Instantaneous vs. continuous admixture dynamics (Jin et al. 2012)

A new paper in AJHG discusses the distribution of chromosomal segments of distinct ancestry (CSDAs) under three different models of admixture dynamics (left). In the hybrid isolation (HI) model, admixture is instantaneous and results in a hybrid population that evolves with drift and recombination only. In the gradual admixture (GA) model, the hybrid population continues to receive admixture from the unadmixed parental populations. Finally, in the continuous gene flow model (CGF), one of the populations becomes admixed while the other continues to exist unadmixed and to contribute to the admixed one.

In practical terms, the HI model results in the diminution of CSDA length due to recombination over time, and at "present" there is a paucity of long CSDAs. In the GA model there are more long CSDAs for both populations, while in the CGF model there is an asymmetry in the CSDAs donated by Pop1 and Pop2, with those from the "donor" population being longer (because fresh "long" segments are added in every generation).

The conclusions of the paper regarding some particular admixture cases are also interesting. For African Americans:

Although the actual population admixture of African Americans might be more complex than what our simulation suggested, the CGF1 model setting at 14 generations was found to be reasonably  epresentative, capturing the main pattern of the population admixture dynamics.

The CGF1 model has Africans as recipients and Europeans as donors. This makes sense, since African Americans are descended from slaves who were transported to the New World, with the slave trade ending centuries ago, hence there was mostly no replenishment of the AA population with fresh African-origin individuals. On the other hand, European Americans, both due to social dynamics and their numerical majority continued to exist as a distinct population that contributed to the AA population.

I should mention that according to HAPMIX, the admixture time was 7 generations, with is close to the 6 +/- 1 generations inferred by rolloff analysis by Moorjani et al. So, in this case this admixture time appears to be an "average" of a continuing process of admixture that began 14 generations ago.

Onto Mexicans:

In short, the GA model at 24 generations fit the empirical data best among all these simulated scenarios, as indicated by the distribution of EMDs.

Again, this makes sense, because in Mexico there continued to exist unadmixed populations of Europeans and Amerindians that contributed to the Mestizo population of the country.

On the African admixture in Mozabites:

Comparing the empirical distribution of CSDAs with that simulated, we found that the Mozabite admixture process essentially fit the HI model with 100 generations since admixture. There was an almost complete absence of recent gene flow from European populations to the Mozabite gene pool (Figure 6A). For the Sub-Saharan African ancestral component, there were more long CSDAs at the tail of empirical distribution than those in the HI model, which confirmed that recent gene flow from African populations had contributed to the Mozabite gene pool (Figure 6B). 

Again, this makes sense: Berber groups were not replenished from other Caucasoid sources, so their original admixture with native Africans resulted in a blend that persisted largely unaffected by "Europeans", but did find occasion of admixture with Sub-Saharans. Hence, the asymmetry in the presence of long "European" vs. "Sub-Saharan" segments.

A similar pattern was evident for Bedouin, Palestinians, and Druze:

Analyses of European ancestral component in Bedouin and Palestinian populations also showed that the empirical distributions essentially fit the HI model for both populations (Figures 6C and 6E). Although the empirical CSDA distribution of Sub-Saharan African ancestral component also fit the HI model  best, both distributions showed a long tail at the right compared with those under the HI model, indicating that recent gene flow from Sub-Saharan Africans also contributed to the two admixed populations (Figures 6D and 6F). ... For Druze, their European component of ancestry fit the HI model very well. However, their African ancestral component contained much shorter CSDAs than those of simulated (Figure S14), which might indicate that previous studies had underestimated the admixture time of Druze. In addition, populations receiving recent gene flow from their parental populations showed higher variation of individual ancestral proportions than those who did not (Figure S13).

The Druze have well-known Egyptian connections, and they may have largely avoided Sub-Saharan African admixture during the Islamic period, principally because of its avoidance of proselytism. Hence, their African admixture may stem from Egyptian adherents who were themselves a product of much earlier Caucasoid/Sub-Saharan admixture during the course of pre-Islamic Egypt.


