New A00 project

A new project dedicated to Y-haplogroup A00 is seeking funding. A00 is the most basal clade of the human Y-chromosome phylogeny and has so far been found in African Americans and Mbo people from Cameroon. This is how the funds raised will be used:

In this campaign, we're seeking the funds we need to launch our first phase of fieldwork in late August, 2013. Our overall research plan includes five field trips to sample peoples in different regions of the country. In the first trip, Matthew will travel to the remote rural villages where he was raised, in the mountainous, forested Nkongho-Mbo region, and collect at least 100 samples from three villages, which will then be sent to a lab to be screened for A00. More in-depth testing will focus on those A00 samples. 

Planning and discussions are underway regarding which labs, probably more than one, will perform both SNP and STR testing on the samples. A full Y-chromosome sequence is on our wish list. This fundraising campaign, our first, will be limited to funding the DNA collection fieldwork. We'll be asking for your donations for lab testing in a separate campaign, in the near future. We need to limit the total amount of each fundraising campaign's goal to a modest amount we have some confidence of achieving within the set time, due to the all-or-nothing system used by Microryza.

 A00 is separated from the rest of mankind by >200 thousand years, but how closely related are different A00 chromosomes? It is necessary to have multiple samples to attempt to answer that question; I think it is quite probable that A00 is not limited to the area of Cameroon where it was discovered, but it probably makes sense to focus on it, since it is most likely to yield additional A00 samples given a sample size of 100.

A full Y-chromosome sequence of an A00 chromosome would also be very useful, since it would allow us to estimate its divergence from the A0-T remainder of mankind more securely.

The $2,500 they are seeking to launch their first field trip seems like a bargain to me.

Phylogeography of Bantu languages (Currie et al. 2013)

Proc. R. Soc. B 7 July 2013 vol. 280 no. 1762 20130695

Cultural phylogeography of the Bantu Languages of sub-Saharan Africa

Thomas E. Currie et al.

There is disagreement about the routes taken by populations speaking Bantu languages as they expanded to cover much of sub-Saharan Africa. Here, we build phylogenetic trees of Bantu languages and map them onto geographical space in order to assess the likely pathway of expansion and test between dispersal scenarios. The results clearly support a scenario in which groups first moved south through the rainforest from a homeland somewhere near the Nigeria–Cameroon border. Emerging on the south side of the rainforest, one branch moved south and west. Another branch moved towards the Great Lakes, eventually giving rise to the monophyletic clade of East Bantu languages that inhabit East and Southeastern Africa. These phylogenies also reveal information about more general processes involved in the diversification of human populations into distinct ethnolinguistic groups. Our study reveals that Bantu languages show a latitudinal gradient in covering greater areas with increasing distance from the equator. Analyses suggest that this pattern reflects a true ecological relationship rather than merely being an artefact of shared history. The study shows how a phylogeographic approach can address questions relating to the specific histories of certain groups, as well as general cultural evolutionary processes.

Link

Extremely old (237–581 kya) root of human Y-chromosome phylogeny

I had mentioned this research before, and now it has officially been published. There are three things to be excited about this new paper:

First, it forces us to consider the possibility of either (i) archaic admixture in Africa, or (ii) a much more ancient time depth of modern humans than the first fossils from Ethiopia dated to about ~200 thousand years ago.

Second, it underscores the importance of collaboration between academia and regular folk, since it was the combined contributions of academics, genetic genealogists, and the owners of the new A00 basal Y-chromosomes that made this new discovery possible.

And, third, it shows that the extraordinary can be discovered without contacting isolated tribes or seeking human bones in remote regions, but rather through careful scrutiny of large volumes of data for the proverbial needle in the haystack.

