reduced by half. This NIH funded research provides a basis for further appreciating how the mother’s body and responses in addition to the infant sleeping on its back can create an adaptive “micro-environment” for the human infant, and how both the mother and infant, by virtue of their sensory interactions, changes each other’s physiological status. 15 routinely solitary sleeping breastfeeding infants and their mothers and 23 routinely bed sharing breastfeeding mother-baby pairs sleeping apart and together over three consecutive nights were filmed using infrared cameras. Data collected on body orientation, sleep position, crying, breastfeeding, and maternal responses, as mothers and infants shift between bedsharing and separate room sleeping reveal changes in maternal-infant interactions involving partner-induced arousal patterns and overall sleep duration. Breastfeeding doubled when mother and their infants slept together, and infants cried significantly less. Decreased infant crying may be related to the shortened temporal latencies between when the infant aroused and when their bedsharing mothers responded. This makes problematic a 1999 recommendation by the American Consumer Product Safety Commission, to “never sleep with a baby.”

Ethnic and biological identity in New Kingdom Nubia.

M.R. Buzon

The populations of Nubia and Egypt have had a long history of interaction. While past studies have often focused on the unidirectional changed forced on Nubia by Egypt, more recent paradigms emphasizing the dynamic and bidirectional nature of these power relations are more appropriate for this situation. The events that occurred around the time of the Egyptian New Kingdom occupation of Nubia are significant. It is during this time that the foundations of the Nubian Napatan Kingdom, which ruled Egypt as the 25th Dynasty, were being built. Scholars disagree about who controlled Nubia during this important time: Egyptian colonists or native leaders. In this paper, these issues are addressed using a bioarchaeological approach.

The people buried using Egyptian and Nubian ritual at the New Kingdom site of Tombos, located at the third cataract of the Nile in Nubia, are the focus of this research (N=100). In addition, 1,287 individuals from contemporaneous Egyptian and Nubian sites are examined in order to comparatively assess the Tombos population. Multivariate statistical analyses of cranial measurements and cranial non-metric traits are used to evaluate the genetic relationships between Tombos and these comparative populations. The analyses of genetic affinities suggest that the cranial morphology of the Tombos population is more heterogeneous than that of the Egyptian populations. This heterogeneity, however, is also characteristic of the native Nubian populations. Combined with the mixed ethnicity portrayed through archaeological indications of burial ritual, it is apparent that Tombos was comprised of an ethnically and biologically mixed group of people.

Artificial cranial deformation in the prehistoric lower Mississippi river valley.

S.N. Byers

A study was performed on the cranial deformation found among prehistoric individuals from Louisiana. The type, degree, and characteristics of the deformation are presented. In addition, hypotheses are tested concerning the association between presence or degree of cranial deformation and social/biological groups: warriors vs. non-warriors, elites vs. commoners, priests vs. commoners, male vs. female, and all members of society. Testing protocols are generated for each hypothesis and the fit between the data and the protocols tested. The results of these tests indicate that cranial deformation is not more common in some groups than in all members of society, indicating that the practice was not limited to groups such as warriors, elite, priests, or even only one of the sexes. The major finding is that this cultural practice appeared to increase in frequency through time from the oldest to the youngest site.

A reassessment of human cranial metric and nonmetric trait heritabilities.

E.A. Carson

Quantitative genetics models of human populations often rely on trait heritability rates to represent the genetic variability of phenotype. The heritability ‘gold standard’ was established 20 years ago by Sjøvold (1984) and Devor (1987), whose estimates of genetic inheritance for craniometric and, in Sjøvold’s case, cranial nonmetric traits are universally used and often averaged to obtain an overall heritability rate for population genetics models. Each of these studies, however, is problematic. The heritabilities reported by Sjøvold were calculated using linear regression, a technique which makes assumptions regarding the variance matrices and parental-offspring environmental correlation that are not valid for humans. In addition, measures typically included in anthropological studies such as nasal breadth, maximum cranial length and breadth, were not assessed in Sjøvold’s study. While Devor (1987) did report heritabilities for these established cranial dimensions, his data were collected on living humans; the use of soft tissue measurements as a proxy for skeletal dimensions has since been called into question.

The current study addresses each of these problems by utilizing maximum likelihood variance component analysis to calculate heritability estimates from a sample of 200 parental-offspring pairs of crania from the Hallstatt, Austria ossuary, the same skeletal population assessed by Sjøvold. Metric data were collected on 58 standard cranial landmarks using a Microscribe 3-D digitizer that allow for the calculation of 36 linear cranial measurements commonly used by physical anthropologists (Howells, 1989). This poster presents updated heritability estimates for these measures, as well as for 36 standard cranial non-metric traits.

Longevity in the Middle Paleolithic: Did modern humans live longer than Neandertals?

R. Caspari

Increased longevity, expressed as the number of individuals surviving to older adulthood, represents one of the ways that Upper Paleolithic Europeans differ from earlier European populations. It remains unclear whether this increase in adult survivorship is an attribute of the Upper Paleolithic itself, or whether it occurred in earlier anatomically modern humans migrating into Europe from elsewhere. In this paper we address this issue by comparing anatomically modern humans associated with the Middle Paleolithic of Western Asia to their Upper Paleolithic counterparts.

