January 28, 2009

AAPA 2009 abstracts

The book of abstracts (pdfs) from the 2009 conference of the American Association of Physical Anthropologists has many interesting and important topics. I list the titles of those that caught my eye, with the full abstracts and some comments on some of them.

The first one is very important since it shows continuity between ancient Etruscans and medieval/Renaissance Tuscans, and discontinuity between the latter and modern Tuscans.

Recent demographic changes account for the genealogical discontinuity between Etruscan, Medieval and modern Tuscans. GUIDO BARBUJANI, SILVIA GUIMARAES, ANDREA BENAZZO, LUCIO MILANI , DAVID CARAMELLI.
The available mitochondrial DNA
data appear incompatible with the
view that modern Tuscans are
descended from the Etruscans who
inhabited the same region 2,500
years ago. To understand how and
when such a genetic discontinuity
may have arisen, we extracted and
typed the mtDNAs of 27 medieval
Tuscans from an initial sample of
61, spanning a time period between
the 10th and 15th centuries A.D..
Etruscans and medieval Tuscans
share four mitochondrial
haplotypes, and serial coalescent
simulations show a clear
genealogical continuity between
them. By contrast, it was
impossible to fit into the same
mtDNA genealogy modern
inhabitants of the same area,
including those (Murlo, Volterra,
Casentino) who were recently
claimed to be of Etruscan descent.
These data strongly suggest that the
Etruscans did not get extinct when
their culture disappeared with the
Roman assimilation. However, they
contributed little to the modern
mitochondrial gene pool, probably
because of extensive immigration
after 1500 A.D.. No evidence of
excess mutation was found in the
ancient DNA by a Bayesian test,
and so there is no reason to suspect
that these results be biased by
laboratory artefacts in the ancient
sequences. Genealogical continuity
between ancient and modern
populations of the same area does
not seem a safe general assumption,
but rather a hypothesis that should
and can be tested using ancient
DNA analysis.
Stable isotope and mtDNA evidence for geographic origins at the site of Vagnari
(2nd- 4th centuries AD), Italy. T.L. PROWSE, T.E. VON HUNNIUS, AND J.L. BARTA.

Arsinoe IV of Egypt, sister of Cleopatra identified? Osseous and molecular challenges. F. KANZ, K. GROSSSCHMIDT, J. KIESSLICH.
Arsinoe IV of Egypt, the younger
sister of Cleopatra, was murdered
between the ages of 16 and 18 on
the order of Marc Antony in 41 BC
while living in political asylum at
the Artemision in Ephesus
(Turkey). Archaeological findings
and architectural features point to
the skeletal remains found in the socalled
Oktogon - Heroon in the
center of ancient Ephesus - to being
those of Arsinoe IV. Respective
remains were dated and
investigated by forensic osteology,
radiology and ancient DNA
analysis to assess identification:
Radiocarbon dating (VERA-4104)
isolated the period between 210 and
20 BC (94 % prob.).
Morphological features suggest a
female with an estimated body
height of 154 cm (+/- 3 cm) and
with limbs in good proportion to
one another. Epiphyseal closure and
histological age estimation (femoral
cross sections) revealed a consistent
age at death between 15 and 17
years. The whole skeleton appeared
to belong to a slim and fragile
individual (soft tissue
reconstruction was applied and
compared to ancient sources).
Stress markers, like Harris’ lines
were absent and no sings for heavy
workload or pre- or perimortal
traumas were found. Ancient DNA
analysis was carried out for several
bone samples. No nuclear DNA
was detected, most likely due to
diagenetic factors and storage
conditions. Endeavors to find
mitochondrial DNA are currently in
progress. Investigations could
neither verify nor disprove the
theory on the origin of the remains.
However, after successful mtDNA
typing a maternal relative reference
sample would be required for final

The importance of slavery in agriculture: paleopathological evidence from Classical Thebes, Greece. E. VIKA
A hypothesis endorsed by many
writers is that, in the social system
of Classical times, citizens did not
work for a living. This is supported
by iconography and literary
evidence, which presents a wellestablished
life of leisure for the
free. Therefore, slaves were solely
responsible for the cultivation of
land, forming a powerful
However, social organization in
Classical Thebes may have been
very different from what is known
for Classical Athens, and indeed
many writers caution against
applying the Athenian model to all
Greek cities of the period. It may be
more likely that in Thebes, were
population density was such, that
people lived under maximum land
capacity, the need for labor force
was extreme. In this case, slaves
would have joined families and
worked with them.
Physical anthropology can provide
compelling evidence in the matter
of the division of labor in antiquity,
clearly portraying individuals not
involved in manual labor. The
present study examined 50
skeletons from Thebes’ most
extensive historical cemetery. The
results show that activity-related
skeletal alterations, traumas and
pathologies had affected the entire
population, verifying that slaves
and freemen were equally involved
in agricultural activities. This
evidence is important in
reconstructing social structure in
Thebes, moves away from the
domination of the paradigm of
Classical Athens and provides apt
information for the extreme need of
agricultural labor in the area during
this time.

Identification of infanticide in the Greco-Roman world: a contrary view from the Agora of Athens. M.A. LISTON.
The identification of infanticide in
perinatal skeletons is a topic that
has engendered considerable
controversy; distinguishing normal
infant mortality from catastrophic
death or large-scale infanticide is
difficult at best. Roman-era infant
skeletons deposited in a sewer at
Ashkelon, Israel (Smith and Kahila
1992) have been identified as
victims of infanticide, based
primarily on the age-at-death
distributions and the lack of formal
burial. Similar age distributions
from Roman cemetery burials have
been interpreted both as infanticide
in Britain (Mays 1993) and natural
infant mortality in Egypt (Tocheri
et al. 2005). Analysis of a late
Hellenistic/early Roman group of
perinatal infant skeletons (n=457)
deposited in a well in the Athenian
Agora, suggests that infanticide
may not be the appropriate
interpretation of perinatal mortality,
even in the absence of formal
burial. The frequency distributions
of long bone lengths indicate that
all of these sites have similar
patterns, but the Agora infants also
have been demonstrated to have
died from a variety of natural
causes including premature birth
and infectious disease (Liston
AAPA 2007). The age distribution
is similar to that found in other
collections of infants, all identified
as natural perinatal mortality. As
further evidence against widespread
infanticide, morphological
evaluation of the 321 preserved ilia
from the Agora tentatively suggests
a nearly balanced sex ratio as
expected with natural deaths, in
contrast to a subsample from
Ashkelon (Mays and Faerman
2001). However, the identification
of developmental defects in at least
nine Agora infants suggests that
infanticide may be implicated in
some infant deaths.
This seems quite interesting, the frequency of J2 (12%) and G (6%) seem to be quite high in this sample compared to white Americans and Britons.

Finding the Scot in the Scottish-American: Examination of ethnic identity through the Y-chromosome. K.G. BEATY AND M.L. MEALEY.
It is estimated that over 12 million
Americans claim Scottish ancestry.
To determine whether individuals
self-identifed as Scottish carry
Scottish genetics markers in their
genes, samples were collected from
50 males at the 2006 Kansas City
Highland Games. All individuals in
the sample identified themselves as
“Scottish.”. To determine possible
contribution from a paternal line,
surnames where analyzed. All but
6% of the individuals have
surnames that are currently found in
Scotland, with most surnames
having been present in the historical
records the since the mid 1500’s.
Analysis of 9 short-tandem repeats
on the Y-chromosome (YSTRs)
identified probable Y haplogroup
assignment. Individuals in this
sample represented the following
haplogroups: R1b, R1a (3%), I
(11%), J2 (12%), G (6%) and E3b
(4%). Haplogroup R1b dominates
the sample at 64%, as would be
suspected of a population with
origins in Western Europe.
Haplogroup frequencies are found
at those similar to the current
Scottish population, as well as in
similar frequencies to the rest of the
British Isles. All but six Y-STR
haplotypes matched individuals in
the current Scottish population.
Paleoamericans in a Late Pleistocene context: assessing morphological affinities. M. HUBBE, K. HARVATI, W. A. NEVES.

Biological variation resulting from Inka imperialism. J.D. BETHARD.

Craniometric divergence of Japanese inhabitants due to gene flows from Prehistoric Northeast Asians. H. ISHIDA, T. HANIHARA, O. KONDO.

The Swatis of northern Pakistan—Emigrants from Central Asia or colonists from peninsular India?: a dental morphometric investigation. B.E. HEMPHILL.

Considerations for the Population History of the Wakhan Corridor: An Odontometric Investigation of Wakhi Biological Affinity and Diachronic Analysis of Biological Interaction Between Northern Pakistan and South Asia. P.W. O’NEILL AND B.E. HEMPHILL.