The paper developed a model of Y-chromosome mutation based on the estimate of Kong et al. Significantly, though:

If we were to use the higher mutation rate (1.0x10^-9 per base per year6) rather than a realistic range derived from whole-genome sequencing (4.39x10^-9  -   7.07x10^- 9), the estimated TMRCA for the tree incorporating A00 as the basal lineage would be 209 kya, which is only slightly older than current estimates of the TMRCA of mtDNA and the age of the oldest AMH fossil remains. We note, however, that the higher mutation rate produces an estimate for the common ancestor of all non-African Y chromosome haplogroups (C through T) of ~39 kya6 (i.e., versus ~63 kya for the mutation rate used here).

A 39kya common ancestor for Eurasian Y-chromosomes makes no sense, since we now know for sure that by that time, the differentiation of Eurasians was already well on its way and modern humans in remote parts of the Old World have been documented much earlier than that time.

A ~63kya common ancestor, on the other hand, fits nicely with my "two deserts" theory of modern human origins, according to which the ancestors of Eurasians faced an ecological crisis in Arabia when it became much drier post-70kya; that seems like a most opportune time for the major Eurasian bottleneck and the corresponding coalescence of Eurasian Y-chromosomes to a single man. And, while there is no a priori reason for Y chromosomes and mtDNA to behave similarly, the age of the "older" Eurasian ur-mother, haplogroup N at 59 thousand years, with presumably an older ancestor within mtDNA haplogroup L3 founding the Eurasian population.

Also, if modern human-Neandertal admixture had occurred  "most likely 47,000–65,000 years ago", then the expansion of modern Proto-Eurasians within a 70-60kya timeframe north Out-of-Arabia would have brought them in contact with their northern Neandertal neighbors. On the other hand, it would be incredible if modern humans experienced admixture with Neandertals but were still much later a very small population (to allow for the coalescence of their Y-chromosomes to one man ~39kya).


So, in summary, the mutation rate used by the authors seems consistent with what we know about an important calibration point of the human story.

But, who were the people in Africa responsible for the introgression of A00 chromosomes? Mendez et al. used the haplotype of the African American A00 individual and discovered his patrilineal kin among the Mbo of Cameroon, who are Bantu farmers. 

I have observed before that Pygmies and Bushmen represent only a tiny fraction of pre-existing African genetic diversity, the part that had not yet been absorbed into the farmers' expanding population by the time that Africa came to the attention of of modern science. We see traces of Pygmy and Bushman ancestry in some African farmers, and there were probably other groups, no longer extant as distinct ethno-cultural entities, but, nonetheless, surviving as genetic fragments in the genomes of the farmers.

Thus, while it still makes sense to study the surviving hunter-gatherers of Africa who make up perhaps a percent or less of the population of Africa, it may be equally important to study different groups of African farmers who may possess a much richer treasure trove (albeit diluted) of such "Palaeoafrican" ancestry.

Finally:

Although the stochastic nature of the evolutionary process can explain the aforementioned incongruences, the extreme age and rarity of the A00 lineage point to the possibility of a highly structured ancestral population, consistent with recent work on the autosomes.40,41,43,44 This could take the form of long-standing population structure among AMH populations45 or archaic introgression from an archaic form into the ancestors of AMHs.46 Interestingly, the Mbo live less than 800 km away from a Nigerian site known as Iwo Eleru, where human skeletal remains with both archaic and modern features were found and dated to ~13 kya.47 Further surveys in sub- Saharan Africa and in the African Diaspora might uncover more diverged basal lineages, which will help to disentangle some of the complex evolutionary processes that shape patterns of Y chromosome diversity.

AJHG 10.1016/j.ajhg.2013.02.002

An African American Paternal Lineage Adds an Extremely Ancient Root to the Human Y Chromosome Phylogenetic Tree 

Fernando L. Mendez et al.