We examined differences in longevity by assessing the ratio of older to younger adults (OY ratios) in two earlier penecontemporary dental samples, both associated with the Middle Paleolithic: Neandertals and fossils considered anatomically modern Homo sapiens from Western Asia. Younger and older adult status was assessed by M3 eruption and wear seriation of each sample: M3 eruption indicated adulthood, and older adulthood was defined as the age at which individuals could first potentially become a grandparent (double the age of M3 eruption). Significance of the difference in ratios between the groups was tested using distributions generated by random resampling with replacement. Our results do not reject the null hypothesis of no difference between the two Middle Paleolithic populations. We conclude that the dramatic increase in adult survivorship was not a hallmark of the earliest modern humans, but instead occurred more recently coinciding with the Upper Paleolithic. Whether or not modern humans and Neandertals were conspecifics, this suggests that the increase in adult survivorship associated with the Upper Paleolithic was not directly linked to speciation.

The truth is out there: how NOT to use FORDISC.

D. Freid

FORDISC is an interactive computer program designed to classify an unknown adult cranium based on the reference samples in its database. FORDISC uses discriminant functions to construct a classification matrix and assign group membership of the unknown cranium into one of the selected reference groups. The researcher guides the analysis by choosing the populations against which to classify the unknown, choosing from eleven population samples from the Forensic Anthropology Data Bank or twenty-eight population samples from Howells’ (1989) worldwide database. The utility and efficacy of FORDISC has been criticized for providing ‘incorrect’ classifications, however these disputed results are often due to inappropriate reference samples and failure to properly evaluate the typicality and posterior probabilities provided by the program. In this paper, unknown crania from populations known not to belong to any of the reference samples will be analyzed, demonstrating the interpretation of posterior and typicality probabilities provided in the FORDISC output and the importance of the use of an appropriate reference sample.

An application of ancient DNA analysis to an early Byzantine monastic community.

A.M. French et al.

The degree of contact among ancient populations and the extent of human historical movement have long been topics of interest and debate. While archaeological, linguistic, and textual evidence provide much information on historical patterns of migration, the record is often incomplete. A combination of biological and historical data and the introduction of methods such as ancient DNA analysis provide a more complete picture of historical migration patterns. Populations from the early Byzantine period (5th – 7th c. C.E.), when cultural and probably biological interaction among peoples of different geographic regions was common, are especially appropriate for such an analysis. An examination of genetic material from adult and subadult remains at St. Stephen’s, a Byzantine monastery in Jerusalem, has proven particularly useful in revealing some patterns of migration during the Byzantine period.

In this study, levels of genetic heterogeneity of mitochondrial DNA both within and between the subadult and adult populations at St. Stephen’s are examined to determine the likelihood that the individuals were members of the same genetic population. As many of the subadults are too young to be pilgrims they are, most likely, representative of the local region. Additionally, the sequences from the St. Stephen’s collection are compared with genetic data from worldwide populations in order to determine the most likely place(s) of origin for members of the St. Stephen’s assemblage. The genetic data, in conjunction with textual and archaeological evidence, illuminates some patterns of population movement during the Early Byzantine era into Jerusalem, especially those associated with ecclesiastical institutions.

A measure of biological distance in Nubians: a look at intrapopulation variation.

K. Godde. California State University, Sacramento.

Biological distance studies typically measure the genetic distance between populations. However, little has been done to assess the distance within specific populations. This study looked at six subpopulations of Nubians separated geographically and/or temporally to determine if variability within populations was statistically significant. In order to measure this, twenty nonmetric traits were observed on a total of 319 skulls, representing three temporally distinct periods from Semna South, including the Meroitic, X-Group, and Christian eras. Tsuneko Hanihara provided data on 180 additional crania (personal communication) from three other Nubian subpopulations that were spatially and temporally distinct from the other groups. These data were from the sites of Kerma (12th –13th dynasty), Sesebi (recent population), and the islands of Hesa and Biga (pre-Christian). All six subpopulations were compared to one another using Mean Measure of Divergence (MMD), its variance, standard deviation and the standardized MMD. The results of the statistical analysis showed that there was little variability between most of the samples. However, the MMD results of the Meroitics and Hesa and Biga were only .01 away from being statistically significant at the .05 level. Additionally, the difference between Kerma and the Meroitics was statistically significant at the .05 level. These samples were not separated by the greatest amount of geographic or temporal distance, and thus these explanations cannot completely account for the difference. In light of this study, further analysis should address whether it is necessary to separate highly variable subpopulations when attempting to measure biological distance on a global scale.

Variation in the juvenile craniofacial form: a pilot study.

R.A. Gonzalez

Much research has been conducted in the area of age determination of juvenile skeletal remains for biological profiling purposes within a medico-legal context. However, the ability to determine sex and group affiliation from juvenile skeletons is limited and often unreliable (Kerley, 1976). In fact, identifying sex and group specific differences with any degree of reliability is one of the major problems in the analysis of juvenile skeletal remains (Scheuer and Black, 2000).

This pilot study presents initial findings of human variation as expressed in the juvenile craniofacial form. A sample of 28 groups divided according to age, sex, and group affiliation was studied utilizing 22 common cephalometric measurements of American children of African and European descent. A glm manova procedure and principal component analysis served to test for the presence of sex and group specific features in the juvenile craniofacial skeleton throughout development.

The findings of this initial investigation demonstrate a statistically meaningful sex and group specific pattern of size and shape differences throughout development. Additionally, this study suggests that for each age group category utilized in the analysis, ages 6-12, it is possible to clearly identify the sex and group affiliation of juvenile skeletal remains for forensic biological profiling purposes. If the preliminary results are correct, then this investigation provides evidence of morphological differences that can be accurately identified throughout craniofacial development. These findings provide the basis for future research in which this investigator will use to develop biological profiling standards for juvenile skeletal remains.

Sequence data from the autosomes and X chromosome: Evidence for ancient admixture in the history of H. sapiens?