The people of the Xiongnu culture (3rd century B.C. to 2nd century A.D.): Insights into the biological diversity of the earliest Eurasian nomadic steppe empire. R.W. SCHMIDT, B. CHRISTY, A. BURCH, A.R. NELSON, N. SEGUCHI.

Rome if you want to: immigrants in the Empire. K. KILLGROVE.

Recognizing population displacements and replacements in prehistory: A view from North Africa. C.M. STOJANOWSKI.

The working class at Hierakonpolis. Nubian or Egyptian?. K. GODDE.

Craniofacial evolution in Polynesia: A geometric morphometric study of population diversity. T.J. BUCK, U. STRAND VIÐARSDÓTTIR

The state of health of Roman Republic to Imperial Roman period burials from the necropolis of Aquinum, Italy. R.R. PAINE, R. VARGIU, G.R. BELLINI, D. MANCINELLI, P. SANTORO, A. COPPA.

Health and lifestyle of ancient pastoralists from Mongolia. J.J. BEACH, M.L. MACHICEK, A.R. NELSON.

Regional patterns among Holocene hunter-gatherers of southern Africa. SUSAN PFEIFFER AND JUDITH SEALY

Ecogeographic variation in the ontogeny of hunter-gatherer physique and skeletal robusticity. JAY STOCK

Hunter-fisher-gatherer dietary adaptations in Neolithic and Bronze Age Siberians. M.A. KATZENBERG, H.G. MCKENZIE, A.W. WEBER AND O.I. GORIUNOVA.

Basques in an Indo-European sea: a perspective from tooth crown morphology. SCOTT GR

Session 5. Reconstructing Health and Disease in Europe: The Early Middle Ages through the
Industrial Period. Invited poster symposium. River Exhibition Hall B.

Stable isotope analysis of diet among Bronze Age and Iron Age inhabitants of Xinjiang Uyghur Autonomous Region, China. J.T. ENG, Q. ZHANG, H. ZHU.

The nasal cavity of Pleistocene hominins: implications of climate-related variation among modern humans. M.L. NOBACK, F. SPOOR.

Inferred body proportions of a southern European Neandertal, Palomas 92. E. TRINKAUS, M.J. WALKER, J. MAKI, M.V. LÓPEZ, J. ORTEGA.

Buccal dental microwear and tooth crown morphology in Neandertals and modern humans show significant correlations with prevailing climatic conditions throughout the Middle and Upper Paleolithic in Europe. B. PINILÑLA, A. PÉREZ-PÉREZ.

Geographic structure of global craniometric variation. J.H. RELETHFORD

Australian craniofacial evolution: drift, selection, or all of the above? E.A. CARSON.

Identifying selection and genetic drift in the landmark-based 3D cranial morphology of modern humans. H.F. SMITH

The paradox of human cranial variation. T.D. WEAVER

Geographic structure of craniofacial variation in modern human populations: an R-matrix approach. T. HANIHARA, H. ISHIDA.

Population history and cranial morphology in a large human skeletal dataset. K. HARVATI, M. HUBBE, D.V. BERNARDO, T. HANIHARA

Natural selection, random genetic drift, and the study of morphological variation. C.C. ROSEMAN.

Quantitative genetic insights on the evolutionary processes operating on human skull shape. N.

Ancient demography, not climate, explains within-population phenotypic diversity in humans. A.

Evidence for the influence of diet on cranial form and robusticity. R.A. MENEGAZ, S.V. SUBLETT, S.D. FIGUEROA, T.J. HOFFMAN, M.J. RAVOSA, AND K. ALDRIDGE.

New Frameworks of Understanding for the Origins of Agriculture. BRUCE SMITH

Natural selection, longevity, and the Neandertal-modern interface. J. HAWKS.

The Neanderthal face is not cold adapted. T. C. RAE, T. KOPPE, C. B. STRINGER.

Functional implications of the unique Neandertal face. A. MAROM, Y. RAK.

Using 3-D geometric morphometric techniques to further understand the relationship between Neanderthals and Homo sapiens. J.A. MINETZ.

Qualitative and quantitative analyses of the Holocene Khoesan dentition. W. BLACK.

The brain morphology of Homo Liujiang cranium fossil by 3-D CT. X.J. WU, W. LIU. W. DONG, J.Q. QUE, Y.F. WANG

Scurvy in a Late Roman Greek child: multiple lines of evidence. S. GARVIE-LOK, C. PENNYCOOK, R. STARK.

Genetics, Selection, Perception and the Human Face. M.D. SHRIVER, D. LIBERTON, AND K. MATTHES, J. BOSTER AND D.A. PUTS.

Evolution and natural selection of skin color. E.J. PARRA

Late Pleistocene/Holocene human populations transition in Old World: the analysis of morphological dental traits. A. COPPA, F. CANDILIO, A. CUCINA, F. DEMETER, A.KUTTERER, M. LUCCI, F. MANNI, A. OUJAA, S. ROUDESLI-CHEBBI, R. VARGIU.

Morphometric analysis of the Herto cranium (BOU-VP-16-1): Where does it fit? K.D. LUBSEN, J.L. MAYHER, R.S. CORRUCCINI.

Assessing the relationship between craniofacial morphology and genetic variation in a population with admixed ancestry. F.I. MARTINEZ, D. BUSEL, M. MORAGA, G. MANRÍQUEZ, M. BELLATTI, F. LAHR, M.M. LAHR

A genetic association study of normal variation in facial features. D.K. LIBERTON, K.A. MATTHES, B. MCEVOY, R. PEREIRA, T. FRUDAKIS, M.D. SHRIVER.

Dissimilarity fraction for metrical traits of human skull: comparison with genetic studies. A.M. STRAUSS, M. HUBBE.

Cranial nonmetric study of archaeological populations from different historical periods of Mongolia ERDENE MYAGMAR.

Genetic and Linguistic Coevolution in Native Latin America. N.J. SCHNEIDER, K.L. HUNLEY,

Analysis of aDNA From Maya Skeletal Remains Using the Mitochondrial Control Region. ELIZABETH LAVOIE.

Search for founder mitochondrial lineages in Holocene human remains in Patagonia. M. MORAGA, E. ASPILLAGA, F. MENA.

Genetic diversity in South Amerindian populations. M.L. PAROLIN, A.S. GOICOECHEA, C.B. DEJEAN, S.A. AVENA, F.R. CARNESE.

Global human population structuring seen from craniometric data. D. V. BERNARDO, T. F. ALMEIDA, W. A. NEVES, T. HANIHARA


The operational sex ratio (OSR) among hunter-gatherers: cause or effect of male-male competition? MARLOW, FW AND BERBESQUE, JC

Mitochondrial DNA diversity of Yemenite and Ethiopian Jewish populations. NON, AMY L.

Genetic structure of the Spanish populations: the end of the Basque singularity? F. CALAFELL, H. LAAYOUNI, P. GARAGNANI, A. GONZÁLEZ-NEIRA, J. BERTRANPETIT.

Inferring human gene flow over Mediterranean space towards Iberian Peninsula based on Y-chromosomal haplogroups E and J in a coastal Andalusian population (Southern Spain). R. CALDERÓN, B. AMBROSIO, J.M. DUGOUJON, C. HERNÁNDEZ, D. DE LA FUENTE, A. GONZÁLEZ-MARTÍN, J.N. RODRÍGUEZ, A. NOVELLETTO.

Evidence supporting two centers of population differentiation in East Asia: Siberia and SE Asia. M.S. SCHANFIELD, S. MILLER, R. SHYU,M. MOUNT, H.F. POLESKY, R. CASTRO, H. EHRLICH, U. EKE, S. MACK, R.J. MITCHELL, M. COBLE, K. MELVIN, M. H. CRAWFORD.

Climate and Craniofacial shape variation among major human populations: a geometric morphometric approach. M. FRIESS.

Sign, sign, everywhere a sign: high density haplotype maps of the dog, human, and cow genomes reveal extensive human reorganization of domesticated genomes. CARLOS D. BUSTAMANTE, ELAINE A. OSTRANDER, MAGNUS NORDBORG, MATTHEW R. NELSON, MICHELE CARGILL, RICHARD A. GIBBS, AND ROBERT K. WAYNE

Insights from sequencing the Neandertal genome. J. KRAUSE, R. E. GREEN, A.W. BRIGGS, U. STENZEL, K. PRUEFER, T. MARICIC, M. KICHNER, J. KELSO, D. REICH, J. C. MULLIKIN, M. EGHOLM & S. PÄÄBO

Layers of history within humanity's genomes. J.L. MOUNTAIN.

The genetic basis of phenotypic variation in Africa: Evidence for local adaptation. S. A. TISHKOFF, M. CAMPBELL, A. FROMENT, J. HIRBO, M. IBRAHIM, S. OMAR, A. RANCIARO.

