- 0.57 in Iran
- 0.47 in Pakistan
- 0.36 in India
See also STR variance of haplogroup J2 in the Balkans and Anatolia.
January 05, 2006
J variance in Iran, Pakistan, India, Turkey, and the Balkans
Quintana-Murci et al. reported that the STR variance in haplogroup J is
See also STR variance of haplogroup J2 in the Balkans and Anatolia.
See also STR variance of haplogroup J2 in the Balkans and Anatolia.
Correlations of US height and body mass index
Journal of Biosocial Science (online early)
SPATIAL CORRELATES OF US HEIGHTS AND BODY MASS INDEXES, 2002
JOHN KOMLOS and BENJAMIN E. LAUDERDALE
Abstract
Aiming to further explore possible underlying causes of the recent remarkable stagnation and relative decline in American heights, this paper describes the result of analysis of the commercial US Sizing Survey (2002). Heights are correlated positively with income and education among both white males and females while Body Mass Index (BMI) is correlated negatively among females, as in other samples. In contrast to much of the literature, this paper considers geographic correlates of height such as local poverty rate, median income and population density at the zip code level of resolution. After adjusting for confounding factors that influence height such as income and education, population density is found to be strongly and negatively correlated with height among white men, but less so among white women. The effect on BMIs less convincing. Other ethnic groups are not analysed in detail because of the small number of observations available. Local economic conditions as measured by median income, unemployment and poverty rate do not have a strong correlation with height or BMI after adjusting for individual income and education.
Link
SPATIAL CORRELATES OF US HEIGHTS AND BODY MASS INDEXES, 2002
JOHN KOMLOS and BENJAMIN E. LAUDERDALE
Abstract
Aiming to further explore possible underlying causes of the recent remarkable stagnation and relative decline in American heights, this paper describes the result of analysis of the commercial US Sizing Survey (2002). Heights are correlated positively with income and education among both white males and females while Body Mass Index (BMI) is correlated negatively among females, as in other samples. In contrast to much of the literature, this paper considers geographic correlates of height such as local poverty rate, median income and population density at the zip code level of resolution. After adjusting for confounding factors that influence height such as income and education, population density is found to be strongly and negatively correlated with height among white men, but less so among white women. The effect on BMIs less convincing. Other ethnic groups are not analysed in detail because of the small number of observations available. Local economic conditions as measured by median income, unemployment and poverty rate do not have a strong correlation with height or BMI after adjusting for individual income and education.
Link
January 04, 2006
The prion protein gene in humans revisited
A few years ago, in a widely reported study, it was postulated that cannibalism may have been quite frequent in human evolutionary history. This conclusion was reached by the study of genes which protect people from brain-related diseases associated by cannibalism, similar to "mad cow disease". Now, a new study throws doubt on these earlier findings, showing that there was no rampant general cannibalism in the human past.
See also History of human cannibalism eats away at researchers.
Genome Res. 2005 Dec 20; [Epub ahead of print]
The prion protein gene in humans revisited: Lessons from a worldwide resequencing study.
Soldevila M, Andres AM, Ramirez-Soriano A, Marques-Bonet T, Calafell F, Navarro A, Bertranpetit J.
Ample evidence has accumulated showing that different coding variants of the PRNP gene confer differential susceptibility for prion diseases. Here we evaluate the patterns of nucleotide variation in PRNP exon 2, which includes all the protein-coding sequence, by resequencing a worldwide sample of 174 humans for 2378 bp. In line with previous studies, we found two main haplotypes differentiated by nonsynonymous substitution in codon 129. Our analyses reveal the worldwide pattern of variation at the PRNP gene to be inconsistent with neutral expectations, indicating instead an excess of low-frequency variants, a footprint of the action of either positive or purifying selection. A comparison of neutrality test statistics for PRNP with other human genes indicates that the signal of positive selection on PRNP is stronger than expected from a possible confounding genome-wide background signal of population expansion. Two main conclusions arise from our analysis. First, the existence of an ancient, stable, balanced polymorphism that has been claimed in a previous study and related to cannibalism can be rejected and is shown to be due to ascertainment bias. Second, our results are consistent with a complex history of selection including mainly positive selection, even if short local periods of balancing selection (Kuru-like episodes), or even a weak purifying selection model, are consistent with our data.
Link
See also History of human cannibalism eats away at researchers.
Genome Res. 2005 Dec 20; [Epub ahead of print]
The prion protein gene in humans revisited: Lessons from a worldwide resequencing study.
Soldevila M, Andres AM, Ramirez-Soriano A, Marques-Bonet T, Calafell F, Navarro A, Bertranpetit J.
Ample evidence has accumulated showing that different coding variants of the PRNP gene confer differential susceptibility for prion diseases. Here we evaluate the patterns of nucleotide variation in PRNP exon 2, which includes all the protein-coding sequence, by resequencing a worldwide sample of 174 humans for 2378 bp. In line with previous studies, we found two main haplotypes differentiated by nonsynonymous substitution in codon 129. Our analyses reveal the worldwide pattern of variation at the PRNP gene to be inconsistent with neutral expectations, indicating instead an excess of low-frequency variants, a footprint of the action of either positive or purifying selection. A comparison of neutrality test statistics for PRNP with other human genes indicates that the signal of positive selection on PRNP is stronger than expected from a possible confounding genome-wide background signal of population expansion. Two main conclusions arise from our analysis. First, the existence of an ancient, stable, balanced polymorphism that has been claimed in a previous study and related to cannibalism can be rejected and is shown to be due to ascertainment bias. Second, our results are consistent with a complex history of selection including mainly positive selection, even if short local periods of balancing selection (Kuru-like episodes), or even a weak purifying selection model, are consistent with our data.
Link
STR variance of haplogroup J2 in the Balkans and Anatolia
I have calculated the STR variance of haplogroup J2 chromosomes in the Balkans, based on the recent study by Bosch et al. and in Anatolia, reported by Cinnioglu et al. Since Bosch et al. studied more microsatellites, and microsatellite mutation rates are variable, I have made the comparison based on the 10 microsatellites used by Cinnioglu et al. (DYS19 DYS388 DYS390 DYS391 DYS392 DYS393 DYS389I(CD) DYS389II(AB) DYS439 DYSA7.2). I have also adjusted the DYS389ii value reported by Bosch et al. to conform to the Cinnioglu et al. convention.
STR variance in J2 chromosomes in Turkey is 0.52, precisely as originally reported by Cinnioglu et al. The corresponding value for the Balkan populations sampled by Bosch et al. is 0.56.
Please, also note that Bosch et al. report two haplotypes #145 and #166 that occur in 19 and 17 cases, and may represent a founder effect in specific populations.
The results of these two studies are broadly compatible with the observations of Malaspina et al. on STR variatiance within haplogroup J2a1.
Update
Behar et al. also report allele variances for Ashkenazi Jewish (0.28) and non-Jewish Europeans (0.37). They include the DYS426 locus instead of DYS461/DYS A7.2. Their European sample did not include Balkan populations, except for some Romanians.
Update 2
The STR variance of J2a in India is 0.34 (data from Sengupta 2006). The variance of J2b is 0.34.
Update 3
The variance of J2a in Turkey is 0.47. The variance of J2b is 0.24.
STR variance in J2 chromosomes in Turkey is 0.52, precisely as originally reported by Cinnioglu et al. The corresponding value for the Balkan populations sampled by Bosch et al. is 0.56.
Please, also note that Bosch et al. report two haplotypes #145 and #166 that occur in 19 and 17 cases, and may represent a founder effect in specific populations.
The results of these two studies are broadly compatible with the observations of Malaspina et al. on STR variatiance within haplogroup J2a1.