M.F. Hammer et al.

A longstanding question in anthropology asks whether the history of our species is characterized by an expansion from an isolated panmictic population with complete replacement of archaic forms, or by admixture among divergent allotaxa. While mtDNA data support a recent and complete replacement model, nuclear loci present a more complicated picture. Two major problems associated with interpreting the heterogeneous patterns of variation observed at multiple nuclear loci are that sampling procedures vary across studies, and experimental designs generally lack statistical power to detect archaic admixture. We are undertaking a systematic survey of DNA sequence variation at 90 unlinked nuclear loci and developing a statistical framework (to be presented by Jeff Wall) to explicitly test the hypothesis of no admixture between modern and archaic forms, and for estimating the admixture ratio (if the null hypothesis is rejected). Our approach involves sequencing three windows of ~2 kb spanning ~16 kb at each locus in a panel of 90 individuals from 6 populations. Preliminary data from two loci that show evidence of ancient admixture will be discussed. A gene tree constructed from sequence data at the first locus roots in East Asia and has a most recent common ancestor ~2 million YBP. The pattern of nucleotide variation at the second locus reveals two major lineages that have not undergone recombination for over 2 million years, and statistically rejects the null hypothesis of panmixia during the early ancestry of modern humans.

MtDNA variation in North, East, and Central African populations gives clues to a possible back-migration from the Middle East.

A.D. Holden et al.

The general timeline for human occupation of Africa has been studied extensively. However, questions involving Upper Palaeolithic migrations still persist. One remaining question is the presence of the mitochondrial M1 haplogroup in North and East Africa. Some (Quintana-Murci et al. 2004, 1999) argue that the presence of M1 in modern Africans is a remnant of the original M haplogroup that left Africa 60 kya via the Horn of Africa. Others (Forster, 2004) propose that it is instead the result of a back-migration from the Arabian Peninsula from 20 kya. This research aims to test these two competing hypotheses.

We analysed mtDNA variation in ~250 persons from Libya, Somalia, and Congo/Zambia, as representatives of the three regions of interest. Our initial results indicate a sharp cline in M1 frequencies that generally does not extend into sub-Saharan Africa. While our North and especially East African samples contained frequencies of M1 over 20%, our sub-Saharan samples consisted almost entirely of the L1 or L2 haplogroups only. In addition, there existed a significant amount of homogeneity within the M1 haplogroup.

This sharp cline indicates a history of little admixture between these regions. This could imply a more recent ancestry for M1 in Africa, as older lineages are more diverse and widespread by nature, and may be an indication of a back-migration into Africa from the Middle East. Further research on this topic includes more extensive population samples from the Middle East, as well as possible correlations of M1 to the Afro-Asiatic language family.

Rejection of isolation by distance for human gene geography and suggested alternatives.

K. Hunley et al.

Isolation by distance population structure is tested for the worldwide pattern of human genetic diversity using a large short tandem repeat (STR) data set (Cann et al., 2002, Science, 298: 261-2). A subset of 27 populations, chosen on the basis sample size, was analyzed. Each individual was represented by 377 autosomal short tandem repeat (STR) genotypes. Malecot’s genetic kinship was calculated between population pairs. Scatterplots and regression methods were applied analyze the relationship between genetic kinship and geographic distance.

All African/non-African population pairs show about the same degree of genetic kinship, regardless of geographic distance. European/non-European comparisons show two strata of genetic kinship. The first stratum presents European/African pairs, while the second stratum contains European/Asian and European/Native American pairs. There is no trend for genetic kinship to decrease with increasing geographic distance. Finally, comparisons between Asian with non-Asian samples reveal three strata, the first stratum includes Asian/African pairs, the second stratum includes Asian/European pairs, and the third stratum includes Asian/Native American pairs. The pattern is remarkable. Rather than isolation by distance, it reflects a pattern of nested subsets. Non-Africans possess a subset of the variation in Africans; Asians and Native Americans possess a subset of the variation in Non-Africans; and Native Americans possess a subset of the variation in Asians. The nested subset pattern of genetic diversity is consistent with a model that postulates a succession of ancient founder events that occurred as the human species expanded its range and occupied new continents.

The relationship between a quantitative measure of facial harmony and subjective measures of facial attractiveness.

P.L. Jamison et al.

The craniofacial variability index (CVI) summarizes the variation in Z-scores across a set of sixteen common craniofacial measurements and can be used as a measure of facial harmony. Previously we have shown that high values of this summary statistic correlate strongly with individuals known to have congenital craniofacial syndromes. In the present study we hypothesized that low values of this measure correlate with attractive or harmonious faces. The CVI was calculated for 205 adult females who had previously been ranked for attractiveness using a panel of male and female judges. The judges used a seven point Likert scale to rate each subject from above average in appearance to below average in appearance. Mean ranking scores for each subject were then used to create three groups, above average (n-34), average (n=145), and below average (n=21). ANOVA demonstrated significant differences in CVI scores of the three groups and Bonferroni post hoc tests revealed that the subjects in the “above average” group had significantly lower CVI scores than the subjects in the other two groups. Mean CVI did not differ significantly between the average and below average groups. These results indicate that the CVI is an effective measure of facial harmony and suggest that it may be a useful tool in testing some of the hypotheses that have been put forward regarding physical attractiveness and reproductive fitness.

Environmental variability, life history tactics, and the Neanderthal extinction.