Seasonality and Brain Size: What’s the Link? J.T. VAN WOERDEN, K. ISLER, C.P. VAN SCHAIK.

Y chromosome haplogroup I and rapid HIV progression

This is one of few substantiated cases of possible selection acting on a Y-chromosome haplogroup. Another one involved interaction between haplogroup R and mtDNA haplogroup H. Selection is one of the mechanisms that can account for the fact that Y-chromosome lineages have grown to demographic sizes that far exceed expectation under genetic drift.

Human Genetics doi:10.1007/s00439-008-0620-7

Association of Y chromosome haplogroup I with HIV progression, and HAART outcome

Efe Sezgin et al.


The host genetic basis of differential outcomes in HIV infection, progression, viral load set point and highly active retroviral therapy (HAART) responses was examined for the common Y haplogroups in European Americans and African Americans. Accelerated progression to acquired immune deficiency syndrome (AIDS) and related death in European Americans among Y chromosome haplogroup I (Y-I) subjects was discovered. Additionally, Y-I haplogroup subjects on HAART took a longer time to HIV-1 viral suppression and were more likely to fail HAART. Both the accelerated progression and longer time to viral suppression results observed in haplogroup Y-I were significant after false-discovery-rate corrections. A higher frequency of AIDS-defining illnesses was also observed in haplogroup Y-I. These effects were independent of the previously identified autosomal AIDS restriction genes. When the Y-I haplogroup subjects were further subdivided into six I subhaplogroups, no one subhaplogroup accounted for the effects on HIV progression, viral load or HAART response. Adjustment of the analyses for population stratification found significant and concordant haplogroup Y-I results. The Y chromosome haplogroup analyses of HIV infection and progression in African Americans were not significant. Our results suggest that one or more loci on the Y chromosome found on haplogroup Y-I have an effect on AIDS progression and treatment responses in European Americans.


Heritability of Human cranial dimensions

J Anat. 2009 Jan;214(1):19-35.

Heritability of human cranial dimensions: comparing the evolvability of different cranial regions.

Martínez-Abadías N, Esparza M, Sjøvold T, González-José R, Santos M, Hernández M.

Quantitative craniometrical traits have been successfully incorporated into population genetic methods to provide insight into human population structure. However, little is known about the degree of genetic and non-genetic influences on the phenotypic expression of functionally based traits. Many studies have assessed the heritability of craniofacial traits, but complex patterns of correlation among traits have been disregarded. This is a pitfall as the human skull is strongly integrated. Here we reconsider the evolutionary potential of craniometric traits by assessing their heritability values as well as their patterns of genetic and phenotypic correlation using a large pedigree-structured skull series from Hallstatt (Austria). The sample includes 355 complete adult skulls that have been analysed using 3D geometric morphometric techniques. Heritability estimates for 58 cranial linear distances were computed using maximum likelihood methods. These distances were assigned to the main functional and developmental regions of the skull. Results showed that the human skull has substantial amounts of genetic variation, and a t-test showed that there are no statistically significant differences among the heritabilities of facial, neurocranial and basal dimensions. However, skull evolvability is limited by complex patterns of genetic correlation. Phenotypic and genetic patterns of correlation are consistent but do not support traditional hypotheses of integration of the human shape, showing that the classification between brachy- and dolicephalic skulls is not grounded on the genetic level. Here we support previous findings in the mouse cranium and provide empirical evidence that covariation between the maximum widths of the main developmental regions of the skull is the dominant factor of integration in the human skull.


January 26, 2009

Bayesian phylogenetics of languages and the timing of Austronesian settlement of the Pacific from Taiwan

The same Bayesian methodology was used by the first author to conclude that the spread of Indo-European languages began in Asia Minor during the Neolithic.

From the paper:

The innovationist "pulse-pause" scenario posits that the Austronesians originated in Taiwan around 5500 years ago and spread through the Pacific in a sequence of expansion pulses and settlement pauses (2, 4–6).


The divergence time estimates for the age of the Austronesian language family support the pulse-pause scenario (Fig. 2). The estimated root age of Austronesian across all the post–burn-in trees has a mean of 5230 years [95% highest posterior density (HPD) interval, 4750 to 5800 years B.P.). The divergence time estimates were robust across a range of calibrations and different models (28).
The concordance of Bayesian linguistics with the pulse-pause archaeological model is remarkable. So, how was the slow-boat model supported in the first place?
In contrast, proponents of the slow-boat scenario argue that the Austronesians emerged from an extensive sociocultural network of maritime exchange in Wallacea (in the region of modern day Sulawesi and the Moluccas) around 13,000 to 17,000 years B.P. based on the dating of mitochondrial lineages (11, 12).


Our estimates for the age of the Austronesian expansion are considerably younger than the deep age estimates of the slow-boat scenario (11, 12, 15). One possibility is that these deep estimates are artifacts due to problems with accurately dating genetic change. There is increasing evidence that rates of genetic change estimated over thousands of years are substantially higher than the long-term substitution rate (21). This violation of the molecular clock leads to the systematic overestimation of recent divergence times.
The problem was that a calibrated evolutionary mutation rate was used to estimate these ages, making them about 3 times older than the Austronesian expansion. Sound familiar?

Science DOI: 10.1126/science.1166858

Language Phylogenies Reveal Expansion Pulses and Pauses in Pacific Settlement

R. D. Gray et al.


Debates about human prehistory often center on the role that population expansions play in shaping biological and cultural diversity. Hypotheses on the origin of the Austronesian settlers of the Pacific are divided between a recent "pulse-pause" expansion from Taiwan and an older "slow-boat" diffusion from Wallacea. We used lexical data and Bayesian phylogenetic methods to construct a phylogeny of 400 languages. In agreement with the pulse-pause scenario, the language trees place the Austronesian origin in Taiwan approximately 5230 years ago and reveal a series of settlement pauses and expansion pulses linked to technological and social innovations. These results are robust to assumptions about the rooting and calibration of the trees and demonstrate the combined power of linguistic scholarship, database technologies, and computational phylogenetic methods for resolving questions about human prehistory.


January 25, 2009

Magyars and Madjars

American Journal of Physical Anthropology doi:10.1002/ajpa.20984

A Y-chromosomal comparison of the Madjars (Kazakhstan) and the Magyars (Hungary)

A.Z. Bíró et al.


The Madjars are a previously unstudied population from Kazakhstan who practice a form of local exogamy in which wives are brought in from neighboring tribes, but husbands are not, so the paternal lineages remain genetically isolated within the population. Their name bears a striking resemblance to the Magyars who have inhabited Hungary for over a millennium, but whose previous history is poorly understood. We have now carried out a genetic analysis of the population structure and relationships of the Madjars, and in particular have sought to test whether or not they show a genetic link with the Magyars. We concentrated on paternal lineages because of their isolation within the Madjars and sampled males representing all extant male lineages unrelated for more than eight generations (n = 45) in the Torgay area of Kazakhstan. The Madjars show evidence of extensive genetic drift, with 24/45 carrying the same 12-STR haplotype within haplogroup G. Genetic distances based on haplogroup frequencies were used to compare the Madjars with 37 other populations and showed that they were closest to the Hungarian population rather than their geographical neighbors. Although this finding could result from chance, it is striking and suggests that there could have been genetic contact between the ancestors of the Madjars and Magyars, and thus that modern Hungarians may trace their ancestry to Central Asia, instead of the Eastern Uralic region as previously thought.


January 23, 2009

Indian origin of haplogroup R1a1 (?)

The paper does not appear to be live yet, so I cannot comment on the specifics. However, judging from the abstract I see no reason to agree with the authors' conclusions. My most recent observations on the topic can be found in Origin of Hindu Brahmins. The authors' observation of paragroup R1a* Y-chromosomes in India is in itself unremarkable, as such chromosomes have been found outside India, e.g., in North Iran, Crete, and Greek Macedonia (and I'm sure elsewhere). The argument about the presence of R1a1 in tribals does not carry force, as its presence there (at much lower frequencies than in Brahmin groups) can be explained as the result of occasional admixture. Moreover, India is exceptionally notable for its lack (except in a few erratics) of the related haplogroup R1b, which once again argues against the emergence of R1a in India itself.

See also another recent study which considers R1a1 extraneous in India, and which includes links to various other blog posts on the topic.

Perhaps I will have more on this when I read the paper (feel free to send me a copy to my e-mail address).

J Hum Genet. 2009 Jan 9. [Epub ahead of print]

The Indian origin of paternal haplogroup R1a1(*) substantiates the autochthonous origin of Brahmins and the caste system.

Sharma S. et al.