The American Journal of Human Genetics, 25 October 2012 doi:10.1016/j.ajhg.2012.09.008

Exploring Population Admixture Dynamics via Empirical and Simulated Genome-Wide Distribution of Ancestral Chromosomal Segments

Wenfei Jin et al

Abstract

The processes of genetic admixture determine the haplotype structure and linkage disequilibrium patterns of the admixed population, which is important for medical and evolutionary studies. However, most previous studies do not consider the inherent complexity of admixture processes. Here we proposed two approaches to explore population admixture dynamics, and we demonstrated, by analyzing genome-wide empirical and simulated data, that the approach based on the distribution of chromosomal segments of distinct ancestry (CSDAs) was more powerful than that based on the distribution of individual ancestry proportions. Analysis of 1,890 African Americans showed that a continuous gene flow model, in which the African American population continuously received gene flow from European populations over about 14 generations, best explained the admixture dynamics of African Americans among several putative models. Interestingly, we observed that some African Americans had much more European ancestry than the simulated samples, indicating substructures of local ancestries in African Americans that could have been caused by individuals from some particular lineages having repeatedly admixed with people of European ancestry. In contrast, the admixture dynamics of Mexicans could be explained by a gradual admixture model in which the Mexican population continuously received gene flow from both European and Amerindian populations over about 24 generations. Our results also indicated that recent gene flows from Sub-Saharan Africans have contributed to the gene pool of Middle Eastern populations such as Mozabite, Bedouin, and Palestinian. In summary, this study not only provides approaches to explore population admixture dynamics, but also advances our understanding on population history of African Americans, Mexicans, and Middle Eastern populations.

Link

Refinement of ancestry informative markers in Europeans (Tian et al. 2009)

From the paper:

In general, Fst values corresponded to geographical relationships with smaller values between population groups with origins in neighboring countries/regions (e.g. Tuscan/Greek, Fst = 0.001) compared with those from very different regions in Europe (e.g. Russian/Palestinian, Fst = 0.020) similar to previous studies [10].

...

The current study extends the analysis of European population genetic structure to include additional southern European groups and Arab populations. Even within Italy, the relative position of northern Italians compared with subjects from Tuscany is consistent with the general geographic correspondence of PCA results. Interestingly, the majority of Italian Americans (NYCP 4 grandparent defined) appear to derive from southern Italy and overlap with subjects of Greek heritage. Both of these observations are consistent with previous historical information [30,31].

The paired Fst table confirms that the closest population to Greeks are Italians (negative Fst=-0.0001) and Tuscans (Fst=0.0005). Much further apart are Spaniards (Fst=0.0035) and Germans (Fst=0.0039), who are still much closer than the most distant Russians (Fst=0.0108) and Orcadians (Fst=0.103).

The low genetic distance between Greeks and Italians (the lowest in the table), suggests, once again, that southern Italians are little more than Latin-speaking Greeks as their history suggests, without discounting the possibility that they have experienced some non-Greek admixture.

Also of interest is the proximity of Ashkenazi Jews to Greeks and Italians which are about twice closer to them than Bedouins, Palestinians, or Druze from the Near East. As I have argued before, a major component in the ancestry of Jews was picked up in Hellenistic-Roman times; most published models of Ashkenazi Jewish origins have only considered admixture between a Near Eastern component with a northern European (German-Slavic) component. Indeed, Ashkenazi Jews are closer to several European populations than they are to Middle Eastern ones

However, as the PCA analysis shows, Ashkenazi Jews are distinct from both Europeans and non-Jewish Middle Eastern populations and cannot be viewed as a simple mix of the two; their distinctiveness must be -in part- due to the specific features of the small founder population of that community after it became effectively reproductively semi-isolated from gentiles after Roman times. It would be interesting to see different Jewish communities studied in the context of a broad variety of European and Middle Eastern populations, to determine whether Ashkenazi distinctiveness is specifically Ashkenazi or more generally Jewish distinctiveness; I would bet on a combination of the two.

Also of interest is the analysis of European populations in comparison to South Asian Burusho and Balochi, which shows on the one hand, substantial homogeneity of West Eurasians compared to South Asians, but also, to some extent, the transitional nature of some populations such as Bedouins or Adygei.

Related: A previous article by Tian et al.