J.H. Jones

In this paper, I use the demographic theory for structured populations in variable environments to shed light on the demise of the Neanderthals. Humans are – and probably most hominins were – characterized by highly structured life cycles. That is, age-specific schedules of reproductive investment are far from constant across the life cycle. In the presence of environmental variability, this structure induces correlations in vital rates across environments that can fundamentally alter optimal life history tactics. I present stochastic models of human population dynamics in a variety of stochastic environments showing that, in general, increased variability favors (1) delayed age at maturity and (2) long reproductive span. Recent histological analyses of Neanderthal teeth suggest their age at maturity was significantly earlier than that of anatomically modern humans. I show that under a reasonable range of demographic schedules, this early age at maturity would have increased the probability of extinction of Neanderthal populations under the right environmental conditions. Drawing upon Pleistocene temperature proxy data from the Greenland Ice Core Project, I show that high-frequency fluctuations increased significantly in the period more or less coincident with the disappearance of Neanderthals, consistent with this hypothesis. These results suggest the possibility that Neanderthal extinction was driven by intrinsic features of their biology and not through competition with anatomically modern humans.

Population expansions in South Indian caste and tribal populations: inferences from genetic data.

L.B. Jorde et al.

The origins and affinities of Hindu caste populations remain poorly understood. To investigate the relationships between Hindu caste populations, Indian tribal populations, and other populations, we have genotyped 45 short tandem repeat polymorphisms (STRPs) in 151 members of tribal populations and 437 members of caste populations from South India. These same STRPs have also been assayed in 142 Africans, 117 Europeans, and 61 East Asians. STRP heterozygosity was quite similar among all caste populations, with an average of 69%. The average heterozygosity among tribal groups was somewhat lower (66%), and it varied considerably among populations, with a range of 54% to 74%. The Fst value for the caste populations was relatively small (0.9), but the Fst value for the tribal populations (4.8%) was slightly higher than for our collection of sub-Saharan African populations (3.7%). Genetic distance analyses show that the caste and tribal populations occupy a position intermediate between E. Asian and European populations, as expected. In marked contrast to the caste populations, several of the tribal populations (Yanadi, Kattuniaken, Paniyan, and Chenchu) are extreme outliers on a neighbor-joining tree. These results are all highly similar using either STRPs or Alu insertion polymorphisms, and they are consistent with a much higher rate of genetic drift in the tribal populations than in caste populations. The matrix coalescent approach was applied to these data to estimate population growth parameters in caste vs. tribal populations, and these results will be discussed.

Mitochondrial DNA variation among populations of Mesoamerica and the American Southwest: Does Uto-Aztecan represent a biological unit?

B.M. Kemp et al.

Anthropologists have long noted the archaeological, cultural, and linguistic parallels between indigenous populations residing in Mesoamerica and the American Southwest. The most notable ties are the northward spread of agriculture from central Mexico into the Southwest and the presence of Uto-Aztecan speaking populations in both regions. Thus, it has been suggested that proto-Uto-Aztecan speakers were responsible for the spread of agriculture, possibly taking the form of a northward human migration. If true, Uto-Aztecan speakers from both areas should be more genetically related than they are to non-Uto-Aztecan speaking populations, regardless of geographic location.

This hypothesis was evaluated by assigning the mtDNA of over 900 individuals from fourteen extant populations (Uto-Aztecan and non-Uto-Aztecan from the Southwest and Mesoamerica) and one pre-Columbian population (Aztecs from Tlatelolco, Mexico) to one of the five Native American haplogroups: A, B, C, D, or X. These data exhibit a pattern of regional continuity and, therefore, substantial difference between regions. Additionally, the haplotypes (from the sequence of hypervariable regions I, II, and III) of over 700 of these individuals were identified. Analyses of these data demonstrate that very few maternal lineages are shared between populations and network analyses demonstrate that the majority of clades are geographic, not linguistic. The patterning of mtDNA variation suggests these regional genetic differences are of great antiquity and opposes an accompanying human migration with the spread of agriculture. We, however, point out alternative possibilities not covered by our investigation, but that are currently being tested by other colleagues.

Comparison of genetic and linguistic phylogenetic reconstructions as a means of investigating the evolution of the Semitic language family.

A. Kitchen et al.

Inference of the history of the Semitic language family has long been controversial. In order to address this problem, we have taken an interdisciplinary approach in which genetic and linguistic evolutionary relationships are compared through independent phylogenetic reconstructions of genetic and lexical data.

Our phylogenetic analyses of genetic data (mitochondrial control region DNA sequence from three Semitic-speaking populations) demonstrates that Ethiopic Semitic populations are basal relative to non-African Semitic-speakers. While greater antiquity of African populations relative to non-Africans is not surprising, genetic diversity has never been explicitly compared between African and non-African Semitic-speakers. This result suggests that if Ethiopian Semitic did originate in Arabia, it may have been introduced to Ethiopia in the absence of significant gene flow from a less diverse and evolutionary younger non-African population.

Concurrent analysis of lexical data (Bender’s modification of Swadesh’ 100-word lists for 15 Ethio-Semitic populations) using phylogenetic techniques borrowed from evolutionary systematics allows us to contrast population history, gene-flow and linguistic evolution within Semitic populations. Applying maximum parsimony and distance phylogenetic reconstruction methods to our lexical dataset, and comparing the resulting lexical and genetic phylogenies, we test alternative hypotheses of Ethio-Semitic language evolution. Our results largely support Bender's original classificatory scheme of Ethio-Semitic languages. Comparative analyses of genetic and linguistic phylogenetic reconstructions of Semitic-speaking populations should help resolve questions concerning the genetic and geographic origin of the language family.

Polygenotype-environment interaction and the Boas immigrant data.