We report the discovery of an African American Y chromosome that carries the ancestral state of all SNPs that defined the basal portion of the Y chromosome phylogenetic tree. We sequenced ∼240 kb of this chromosome to identify private, derived mutations on this lineage, which we named A00. We then estimated the time to the most recent common ancestor (TMRCA) for the Y tree as 338 thousand years ago (kya) (95% confidence interval = 237–581 kya). Remarkably, this exceeds current estimates of the mtDNA TMRCA, as well as those of the age of the oldest anatomically modern human fossils. The extremely ancient age combined with the rarity of the A00 lineage, which we also find at very low frequency in central Africa, point to the importance of considering more complex models for the origin of Y chromosome diversity. These models include ancient population structure and the possibility of archaic introgression of Y chromosomes into anatomically modern humans. The A00 lineage was discovered in a large database of consumer samples of African Americans and has not been identified in traditional hunter-gatherer populations from sub-Saharan Africa. This underscores how the stochastic nature of the genealogical process can affect inference from a single locus and warrants caution during the interpretation of the geographic location of divergent branches of the Y chromosome phylogenetic tree for the elucidation of human origins.

Link

New evidence for archaic admixture in African hunter gatherers (Lachance et al. 2012)

At the end of last year I predicted that full genome sequencing would begin turning up evidence for more archaic admixture in Africa. Halfway into the year, it appears that my prediction has proven to be correct: a new study in Cell by Lachance et al. documents the existence of such admixture between an archaic hominin and Pygmies from Cameroon, and the East African Hadza and Sandawe.

Archaic admixture in Biaka and San was previously detected by Hammer et al. Hence, we now have evidence for archaic admixture from several regions that encompass all major regions within sub-Saharan Africa. It seems that my old idea about layers of Palaeoafricans being absorbed by early modern humans in Africa was basically correct, and that some of these layers correspond to archaic African populations.

But not all agree. The New York Times coverage of the paper suggests that there is a controversy surrounding the new study:

All human fossil remains in Africa for the last 100,000 years, and probably the last 200,000 years, are of modern humans, providing no support for a coexistent archaic species. 

... 

Paleoanthropologists like Dr. Klein consider it “irresponsible” of the geneticists to publish genetic findings about human origins without even trying to show how they may fit in with the existing fossil and archaeological evidence. Dr. Akey said he agreed that genetics can provide only part of the story. “But hopefully this is just a period when new discoveries are being made and there hasn’t been enough incubation time to synthesize all the disparities,” he said.

This is of course completely wrong; as Chris Stringer mentions in the NY Times piece, there is ample evidence for archaic Africans down to quite recent times in the form of Iwo Eleru and Ishango, and there is more evidence besides. Indeed, it does not appear at all that there was a punctuational event that replaced archaic hominins with a new Homo sapiens species. If anyone wants to criticize the new study, complaining about it being in disharmony with physical anthropology is not a good way to go about it. Nor is it, of course, "irresponsible" to report the new findings.  And, apparently, there is more on the way:

In a report still under review, a third group of geneticists says there are signs of Neanderthals having interbred with Asians and East Africans. But Neanderthals were a cold-adapted species that never reached East Africa.

Things are bound to become quite interesting.

From the paper:

A striking finding in our data set is that compelling evidence exists that extant hunter-gatherer genomes contain introgressed archaic sequence, consistent with previous studies (Hammer et al., 2011; Plagnol and Wall, 2006; Reich et al., 2010; Shimada et al., 2007; Wall et al., 2009). We note that unambiguous evidence of introgression is difficult to obtain in the absence of an archaic reference sequence, which currently does not exist and may never be feasible given the rapid decay of fossils in Africa. Although we carefully filtered our data set in an attempt to analyze only high-quality sequences (Supplementary Information), it is possible that unrecognized structural variants or other alignment errors could generate a spurious signature similar to introgression. Encouragingly, we did not see an enrichment of structural variation calls in our candidate introgression regions. Additionally, through extensive simulations and analysis of European whole-genome sequences (Supplementary Information), we have demonstrated that the signatures of introgression that we observed are unlikely to be entirely accounted for due to other aspects of population demographic history, natural selection, or sequencing errors. Moreover, we did not find strong evidence that introgressed regions were clustered in the genome more often than expected by chance (p > 0.05; Supplemental Information). Nor did we find significant evidence that introgressed regions were enriched in genic regions (p > 0.05); rather, genic regions were significantly depleted for introgression in several populations (Supplemental Information). Therefore, the simplest interpretation of these data is that introgressed regions in extant human populations represent neutrally evolving vestiges of archaic sequences. In short, we find that low levels of introgression from an unknown archaic population or populations occurred in the three African hunter-gatherer samples examined, consistent with findings of archaic admixture in non-Africans (Reich et al., 2010). 