Many major rival models of the origin of the Hindu caste system co-exist despite extensive studies, each with associated genetic evidences. One of the major factors that has still kept the origin of the Indian caste system obscure is the unresolved question of the origin of Y-haplogroup R1a1(*), at times associated with a male-mediated major genetic influx from Central Asia or Eurasia, which has contributed to the higher castes in India. Y-haplogroup R1a1(*) has a widespread distribution and high frequency across Eurasia, Central Asia and the Indian subcontinent, with scanty reports of its ancestral (R(*), R1(*) and R1a(*)) and derived lineages (R1a1a, R1a1b and R1a1c). To resolve these issues, we screened 621 Y-chromosomes (of Brahmins occupying the upper-most caste position and schedule castes/tribals occupying the lower-most positions) with 55 Y-chromosomal binary markers and seven Y-microsatellite markers and compiled an extensive dataset of 2809 Y-chromosomes (681 Brahmins, and 2128 tribals and schedule castes) for conclusions. A peculiar observation of the highest frequency (up to 72.22%) of Y-haplogroup R1a1(*) in Brahmins hinted at its presence as a founder lineage for this caste group. Further, observation of R1a1(*) in different tribal population groups, existence of Y-haplogroup R1a(*) in ancestors and extended phylogenetic analyses of the pooled dataset of 530 Indians, 224 Pakistanis and 276 Central Asians and Eurasians bearing the R1a1(*) haplogroup supported the autochthonous origin of R1a1 lineage in India and a tribal link to Indian Brahmins. However, it is important to discover novel Y-chromosomal binary marker(s) for a higher resolution of R1a1(*) and confirm the present conclusions.


Another paper on Ashkenazi Jewish distinctiveness

Gene Expression points me to a new paper which demonstrates that Ashkenazi Jews can be distinguished perfectly from non-Jewish European Americans. This was previously seen, but it is nice to see it confirmed once more. Some previous studies:
  1. New paper on genomic differences between Ashkenazi Jews and Europeans
  2. 300K SNP paper on European genetic substructure
  3. European population substructure revealed by genetics
The authors also observed that heterozygosity among Ashkenazi Jews is higher than in European Americans. This is fairly conclusive evidence that Ashkenazi Jews are not so distinctive because they passed through a genetic bottleneck that shifted their allele frequencies in a direction specific to their group.

On the other hand, the conclusion that the genetic distinctness of Ashkenazi Jews is due to Middle Eastern ancestry is not demonstrated by this study. For example, the Uyghur of Central Asia are distinct from both East Asians and Caucasoids, but this is not due to any mysterious "Central Asian" component in them, but rather due to the fact that they are an admixed population of Caucasoids and Mongoloids.

To demonstrate the specific Middle Eastern background of Ashkenazi Jews, it would be a good idea to also study other Jewish groups. If it is shown that the various Jewish groups possess a common autosomal genetic component, then the simplest explanation would be that this component stems from the ancestral Jewish population of the 1st millennium AD, prior to the separation of the various Jewish groups from each other.

Moreover, the genetic distinctiveness of Ashkenazi Jews does not in itself say anything about the extent of Middle Eastern ancestry in this group. For example, in this paper, the Middle Eastern groups (mostly non-Jewish Semitic groups recruited in Israel) were different from other Caucasoids by the possession of a specific ancestral component (color-coded brown), but the extent of this component differed among them.

With that said, I do suspect that the distinctiveness of the Ashkenazi Jews is in part due to the possession of a Middle Eastern component of unspecified strength. I base this hypothesis on the results reported to me about the EURO-DNA-CALC test. This test distinguishes between NW, SE Europeans and Ashkenazi Jews; a few Arab individuals who have communicated their results to me have reported fairly high AJ components, indicating that part of what distinguishes an AJ from Europeans is related to the Middle Eastern Semitic background of that group.

The way forward is of course to perform a comprehensive admixture analysis where Europeans, various Jewish groups, and various non-Jewish Middle Eastern groups will be represented. That is the only way to ascertain the ancestral components of the various Jewish groups. Moreover, such an analysis would establish the extent of the common genomic element between the various Jewish groups, which -so far- has been established for a limited number of Y-chromosome and mtDNA lineages.

UPDATE: While a formal admixture analysis is not performed, the EIGENSOFT plot is suggestive of what common sense would dictate, namely that Ashkenazi Jews (reds) are intermediate between a native Near Eastern group (the Druze) and Europeans. Unfortunately the inclusion of the Mozabites (off the chart to the left) who have substantial Sub-Saharan ancestry, makes the resolution of the visible part of the chart less than desirable.

Genome Biology doi:10.1186/gb-2009-10-1-r7

A genome-wide genetic signature of Jewish ancestry perfectly separates individuals with and without full Jewish ancestry in a large random sample of European Americans

Anna C Need et al.



It was recently shown that the genetic distinction between self-identified Ashkenazi Jewish and non-Jewish individuals is a prominent component of genome-wide patterns of genetic variation in European Americans. No study however has yet assessed how accurately self-identified (Ashkenazi) Jewish ancestry can be inferred from genomic information, nor whether the degree of Jewish ancestry can be inferred among individuals with fewer than four Jewish grandparents.


Using a principal components analysis, we found that the individuals with full Jewish ancestry formed a clearly distinct cluster from those individuals with no Jewish ancestry. Using the position on the first principal component axis, every single individual with self-reported full Jewish ancestry had a higher score than any individual with no Jewish ancestry.


Here we show that within Americans of European ancestry there is a perfect genetic corollary of Jewish ancestry which, in principle, would permit near perfect genetic inference of Ashkenazi Jewish ancestry. In fact, even subjects with a single Jewish grandparent can be statistically distinguished from those without Jewish ancestry. We also found that subjects with Jewish ancestry were slightly more heterozygous than the subjects with no Jewish ancestry, suggesting that the genetic distinction between Jews and non-Jews may be more attributable to a Near-Eastern origin for Jewish populations than to population bottlenecks.

Link (pdf)

January 22, 2009

Best overall matching in Europeans

I was planning to do a post on the meaning of cluster separability, but this new paper actually demonstrates the main point I was going to investigate.

Over the last years, studies such as this have shown that is possible to distinguish between many European population groups.

However, clusters that are completely separable, may still harbor a substantial amount of internal variation. To see this, consider the following example of two groups, each consisting of 3 individuals and 5 markers:





It can be easily seen that group 1 is perfectly separable from group 2, in this case simply by looking at the first marker where group 1 has invariably an A, and group 2 has invariably a C.

But, if we try to see what the "best match" is for these individuals, we see that e.g., for individual a of group 1, the best match is d from group 2, for b it is e and for c it is f.

Now, for very distant populations, the scenario described above will almost never occur. Using 10K SNPs from the HGDP data, for the post I was preparing, I was able to conclude, for example, that any pair of Oroqen is always closer to each other than an Oroqen is to any Bantu sample.

This new study answers this question in the case of closely related European groups, showing that it is not the case that an individual will always have a member of his own group as his "best overall match" (BOM). Finns, for example, who appear as most distinct, have a Finnish BOM some 39 (out of 47) times, while some Finns have a Norwegian, German, or Polish BOM.

Moving into Central Europe, we see some counterintuitive results: no Austrian has an Austrian BOM, for example, but British, Danish, Dutch, German, Italian, and Polish ones.

Sample sizes play a role, however. For example, 25 out of 51 Greeks have Germans as their BOM, and only 7 out of 51 have Greek BOM's. But, since there is a sample of 983 Germans overall, Greeks are in fact 5.4 times more likely to match a Greek than a German.

Some markers and combinations of markers do differ between groups in a systematic way, like the A/C in the simple example above. Such markers allow us to separate groups, and distinguish between them. But, if we look at the overall genetic similarity between individuals, it turns out that members of one group may be more similar to some members of another than to their own.

So, if one were to be in a room with people from all over Europe, say during a meeting of the European Parliament, he might share some traits with people from his own country, but his best overall genetic match might be quite different.

Someone with the computing power and patience should carry out this investigation with the large HGDP dataset, to see which groups are strongly separable in the Oroqen-Bantu sense, and which ones are more weakly separable as in the European sense.

European Journal of Human Genetics doi: 10.1038/ejhg.2008.266

An evaluation of the genetic-matched pair study design using genome-wide SNP data from the European population

Timothy Tehva Lu et al.