L.W. Konigsberg et al.

The Boas immigrant dataset has recently seen a resurgence of interest, with a number of studies published using methods not available to Boas in the pre-computer era. These analyses have tended to take alternative views on the importance of polygenotypic effects as versus environmental plasticity. In this paper we re-analyze the Boas dataset with an eye to characterizing the effect of polygenotype-environment interaction on the cephalic index.

We use data on 13,732 individuals taken from Clarence Gravlee’s website (http://lance.qualquant.net/boas/data.htm). Treating the data as composed of many unrelated families and controlling for age at measurement and immigration status we estimate a narrow sense heritability for the cephalic index of about 0.74. This figure is an overestimate because it does not account for the different familial ancestries. Allowing for the original seven groups defined in Boas’s study, the within-group heritabilities are substantially lower with none reaching above 0.60. This analysis shows that we cannot ignore the existence of group-structure in the Boas data, for to do so causes cephalic index to look “more genetic” (because of increasing the genetic variation around a grand mean). Neither can we ignore the effect of the environment, for as Boas and subsequent studies (as well as this one) amply demonstrate, groups’ cephalic indexes are subject to differential responses following immigration to the United States. Consequently, the Boas data do not tell us whether cephalic index is about genes versus environment, but rather that the index is about genes and the environment.

Grandma’s right: A sleeping baby may be a growing baby.

M. Lampl

The irregularity of infant sleeping behavior is a significant biocultural issue, with much advice-seeking and offering with little scientific basis. This study aimed to investigate whether infant sleep patterns were a biobehavioral indicator of growth. Three independent statistical methods were used to test the hypothesis that the irregular increases and decreases in infant sleeping behaviors were related to episodic (saltatory) spurts in infant body length growth. Detailed daily diaries recorded the continuous patterns of sleep for twenty-four infants (15 females, 9 males) during the first year of life for durations of 4 to 12 months (n= 5660 daily records). Total daily hours of sleep and number of episodes were the variables studied. A pulse detection algorithm (CLUSTER) clarified that infant sleep irregularity consisted of sleeping peaks and troughs for all infants with an average of 4.7 more hours and/or 3 more naps per day for two days during peaks. These patterns were compared to previously identified growth spurts in body length by coincident analysis. Significant nonrandom copulsatility was identified between the two independently collected data sets (physical growth and sleep patterns) suggesting that daily sleeping behavior and growth in infant body length are a coupled biological process. Maximum likelihood logistic regression models quantified a 25% increased likelihood of a growth spurt for each hour the infants slept above their non-growth interval sleeping averages.

These data link behavioral state changes and the biological mechanisms underlying the timing and control of human growth spurts, adding growth biology to the enigmatic question of “why do we sleep?”

Changes in sexual dimorphism in Europeans in the last 30,000 years.

S.-H. Lee ET AL.

In Europe, sexual dimorphism decreased from the Upper Paleolithic through the Mesolithic followed by a slight increase from the Mesolithic to the Neolithic. In all, the level of sexual dimorphism typical of recent Europeans was reached by the end of the Neolithic. Earlier work (Frayer, 1980) documented these trends by plotting means in sexual dimorphism in dental, cranial and postcranial metrics for the three periods, attributing the reduction trend to greater gracilization in males from the Upper Paleolithic to the Mesolithic. The subsequent increase in sexual dimorphism was a result of stabilization of the male trend, coupled with a decrease in female metrics from the Mesolithic to the Neolithic.

The previous study was conducted by pooling data into three time periods and testing for differences across these divisions. In this study, the pattern of gracilization over time was examined by tracking male and female metrics separately through the entire time span. Here, we treat the time period as a continuous sample and use an updated data set to address two questions: 1) the pattern of change in sexual dimorphism; and 2) the contribution of changes in each sex over time to the observed pattern of variation. We apply a data re-sampling approach and ask if changes occurred gradually through the 30,000 year time span. Our results confirm earlier work, but deepen the understanding of the temporal patterning of trends of sexual dimorphism in post-Neandertal European populations.

Predictions of isolation by distance and alternatives for human gene geography.

J.C. Long et al.

Many human genetic examples of correlations between genetic and geographic distances are attributed to isolation by distance, meaning a population structure where the reproductive dispersal of individuals is restricted relative to the range of the entire population. Wright, Malecot, Kimura, and Slatkin have developed the rigorous genetic theory of isolation by distance. While each architect of the theory has developed a slightly different version, the common result is that at equilibrium there is a titration between genetic differentiation and the geographic distance between localities. Isolation by distance implies for the human data that genetic drift and local dispersal have shaped the genetic structure of our species.

Alternatively, other mechanisms such as a step-wise range expansion can create a correlation between genetic and geographic distance. In this circumstance, the correlation between genetic and geographic distance does not reflect local dispersal. Rather, it reproduces the migration paths and succession of founder events that occurred during the process of range expansion.

The purpose of this paper is to show how hierarchical F-statistics can distinguish between these two alternative population structures. Computer simulations are used to illustrate the approach and potential outcomes. We use these simulations to determine the number of genetic loci that must be assayed in order to reliably distinguish patterns of genetic divergence. In addition, we explore the effect of systematic sampling biases such as sampling clusters of widely dispersed populations on the outcome of analyses.

Analysis of mtDNA haplogroup monomorphism in a sample of a Native American population combining modern and ancient DNA research.

E. Marchani et al.

We observe a lack of mitochondrial haplogroup variation not only among modern Eastern Inuit, but also among their ancestors, the Thule. Both groups possess haplogroup A exclusively, in contrast to other Native American groups, who possess some combination of haplogroups A, B, C, D, and X.