What are the implications of the new research? Where did modern humans actually originate and how can their archaic admixture be explained?

One possible explanation, consistent with multi-regional evolution (MRE) theory, is that modern humans didn't originate anywhere in particular; they emerged out of Homo populations that lived everywhere. And, certainly, the discovery of archaic admixture of a local origin is quickly reducing the number of places where the common ancestors of modern humans could have begun their expansion. Western Eurasia is out due to Neandertals; East Eurasia and Oceania is out due to Denisovans; the entirety of Sub-Saharan Africa seems to also be out. North Africa and Southwest Asia appear to be the only remaining candidates.

I don't particularly agree with MRE; one of its predictions (about the relevance of archaic hominins to the human story) has proven to be correct: it increasingly seems that there never was a new Homo sapiens species that was in reproductive isolation from the rest of the Homo genus. On the other hand, the existence of local admixture with different sets of archaic hominins, together with the relative homogeneity of our species is indicative of a range expansion that largely replaced archaic humans -- but not completely.

There does seem to have been a Big Bang of modern humans which caused the demographical explosion of a particular subset of genetic variation. This Big Bang is often associated with Out-of-Africa, but there are good reasons to doubt the traditional 60,000-year old Out-of-Africa theory, according to which humans from South or East Africa crossed into Arabia and followed the coast to populate the world. We now have more reasons to doubt this: evidence of archaic admixture in both the postulated homelands: South Africa, often cited as the region where the first signs of behavioral modernity appear, and East Africa, where the earliest anatomically modern human fossils appear.

My money continues to be on the "two deserts" theory I have proposed some time ago:

• A green Sahara pumping the ancestors of modern humans pre-100 thousand years ago, and 
• a deteriorating green Arabia pumping them post-70 thousand years ago, with some back-migration into Africa.

This would relate the two regions where no evidence (yet?) for archaic humans exist (North Africa and South West Asia), explain the causes of their dispersal (climate change), and harmonize with the evidence for archaic admixture, since the expanding wave of modern humans would partially absorb pre-existing hominins in both Sub-Saharan Africa and across Eurasia.


It must be noted that scientists have been rather conservative in their estimates of archaic admixture in the absence of ancient DNA sequence. Recombination obliterates traces of really old admixture, because introgressed segments become ever smaller, resulting in a pastiche of modern and archaic sequence that no longer looks statistically archaic. But, hopefully, the ever-solidifying case for archaic admixture in our species will finally deal the death blow to tree models, and reveal a much more interesting story of our origins.


Other coverage of the new paper: Nature, Science, ScienceDaily, EurekAlert, Washington Post, SciAm.


Cell doi:10.1016/j.cell.2012.07.009

Evolutionary History and Adaptation from High-Coverage Whole-Genome Sequences of Diverse African Hunter-Gatherers

Joseph Lachance et al.


To reconstruct modern human evolutionary history and identify loci that have shaped hunter-gatherer adaptation, we sequenced the whole genomes of five individuals in each of three different hunter-gatherer populations at >60x coverage: Pygmies from Cameroon and Khoesan-speaking Hadza and Sandawe from Tanzania. We identify 13.4 million variants, substantially increasing the set of known human variation. We found evidence of archaic introgression in all three populations, and the distribution of time to most recent common ancestors from these regions is similar to that observed for introgressed regions in Europeans. Additionally, we identify numerous loci that harbor signatures of local adaptation, including genes involved in immunity, metabolism, olfactory and taste perception, reproduction, and wound healing. Within the Pygmy population, we identify multiple highly differentiated loci that play a role in growth and anterior pituitary function and are associated with height.