Genetic matching potentially provides a means to alleviate the effects of incomplete Mendelian randomization in population-based gene–disease association studies. We therefore evaluated the genetic-matched pair study design on the basis of genome-wide SNP data (309 790 markers; Affymetrix GeneChip Human Mapping 500K Array) from 2457 individuals, sampled at 23 different recruitment sites across Europe. Using pair-wise identity-by-state (IBS) as a matching criterion, we tried to derive a subset of markers that would allow identification of the best overall matching (BOM) partner for a given individual, based on the IBS status for the subset alone. However, our results suggest that, by following this approach, the prediction accuracy is only notably improved by the first 20 markers selected, and increases proportionally to the marker number thereafter. Furthermore, in a considerable proportion of cases (76.0%), the BOM of a given individual, based on the complete marker set, came from a different recruitment site than the individual itself. A second marker set, specifically selected for ancestry sensitivity using singular value decomposition, performed even more poorly and was no more capable of predicting the BOM than randomly chosen subsets. This leads us to conclude that, at least in Europe, the utility of the genetic-matched pair study design depends critically on the availability of comprehensive genotype information for both cases and controls.


January 21, 2009

North African male legacy in southern Europe quantified

This seems like an improvement over previous attempts at quantification of the genetic effects of the historical occupation of parts of southern Europe. The researchers looked at haplotypes within three haplogroups that are likely to share common ancestry with North Africans within the relevant time frame:
Haplogroups E1b1b1b(M81 derived), E1b1b1a-β (M78 derived chromosomes showing the rare DYS439 allele 10) and a subset of J1 (M267 derived) were identified in the literature as being NWAfrica specific, together accounting for between 58 and 90% of males in populations from this area, but never above 13% in Europe.


Therefore, following this, European Y chromosomes within the three haplogroups identical to, or with one mutational difference from, NW African STR haplotypes were considered compatible with an MNA ancestry. In Iberia and peninsular Italy, they account for 90, 78 and 42% of the E1b1b1b, E1b1b1a-b and J1 chromosomes respectively.

It seems that E-M81 in Europe is indeed largely of recent North African origin, E-M78β is largely so, but J1 only partly so; perhaps the rest of it is due to other (pre)-historic movements of people from West Asia directly into Europe.

Estimates of the NW African types ranged from 0 to 18.6% (in Cantabria). For Sicily, the estimate was 7.5%, similar to the 6% reported recently. NW Apulia is second in Italy at 6.5% and E Campania third at 4.8%. The remaining Italian regions have lower than 2%, except Lucera (3.3%) and Central Tuscany (2.4%). W Calabria comes in at 0% as do some other Italian regions.

In Portugal, the total contribution is 7.1% and in Spain 7.7%. Higher than average is the aforementioned Cantabria and Galicia (6.8%).

It is noteworthy that in all the regions, E-M81 seems to be the main component of the NW African element, but the situation in Sicily is reversed: Sicily is highest in J1 and second-highest in E-M78β and not particularly high in E-M81.

European Journal of Human Genetics doi:10.1038/ejhg.2008.258

Moors and Saracens in Europe: estimating the medieval North African male legacy in southern Europe

Cristian Capelli et al.


To investigate the male genetic legacy of the Arab rule in southern Europe during medieval times, we focused on specific Northwest African haplogroups and identified evolutionary close STR-defined haplotypes in Iberia, Sicily and the Italian peninsula. Our results point to a higher recent Northwest African contribution in Iberia and Sicily in agreement with historical data. southern Italian regions known to have experienced long-term Arab presence also show an enrichment of Northwest African types. The forensic and genomic implications of these findings are discussed.


January 20, 2009

Epigenetics via twin studies

Coverage elsewhere:
Epigenetics reveals unexpected, and some identical, results
Inherited traits may explain differences in 'identical' twins
Related: In search of the Hidden Heritability

Nature Genetics doi: 10.1038/ng.286

DNA methylation profiles in monozygotic and dizygotic twins

Zachary A Kaminsky et al.


Twin studies have provided the basis for genetic and epidemiological studies in human complex traits. As epigenetic factors can contribute to phenotypic outcomes, we conducted a DNA methylation analysis in white blood cells (WBC), buccal epithelial cells and gut biopsies of 114 monozygotic (MZ) twins as well as WBC and buccal epithelial cells of 80 dizygotic (DZ) twins using 12K CpG island microarrays. Here we provide the first annotation of epigenetic metastability of approx6,000 unique genomic regions in MZ twins. An intraclass correlation (ICC)-based comparison of matched MZ and DZ twins showed significantly higher epigenetic difference in buccal cells of DZ co-twins (P = 1.2 times 10-294). Although such higher epigenetic discordance in DZ twins can result from DNA sequence differences, our in silico SNP analyses and animal studies favor the hypothesis that it is due to epigenomic differences in the zygotes, suggesting that molecular mechanisms of heritability may not be limited to DNA sequence differences.


January 17, 2009

Things that smell nice to both humans and mice

PLoS ONE doi: 10.1371/journal.pone.0004209

Humans and Mice Express Similar Olfactory Preferences

Nathalie Mandairon et al.


In humans, the pleasantness of odors is a major contributor to social relationships and food intake. Smells evoke attraction and repulsion responses, reflecting the hedonic value of the odorant. While olfactory preferences are known to be strongly modulated by experience and learning, it has been recently suggested that, in humans, the pleasantness of odors may be partly explained by the physicochemical properties of the odorant molecules themselves. If odor hedonic value is indeed predetermined by odorant structure, then it could be hypothesized that other species will show similar odor preferences to humans. Combining behavioral and psychophysical approaches, we here show that odorants rated as pleasant by humans were also those which, behaviorally, mice investigated longer and human subjects sniffed longer, thereby revealing for the first time a component of olfactory hedonic perception conserved across species. Consistent with this, we further show that odor pleasantness rating in humans and investigation time in mice were both correlated with the physicochemical properties of the molecules, suggesting that olfactory preferences are indeed partly engraved in the physicochemical structure of the odorant. That odor preferences are shared between mammal species and are guided by physicochemical features of odorant stimuli strengthens the view that odor preference is partially predetermined. These findings open up new perspectives for the study of the neural mechanisms of hedonic perception.


Sons of billionaires

From the paper:
For species where one sex has more variable reproductive success (males in polygynous species), the TWH predicts that 1) a mother with more resources to invest would be advantaged by producing a son, as a successful son would out-compete a successful daughter (constrained to a less variable reproductive rate), and 2) a mother with less resources to invest would be advantaged by producing a daughter, as her daughter would out-reproduce an unsuccessful son. Alternatively, if sons are more costly than daughters, only mothers in good condition could bear this cost [2].

PLoS ONE doi: 10.1371/journal.pone.0004195

A Trivers-Willard Effect in Contemporary Humans: Male-Biased Sex Ratios among Billionaires

Elissa Z. Cameron, Fredrik Dalerum



Natural selection should favour the ability of mothers to adjust the sex ratio of offspring in relation to the offspring's potential reproductive success. In polygynous species, mothers in good condition would be advantaged by giving birth to more sons. While studies on mammals in general provide support for the hypothesis, studies on humans provide particularly inconsistent results, possibly because the assumptions of the model do not apply.

Methodology/Principal Findings

Here, we take a subset of humans in very good condition: the Forbe's billionaire list. First, we test if the assumptions of the model apply, and show that mothers leave more grandchildren through their sons than through their daughters. We then show that billionaires have 60% sons, which is significantly different from the general population, consistent with our hypothesis. However, women who themselves are billionaires have fewer sons than women having children with billionaires, suggesting that maternal testosterone does not explain the observed variation. Furthermore, paternal masculinity as indexed by achievement, could not explain the variation, since there was no variation in sex ratio between self-made or inherited billionaires.


Humans in the highest economic bracket leave more grandchildren through sons than through daughters. Therefore, adaptive variation in sex ratios is expected, and human mothers in the highest economic bracket do give birth to more sons, suggesting similar sex ratio manipulation as seen in other mammals.


IQ and death from unintentional injury

Am J Epidemiol. 2009 Jan 15. [Epub ahead of print]

IQ in Early Adulthood, Socioeconomic Position, and Unintentional Injury Mortality by Middle Age: A Cohort Study of More Than 1 Million Swedish Men.

Batty GD, Gale CR, Tynelius P, Deary IJ, Rasmussen F.

The authors evaluated the little-examined association between intelligence (IQ) and injury mortality and, for the first known time, explored the extent to which IQ might explain established socioeconomic inequalities in injury mortality. A nationwide cohort of 1,116,442 Swedish men who underwent IQ testing at about 18 years of age was followed for mortality experience for an average of 22.6 years. In age-adjusted analyses in which IQ scores were classified into 4 groups, relative to the highest scoring category, the hazard ratio in the lowest was elevated for all injury types: poisonings (hazard ratio (HR) = 5.82, 95% confidence interval (CI): 4.25, 7.97), fire (HR = 4.39, 95% CI: 2.51, 7.77), falls (HR = 3.17, 95% CI: 2.19, 4.59), drowning (HR = 3.16, 95% CI: 1.85, 5.39), and road injury (HR = 2.17, 95% CI: 1.91, 2.47). Dose-response effects across the full IQ range were evident (P-trend < 0.001). Control for potential covariates, including socioeconomic position, had little impact on these gradients. When socioeconomic disadvantage-indexed by parental and subject's own occupational social class-was the exposure of interest, IQ explained a sizable portion (19%-86%) of the relation with injury mortality. These findings suggest that IQ may have an important role both in the etiology of injuries and in explaining socioeconomic inequalities in injury mortality.