Update
Behar et al. also report allele variances for Ashkenazi Jewish (0.28) and non-Jewish Europeans (0.37). They include the DYS426 locus instead of DYS461/DYS A7.2. Their European sample did not include Balkan populations, except for some Romanians.
Update 2
The STR variance of J2a in India is 0.34 (data from Sengupta 2006). The variance of J2b is 0.34.
Update 3
The variance of J2a in Turkey is 0.47. The variance of J2b is 0.24.
January 03, 2006
On Genetic Palimpsests
Most of the genetic markers used in human phylogeographic studies have been dated to the prehistoric period, and the majority of them are of Upper Paleolithic origin.
Lately, subclades identified within some human lineages on the Y-chromosome have crossed the Neolithic barrier, and in even rarer cases, "signatures" of historical events, such as the dominance of the Mongols, the Manchu, or the Ui Neill.
As a result, most markers are suitable for examining events of human prehistory, and not of historical ethnic groups.
Of course, scientists have tried to apply genetic information to historical processes, e.g., in the case of Jewish origins, but it turns out that the "Jewish gene" or Cohen Modal Haplotype actually turns out to to be much older and not particularly Jewish after all.
Even with old markers, it is still possible to reason about historical events. For example, the theories of white nationalist Arthur Kemp about the widespread prevalence of black African slavery in the classical world have been squarely defeated by the near-complete absence of Sub-Saharan African markers in the Italian and Balkan peninsulas. Similar theories propagated by Gustav Kossina and the Aryan-Nordic camp about the Northern European origin of the Indo-Europeans of India have similarly been defeated, since Indians completely lack haplogroup I chromosomes that are frequent in European Nordic populations.
So, even though the markers in question are very old (I is of Upper Paleolithic age), we can still reason historically with them.
Often, this historical reasoning can be shaky. For example, Spencer Wells has made tall claims about the Phoenicians, the Sea Peoples, and the Carthaginians in a National Geographic article which were based on the analysis of haplogroup J and E distribution in the Levant and North Africa.
For example, he found that there was little impact of Phoenicians on Carthage, but his conclusions are based on the paucity of haplogroup J in modern North African populations, who are a much broader-group than the socially and geographically constrained group of the ancient Carthaginians. Similar claims were made regarding the non-impact of the Sea Peoples in the Levant, but again, this is based on the similarity between coastal and non-coastal populations.
But, for all we know subdivisions of haplogroup J and other Near Eastern markers may differ between coastal and non-coastal populations, or perhaps, the Sea Peoples did initially affect the coastal peoples, but later their genes diffused into non-coastal populations, removing the distinctiveness of the two.
Let us take a further example of Sicily. The island of Sicily was colonized initially by farmers, and later by Greeks and Phoenicians. All three groups are believed to have contained some "Neolithic" markers, such as haplogroups J, E3b, and G, so any inferences about the relative contributions of the three groups are on very shaky ground.
For example, Semino et al. proposed that only 7% of Calabrian Y-chromosomes are of Greek with the assumption that J2a and E3b represent Anatolian and Greek lineages respectively. But, the frequency of E3b in modern Peloponnesians is not necessarily representative of its frequency in the very specific ancient city states and medieval Greek populations that colonized Southern Italy, and J2a may have arrived in Calabria either from Anatolia, e.g., during the Neolithic, or from Greece, during the age of colonization.
Things become even more complex when we turn to the Balkans or to Anatolia. For example, I playfully recounted some random facts about Phrygo-Armenians, but these hardly scratch the surface of the problem. Hittites, themselves either native or intrusive, were unseated by Phrygians, who were conquered by Persians, who were conquered by Macedonian Greeks, who were conquered by Romans, who were conquered by Turks. Not to mention the Galatians of Ancyra, or the ubuiquitous Armenians of the Byzantine Empire, or even the Jews of both the ancient and more recent origin, and of course the Turks themselves as well as imported Muslims from former provinces or vassals of the Ottoman Empire. And, of course, we should not forget that present-day Anatolians are only a subset of very recent Anatolians, several million of who were liquidated or deported following World War I.
These remarks underscore the near hopelessness of untangling historical patterns on the basis of phylogeography. Is there a way out?
Part of the solution will consist of performing huge studies with large sample sizes and very recently derived genetic markers, augmented by separate genome-wide autosomal clustering methods that may unmask latent genetic components that may be correlated with historical groups. Such studies will be very costly, even though the price of DNA testing is likely to go down, because ultimately the hard work of sample collection has to be done and paid for.
The ultimate solution, would be some significant progress in ancient DNA extraction. At present, mtDNA is the only game in town, and inferences from mtDNA are always up for grabs, due to the potential for contamination, uncertainties about selection, and of course the simple fact that ancient civilizations were largely patriarchal.
An even more exciting development would be the discovery -in modern human populations- of the genetics underlying common human variation in metric and morphological traits. Then, by examing ancient skeletal remains, we will be able to estimate the genetic identity of populations even if DNA cannot be directly observed.
The technical challenges are enormous, but -in my opinion- are not the main challenges at all. As hinted in Genetic vs. Mythical Origins, the study of the past forces us to question our ideas of descent and ethnicity. In the end, will it lead to an erosion of ethnic identity, or to its reinforcement along genetic and hence "objective" lines?
Lately, subclades identified within some human lineages on the Y-chromosome have crossed the Neolithic barrier, and in even rarer cases, "signatures" of historical events, such as the dominance of the Mongols, the Manchu, or the Ui Neill.
As a result, most markers are suitable for examining events of human prehistory, and not of historical ethnic groups.
Of course, scientists have tried to apply genetic information to historical processes, e.g., in the case of Jewish origins, but it turns out that the "Jewish gene" or Cohen Modal Haplotype actually turns out to to be much older and not particularly Jewish after all.
Even with old markers, it is still possible to reason about historical events. For example, the theories of white nationalist Arthur Kemp about the widespread prevalence of black African slavery in the classical world have been squarely defeated by the near-complete absence of Sub-Saharan African markers in the Italian and Balkan peninsulas. Similar theories propagated by Gustav Kossina and the Aryan-Nordic camp about the Northern European origin of the Indo-Europeans of India have similarly been defeated, since Indians completely lack haplogroup I chromosomes that are frequent in European Nordic populations.
So, even though the markers in question are very old (I is of Upper Paleolithic age), we can still reason historically with them.
Often, this historical reasoning can be shaky. For example, Spencer Wells has made tall claims about the Phoenicians, the Sea Peoples, and the Carthaginians in a National Geographic article which were based on the analysis of haplogroup J and E distribution in the Levant and North Africa.
For example, he found that there was little impact of Phoenicians on Carthage, but his conclusions are based on the paucity of haplogroup J in modern North African populations, who are a much broader-group than the socially and geographically constrained group of the ancient Carthaginians. Similar claims were made regarding the non-impact of the Sea Peoples in the Levant, but again, this is based on the similarity between coastal and non-coastal populations.
But, for all we know subdivisions of haplogroup J and other Near Eastern markers may differ between coastal and non-coastal populations, or perhaps, the Sea Peoples did initially affect the coastal peoples, but later their genes diffused into non-coastal populations, removing the distinctiveness of the two.
Let us take a further example of Sicily. The island of Sicily was colonized initially by farmers, and later by Greeks and Phoenicians. All three groups are believed to have contained some "Neolithic" markers, such as haplogroups J, E3b, and G, so any inferences about the relative contributions of the three groups are on very shaky ground.