UPDATE (Aug 29)

The PCA analysis is also quite interesting:

Some observations:

• In Α we see a west-east differentiation in northern Europe, with Irish and Russians in the two ends of PC1.
• In Β we see differentiation of non-Jewish southern European populations from Ashkenazi Jews along PC1 and from Druze, Palestinians, and Bedouins, along PC2. Greeks are concentrated near the center at the lower left quadrant.
• In C we see all the populations using only ancestry-informative markers and in D with all 270k markers. The two plots are similar, although use of the full set results in clearer results. We observe a cline of populations from the Near East to Northern Europe at the bottom. A little discontinuity between Greeks and Arabs would probably disappear if geographically intermediate populations had been included. Ashkenazi Jews are differentiated from the entire sample, suggesting that due to genetic drift, selection, or cryptic other ancestry (?) they cannot be reckoned as a simple European-Near Eastern mix genetically.

UPDATE (Aug 30):

Here is a dendrogram I created based on the paired Fst table from the paper. It is of course better to refer to the original table, but the plot, nonetheless shows in a different form "southern" (divided into European and Arab clusters) and "northern" (divided into "western" and "eastern" clusters).

Also a dendrogram after removing the island populations of Orkney and Sardinia, and the non-IE Basques.

Mol Med. 2009 Aug 24. [Epub ahead of print]

European Population Genetic Substructure: Further Definition of Ancestry Informative Markers for Distinguishing Among Diverse European Ethnic Groups.

Tian C, Kosoy R, Nassir R, Lee A, Villoslada P, Klareskog L, Hammarström L, Garchon HJ, Pulver AE, Ransom M, Gregersen PK, Seldin MF.

The definition of European population genetic substructure and its application to understanding complex phenotypes is becoming increasingly important. In the current study using over 4000 subjects genotyped for 300 thousand SNPs we provide further insight into relationships among European population groups and identify sets of SNP ancestry informative markers (AIMs) for application in genetic studies. In general, the graphical description of these principal components analyses (PCA) of diverse European subjects showed a strong correspondence to the geographical relationships of specific countries or regions of origin. Clearer separation of different ethnic and regional populations was observed when northern and southern European groups were considered separately and the PCA results were influenced by the inclusion or exclusion of different self-identified population groups including Ashkenazi Jewish, Sardinian and Orcadian ethnic groups. SNP AIM sets were identified that could distinguish the regional and ethnic population groups. Moreover, the studies demonstrated that most allele frequency differences between different European groups could be effectively controlled in analyses using these AIM sets. The European substructure AIMs should be widely applicable to ongoing studies to confirm and delineate specific disease susceptibility candidate regions without the necessity to perform additional genome-wide SNP studies in additional subject sets.

Link

The Druze as a population genetic refugium of the Near East

Table S2 has the data.

PLoS ONE 3(5): e2105. doi:10.1371/journal.pone.0002105

The Druze: A Population Genetic Refugium of the Near East

Liran I. Shlush et al.

Abstract

Background

Phylogenetic mitochondrial DNA haplogroups are highly partitioned across global geographic regions. A unique exception is the X haplogroup, which has a widespread global distribution without major regions of distinct localization.

Principal Findings

We have examined mitochondrial DNA sequence variation together with Y-chromosome-based haplogroup structure among the Druze, a religious minority with a unique socio-demographic history residing in the Near East. We observed a striking overall pattern of heterogeneous parental origins, consistent with Druze oral tradition, together with both a high frequency and a high diversity of the mitochondrial DNA (mtDNA) X haplogroup within a confined regional subpopulation. Furthermore demographic modeling indicated low migration rates with nearby populations.

Conclusions

These findings were enabled through the use of a paternal kindred based sampling approach, and suggest that the Galilee Druze represent a population isolate, and that the combination of a high frequency and diversity of the mtDNA X haplogroup signifies a phylogenetic refugium, providing a sample snapshot of the genetic landscape of the Near East prior to the modern age.

Link

Christian and Muslim Lebanese do differ from each other after all

Like I said they did in 2007. BBC has a story about this:

The team analysed the Y chromosomes of 926 Lebanese males and found that patterns of male genetic variation in Lebanon fell more along religious lines than along geographical lines.

A genetic signature on the male chromosome called WES1, which is usually only found in European populations, was found among the Lebanese men included in the study.