This lack of variation might have been caused by genetic drift, given a recent history of small effective population size. This hypothesis seems plausible, given archaeological evidence that the Thule expanded rapidly across the far north approximately 1000 years ago from a relatively small founding population. Here, we ask what hypotheses about population history can be excluded on the basis of the observed absence of mitochondrial haplogroup variation.

We test hypotheses about population history using coalescent simulations. We are able to exclude hypotheses of a bottleneck in the distant past, while we are not able to reject hypotheses of a bottleneck within the recent past. Our results both describe and help to explain the demographic and biological processes that result in the unique phenomenon of mitochondrial haplogroup monomorphism.

Population structure in sub-Saharan Africans based on mitochondrial, Y chromosomal and X chromosomal DNA sequences.

M. Metni Pilkington et al.

Africans harbor the greatest genetic diversity, the deepest TMRCA estimates, and the largest effective population size of humans. Here we ask whether the large effective population size is associated with a highly structured population and how population structure compares across loci. We address these questions using DNA sequence data from the mitochondrial (mtDNA) COIII locus, anonymous sequences from the non-recombining portion of the Y chromosome (NRY), and two X chromosomal genes (PDHA1 and RRM2P4). A total of 13.8 kb of DNA sequence was examined in each of 160 individuals from five geographically diverse African populations: the Dinka of Sudan, the Dogon of Mali, the Bakola of Cameroon, and the Khoisan and southeast Bantu from southern Africa.

Estimates of subdivision based on mtDNA and the NRY reveal relatively high levels of population differentiation (FST = 0.284 and 0.236, respectively). Similar levels of population structure for these loci provides no evidence for sex-specific differences in migration rate among these populations. These FST values are only ~20-30% higher than we observe for the same loci sampled in six non-African populations (data not shown). FST values based on the two X chromosome loci (PDHA1 and RRM2P4) were lower (FST = 0.090 and 0.073), but not unexpected because of their 3-fold higher effective population size compared with the haploid loci. These results may be explained by a long period of ongoing gene flow among widely scattered African populations.

Quantitative analysis of modern human and fossil mandibles using 3-D geometric morphometrics.

E. Nicholson et al.

The study of the human mandible has been relatively neglected in comparison to the cranium. Mandibular morphology is often thought to reflect function and not to contain phylogenetic information. Previous descriptions show variation in ramal height and breadth to be the strongest difference among recent human groups. Populations also are thought to vary in corpus robusticity, obliqueness of the ramus, sigmoid notch depth, bicondylar breadth and mental foramen position. Several mandibular traits are believed to differentiate Neanderthals from modern humans: greater robusticity, a receding symphysis, a large retromolar space, a rounder gonial area, an asymmetric sigmoid notch and a posteriorly positioned mental foramen in Neanderthals.

This study quantitatively evaluated some of the proposed differences among modern human groups and between modern and fossil humans and explored these differences to test phylogenetic and functional hypotheses. 28 landmarks were digitized on 134 modern human mandibles from 10 geographic populations. 13 fossil specimens from Europe, the Near East and Africa were also measured. Data were collected with a Microscribe 3DX. A GPA was performed in Morpheus. The fitted coordinates were analyzed in SAS using PCA, CVA, Mahalanobis D2 and Discriminant Analysis. Shape differences were explored using Morphologika.

Modern human mandibular shape shows some geographic patterning. Australians, Polynesians and, to a lesser extent, the Arctic population, are most distinct. Most shape differences between fossil and modern groups, but not among modern humans, are related to differences in centroid size. Functional implications are explored.

Using measures of locus-specific differentiation to find genes underlying traits subject to recent genetic adaptation: a test case using skin pigmentation.

H. Norton et al.

A number of DNA sequence-based statistics are available to identify signatures of natural selection. However, sequencing large numbers of individuals across multiple genes can be costly and time consuming. An alternate method that uses allele frequency data has received less attention, but may be more efficient for large screening studies. This method is based on the idea that demographic events affect loci across the genome equally, while adaptation affects individual genes and nearby markers. We have applied the locus-specific pairwise FST (lspFST) to survey seven pigmentation candidate genes from six geographically diverse populations. Using the allele frequencies at these genes, we calculated the lspFST statistic and compared it to an empirical distribution based on 11,078 SNPs analyzed in the same populations. With this comparison we are able to take into consideration the demographic histories of the populations and calculate likelihoods of the data given neutral evolution. Several pigmentation candidate genes show evidence of non-neutral patterns of differentiation. Interestingly, population differentiation at pigmentation candidate SNPs was observed both for populations differing in pigmentation phenotype (ASIP and OCA2), as well as for populations similar in pigmentation phenotype (TYR). Additionally, SNPs in MATP show high levels of European-specific population differentiation. These results suggest a strong role for natural (and/or sexual) selection in shaping human pigmentation variation. Patterns of allele frequency and lspFST variation at TYR and MATP between Europeans and East Asians raise the possibility that natural selection may have acted on different alleles to produce a similar adaptive phenotype in these populations.

The effect of breastfeeding intensity on bone mineral density.