For example, Semino et al. proposed that only 7% of Calabrian Y-chromosomes are of Greek with the assumption that J2a and E3b represent Anatolian and Greek lineages respectively. But, the frequency of E3b in modern Peloponnesians is not necessarily representative of its frequency in the very specific ancient city states and medieval Greek populations that colonized Southern Italy, and J2a may have arrived in Calabria either from Anatolia, e.g., during the Neolithic, or from Greece, during the age of colonization.
Things become even more complex when we turn to the Balkans or to Anatolia. For example, I playfully recounted some random facts about Phrygo-Armenians, but these hardly scratch the surface of the problem. Hittites, themselves either native or intrusive, were unseated by Phrygians, who were conquered by Persians, who were conquered by Macedonian Greeks, who were conquered by Romans, who were conquered by Turks. Not to mention the Galatians of Ancyra, or the ubuiquitous Armenians of the Byzantine Empire, or even the Jews of both the ancient and more recent origin, and of course the Turks themselves as well as imported Muslims from former provinces or vassals of the Ottoman Empire. And, of course, we should not forget that present-day Anatolians are only a subset of very recent Anatolians, several million of who were liquidated or deported following World War I.
These remarks underscore the near hopelessness of untangling historical patterns on the basis of phylogeography. Is there a way out?
Part of the solution will consist of performing huge studies with large sample sizes and very recently derived genetic markers, augmented by separate genome-wide autosomal clustering methods that may unmask latent genetic components that may be correlated with historical groups. Such studies will be very costly, even though the price of DNA testing is likely to go down, because ultimately the hard work of sample collection has to be done and paid for.
The ultimate solution, would be some significant progress in ancient DNA extraction. At present, mtDNA is the only game in town, and inferences from mtDNA are always up for grabs, due to the potential for contamination, uncertainties about selection, and of course the simple fact that ancient civilizations were largely patriarchal.
An even more exciting development would be the discovery -in modern human populations- of the genetics underlying common human variation in metric and morphological traits. Then, by examing ancient skeletal remains, we will be able to estimate the genetic identity of populations even if DNA cannot be directly observed.
The technical challenges are enormous, but -in my opinion- are not the main challenges at all. As hinted in Genetic vs. Mythical Origins, the study of the past forces us to question our ideas of descent and ethnicity. In the end, will it lead to an erosion of ethnic identity, or to its reinforcement along genetic and hence "objective" lines?
Looking forward to in 2006
I have already posted some of the highlights of the past year. Here are some of the things that I am looking forward to this year, partly inspired by John Hawks' oracles:
- The first study on ancient Mycenaean and Minoan mtDNA.
- A study on haplogroup E-M78 subdivisions.
- A study on Minoan civilization origins.
- Successful extraction of autosomal DNA from prehistoric humans.
- Correlation of recently selected genes with IQ and/or personality.
- Even more debate between demists and acculturationists regarding the spread of the Neolithic.
- Even more debate between assimilationists and non-assimilationists about the Neandertals.
- At least one paper from the Genographic project in a venue other than National Geographic about some obscure people that no one has heard about but everyone will talk about for days. The paper will have a feel-good message about the unity of mankind.
- The French will continue to remain a genetic mystery, but there will be at least three more studies on Jewish population genetics.
January 02, 2006
Some aspects of J2 distribution
Haplogroup J2 consists exclusively of two separate subclades: J2a-M410 and J2b-M12.
Crete, occupying the southmost of the Greek world has an M12/M172 ratio of 2.2% [1]. This ratio is 20% [1] or 42.2% [2], a weighted average of 26%. In Northern Greece (Macedonia) it is 43.2% [2].
In Albania, the same ratio is 100% in the small sample of [1] and 54.6% as reported by [2], a weighted average of 55%.
In Bulgaria, the ratio is 28.6% [1] and in Romania, the ratio is 0% in the good sample of [1]. In the Ukraine it is 32.9% [2]
According to [3], the ratio is high in Serbs (66.3%). The few Croatians and Herzegovinians belonging in haplogroup J2 belong to the M12 clade, giving a ratio of 100% [2,3]. Similarly in Poland (100%) [2], and Czech Republic/Slovakia (50%) [1].
The distinction between the Western and Eastern Balkans that I have spoken of before is clear in this regard. M12 clade comprises the majority of J2 in the West and the minority in the East. Moreover, Slavic speakers of continental Europe belong more to the M12 clade, whereas those bordering Black Sea are more inclined to have a low frequency of M12, including the non-Slavic Romanians who lack M12 altogether. In historical times, the Balkans were inhabited by several Indo-European peoples which could be classified in the macro-groups of Illyrians (west) and Thracians (east). Greek trade and settlement occurred in both the Adriatic and the Black Sea, but the Greek presence was probably heavier and more long-lasting (until recent times) in the latter region.
Italy resembles the Greek-Black Sea area. Southern Italy has a ratio of 12.4%, while Northern Italy has a ratio of 25% [1]. North-Central Italy (35.7%), and two Calabrian samples (1%), and Sicily (0%). The latter two locations were Greek speaking for the major part of their recorded history.
Turkey resembles the Greek-Black Sea-South Italian area with an overall ratio of 7.1% [4]. Turkey was primarily Greek, Armenian and Kurdish speaking before the arrival of the Altaic-speaking Turks. Before that, it was also home to a variety of languages, including several extinct languages of the Indo-European family such as Hittite, Luvian, Palaic, Lydian, Lycian, Phrygian, and Celtic.
[1] Di Giacomo (2004)
[2] Semino (2004)
[3] Pericic (2006)
[4] Cinnioglu (2004)
Crete, occupying the southmost of the Greek world has an M12/M172 ratio of 2.2% [1]. This ratio is 20% [1] or 42.2% [2], a weighted average of 26%. In Northern Greece (Macedonia) it is 43.2% [2].
In Albania, the same ratio is 100% in the small sample of [1] and 54.6% as reported by [2], a weighted average of 55%.
In Bulgaria, the ratio is 28.6% [1] and in Romania, the ratio is 0% in the good sample of [1]. In the Ukraine it is 32.9% [2]
According to [3], the ratio is high in Serbs (66.3%). The few Croatians and Herzegovinians belonging in haplogroup J2 belong to the M12 clade, giving a ratio of 100% [2,3]. Similarly in Poland (100%) [2], and Czech Republic/Slovakia (50%) [1].
The distinction between the Western and Eastern Balkans that I have spoken of before is clear in this regard. M12 clade comprises the majority of J2 in the West and the minority in the East. Moreover, Slavic speakers of continental Europe belong more to the M12 clade, whereas those bordering Black Sea are more inclined to have a low frequency of M12, including the non-Slavic Romanians who lack M12 altogether. In historical times, the Balkans were inhabited by several Indo-European peoples which could be classified in the macro-groups of Illyrians (west) and Thracians (east). Greek trade and settlement occurred in both the Adriatic and the Black Sea, but the Greek presence was probably heavier and more long-lasting (until recent times) in the latter region.
Italy resembles the Greek-Black Sea area. Southern Italy has a ratio of 12.4%, while Northern Italy has a ratio of 25% [1]. North-Central Italy (35.7%), and two Calabrian samples (1%), and Sicily (0%). The latter two locations were Greek speaking for the major part of their recorded history.
Turkey resembles the Greek-Black Sea-South Italian area with an overall ratio of 7.1% [4]. Turkey was primarily Greek, Armenian and Kurdish speaking before the arrival of the Altaic-speaking Turks. Before that, it was also home to a variety of languages, including several extinct languages of the Indo-European family such as Hittite, Luvian, Palaic, Lydian, Lycian, Phrygian, and Celtic.