"It seems to have come in from Europe and is found mostly in the Christian population," said Dr Spencer Wells, director of the Genographic Project.

"This is odd because typically we don't see this sort of stratification by religion when we are looking at the relative proportions of these lineages - and particularly immigration events."

He told BBC News: "Looking at the same data set, we saw a similar enrichment of lineages coming in from the Arabian Peninsula in the Muslim population which we didn't see [as often] in the Christian population."

Lebanese Muslim men were found to have high frequencies of a Y chromosome grouping known as J1. This is typical of populations originating from the Arabian Peninsula, who were involved in the Muslim expansion.

As I predicted, the finding of similarity between Christian and Muslim Lebanese in the older National Geographic story on Wells' and Zalloua's work was premature, based on their common possession of Y-haplogroup J, because it did not look at downstream markers which differentiate between Christians and Muslims. As I observed based on the work of Capelli et al., it is the overrepresentation of Y-haplogroup J*(xJ2), which comprises almost entirely of J1 chromosomes that is the mark of the Arab descent of Muslim Lebanese.

I will post the abstract of this study and any further comments when I see it.

UPDATE: The Genographic project has its own page on this research, as well as a link to the paper (pdf).

Y-Chromosomal Diversity in Lebanon Is Structured by Recent Historical Events

Pierre A. Zalloua et al.

Lebanon is an eastern Mediterranean country inhabited by approximately four million people with a wide variety of ethnicities and religions, including Muslim, Christian, and Druze. In the present study, 926 Lebanese men were typed with Y-chromosomal SNP and STR markers, and unusually, male genetic variation within Lebanon was found to be more strongly structured by religious affiliation than by geography.We therefore tested the hypothesis that migrations within historical times could have contributed to this situation. Y-haplogroup J*(xJ2) was more frequent in the putative Muslim source region (the Arabian Peninsula) than in Lebanon, and it was also more frequent in Lebanese Muslims than in Lebanese non-Muslims. Conversely, haplogroup R1b was more frequent in the putative Christian source region (western Europe) than in Lebanon and was also more frequent in Lebanese Christians than in Lebanese non-
Christians. The most common R1b STR-haplotype in Lebanese Christians was otherwise highly specific for western Europe and was unlikely to have reached its current frequency in Lebanese Christians without admixture.We therefore suggest that the Islamic expansion from the Arabian Peninsula beginning in the seventh century CE introduced lineages typical of this area into those who subsequently became Lebanese Muslims, whereas the Crusader activity in the 11th-13th centuries CE introduced western European lineages into Lebanese Christians.

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.

Samaritan mtDNA and Y chromosomes

Hum Mutat. 2004 Sep;24(3):248-60.

Reconstruction of patrilineages and matrilineages of Samaritans and other Israeli populations from Y-Chromosome and mitochondrial DNA sequence Variation.

P. Shen et al.

The Samaritan community, which numbered more than a million in late Roman times and only 146 in 1917, numbers today about 640 people representing four large families. They are culturally different from both Jewish and non-Jewish populations in the Middle East and their origin remains a question of great interest. Genetic differences between the Samaritans and neighboring Jewish and non-Jewish populations are corroborated in the present study of 7,280 bp of nonrecombining Y-chromosome and 5,622 bp of coding and hypervariable segment I (HVS-I) mitochondrial DNA (mtDNA) sequences. Comparative sequence analysis was carried out on 12 Samaritan Y-chromosome, and mtDNA samples from nine male and seven female Samaritans separated by at least two generations. In addition, 18-20 male individuals were analyzed, each representing Ethiopian, Ashkenazi, Iraqi, Libyan, Moroccan, and Yemenite Jews, as well as Druze and Palestinians, all currently living in Israel. The four Samaritan families clustered to four distinct Y-chromosome haplogroups according to their patrilineal identity. Of the 16 Samaritan mtDNA samples, 14 carry either of two mitochondrial haplotypes that are rare or absent among other worldwide ethnic groups. Principal component analysis suggests a common ancestry of Samaritan and Jewish patrilineages. Most of the former may be traced back to a common ancestor in the paternally-inherited Jewish high priesthood (Cohanim) at the time of the Assyrian conquest of the kingdom of Israel.

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