January 16, 2009

Y chromosomes and mtDNA of Koreans

Table 2 has a very useful listing of mtDNA haplogroup frequencies in several East Asian populations.

Table 5 has admixture estimates of NE and SE Asians in Korean populations; notice the gender asymmetry, with males of more southern origin than females.

Table S3 (Excel) has Y-chromosome haplogroup frequencies.

From the paper:
What could be the origin of the male-biased southern contribution to Korean gene pool illustrated, for example, by haplogroups O-M122 (42.2%) and O-SRY465 (20.1%) [29]. Recent molecular genetic analyses and the geographical distribution of haplogroup O-M122 lineages, found widely throughout East Asia at high frequencies (especially in southern populations and China), have suggested a link between these Y-chromosome expansions and the spread of rice agriculture in East Asia [62]–[64]. In general, Y-chromosomes might be spread via a process of demic diffusion during the early agricultural expansion period [65], [66]. If this interpretation were substantiated, the spatial pattern of Y-haplogroup O would imply a genetic contribution to Korea through the spread of male-mediated agriculture.

PLoS ONE 10.1371/journal.pone.0004210

The Peopling of Korea Revealed by Analyses of Mitochondrial DNA and Y-Chromosomal Markers

Han-Jun Jin, Chris Tyler-Smith, Wook Kim



The Koreans are generally considered a northeast Asian group because of their geographical location. However, recent findings from Y chromosome studies showed that the Korean population contains lineages from both southern and northern parts of East Asia. To understand the genetic history and relationships of Korea more fully, additional data and analyses are necessary.

Methodology and Results

We analyzed mitochondrial DNA (mtDNA) sequence variation in the hypervariable segments I and II (HVS-I and HVS-II) and haplogroup-specific mutations in coding regions in 445 individuals from seven east Asian populations (Korean, Korean-Chinese, Mongolian, Manchurian, Han (Beijing), Vietnamese and Thais). In addition, published mtDNA haplogroup data (N = 3307), mtDNA HVS-I sequences (N = 2313), Y chromosome haplogroup data (N = 1697) and Y chromosome STR data (N = 2713) were analyzed to elucidate the genetic structure of East Asian populations. All the mtDNA profiles studied here were classified into subsets of haplogroups common in East Asia, with just two exceptions. In general, the Korean mtDNA profiles revealed similarities to other northeastern Asian populations through analysis of individual haplogroup distributions, genetic distances between populations or an analysis of molecular variance, although a minor southern contribution was also suggested. Reanalysis of Y-chromosomal data confirmed both the overall similarity to other northeastern populations, and also a larger paternal contribution from southeastern populations.


The present work provides evidence that peopling of Korea can be seen as a complex process, interpreted as an early northern Asian settlement with at least one subsequent male-biased southern-to-northern migration, possibly associated with the spread of rice agriculture.


Ancient mtDNA from Iceland

From the paper:
Using the sequence data described in Table 1, we obtained an estimate of 58% ancestry from Scotland and Ireland for contemporary Icelanders (95% C.I.: 44.6–71.2%). In comparison, the IEMS [DP: Iceland Early Medieval Sample] yielded an estimate of 64.7% (95% C.I.: 36.8–90.3%), indicating a similar excess of matrilineal ancestry from Scotland and Ireland.
PLoS Genetics doi: 10.1371/journal.pgen.1000343

Sequences From First Settlers Reveal Rapid Evolution in Icelandic mtDNA Pool

Agnar Helgason et al.


A major task in human genetics is to understand the nature of the evolutionary processes that have shaped the gene pools of contemporary populations. Ancient DNA studies have great potential to shed light on the evolution of populations because they provide the opportunity to sample from the same population at different points in time. Here, we show that a sample of mitochondrial DNA (mtDNA) control region sequences from 68 early medieval Icelandic skeletal remains is more closely related to sequences from contemporary inhabitants of Scotland, Ireland, and Scandinavia than to those from the modern Icelandic population. Due to a faster rate of genetic drift in the Icelandic mtDNA pool during the last 1,100 years, the sequences carried by the first settlers were better preserved in their ancestral gene pools than among their descendants in Iceland. These results demonstrate the inferential power gained in ancient DNA studies through the application of population genetics analyses to relatively large samples.


Selection on human mtDNA from ratio of nonsynonymous to synonymous mutations

Molecular Biology and Evolution, doi:10.1093/molbev/msp005

Temporal trails of natural selection in human mitogenomes

Sankar Subramanian


Mildly deleterious mutations initially contribute to the diversity of a population but later they are selected against at high frequency and are eliminated eventually. Using over 1500 complete human mitochondrial genomes along with those of Neanderthal and Chimpanzee, I provide empirical evidence for this prediction by tracing the footprints of natural selection over time. The results show a highly significant inverse relationship between the ratio of nonsynonymous- to synonymous divergence (dN/dS) and the age of human haplogroups. Furthermore this study suggests that slightly deleterious mutations constitute up to 80% of the mitochondrial amino acid replacement mutations detected in human populations and that over the last 500,000 years these mutations have been gradually removed.


January 13, 2009

Population history of ancient Egyptians

The non-inclusion of population samples from outside Egypt for comparison makes it difficult to assess the population affinities of ancient Egyptians. Nonetheless, this study is to be commended for trying different biodistance measures on the skeletal samples. From the paper:
The relative uniqueness of Gebel Ramlah suggests that this particular Neolithic group did not contribute substantially to the ancestry of subsequent predynastic Nile Valley groups. It is important to note that Gebel Ramlah is also geographically distant from the Nile Valley. Similarly, because the Greek Egyptian sample is an outlier across MDS plots, genetic isolation from local Egyptians seems likely.
American Journal of Physical Anthropology doi: 10.1002/ajpa.20976

Further analysis of the population history of ancient Egyptians

Michael A. Schillaci, Joel D. Irish, Carolan C.E. Wood


The origins of state formation in ancient Egypt have been the focus of recent research utilizing biological data to test hypotheses regarding in situ development of local groups, or large-scale in-migration, possibly by an invading army. The primary goal of the present research is to further test these hypotheses. Our secondary goal is to compare different distance measures and assess how they might affect interpretation of population history. We analyze craniodental nonmetric data using several different measures of biological distance, as well as a method for estimating group diversity using multidimensional scaling of distance estimates. Patterns of biological variation and population relationships were interpreted in temporal and geographic contexts. The results of our analyses suggest that the formation of the ancient Egyptian state likely included a substantial in situ process, with some level of contribution by outside migrants probable. The higher level of population structure in Lower Egypt, relative to Upper Egypt, suggests that such influence and migration by outsiders may not have been widespread geographically. These findings support, but serve to refine further those obtained by the second author in a previous study. Moreover, our comparison of distance measures indicates that the choice of measure can influence identification and interpretation of the microevolutionary processes shaping population history, despite being strongly correlated with one another.


January 12, 2009

mtDNA of Tunisian centenarians

Mech Ageing Dev. 2008 Dec 24.

Data from complete mtDNA sequencing of Tunisian centenarians: Testing haplogroup association and the "golden mean" to longevity.

Costa MD, Cherni L, Fernandes V, Freitas F, Ammar El Gaaied AB, Pereira L.

Since the mitochondrial theory of ageing was proposed, mitochondrial DNA (mtDNA) diversity has been largely studied in old people, however complete genomes are still rare, being limited to Japanese and UK/US samples. In this work, we evaluated possible longevity associated polymorphisms/haplogroups in an African population, from Tunisia, by performing complete mtDNA sequencing. This population has a mixed Eurasian/sub-Saharan mtDNA gene pool, which could potentially facilitate the evaluation of association for sub-Saharan lineages. Sub-Saharan haplogroups were shown to be significantly less represented in centenarians (9.5%) than in controls (54.5%), but it is not possible to rule out an influence of population structure, which is high in these populations. No recurrent polymorphism were more frequent in centenarians than in controls, and although the Tunisian centenarians presented less synonymous and replacement polymorphisms than controls, this difference was not statistically significant. So far, it does not seem that centenarians have significantly less mildly deleterious substitutions, not only in Tunisia but also in Japanese and UK/US samples, as tested here, not favouring a "golden mean" to longevity.