[1] Di Giacomo (2004)
[2] Semino (2004)
[3] Pericic (2006)
[4] Cinnioglu (2004)
Some random (?) facts
"The Phrygians had an equipment very like that of the Paphlagonians with some slight difference. Now the Phrygians, as the Macedonians say, used to be called Brigians during the time that they were natives of Europe and dwelt with the Macedonians; but after they had changed into Asia, with their country they changed also their name and were called Phrygians. The Armenians were armed just like the Phrygians, being settlers from the Phrygians. Of these two together the commander was Artochmes, who was married to a daughter of Dareios." Herodotus, vii, 73
"Phrygia is the Greek name of an ancient state in western-central Anatolia (modern Turkey), extending from the Eskishehir area east to (perhaps) Bogazköy and Alishar Hüyük within the Halys River bend. The Assyrians, a powerful state in northern Mesopotamia to the south, called the state Mushki; what its own people called it is unknown. We know from their inscriptions that the Phrygians spoke an Indo-European language. Judging from historical records supported by ceramic evidence, settlers migrating from the Balkans in Europe first settled here a hundred or more years following the destruction of the Hittite empire (ca. 1200 BC)." The Metropolitan Museum of Art: 'Phrygia, Gordion, and King Midas in the Late Eighth Century B.C.'
"There is evidence that in ancient times a distinct subfamily of Indo-European languages existed that is now called Thraco-Phrygian. To it belonged Phrygian (an ancient and now extinct Indo-European language of Anatolia) and Thracian (a now dead Indo-European tongue of the Balkans in antiquity). Modern Armenian may well be a direct descendant of Phrygian." The Columbia Encyclopedia: 'Armenian language'
"All the unrooted trees agree that there are four supergroups of IE languages (Balto-Slavonic, Romano-Germano-Celtic, Armenian-Greek, and Indo-Iranian)" Rexova K. (2003) Cladistic analysis of languages: Indo-European classification based on lexicostatistical data, Cladistics 19(2)
Interpolated map of haplogroup J2a frequency. Extracted from Sengupta et al. (in press).
Ancient Phrygia, map extracted from Ancient Anatolia web site.
December 29, 2005
The questionable contribution of the Neolithic and the Bronze Age to European craniofacial form (?)
C. Loring Brace and colleagues have published a new paper in PNAS which examines several populations from West Eurasia and Africa based on 24 cranial measurements.
The first canonical variate (horizontal) clearly separates the Niger-Congo group from the other populations:
According to Brace et al:
Brace et al. also combined samples into regional groups. The canonical variate plot again shows the separate of the Niger-Congo group, and the intermediacy of the Natufians between West Eurasians and North/East Africans and Eurasians.
The raw Mahalanobis distances are quite informative.
It can be easily seen that the Niger-Congo have high distances from all other populations, except Northeast Africans. Northeast Africans are however closer to Late Prehistoric Eurasians and Modern Europeans than to the Niger-Congo group. This, once more, establishes the intermediacy of Northeast Africans between Caucasoids and Sub-Saharan Africans.
All populations except the Niger-Congo and the Natufians are close to each other. The Natufians have very high distances from other samples. Their closest neighbors are first, Late Prehistoric Eurasia, and second, Niger-Congo.
According to Brace:
Brace's conclusion is stated in conditional form:
Brace finds similarities between the ancient Neolithic culture-bearers and modern Mediterranean populations, which is no doubt accurate. On the other hand, in continental Europe, the "signal" of the Neolithic populations has been absorbed by the indigenous inhabitants. This is all fine, and agrees nicely with the picture presented sixty five years ago by Carleton Coon, whereby the invasion of Europe by gracile dolichomorphs (skeletally Mediterranean) populations was followed by a period of absorption and "re-emergence" of the Upper Paleolithic types and their mixtures with the Mediterraneans.
Indeed, the early inhabitants of Northern Europe were robust broad-faced Cro-Magnoids, unlike the gracile narrow-faced Mediterraneans which diffused through Central Europe from a proximate Southeastern European source. Brace studies Cro-Magnon to propose that:
The retention of the "Upper Paleolithic" signal in modern Europeans is quite impressive, since Europe's colonization did not cease with Cro-Magnon in the first Upper Paleolithic.
Cro-Magnon was a coarse-featured and robust skull atypical of modern Europeans, but one may still find individuals in Europe which resemble him: Brace et al. did not test for his resemblance to individuals. Moreover, he did not test Cro-Magnon against individual European populations. For example, Jantz and Owsley concluded that:
I have sent the following questions to Dr. Brace regarding his study. If and when he responds, and if I am granted permission to publish his response, I will do so in these entry:
Proc. Natl. Acad. Sci. USA, 10.1073/pnas.0509801102
The questionable contribution of the Neolithic and the Bronze Age to European craniofacial form
C. Loring Brace et al.
Many human craniofacial dimensions are largely of neutral adaptive significance, and an analysis of their variation can serve as an indication of the extent to which any given population is genetically related to or differs from any other. When 24 craniofacial measurements of a series of human populations are used to generate neighbor-joining dendrograms, it is no surprise that all modern European groups, ranging all of the way from Scandinavia to eastern Europe and throughout the Mediterranean to the Middle East, show that they are closely related to each other. The surprise is that the Neolithic peoples of Europe and their Bronze Age successors are not closely related to the modern inhabitants, although the prehistoric/modern ties are somewhat more apparent in southern Europe. It is a further surprise that the Epipalaeolithic Natufian of Israel from whom the Neolithic realm was assumed to arise has a clear link to Sub-Saharan Africa. Basques and Canary Islanders are clearly associated with modern Europeans. When canonical variates are plotted, neither sample ties in with Cro-Magnon as was once suggested. The data treated here support the idea that the Neolithic moved out of the Near East into the circum-Mediterranean areas and Europe by a process of demic diffusion but that subsequently the in situ residents of those areas, derived from the Late Pleistocene inhabitants, absorbed both the agricultural life way and the people who had brought it.
Link
The first canonical variate (horizontal) clearly separates the Niger-Congo group from the other populations:
According to Brace et al:
When the samples used in Fig. 1 are compared by the use of canonical variate plots as in Fig. 2, the separateness of the Niger-Congo speakers is again quite clear. Interestingly enough, however, the small Natufian sample falls between the Niger-Congo group and the other samples used. Fig. 2 shows the plot produced by the first two canonical variates, but the same thing happens when canonical variates 1 and 3 (not shown here) are used. This placement suggests that there may have been a Sub-Saharan African element in the make-up of the Natufians (the putative ancestors of the subsequent Neolithic), although in this particular test there is no such evident presence in the North African or Egyptian samples. As shown in Fig. 1, the Somalis and the Egyptian Bronze Age sample from Naqada may also have a hint of a Sub-Saharan African component. That was not borne out in the canonical variate plot (Fig. 2), and there was no evidence of such an involvement in the Algerian Neolithic (Gambetta) sample.
Brace et al. also combined samples into regional groups. The canonical variate plot again shows the separate of the Niger-Congo group, and the intermediacy of the Natufians between West Eurasians and North/East Africans and Eurasians.
The raw Mahalanobis distances are quite informative.
It can be easily seen that the Niger-Congo have high distances from all other populations, except Northeast Africans. Northeast Africans are however closer to Late Prehistoric Eurasians and Modern Europeans than to the Niger-Congo group. This, once more, establishes the intermediacy of Northeast Africans between Caucasoids and Sub-Saharan Africans.
All populations except the Niger-Congo and the Natufians are close to each other. The Natufians have very high distances from other samples. Their closest neighbors are first, Late Prehistoric Eurasia, and second, Niger-Congo.