K. Pearce. University of Massachusetts, Amherst.

Breastfeeding women from Massachusetts (n=35) participated in a study measuring the effect of breastfeeding variation on BMD. Breastfeeding diaries and repeated measures of BMD (DEXA) were used to categorize breastfeeding intensity and changes in BMD throughout the postpartum period. Women entered the study between 2 weeks and 3 years postpartum. The central hypothesis tested was whether variation in breastfeeding intensity affected the rate of change in BMD during lactational amenorrhea (LA) and/or after menses resumed. Multilevel modeling was used to interpret the data. Repeated BMD measures were viewed as nested within individuals. Individuals were nested within groups based on breastfeeding intensity (low, medium-low, medium-high, or high), calcium intake (low or high), and familial history of osteoporosis (yes or no). Results show that BMD decreased during lactation and increased after menses resumed. High breastfeeding intensity had a greater effect on the increase of BMD after menses returned than it had on the loss of bone during LA. High intensity was associated with a .04 g/cm2 increase in BMD (t = 24.1, p=.000) for every three months of post-menses breastfeeding. The same level of breastfeeding intensity during LA was associated with a decrease of .01 g/cm2 BMD, also statistically significant (t = 4.3, p=.01). This study suggests that high intensity post-menses breastfeeding may be an important factor in attaining a net gain in BMD during lactation, with implications for osteoporosis studies of contemporary women and archaeological populations.

Demographic and selective history of African populations inferred from genome wide genetic markers.

F.A. Reed et al.

In collaboration with the Marshfield Medical Research Foundation, a large multi-locus dataset (>2,000,000 genotypes) has been generated from 1,070 microsatellite and in/del markers from ~2,000 individuals originating from >60 ethnically defined populations in Africa and in 100 African Americans. This resource has the potential to answer many questions about the history of humans both within Africa as well as history of the African diaspora into the Americas. These data have been compared to previously published analysis of the same markers in the CEPH diversity panel (Rosenberg et al., 2002). Here we present the results of our analysis of population structure within Africa and African population history. Initial results indicate considerable levels of substructure, even within small geographic regions. We are also able to infer and address several hypotheses regarding the origin of Pygmy populations in Africa, as well as the ancestry of Nilo-Saharan, Niger-Kordofanian, Afro-Asiatic, and Khoisan speaking populations. Additionally, we describe our current efforts at developing acceptance-rejection composite likelihood-approximations to estimate parameters of interest (of demography and selection) from these microsatellite data.

The distribution of ancestral alleles among populations.

A.R. Rogers et al.

The “ancestral allele” at a given locus is the allele thought to have been carried by the last common ancestor (LCA) of all humans. These are only estimates, of course, but they are often relatively good ones. Thus, it is interesting that human ancestral alleles are usually most common in Africa. Some claim that the ancestral allele should be most common in Africa, because it is the ancestral population. We argue otherwise. In the absence of selection or ascertainment bias, the expected frequency of the ancestral allele is the same in each modern population, regardless of the history of population size, subdivision, or gene flow. The observed tendency of ancestral alleles to cluster in Africa argues either for some form of ascertainment bias or for some form of selection.
We attribute the pattern to two forms of ascertainment bias, which affect different sorts of locus. These biases, together with a history of expansion out of Africa, are capable of producing the observed pattern. The only loci that are certainly free of bias are those that sequence arbitrary stretches of DNA far from known genes. In these bias-free systems, there is no tendency for ancestral alleles to be most common in Africa.

Early South Americans in craniofacial metric perspective: Lagoa Santa.

N. Seguchi et al.

We compare the craniofacial morphology of four Sumidouro skulls and one Lund skull, representing South American Paleoindians from Lagoa Santa, Brazil, with worldwide prehistoric and recent human craniofacial metric data. Relationships in these data are illustrated using the neighbor-joining method based on a Mahalanobis distance matrix, discriminant function analysis, canonical variate plots, and posterior and typicality probabilities. We also employed Relethford and Blangero’s R matrix method (Relethford and Blangero 1990, Relethford and Harpending 1994) on the same craniofacial metric data, and generated the neighbor-joining tree and principal coordinate plot. Using Howells’ worldwide comparative dataset, Walter Neves et.al. (2003) recently suggested that Brazilian Paleoamericans probably were closely related to Australian Aborigines and Africans as opposed to Native Americans and Northeast Asians. In contrast, our preliminary results show that Lagoa Santa individuals exhibit stronger morphological affinities with prehistoric Jomon of Japan, recent Patagonia/Tierra del Fuego of South America; present day Mexico, Peru, and Archaic Americans of Windover and Indian Knoll of North America, than with our Australian sample. Moreover, Jomon, Lagoa Santa and Archaic North Americans all present a relatively close relationship, and tie consistently to each other. This suggests that the early inhabitants of South America were probably not related to Australo-Melanesians, but rather the Late Pleistocene descendents of Northeast Asia, such as Jomon. Also, they are related to the Archaic North American populations and recent central, and South Americans.

History of modern human population structure inferred from the worldwide survey on Xp11.22 sequences.

M. K. Shimada et al.

For study of human evolution, using DNA sequence data, long lengths are required because of low mutation rates. However long sequences have a higher probability that recombination has occurred in the region in the evolutionary history. On the other hand, microsatellite data have a high mutation rate but tend to have too much homoplasy. The limitations of different types of data are one reason why different studies have different conclusions regarding human evolutionary history.

We sequenced a 10.1-kilobase pair region of the X chromosome, from 650 individuals from 50 populations. The sequenced region includes two microsatellites. The conjunction of sequence variation with tightly linked microsatellite variation allows each type of data to overcome the limitations of the other.

We found very little evidence of recombination within the region. Most sequences are quite similar to one another, however three sequences differed from the others at an average of 28.6 substitutions. Assuming a molecular clock, and a human/chimpanzee divergence time of 6 million years, the estimated age of the base of the human sequences is 1.1 million years ago, whereas the estimated base of the tree excluding these divergent human sequences is 290,000 years ago. These divergent sequences were found in samples from the Middle East (Druze and Bedouin populations) and North Africa (Mozabite population). The pattern is suggestive of admixture between non-African Archaic humans and Modern Humans.