January 09, 2009

More on Lebanese Phoenicians or mixing Science and Politics

The BBC has a story on Divided Lebanon's common genes.
Dr Zalloua says in Lebanon the Phoenician signature is distributed equally among different groups and that the overall genetic make-up of the Lebanese is proving to be similar across various backgrounds.

"Whether you take a Christian village in the north of Lebanon or a Muslim village in the south, the DNA make-up of its residents is likely to be identical," says Dr Zalloua.

But, from another older BBC story referring to the actual study:
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.

and from the study itself:
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-

If a Christian village and a Muslim village are likely to have "identical" DNA makeup, then why is genetic variation strongly structured by religious affiliation and not by geography?

Since contradictions don't exist in nature, the explanation is simple: in the published scientific article, which had to go through peer-review, someone could not claim that there are no differences between Christian and Muslim Lebanese. But, to the polloi of Lebanon, it is apparently alright to sell a vision of national unity and identity.

I don't know what % of modern Lebanese are descended from Phoenicians, but I detest the idea of mixing science with politics.

More on the topic of "Lebanese Phoenicians":
  1. Muslim and Christian Lebanese or Hasty Conclusions in Human Population Genetics
  2. Christian and Muslim Lebanese do differ from each other after all
  3. "Phoenician" Y-chromosomes

January 08, 2009

Concurrent but distinctive migrations into the Americas

As usual with papers such as this, it is important to note that their age estimates depend on (i) the assumption that coalescence ages of lineages correspond to migration events (in general, they do not), and (ii) the mutation rate used to estimate such ages, which may be time-dependent. In this paper:
We propose here for the first time a new mutation rate taking into account the previous estimates reported by Mishmar [35] for all coding-region base substitutions and by Kivisild [36] for only synonymous transitions. With three decimal digits used throughout, the rounded values were 5140 years per coding-region substitution and 6760 years per synonymous transition, respectively. The rho estimated (average distance of the haplotypes of a clade from the respective root) human coalescence times are then 202 kya according to Mishmar et al. [35] and 160 kya according to Kivisild et al.
The geographic patterns (Pacific coast vs. inland route) seem to be more robust than the conclusions about the supposed ages of the migrations and their temporal concurrency.

The ScienceNews reporting has some contrary views. Some related posts:
  1. Language spread rates in the Americas
  2. Earliest human occupation of southern South America
  3. Three-stage colonization model for Americas reconsidered
  4. Craniofacial shape variation and Native American origins

Current Biology doi:10.1016/j.cub.2008.11.058

Distinctive Paleo-Indian Migration Routes from Beringia Marked by Two Rare mtDNA Haplogroups

Ugo A. Perego et al.



It is widely accepted that the ancestors of Native Americans arrived in the New World via Beringia approximately 10 to 30 thousand years ago (kya). However, the arrival time(s), number of expansion events, and migration routes into the Western Hemisphere remain controversial because linguistic, archaeological, and genetic evidence have not yet provided coherent answers. Notably, most of the genetic evidence has been acquired from the analysis of the common pan-American mitochondrial DNA (mtDNA) haplogroups. In this study, we have instead identified and analyzed mtDNAs belonging to two rare Native American haplogroups named D4h3 and X2a.


Phylogeographic analyses at the highest level of molecular resolution (69 entire mitochondrial genomes) reveal that two almost concomitant paths of migration from Beringia led to the Paleo-Indian dispersal approximately 15–17 kya. Haplogroup D4h3 spread into the Americas along the Pacific coast, whereas X2a entered through the ice-free corridor between the Laurentide and Cordilleran ice sheets. The examination of an additional 276 entire mtDNA sequences provides similar entry times for all common Native American haplogroups, thus indicating at least a dual origin for Paleo-Indians.


A dual origin for the first Americans is a striking novelty from the genetic point of view, and it makes plausible a scenario positing that within a rather short period of time, there may have been several entries into the Americas from a dynamically changing Beringian source. Moreover, this implies that most probably more than one language family was carried along with the Paleo-Indians.


January 07, 2009

Culture, population structure, and low genetic diversity in humans

As I have mentioned in a previous entry, the genetic structure of human populations has been interpreted as the result of a process of "serial bottlenecks", starting from the major "Out of Africa" bottleneck, and followed by a series of other ones, as humans colonized the world. Bottlenecks reduce genetic diversity, but so does selection, and it is imperative to directly sample genetic diversity of past populations, to see how well they conform with the expectations of the "serial bottlenecks" theory, i.e., whether reduced diversity is due to descent from a few individuals whose progeny transcended the bottleneck, or due to selection, which suppresses genetic variation by removing some alleles from the gene pool.

This paper argues in favor of selection as a mechanism for keeping genetic diversity (and hence effective population size) at low levels. This selection process, is not, however, envisioned as affecting the species as a whole, but rather proceeded in its own way in regional subsets of humans. These groups did not exchange genes randomly with other such groups, but rather according to their degree of cultural similarity.

John Hawks has an extensive post on this article, which I recommend.

PNAS doi:10.1073/pnas.0809194105

Culture, population structure, and low genetic diversity in Pleistocene hominins

L.S. Premo, Jean-Jacques Hublin


Paleogenomic research has shown that modern humans, Neanderthals, and their most recent common ancestor have displayed less genetic diversity than living great apes. The traditional interpretation that low levels of genetic diversity in modern humans resulted from a relatively recent demographic bottleneck cannot account for similarly low levels of genetic diversity in Middle Pleistocene hominins. A more parsimonious hypothesis proposes that the effective population size of the human lineage has been low for more than 500,000 years, but the mechanism responsible for suppressing genetic diversity in Pleistocene hominin populations without similarly affecting that of their hominoid contemporaries remains unknown. Here we use agent-based simulation to study the effect of culturally mediated migration on neutral genetic diversity in structured populations. We show that, in populations structured by culturally mediated migration, selection can suppress neutral genetic diversity over thousands of generations, even in the absence of bottlenecks or expansions in census population size. In other words, selection could have suppressed the effective population size of Pleistocene hominins for as long as the degree of cultural similarity between regionally differentiated groups played an important role in mediating intraspecific gene flow.


January 05, 2009

Viaggio nella Calabria Greca - Ταξίδι στην Ελληνική Καλαβρία

An interesting documentary by alexspil on the Greeks of Calabria. Description:

"Viaggio nella Calabria Greca...insieme a un ministro!"
In questo film viene documentata la visita del vice ministro esteri Greco nella zona ellenofona della Calabria, ma anche vari aspetti culturali interessanti di questa minoranza, come per esempio la lingua, la storia, l'arte,delle testiomonianze ecc. La durata totale del documentario è di 70 minuti, ed è diviso in 8 parti. --------------- ------------------- ------------------ ----------------- ΕΛΛΗΝΙΚΑ: "Περιήγηση στην Ελληνόφωνη Καλαβρία...παρέα με έναν υπουργό!"
Το ντοκιμαντέρ αυτό καταγράφει την επίσκεψη του Υφ.Εξωτερικών της Ελλάδας στα ελληνόφωνα χωριά της Καλαβρίας, καθώς και διάφορα ενδιαφέροντα πολιτιστικά στοιχεία αυτής της μειονότητας, όπως π.χ. γλώσσα, ιστορία, τέχνες , διάφορες μαρτυρίες κ.α. Η συνολική του διάρκεια είναι 70 λεπτά, και έχει χωριστεί σε 8 μέρη.

Part 1/8:

The complete YouTube playlist.

January 04, 2009

Language spread rates in the Americas

This paper deals with the issue of how a language family's range (how geographically dispersed it is) provides information about its age (how old it is).

I believe that a similar methodology should be applied to the spread of gene variants as well (e.g., Y-chromosome haplogroups). At present, haplogroup ages are estimated only by internal (genetic) information, e.g., the diversity of linked STR loci. However, as I have argued before, there are additional pieces of information: (i) how big the haplogroup is, and (ii) how geographically dispersed it is. Both (i) and (ii) depend on a haplogroup's age.

CURRENT ANTHROPOLOGY Volume 49, Number 6, December 2008 DOI: 10.1086/592436

Language Spread Rates and Prehistoric American Migration Rates

Johanna Nichols


Spread rates for language families can be calculated from the family's range (which is generally known rather precisely) and age (which is only rarely known precisely but can often be estimated with useful accuracy). Spread rates are calculated here for a number of different language families and subfamilies in different cultural and economic contexts. Deliberate long-distance migrations, imperial conquest, and transport using wheels or sails make for very rapid spread rates. The rate of prestate, pretransport spreads depends primarily on ecology (latitude, coast vs. interior, mountains, vegetation, climate); presence versus absence of food production and movement into inhabited versus abandoned land have little impact on spread rates. This fact makes rates of recent language spreads applicable to early prehistory, where they can be used to model prehistoric colonization rates. Average rates for various ecologies are calculated for a spread from a North American entry point to the archaeological site at Monte Verde, Chile (14,500 calendar years ago). The time required gives a latest possible date for the first settlement of the Americas. Entry dates postdating the end of glaciation all require implausibly fast rates of spread.