According to Brace:
The generally high D2 values for the Natufian sample in Table 3 are almost certainly a reflection of the very small sample size.The Natufian sample consisted of only 4 individuals. Thus, it appears that the high distances of the Niger-Congo group are indicative of its biological distinctiveness, whereas the high distances of the Natufians are due to the small sample size.
Brace's conclusion is stated in conditional form:
If the Late Pleistocene Natufian sample from Israel is the source from which that Neolithic spread was derived, then there was clearly a Sub-Saharan African element present of almost equal importance as the Late Prehistoric Eurasian element. At the same time, the failure of the Neolithic and Bronze Age samples in central and northern Europe to tie to the modern inhabitants supports the suggestion that, while a farming mode of subsistence was spread westward and also north to Crimea and east to Mongolia by actual movement of communities of farmers, the indigenous foragers in each of those areas ultimately absorbed both the agricultural subsistence strategy and also the people who had brought it.The "if" portion of the statement is problematic. While Natufians are widely acknowledged as a culture anticipating the arrival of the Neolithic, they were not the first Neolithic agriculturalists, nor where they the immediate source of the transmission of agriculture. According to Pinhasi and Pluciennik (CURRENT ANTHROPOLOGY Volume 45, Number S4, August-October 2004):
Analysis of the material suggests that there was considerable morphological heterogeneity among the earliest farmers of the Levant belonging to the Pre-Pottery Neolithic but that similar variability is generally not seen among the earliest mainland agriculturalists of south-eastern Europe. We propose that this may be explained by the existence of a genetic "bottleneck" among Anatolian populations and that it supports models of the largely exogenous origin of many early Neolithic populations in this region.Thus, the sample of 4 Natufian individuals does not represent the first pre-pottery Neolithic populations, and moreover, it does not represent the immediate source of the Neolithic in Europe, which was that of the Neolithic agriculturalists of Anatolia. As Pinhasi and Pluciennik state:
Analysis of morphological variability in the Near East and Europe (here and in Pinhasi 2003) suggests that the Epipalaeolithic populations from the Natufian Levant were noticeably different to the Mesolithic populations described from the Danube Gorge, the western Mediterranean, and central Europe. No close similarities were observed between Early Neolithic and Mesolithic European groups in any of the regions studied, with the possible exception of Mediterranean Europe. However, neither were clear affinities observed between Epipalaeolithic Near Eastern groups and any other Neolithic or Mesolithic groups.The last statement is important, because it establishes that the Natufians did not have clear associations with the first Neolithic groups. So, while they are believed to be pre-agricultural culturally they are not related to any Neolithic groups biologically.
Brace finds similarities between the ancient Neolithic culture-bearers and modern Mediterranean populations, which is no doubt accurate. On the other hand, in continental Europe, the "signal" of the Neolithic populations has been absorbed by the indigenous inhabitants. This is all fine, and agrees nicely with the picture presented sixty five years ago by Carleton Coon, whereby the invasion of Europe by gracile dolichomorphs (skeletally Mediterranean) populations was followed by a period of absorption and "re-emergence" of the Upper Paleolithic types and their mixtures with the Mediterraneans.
Indeed, the early inhabitants of Northern Europe were robust broad-faced Cro-Magnoids, unlike the gracile narrow-faced Mediterraneans which diffused through Central Europe from a proximate Southeastern European source. Brace studies Cro-Magnon to propose that:
If this analysis shows nothing else, it demonstrates that the oft-repeated European feeling that the Cro-Magnons are ‘‘us’’ (47) is more a product of anthropological folklore than the result of the metric data available from the skeletal remains.Yes, this bizarre statement is not supported by his own data, which shows that Cro-Magnon shows that the Modern European sample is the only one to which Cro-Magnon is aligned to, however distantly:
The retention of the "Upper Paleolithic" signal in modern Europeans is quite impressive, since Europe's colonization did not cease with Cro-Magnon in the first Upper Paleolithic.
Cro-Magnon was a coarse-featured and robust skull atypical of modern Europeans, but one may still find individuals in Europe which resemble him: Brace et al. did not test for his resemblance to individuals. Moreover, he did not test Cro-Magnon against individual European populations. For example, Jantz and Owsley concluded that:
Using raw measurements, 6 of 8 express an affinity to Norse, and with the shape variables of Darroch and Mosimann ([1985]), 5 of 8 express a similarity to Norse. Using shape variables reduces the Mahalanobis distance, substantially in some cases. Typicality probabilities (Wilson, [1981]), particularly for the shape variables, show the crania to be fairly typical of recent populations. The results presented in Table 1 are consistent with the idea that Upper Paleolithic crania are, for the most part, larger and more generalized versions of recent Europeans. Howells ([1995]) reached a similar conclusion with respect to European Mesolithic crania.UPDATE
I have sent the following questions to Dr. Brace regarding his study. If and when he responds, and if I am granted permission to publish his response, I will do so in these entry:
You state that Modern Europeans are not very closely linked to
Neolithic/Bronze Age Europeans, yet in Table 3, the distance between
"Modern Europe" and "Late Prehistoric Eurasia" is 1.87 which is the
lowest among all population pairs. "Late Prehistoric Eurasia" is
defined as:
"Then Neolithic samples from Denmark, England, France, Germany, and
Portugal were combined with Bronze Age samples from England, Jericho,
and Mongolia to make a ''Late Prehistoric Eurasia'' sample."
This would seem to indicate a strong affinity between Neolithic/Bronze
Age Europeans and modern Europeans.
Moreover, you state that "the oft-repeated European feeling that the
Cro-Magnons are ''us'' (47) is more a product of anthropological
folklore than the result of the metric data available from the
skeletal remains."
But, in Table 4, Cro-Magnon I shows mixed affiliations between Modern
Europe and Late Prehistoric Eurasia. The inability to fall completely
in either Modern Europe or LP Eurasia is not surprising, since Modern
Europe and Late Prehistoric Eurasia are extremely close to each other
(Table 3). So, the data in Table 4 seem to suggest that Cro-Magnon I
did in fact resemble modern Europeans and Late Prehistoric Eurasians.
I would be very interested in hearing your comments.
Proc. Natl. Acad. Sci. USA, 10.1073/pnas.0509801102
The questionable contribution of the Neolithic and the Bronze Age to European craniofacial form
C. Loring Brace et al.
Many human craniofacial dimensions are largely of neutral adaptive significance, and an analysis of their variation can serve as an indication of the extent to which any given population is genetically related to or differs from any other. When 24 craniofacial measurements of a series of human populations are used to generate neighbor-joining dendrograms, it is no surprise that all modern European groups, ranging all of the way from Scandinavia to eastern Europe and throughout the Mediterranean to the Middle East, show that they are closely related to each other. The surprise is that the Neolithic peoples of Europe and their Bronze Age successors are not closely related to the modern inhabitants, although the prehistoric/modern ties are somewhat more apparent in southern Europe. It is a further surprise that the Epipalaeolithic Natufian of Israel from whom the Neolithic realm was assumed to arise has a clear link to Sub-Saharan Africa. Basques and Canary Islanders are clearly associated with modern Europeans. When canonical variates are plotted, neither sample ties in with Cro-Magnon as was once suggested. The data treated here support the idea that the Neolithic moved out of the Near East into the circum-Mediterranean areas and Europe by a process of demic diffusion but that subsequently the in situ residents of those areas, derived from the Late Pleistocene inhabitants, absorbed both the agricultural life way and the people who had brought it.
Link
December 28, 2005
2005 in Review
Some memorable posts/studies from the year that is coming to an end; one per month, most recent first.