Demographic history of African populations inferred from mtDNA analysis.

S.A. Tishkoff et al.

The continent of Africa is thought to be the homeland of all modern humans; it contains the largest amount of human genetic variation, both within and between populations, and the oldest genetic lineages. We have collected an unparalleled resource of genomic DNA samples from >4000 individuals originating from ethnically defined populations across Africa. At the same time, extensive pedigree, linguistic, ethnic, geographic and physiological data was also recorded for many of these individuals. Here we describe our analysis of mtDNA variation obtained from sequencing 1200bp of the control region and genotyping 6 coding-region SNPs mtDNA analysis of a subset of coding-region SNPs in 650 ethnically diverse Tanzanians and from sequencing 40 whole mtDNA genomes (~16,000 bp/genome). We have used coalescence based maximum likelihood simulations to estimate multiple demographic parameters including historic population size, bi-directional migration, time of population divergence, and time of most recent common ancestry of DNA lineages from these data. We observe recent gene flow between populations and phylogenetic analyses show that Tanzanian mtDNA lineages form the most basal branches of the global mitochondrial tree, suggesting that the range expansion of modern humans may have originated in East Africa. Additionally, we find common ancestry of the Hadza and Sandawe Khoisan (click)-speaking populations of Tanzania and that the Sandawe have had historical gene flow and/or common ancestry with southern African !Kung San, supporting the hypothesis that Khoisan speakers may have originated in East Africa.

On the origins of strong polygyny and socially imposed monogamy in humans.

C.P. van Schaik et al.

Because humans show pair-bonding, the environmental potential for despotism is reflected in social polgyny. We first show that increased despotism is expected under a general primate model of male-male coalitions, where the egalitarian system of mobile hunter-gatherers, maintained by large-scale leveling coalitions, is replaced by a despotic system with violent, revolutionary coalitionary takeovers of top ranks. Humans also differ from the other primates in that groups are spatially subdivided, which can produce cliques or class structure. Historically, however, some societies have shown a return to more egalitarian social relationships among males. We present a concession model, in which high-ranking males recruit support from lower-ranking males by granting them more reproductive success. A critical prediction is that transitions to social monogamy or dissolution of castes are found in societies under enemy occupation or involved in a desperate war.

In this paper we investigate the importance of predators in limiting primate populations by testing the following predictions using data taken from the primate literature. First, we predict that habituated primate populations experiencing reduced predation risk due to continuous human presence increase in numbers, at least during the initial years of human presence, whereas unhabituated populations do not. Second, we predict that population densities of primate species in otherwise similar forests in which carnivore predators have disappeared should be lower than those in forests with predators. The results allow us to estimate the relative magnitude of the effect of carnivore predators on primate populations. We discuss the implications of these results for primate population ecology and conservation biology.

A mesio-buccal mandibular molar trait in ancient populations of Ireland.

J.D. Weets

In this poster, previously unpublished variation of a human dental trait in permanent mandibular molars is described. The character, presently labeled IMMP (the Irish Mandibular Molar Pit), is situated anterior to the position occupied by the protostylid on the buccal aspect of cusp 1, and is most commonly found on third molars. IMMP occurred in 32.6% of 126 lower right third molars and 28.3% of 131 lower left third molars from archaeological specimens dating to the Neolithic (c. 4000-1800 BC) through the Early Christian era (c. AD 400-1170) in Ireland. The character was tested for variation in its geographic and temporal distribution across the island. No significant differences were found in its occurrence between time periods, nor between regions of Ireland. But, a lack of significant variation between the island’s ancient populations in other dental traits has been noted by the author in further research. Interestingly, an individual Viking specimen from Ireland exhibited IMMP. Personal correspondence with another dental anthropologist suggests the trait is present, at a much lower rate of expression, in East Asian populations (approximately 1-2% of his sample). These two findings indicate a widespread geographic occurrence that prompts more investigation of IMMP in other populations. Furthermore, marked difference of expression between populations from Ireland and East Asia suggest the trait will distinguish, at the very least, distant geographical populations and may make IMMP a useful addition to the suite of morphological traits utilized by dental anthropologists in biodistancing studies.

Mitochondrial DNA Variation in Northern Altaians: affinities with Siberian and Turkic populations.

S.I. Zhadanov et al.

Altaian peoples are the descendants of ancient (non-Turkic) inhabitants of this mountainous area who mixed with various waves of Turkic speaking nomads, beginning about 2,000 years ago. They are divided into northern and southern groups that are known to be physically, culturally and linguistically distinctive. Morphologically, the Southern Altai-kizhi generally exhibit stronger affinities with Mongolian and East Asian groups, whereas Northern Altaians, including Tubalars, Chelkans and Kumandinians, show some affinities with West Eurasian and Uralic groups. Initial genetic studies involving Altai-kizhi tribes have also revealed them to have considerable genetic diversity with influences from both West and East Eurasian populations. However, Northern Altaian groups as a whole are less well genetically characterized. To clarify this pattern of biological diversity in the Altai region, we surveyed mtDNA variation in several Northern Altaians population from the Altai Republic, and compared the resulting data with the Altai-kizhi and other Siberian and Turkic speaking groups from the region. In addition, we combined the extensive genealogical and demographic data with the mtDNA data from these populations to more accurately reconstruct the prehistory of the Altai Mountain region, including the assessment of Altaian population structure as reckoned by oral histories and tribal clan (seok) membership.