Link

Genetic variation in Cameroon

American Journal of Physical Anthropology doi:10.1002/ajpa.21088

A multi-perspective view of genetic variation in Cameroon

V. Coia et al.

Abstract

In this study, we report the genetic variation of autosomal and Y-chromosomal microsatellites in a large Cameroon population dataset (a total of 11 populations) and jointly analyze novel and previous genetic data (mitochondrial DNA and protein coding loci) taking geographic and cultural factors into consideration. The complex pattern of genetic variation of Cameroon can in part be described by contrasting two geographic areas (corresponding to the northern and southern part of the country), which differ substantially in environmental, biological, and cultural aspects. Northern Cameroon populations show a greater within- and among-group diversity, a finding that reflects the complex migratory patterns and the linguistic heterogeneity of this area. A striking reduction of Y-chromosomal genetic diversity was observed in some populations of the northern part of the country (Podokwo and Uldeme), a result that seems to be related to their demographic history rather than to sampling issues. By exploring patterns of genetic, geographic, and linguistic variation, we detect a preferential correlation between genetics and geography for mtDNA. This finding could reflect a female matrimonial mobility that is less constrained by linguistic factors than in males. Finally, we apply the island model to mitochondrial and Y-chromosomal data and obtain a female-to-male migration N ratio that was more than double in the northern part of the country. The combined effect of the propensity to inter-populational admixture of females, favored by cultural contacts, and of genetic drift acting on Y-chromosomal diversity could account for the peculiar genetic pattern observed in northern Cameroon.

Link

Y chromosomes of the Ruling Dynasty of the Nso' in Cameroon

From the paper:

The groups are (1) the won nto', descendants of a fon down to the third or fourth generation; (2) the duy, descendants of a fon who ruled more than three or four generations ago together with, according to Chem-Langhëë and Fanso (1997), some members of commoner lineages whose heads are descendants of princesses and members of associated patriclans or clan segments, allegedly founded by immigrant royals, that provide state counselors; (3) the nshiylav, subjects born or recruited2 into palace service (patrilineally inherited); and (4) the mtaar, commoners (patrilineally inherited). Although the majority of the Nso' are self-identifying Christians of the Roman Catholic denomination, the fon has, through the generations, maintained a polygynous household, which in 2005 numbered over 70 women.3

...

The most common NRY haplogroup in the won nto' was Y*(xBR,A3b2), with a frequency of 55.6% ( ; table 1). This haplogroup was also found at a frequency of 17.6% in the duy. Furthermore, all Y*(xBR,A3b2) chromosomes had the same microsatellite haplotype (14-12-20-11-14-14; ... For convenience only we refer to Y*(xBR,A3b2) and the associated microsatellite haplotype as the won nto' modal haplotype (WMH); it had ten representatives, while the next most frequent haplotype in the won nto' had only two. The modal NRY haplogroup in the non–won nto' social classes was E3a, with a diverse range of NRY types at the microsatellite haplotype level

...

A principal coordinates analysis plot (fig. 2) based on a pairwise FST distance matrix calculated using NRY haplogroup frequencies (see table F1 for genetic distances and associated P values) clearly distanced the won nto' from both the other Nso' social classes and other ethnic groups, demonstrating that high frequencies of Y*(xBR,A3b2) are not typical of Grassfields and Tikar Plain NRY profiles. Accordingly, because Y*(xBR,A3b2) is typical of a hunter-gatherer population and the WMH is the most likely candidate to be the NRY type of the father of the first Nso' fon, the NRY data favor the oral tradition that the princess married an indigenous Visale, from whom all subsequent fons descend.

Current Anthropology doi: 10.1086/590119

Sex-Specific Genetic Data Support One of Two Alternative Versions of the Foundation of the Ruling Dynasty of the Nso' in Cameroon

Krishna R. Veeramah et al.