- Clusters Strike Back (II)
- mtDNA of early central European farmers
- The Genetic Legacy of the Manchu
- Stop the presses... huge papers on brain evolution in recent humans
- Haplogroup frequency correlations in Southeastern Europe
- Early Modern Humans
- Thomas Jefferson's patrilineal origin
- The mitochondrial time depth of humanity
- Human generation length. Male: 31-32, Autosomal: 28-30, Female: 25-28
- Prehistoric Basques were closer to modern Near Easterners
- Older dates for Omo
- Y-STRs in Europe
Reproductive isolates in Jerba Island
Am J Hum Biol. 2005 Dec 25;18(1):149-153 [Epub ahead of print]
Islands Inside an Island: Reproductive Isolates on Jerba Island.
Loueslati BY, Cherni L, Khodjet-Elkhil H, Ennafaa H, Pereira L, Amorim A, Ben Ayed F, Ben Ammar Elgaaied A.
Jerba Island, located in South Eastern Tunisia, is inhabited by four ethnic groups: Berbers, Arabs, sub-Saharans, and Jews. All live in distinct areas, although the Arabs are also distributed all over the island. The first Arab settlement was founded in the 7th century A.D., so co-existence with Berbers has lasted for more than a millennium. Religious and cultural differences have represented an obstacle to the intermixing of these groups, and among both Arabs and Berbers marriages usually occur between members from the same extended family. Using new mtDNA data and previously described Y-chromosome STR-defined haplotypes, we tested whether this reported inbreeding would be reflected in the differentiation between Berber and Arab communities. Concerning mtDNA, the Berber group presented a greater Eurasian contribution (87%), and, surprisingly, no U6 haplotypes were found; in contrast, the Arabs showed a larger contribution of sub-Saharan lineages (24%) and the U6 haplogroup amounted to 10%. Another source of evidence for the reproductive isolation of the two groups was revealed through the analysis of haplotype matching (both mtDNA and Y-chromosome), showing that matching probabilities between them is of the same order of magnitude of that observed when contrasting samples from different European countries.
Link
Islands Inside an Island: Reproductive Isolates on Jerba Island.
Loueslati BY, Cherni L, Khodjet-Elkhil H, Ennafaa H, Pereira L, Amorim A, Ben Ayed F, Ben Ammar Elgaaied A.
Jerba Island, located in South Eastern Tunisia, is inhabited by four ethnic groups: Berbers, Arabs, sub-Saharans, and Jews. All live in distinct areas, although the Arabs are also distributed all over the island. The first Arab settlement was founded in the 7th century A.D., so co-existence with Berbers has lasted for more than a millennium. Religious and cultural differences have represented an obstacle to the intermixing of these groups, and among both Arabs and Berbers marriages usually occur between members from the same extended family. Using new mtDNA data and previously described Y-chromosome STR-defined haplotypes, we tested whether this reported inbreeding would be reflected in the differentiation between Berber and Arab communities. Concerning mtDNA, the Berber group presented a greater Eurasian contribution (87%), and, surprisingly, no U6 haplotypes were found; in contrast, the Arabs showed a larger contribution of sub-Saharan lineages (24%) and the U6 haplogroup amounted to 10%. Another source of evidence for the reproductive isolation of the two groups was revealed through the analysis of haplotype matching (both mtDNA and Y-chromosome), showing that matching probabilities between them is of the same order of magnitude of that observed when contrasting samples from different European countries.
Link
Back mutation in mtDNA haplogroup C
Am J Hum Biol. 2005 Dec 25;18(1):59-65 [Epub ahead of print]
A revertant of the major founder Native American haplogroup C common in populations from northern South America.
Torres MM, Bravi CM, Bortolini MC, Duque C, Callegari-Jacques S, Ortiz D, Bedoya G, Groot de Restrepo H, Ruiz-Linares A.
We examined the mtDNA RFLP diversity of 17 Native American populations from Colombia. Five of the populations studied were found to have variable frequencies of a mtDNA type lacking the characteristic changes of haplogroups A-D. Sequencing of mtDNA HVS-I and II showed that this "null" RFLP type carries all the substitutions characteristic of Native American founder lineage C. A back mutation has therefore recreated the +13,259 HincII/-13,262 AluI restriction sites that tipify RFLP haplogroup C. This revertant C lineage is further characterized by three changes in HVS-II sequence: C/T transitions at positions 115 and 152, and the deletion of an A residue at position 116. This lineage is observed at high frequency mostly in populations from Greenberg's Equatorial-Tucano linguistic family. Genetic structure analyses are consistent with the reversion mutation occurring at an early stage during the tribalization process.
Link
A revertant of the major founder Native American haplogroup C common in populations from northern South America.
Torres MM, Bravi CM, Bortolini MC, Duque C, Callegari-Jacques S, Ortiz D, Bedoya G, Groot de Restrepo H, Ruiz-Linares A.
We examined the mtDNA RFLP diversity of 17 Native American populations from Colombia. Five of the populations studied were found to have variable frequencies of a mtDNA type lacking the characteristic changes of haplogroups A-D. Sequencing of mtDNA HVS-I and II showed that this "null" RFLP type carries all the substitutions characteristic of Native American founder lineage C. A back mutation has therefore recreated the +13,259 HincII/-13,262 AluI restriction sites that tipify RFLP haplogroup C. This revertant C lineage is further characterized by three changes in HVS-II sequence: C/T transitions at positions 115 and 152, and the deletion of an A residue at position 116. This lineage is observed at high frequency mostly in populations from Greenberg's Equatorial-Tucano linguistic family. Genetic structure analyses are consistent with the reversion mutation occurring at an early stage during the tribalization process.
Link
Y-chromosome diversity in the Solomon Islands
Am J Hum Biol. 2005 Dec 25;18(1):35-50 [Epub ahead of print]
Y-chromosome diversity is inversely associated with language affiliation in paired Austronesian- and Papuan-speaking communities from Solomon Islands.
Cox MP, Mirazon Lahr M.
The Solomon Islands lie in the center of Island Melanesia, bordered to the north by the Bismarck Archipelago and to the south by Vanuatu. The nation's half-million inhabitants speak around 70 languages from two unrelated language groups: Austronesian, a language family widespread in the Pacific and closely related to languages spoken in Island Southeast Asia, and "East Papuan", generally defined as non-Austronesian and distantly related to the extremely diverse Papuan languages of New Guinea. Despite the archipelago's presumed role as a staging post for the settlement of Remote Oceania, genetic research on Solomon Island populations is sparse. We collected paired samples from two regions that have populations speaking Austronesian and Papuan languages, respectively. Here we present Y-chromosome data from these samples, the first from Solomon Islands. We detected five Y-chromosome lineages: M-M106, O-M175, K-M9*, K-M230, and the extremely rare clade, K1-M177. Y-chromosome lineages from Solomon Islands fall within the range of other Island Melanesian populations but display markedly lower haplogroup diversity. From a broad Indo-Pacific perspective, Y-chromosome lineages show partial association with the distribution of language groups: O-M175 is associated spatially with Austronesian-speaking areas, whereas M-M106 broadly correlates with the distribution of Papuan languages. However, no relationship between Y-chromosome lineages and language affiliation was observed on a small scale within Solomon Islands. This pattern may result from a sampling strategy that targeted small communities, where individual Y-chromosome lineages can be fixed or swept to extinction by genetic drift or favored paternal exogamy.
Link
Y-chromosome diversity is inversely associated with language affiliation in paired Austronesian- and Papuan-speaking communities from Solomon Islands.
Cox MP, Mirazon Lahr M.