Waist-to-Hip Ratio across cultures

CURRENT ANTHROPOLOGY Volume 49, Number 6, December 2008
DOI: 10.1086/593036

Waist-to-Hip Ratio across Cultures: Trade-Offs between Androgen- and Estrogen-Dependent Traits

Elizabeth Cashdan


A gynoid pattern of fat distribution, with small waist and large hips (low waist-to-hip ratio, or WHR) holds significant fitness benefits for women: women with a low WHR of about 0.7 are more fecund, are less prone to chronic disease, and (in most cultures) are considered more attractive. Why, then, do nearly all women have a WHR higher than this putative optimum? Is the marked variation in this trait adaptive? This paper first documents the conundrum by showing that female WHR, especially in non-Western populations, is higher than the putative optimum even among samples that are young, lean, and dependent on traditional diets. The paper then proposes compensating benefits to a high WHR that can explain both its prevalence and variation in the trait. The evidence indicates that the hormonal profile associated with high WHR (high androgen and cortisol levels, low estrogens) favors success in resource competition, particularly under stressful and difficult circumstances, even though this carries fitness costs in fecundity and health. Adrenal androgens, in particular, may play an important role in enabling women to respond to stressful challenges.


January 02, 2009

Nicholas Christakis on the Anthroposphere

An interesting answer from the Edge World Question Center 2009. The part in italics reminds me of a previous post I made on Rise of diseases in modern societies is not (usually) due to genetic or environmental factors:
This is a simple consequence of the one reality of life, namely death. The total mortality of the population is always 100%, as we all eventually die. Therefore the prevalence of a particular disease (which brings us closer to death) does not depend exclusively on factors (genetic or environmental) that cause the disease. It also depends on other diseases or lethal factors which might beat them to the punch.

In previous centuries for example, death during childbirth, tuberculosis, death in war, famine etc. were more prevalent. Thus, they took a larger part of the 100% pie. Degenerative diseases were thus correspondingly less important, because irrespective of genes or environments affecting them, we used to die of other causes.
Here is Christakis on the Anthroposphere:
Physician and social scientist, Harvard



The global population stood at one million at 10,000 BC, 50 million at 1,000 BC, and 310 million in 1,000 AD. It stood at about one billion in 1800, 1.65 billion in 1900, and 6.0 billion in 2000. Analysis of these macro-historical trends in human population usually focuses on this population growth and on the "demographic transition" underlying it.

During the first stage of the demographic transition, life—as Hobbes rightly suggested—was nasty, brutish, and short. There was a balance between birth rates and death rates, and both were very high (30-50 per thousand people per year). The human population grew less than 0.05% annually, with a doubling time of over 1,000 years. This state of affairs was true of all human populations everywhere until the late 18th century.

Then, during the second stage, the death rate began to decline—first in northwestern Europe, but then spreading over the next 100 years to the south and east. The decline in the death rate was due initially to improvements in food supply and in public health, both of which reduced mortality, particularly in childhood. As a consequence, there was a population explosion.

During the third stage, birth rates dropped for the first time in human history. The prior decline in childhood mortality probably prompted parents to realize they did not need as many children; and increasing urbanization, increasing female literacy, and (eventually) contraceptive technology also played a part.

Finally, during the fourth stage—in which the developed world presently finds itself—there is renewed stability. Birth and death rates are again in balance, but now both are relatively low. Causes of mortality have shifted from the pre-Modern pattern dominated by infectious diseases, perinatal diseases, and nutritional diseases, to one dominated by chronic diseases, mental illnesses, and behavioral conditions.

This broad story, however, conceals as much as it reveals. There are other demographic developments worldwide beyond the increasing overall size of the population, developments that are still unfolding and that matter much more. Changes in four aspects of population structure are key: (1) sex ratio, (2) age structure, (3) kinship systems, and (4) income distribution.

Sex ratios are becoming increasingly unbalanced in many parts of the world, especially in China and India (which account for 37% of the global population). The normal sex ratio at birth is roughly 106 males for every 100 females, but it may presently be as high as 120 for young people in China, or as high as 111 in India. This shift, much discussed, may arise from preferential abortion or the neglect of baby girls relative to boys. Gender imbalance may also have other determinants, such as large-scale migration of one or the other sex in search of work. This shift has numerous implications. For example, given the historical role of females as caregivers to elderly parents, a shortage of woman to fill this role will induce large-scale social adjustments. Moreover, an excess of low-status men unable to find wives results in an easy (and large) pool of recruits for extremism and violence.

This shift in gender ratios may have other, less heralded implications, however. Some of our own work has suggested that this shift may actually shorten men’s lives, reversing some of the historic progress we have made. Across a range of species, skewed sex ratios result in intensified competition for sexual partners and this induces stress for the supernumerary sex. In humans, it seems, a 5% excess of males at the time of sexual maturity shortens the survival of men by about three months in late life, which is a very substantial loss.

On the other hand, the population worldwide is getting older, especially in the developed world. Globally, the UN estimates that the proportion of people aged 60 and over will double between 2000 and 2050, from 10% to 21%, and the proportion of children will drop from 30% to 21%. This change also has numerous implications, including on the "dependency ratio," meaning that fewer young people are available to provide for the medical and economic needs of the elderly. Much less heralded, however, is the fact that war is a young person’s activity, and it is entirely likely that, as populations age, they may become less aggressive.

The changing nature of kinship networks, such as the growth in blended families—whether due to changing divorce patterns in the developed world or AIDS killing off parents in Africa—has implications for the network of obligations and entitlements within families. Changing kinship systems in modern American society (with complex mixtures of remarried and cohabiting couples, half-siblings, step-siblings, and so on) are having profound implications for caregiving, retirement, and bequests. Who cares for Grandma? Who gets her money when she dies?

Finally, it is not just the balance between males and females, or young and old, that is changing, but also the balance between rich and poor. Income inequality is reaching historic heights throughout the world. The top 1% of the people in the world receives 57% of the income. Income inequality in the US is presently at its highest recorded levels, exceeding even the Roaring Twenties. And while economic development in China has proceeded with astonishing rapidity, income is not evenly distributed; the prospects for conflict in that country as a result seem very high in the coming decades.

Lacking any real predators, a key feature of the human environment is other humans. In our rush to focus on threats such as global warming and environmental degradation, we should not overlook this fact. It is well to look around at who, and not just what, surrounds us. Population structure will change everything. Our health, wealth, and peace depend on it.

Origins of Cholera and Molecular Clock recalibration

A casual 100-fold recalibration of the molecular clock should serve as a warning not to take molecular dating too seriously, or at least to make sure to check the premises on which it is based.

PLoS ONE doi:10.1371/journal.pone.0004053

A Recalibrated Molecular Clock and Independent Origins for the Cholera Pandemic Clones

Lu Feng et al.

Cholera, caused by Vibrio cholerae, erupted globally from South Asia in 7 pandemics, but there were also local outbreaks between the 6th (1899–1923) and 7th (1961–present) pandemics. All the above are serotype O1, whereas environmental or invertebrate isolates are antigenically diverse. The pre 7th pandemic isolates mentioned above, and other minor pathogenic clones, are related to the 7th pandemic clone, while the 6th pandemic clone is in the same lineage but more distantly related, and non-pathogenic isolates show no clonal structure. To understand the origins and relationships of the pandemic clones, we sequenced the genomes of a 1937 prepandemic strain and a 6th pandemic isolate, and compared them with the published 7th pandemic genome. We distinguished mutational and recombinational events, and allocated these and other events, to specific branches in the evolutionary tree. There were more mutational than recombinational events, but more genes, and 44 times more base pairs, changed by recombination. We used the mutational single-nucleotide polymorphisms and known isolation dates of the prepandemic and 7th pandemic isolates to estimate the mutation rate, and found it to be 100 fold higher than usually assumed We then used this to estimate the divergence date of the 6th and 7th pandemic clones to be about 1880. While there is a large margin of error, this is far more realistic than the 10,000–50,000 years ago estimated using the usual assumptions. We conclude that the 2 pandemic clones gained pandemic potential independently, and overall there were 29 insertions or deletions of one or more genes. There were also substantial changes in the major integron, attributed to gain of individual cassettes including copying from within, or loss of blocks of cassettes. The approaches used open up new avenues for analysing the origin and history of other important pathogens.