Abstract

Sex-specific genetic data favor a specific variant of the oral history of the kingdom of Nso' (a Grassfields city-state in Cameroon) in which the royal family traces its descent from a founding ancestress who married into an autochthonous hunter-gatherer group. The distributions of Y chromosome and mitochondrial DNA variation in the Nso' in general and in the ruling dynasty in particular are consistent with specific Nso' marriage practices, suggesting strict conservation of the royal social class along agnatic lines. This study demonstrates the efficacy of using genetics to augment other sources of information (e.g., oral histories, archaeology, and linguistics) when seeking to recover the histories of African peoples.

Link

Campbell & Tishkoff review paper on African genetic diversity

From the paper:

Several studies of nucleotide and haplotype variation have indicated that ancestral African populations were geographically structured prior to the migration of modern humans out of Africa (70, 71, 79, 157, 197, 237). Additionally, a recent study of 800 short tandem repeat polymorphisms (STRPs) and 400 INDELs genotyped in more than 3000 geographically and ethnically diverse Africans indicates the presence of at least 13 genetically distinct ancestral populations in Africa and high levels of population admixture in many regions (F.A. Reed & S.A Tishkoff, unpublished data). Population clusters are correlated with selfdescribed ethnicity and shared cultural and/or linguistic properties (e.g., Pygmies, Khoisanspeaking hunter-gatherers, Bantu speakers, Cushitic speakers). This study reveals extensive admixture between inferred ancestral populations in most African populations. One exception is amongWest African Niger-Kordofanian (i.e., Bantu) speakers who are more genetically homogeneous compared with other African populations, likely reflecting the recent and rapid spread of Bantu speakers from a common origin in Cameroon/Nigeria (although fine-scale genetic structure can be detected amongst these populations). Thus, the pattern of genetic diversity in Africa indicates that African populations have maintained a large and subdivided population structure throughout much of their evolutionary history (Figure 2).

As I have argued before, the great genetic diversity of Sub-Saharan Africans is due to the fact that they are composed of several long-differentiated populations admixed with each other. As Figure 2, mentioned above, indicates, NE Africans are related to Eurasians more closely than other Africans, although there has been subsequent gene flow into NE Africans from other Sub-Saharan Africans. Annual Review of Genomics and Human Genetics Vol. 9 (Volume publication date September 2008) (doi:10.1146/annurev.genom.9.081307.164258) African Genetic Diversity: Implications for Human Demographic History, Modern Human Origins, and Complex Disease Mapping Michael C. Campbell­, Sarah A. Tishkoff­ Comparative studies of ethnically diverse human populations, particularly in Africa, are important for reconstructing human evolutionary history and for understanding the genetic basis of phenotypic adaptation and complex disease. African populations are characterized by greater levels of genetic diversity, extensive population substructure, and less linkage disequilibrium (LD) among loci compared to non-African populations. Africans also possess a number of genetic adaptations that have evolved in response to diverse climates and diets, as well as exposure to infectious disease. This review summarizes patterns and the evolutionary origins of genetic diversity present in African populations, as well as their implications for the mapping of complex traits, including disease susceptibility. Link

mtDNA of Chad Basin populations

Annals of Human Genetics (OnlineEarly Articles)

A Bidirectional Corridor in the Sahel-Sudan Belt and the Distinctive Features of the Chad Basin Populations: A History Revealed by the Mitochondrial DNA Genome