The Solomon Islands lie in the center of Island Melanesia, bordered to the north by the Bismarck Archipelago and to the south by Vanuatu. The nation's half-million inhabitants speak around 70 languages from two unrelated language groups: Austronesian, a language family widespread in the Pacific and closely related to languages spoken in Island Southeast Asia, and "East Papuan", generally defined as non-Austronesian and distantly related to the extremely diverse Papuan languages of New Guinea. Despite the archipelago's presumed role as a staging post for the settlement of Remote Oceania, genetic research on Solomon Island populations is sparse. We collected paired samples from two regions that have populations speaking Austronesian and Papuan languages, respectively. Here we present Y-chromosome data from these samples, the first from Solomon Islands. We detected five Y-chromosome lineages: M-M106, O-M175, K-M9*, K-M230, and the extremely rare clade, K1-M177. Y-chromosome lineages from Solomon Islands fall within the range of other Island Melanesian populations but display markedly lower haplogroup diversity. From a broad Indo-Pacific perspective, Y-chromosome lineages show partial association with the distribution of language groups: O-M175 is associated spatially with Austronesian-speaking areas, whereas M-M106 broadly correlates with the distribution of Papuan languages. However, no relationship between Y-chromosome lineages and language affiliation was observed on a small scale within Solomon Islands. This pattern may result from a sampling strategy that targeted small communities, where individual Y-chromosome lineages can be fixed or swept to extinction by genetic drift or favored paternal exogamy.
Link
December 23, 2005
Y-chromosomes and mtDNA from the Balkans
An important new study on the Balkans, which includes a Greek sample from Thrace, as well as samples from Aromun (Vlach) populations.
UPDATE
It is unfortunate that this study did not study the distribution of deep clades of the Y-chromosomal phylogeny, e.g., in haplogroups J, I, and K*(xP). Nonetheless, the study furthers our understanding of the Y-chromosomal population of Balkan populations, by sampling populations from Albania, the FYRO Macedonia, Romania, and Northeastern Greece, including Vlach (Aromun) speakers.
The shallow depth of the typed markers did not allow the detection of structure. Most haplogroup frequencies occurred in similar frequencies with few significant differences between populations.
Aromuns appear to have a higher frequency overall of haplogroup R1b, which would definitely suggest "Roman" connections, which the authors discount on the basis of searches which they conducted in yhrd. Ultimately, their arguments are not very convincing, since yhrd only allows for exact matches, and any "Roman" contribution to the Aromuns is two thousand years old.
The inclusion of almost all E3b1-M78 chromosomes in the alpha-cluster which is typical of the Balkans was confirmed once again.
R1a1 chromosomes did not exhibit a star-like phylogeny; this may indicate heterogeneity in the origin of R1a1 chromosomes.
Also of interest is the detection of foreign elements in the Balkan population. Such elements were not found in Greeks, but were found occasionally in the form of haplogroups E1 and H in some of the others.
This study seems to agree broadly with my previous observations about the co-occurrence of haplogroups J2 and R1b in the Balkans; these two haplogroups are frequent in most populations, contrasting with most of the Slavs from the western Balkans that have low frequencies.
Annals of Human Genetics (Online Early)
Paternal and maternal lineages in the Balkans show a homogeneous landscape over linguistic barriers, except for the isolated Aromuns
E. Bosch et al.
Summary
The Balkan Peninsula is a complex cultural mosaic comprising populations speaking languages from several branches of the Indo-European family and Altaic, as well as culturally-defined minorities such as the Aromuns who speak a Romance language. The current cultural and linguistic landscape is a palimpsest in which different peoples have contributed their cultures in a historical succession. We have sought to find any evidence of genetic stratification related to those cultural layers by typing both mtDNA and Y chromosomes, in Albanians, Romanians, Macedonians, Greeks, and five Aromun populations. We have paid special attention to the Aromuns, and sought to test genetically various hypotheses on their origins.
MtDNA and Y-chromosome haplogroup frequencies in the Balkans were found to be similar to those elsewhere in Europe. MtDNA sequences and Y-chromosome STR haplotypes revealed decreased variation in some Aromun populations. Variation within Aromun populations was the primary source of genetic differentiation. Y-chromosome haplotypes tended to be shared across Aromuns, but not across non-Aromun populations. These results point to a possible common origin of the Aromuns, with drift acting to differentiate the separate Aromun communities. The homogeneity of Balkan populations prevented testing for the origin of the Aromuns, although a significant Roman contribution can be ruled out.
Link
UPDATE
It is unfortunate that this study did not study the distribution of deep clades of the Y-chromosomal phylogeny, e.g., in haplogroups J, I, and K*(xP). Nonetheless, the study furthers our understanding of the Y-chromosomal population of Balkan populations, by sampling populations from Albania, the FYRO Macedonia, Romania, and Northeastern Greece, including Vlach (Aromun) speakers.
The shallow depth of the typed markers did not allow the detection of structure. Most haplogroup frequencies occurred in similar frequencies with few significant differences between populations.
Aromuns appear to have a higher frequency overall of haplogroup R1b, which would definitely suggest "Roman" connections, which the authors discount on the basis of searches which they conducted in yhrd. Ultimately, their arguments are not very convincing, since yhrd only allows for exact matches, and any "Roman" contribution to the Aromuns is two thousand years old.
The inclusion of almost all E3b1-M78 chromosomes in the alpha-cluster which is typical of the Balkans was confirmed once again.
R1a1 chromosomes did not exhibit a star-like phylogeny; this may indicate heterogeneity in the origin of R1a1 chromosomes.
Also of interest is the detection of foreign elements in the Balkan population. Such elements were not found in Greeks, but were found occasionally in the form of haplogroups E1 and H in some of the others.
This study seems to agree broadly with my previous observations about the co-occurrence of haplogroups J2 and R1b in the Balkans; these two haplogroups are frequent in most populations, contrasting with most of the Slavs from the western Balkans that have low frequencies.
Annals of Human Genetics (Online Early)
Paternal and maternal lineages in the Balkans show a homogeneous landscape over linguistic barriers, except for the isolated Aromuns
E. Bosch et al.
Summary
The Balkan Peninsula is a complex cultural mosaic comprising populations speaking languages from several branches of the Indo-European family and Altaic, as well as culturally-defined minorities such as the Aromuns who speak a Romance language. The current cultural and linguistic landscape is a palimpsest in which different peoples have contributed their cultures in a historical succession. We have sought to find any evidence of genetic stratification related to those cultural layers by typing both mtDNA and Y chromosomes, in Albanians, Romanians, Macedonians, Greeks, and five Aromun populations. We have paid special attention to the Aromuns, and sought to test genetically various hypotheses on their origins.
MtDNA and Y-chromosome haplogroup frequencies in the Balkans were found to be similar to those elsewhere in Europe. MtDNA sequences and Y-chromosome STR haplotypes revealed decreased variation in some Aromun populations. Variation within Aromun populations was the primary source of genetic differentiation. Y-chromosome haplotypes tended to be shared across Aromuns, but not across non-Aromun populations. These results point to a possible common origin of the Aromuns, with drift acting to differentiate the separate Aromun communities. The homogeneity of Balkan populations prevented testing for the origin of the Aromuns, although a significant Roman contribution can be ruled out.
Link
December 22, 2005
Positive selection in NAT2 gene
An interesting new preprint from the AJHG deals with two genes involved in acetylation. The most important finding is that an allele of the NAT2 locus has been under positive selection in Western/Central Eurasians in the last ~6,500 years. According to the researchers' provisional hypothesis:
Deciphering the ancient and complex evolutionary history of human arylamine N-acetyltransferase genes
Etienne Patin et al.