V. Černý et al.

Summary

The Chad Basin was sparsely inhabited during the Stone Age, and its continual settlement began with the Holocene. The role played by Lake Chad in the history and migration patterns of Africa is still unclear. We studied the mitochondrial DNA (mtDNA) variability in 448 individuals from 12 ethnically and/or economically (agricultural/pastoral) different populations from Cameroon, Chad, Niger and Nigeria. The data indicate the importance of this region as a corridor connecting East and West Africa; however, this bidirectional flow of people in the Sahel-Sudan Belt did not erase features peculiar to the original Chad Basin populations. A new sub-clade, L3f2, is described, which together with L3e5 is most probably autochthonous in the Chad Basin. The phylogeography of these two sub-haplogroups seems to indicate prehistoric expansion events in the Chad Basin around 28,950 and 11,400 Y.B.P., respectively. The distribution of L3f2 is virtually restricted to the Chad Basin alone, and in particular to Chadic speaking populations, while L3e5 shows evidence for diffusion into North Africa at about 7,100 Y.B.P. The absence of L3f2 and L3e5 in African-Americans, and the limited number of L-haplotypes shared between the Chad Basin populations and African-Americans, indicate the low contribution of the Chad region to the Atlantic slave trade.

Link

Sexual preferences for human physique in Cameroon

Arch Sex Behav. 2006 Nov 30; [Epub ahead of print]

Human Physique and Sexual Attractiveness: Sexual Preferences of Men and Women in Bakossiland, Cameroon.

Dixson BJ, Dixson AF, Morgan B, Anderson MJ.

Men and women living in a rural community in Bakossiland, Cameroon were asked to rate the attractiveness of images of male or female figures manipulated to vary in somatotype, waist-to-hip ratio (WHR), secondary sexual traits, and other features. In Study 1, women rated mesomorphic (muscular) and average male somatotypes as most attractive, followed by ectomorphic (slim) and endomorphic (heavily built) figures. In Study 2, amount and distribution of masculine trunk (chest and abdominal) hair was altered progressively in a series of front-posed male figures. A significant preference for one of these images was found, but the most hirsute figure was not judged as most attractive. Study 3 assessed attractiveness of front-posed male figures which varied only in length of the non-erect penis. Extremes of penile size (smallest and largest of five images) were rated as significantly less attractive than three intermediate sizes. In Study 4, Bakossi men rated the attractiveness of back-posed female images varying in WHR (from 0.5-1.0). The 0.8 WHR figure was rated markedly more attractive than others. Study 5 rated the attractiveness of female skin color. Men expressed no consistent preference for either lighter or darker female figures. These results are the first of their kind reported for a Central African community and provide a useful cross-cultural perspective to published accounts on sexual selection, human morphology and attractiveness in the U.S., Europe, and elsewhere.

Link

mtDNA of Fulani nomads

Hum Biol. 2006 Feb;78(1):9-27

MtDNA of Fulani nomads and their genetic relationships to neighboring sedentary populations.

Cerný V, Hájek M, Bromová M, Cmejla R, Diallo I, Brdicka R

Despite the large size of the contemporary nomadic Fulani population (roughly 13 million people), the genetic diversity and degree of differentiation of Fulanis compared to other sub-Saharan populations remain unknown. We sampled four Fulani nomad populations (n = 186) in three countries of sub-Saharan Africa (Chad, Cameroon, and Burkina Faso) and analyzed sequences of the first hypervariable segment of the mitochondrial DNA. Most of the haplotypes belong to haplogroups of West African origin, such as L1b, L3b, L3d, L2b, L2c, and L2d (79.6% in total), which are all well represented in each of the four geographically separated samples. The haplogroups of Western Eurasian origin, such as J1b, U5, H, and V, were also detected but in rather low frequencies (8.1% in total). As in African hunter-gatherers (Pygmies and Khoisan) and some populations from central Tunisia (Kesra and Zriba), three of the Fulani nomad samples do not reveal significant negative values of Fu's selective neutrality test. The multidimensional scaling of FST genetic distances of related sub-Saharan populations and the analysis of molecular variance (AMOVA) show clear and close relationships between all pairs of the four Fulani nomad samples, irrespective of their geographic origin. The only group of nomadic Fulani that manifests some similarities with geographically related agricultural populations (from Guinea-Bissau and Nigeria) comes from Tcheboua in northern Cameroon.

Link

Lactase persistence in Africans and non-Africans

I had also posted before about lactose tolerance in Berbers. Interestingly:

While the current distribution of lactase persistence in Eurasia and the African Fulbe seems to be due to the dispersion of a single mutation, it is still unclear what is the significance of the recent finding that –13910*T allele is absent from most African populations in which high frequencies of lactase persistence have been previously found with physiological tests (Mulcare et al. 2004).

Human Genetics (online first)

Microsatellite variation and evolution of human lactase persistence

Margarida Coelho et al.

Abstract The levels of haplotype diversity within the lineages defined by two single-nucleotide polymorphisms (SNPs) (–13910 C/T and –22018 G/A) associated with human lactase persistence were assessed with four fast-evolving microsatellite loci in 794 chromosomes from Portugal, Italy, Fulbe from Cameroon, São Tomé and Mozambique. Age estimates based on the intraallelic microsatellite variation indicate that the –13910*T allele, which is more tightly associated with lactase persistence, originated in Eurasia before the Neolithic and after the emergence of modern humans outside Africa. We detected significant departures from neutrality for the –13910*T variant in geographically and evolutionary distant populations from southern Europe (Portuguese and Italians) and Africa (Fulbe) by using a neutrality test based on the congruence between the frequency of the allele and the levels of intraallelic variability measured by the number of mutations in adjacent microsatellites. This result supports the role of selection in the evolution of lactase persistence, ruling out possible confounding effects from recombination suppression and population history. Reevaluation of the available evidence on variation of the –13910 and –22018 loci indicates that lactase persistence probably originated from different mutations in Europe and most of Africa, even if 13910*T is not the causal allele, suggesting that selective pressure could have promoted the convergent evolution of the trait. Our study shows that a limited number of microsatellite loci may provide sufficient resolution to reconstruct key aspects of the evolutionary history of lactase persistence, providing an alternative to approaches based on large numbers of SNPs.

Link

Back-migration into Cameroon

The presence of R1* Y chromosomes in Cameroon is considered as evidence of a back migration from Eurasia into Sub-Saharan Africa. A new study of mtDNA in the region shows that Eurasian mtDNA is severely underrepresented, and hence either (i) there was biased male-mediated gene flow into the population, or (ii) the Eurasian mtDNA was lost due to drift.

An alternative explanation, not considered by the authors is that mtDNA, known to be involved in energy production, is subject to strong selection in different natural environments, and therefore, there may have been selection against Eurasian mtDNA after its initial introduction into the population.

American Journal of Physical Anthropology
Early View (Articles online in advance of print)

Brief communication: mtDNA variation in North Cameroon: Lack of asian lineages and implications for back migration from Asia to sub-Saharan Africa

Valentina Coia et al.

Abstract

The hypervariable region-1 and four nucleotide positions (10400, 10873, 12308, and 12705) of the coding region of mitochondrial DNA (mtDNA) were analyzed in 441 individuals belonging to eight populations (Daba, Fali, Fulbe, Mandara, Uldeme, Podokwo, Tali, and Tupuri) from North Cameroon and four populations (Bakaka, Bassa, Bamileke, and Ewondo) from South Cameroon. All mtDNAs were assigned to five haplogroups: three sub-Saharan (L1, L2, and L3), one northern African (U6), and one European (U5). Our results contrast with the observed high frequencies of a Y-chromosome haplogroup of probable Asian origin (R1*-M173) in North Cameroon. As a first step toward a better understanding of the evident discrepancy between mtDNA and Y-chromosome data, we propose two contrasting scenarios. The first one, here termed "migration and asymmetric admixture," implies a back migration from Asia to North Cameroon of a population group carrying the haplotype R1*-M173 at high frequency, and an admixture process restricted to migrant males. The second scenario, on the other hand, temed "divergent drift," implies that modern populations of North Cameroon originated from a small population group which migrated from Asia to Africa and in which, through genetic drift, Y-chromosome haplotype R1*-M173 became predominant, whereas the Asian mtDNA haplogroups were lost.

Link

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.