The human N-acetyltransferase genes NAT1 and NAT2 encode two phase II enzymes that metabolize various drugs and carcinogens. Functional variability at these genes has been associated with adverse drug reactions and cancer susceptibility. Mutations in NAT2 leading to the so-called "slow" acetylation phenotype reach high frequencies worldwide, questioning the significance of altered acetylation in human adaptation. To investigate the role of population history and natural selection in shaping NATs variation, we characterized genetic diversity through re-sequencing and genotyping of NAT1, NAT2 and the pseudogene NATP in a collection of 13 different populations with distinct ethnic background and demographic pasts. This combined study-design allowed us to define a detailed map of linkage disequilibrium of the NATs region as well as to perform a number of sequence-based neutrality tests and the Long Range Haplotype (LRH) test. Our data revealed distinctive patterns of variability for the two genes: the reduced diversity observed at NAT1 is consistent with the action of purifying selection while NAT2 functional variation contributes to high levels of diversity. In addition, the LRH test identified a particular NAT2 haplotype (NAT2*5B) under recent positive selection in Western/Central Eurasians. This haplotype harbors the mutation 341T>C and encodes the "slowest" acetylator NAT2 enzyme, suggesting a general selective advantage for the slow acetylator phenotype. Interestingly, the NAT2*5B haplotype, which seems to have conferred a selective advantage during the past ~6,500 years, exhibits today the strongest association with susceptibility to bladder cancer and adverse-drug reactions. On the whole, the patterns observed for NAT2 illustrate well how geographically and temporally-fluctuating xenobiotic environments may have influenced not only our genome variability but also our present-day susceptibility to disease.
In this context, given the geographic distribution of the slow acetylator phenotype and the estimated expansion time of the slowest-encoding 341T>C mutation (5,797-7,005 years ago in West/Central Eurasians), it is tempting to hypothesize that the emergence of agriculture in West Eurasia could be at the basis of such environmental changes. Indeed, there is accumulating evidence that this major transition resulted in a profound modification of human diets and lifestyles (Cordain et al. 2005) and consequently, in the exposure to human chemical environment (Ferguson et al. 2002). Moreover, the highest frequencies of slow acetylators are observed in the Middle East (fig. 5), one of the first regions where agriculture originated ~10,000 years ago, and these frequencies decrease towards Western Europe, North Africa and India, three regions where agriculture was subsequently diffused from the Fertile Crescent (Harris 1996).American Journal of Human Genetics (in press)
Deciphering the ancient and complex evolutionary history of human arylamine N-acetyltransferase genes
Etienne Patin et al.
The human N-acetyltransferase genes NAT1 and NAT2 encode two phase II enzymes that metabolize various drugs and carcinogens. Functional variability at these genes has been associated with adverse drug reactions and cancer susceptibility. Mutations in NAT2 leading to the so-called "slow" acetylation phenotype reach high frequencies worldwide, questioning the significance of altered acetylation in human adaptation. To investigate the role of population history and natural selection in shaping NATs variation, we characterized genetic diversity through re-sequencing and genotyping of NAT1, NAT2 and the pseudogene NATP in a collection of 13 different populations with distinct ethnic background and demographic pasts. This combined study-design allowed us to define a detailed map of linkage disequilibrium of the NATs region as well as to perform a number of sequence-based neutrality tests and the Long Range Haplotype (LRH) test. Our data revealed distinctive patterns of variability for the two genes: the reduced diversity observed at NAT1 is consistent with the action of purifying selection while NAT2 functional variation contributes to high levels of diversity. In addition, the LRH test identified a particular NAT2 haplotype (NAT2*5B) under recent positive selection in Western/Central Eurasians. This haplotype harbors the mutation 341T>C and encodes the "slowest" acetylator NAT2 enzyme, suggesting a general selective advantage for the slow acetylator phenotype. Interestingly, the NAT2*5B haplotype, which seems to have conferred a selective advantage during the past ~6,500 years, exhibits today the strongest association with susceptibility to bladder cancer and adverse-drug reactions. On the whole, the patterns observed for NAT2 illustrate well how geographically and temporally-fluctuating xenobiotic environments may have influenced not only our genome variability but also our present-day susceptibility to disease.
Natural selection in the last 50,000 years
Gene Expression alerts me to a new paper on natural selection in Homo sapiens. Researchers have identified almost 2,000 genes which have been targeted by natural selection in modern humans of the last 50,000 years, i.e., since the emergence of behaviorally modern humanity and its spread around the world.
I will post more from the paper once it becomes "live". For the moment, from ScienceNow:
UPDATE
Here is the abstract and link to the open-access article. With "Darwinian" in the title and "Darwin's fingerprint" in one of the figures, I think that someone is having fun sticking it in to the creationism/ID crowd.
Proc. Natl. Acad. Sci. USA. (published online)
Global landscape of recent inferred Darwinian selection for Homo sapiens
Eric T. Wang et al.
By using the 1.6 million single-nucleotide polymorphism (SNP) genotype data set from Perlegen Sciences [Hinds, D. A., Stuve, L. L., Nilsen, G. B., Halperin, E., Eskin, E., Ballinger, D. G., Frazer, K. A. & Cox, D. R. (2005) Science 307, 1072-1079], a probabilistic search for the landscape exhibited by positive Darwinian selection was conducted. By sorting each high-frequency allele by homozygosity, we search for the expected decay of adjacent SNP linkage disequilibrium (LD) at recently selected alleles, eliminating the need for inferring haplotype. We designate this approach the LD decay (LDD) test. By these criteria, 1.6% of Perlegen SNPs were found to exhibit the genetic architecture of selection. These results were confirmed on an independently generated data set of 1.0 million SNP genotypes (International Human Haplotype Map Phase I freeze). Simulation studies indicate that the LDD test, at the megabase scale used, effectively distinguishes selection from other causes of extensive LD, such as inversions, population bottlenecks, and admixture. The {approx}1,800 genes identified by the LDD test were clustered according to Gene Ontology (GO) categories. Based on overrepresentation analysis, several predominant biological themes are common in these selected alleles, including host-pathogen interactions, reproduction, DNA metabolism/cell cycle, protein metabolism, and neuronal function.
Link (open access)
I will post more from the paper once it becomes "live". For the moment, from ScienceNow:
The genes belong to several biologically important categories, including genes important in defense against disease, controlling the cell cycle, protein metabolism, and nervous system functioning, the researchers report online this week in Proceedings of the National Academy of Sciences.The New Scientist also covers this paper:
One way to look for genes that have recently been changed by natural selection is to study mutations called single-nucleotide polymorphisms (SNPs) – single-letter differences in the genetic code. The trick is to look for pairs of SNPs that occur together more often than would be expected from the chance genetic reshuffling that inevitably happens down the generations.You might also want to read my older post on Human domestication reconsidered, which reports on anthropological changes which are also evidence of human domestication:
Such correlations are known as linkage disequilibrium, and can occur when natural selection favours a particular variant of a gene, causing the SNPs nearby to be selected as well.
...
Moyzis speculates that we may have similarly “domesticated” ourselves with the emergence of modern civilisation.
“One of the major things that has happened in the last 50,000 years is the development of culture,” he says. “By so radically and rapidly changing our environment through our culture, we’ve put new kinds of selection [pressures] on ourselves.”
Genes that aid protein metabolism – perhaps related to a change in diet with the dawn of agriculture – turn up unusually often in Moyzis’s list of recently selected genes. So do genes involved in resisting infections, which would be important in a species settling into more densely populated villages where diseases would spread more easily. Other selected genes include those involved in brain function, which could be important in the development of culture.
Helen Leach is proposing that the Late Pleistocene and early Holocene (archaeologically Neolithic) humans underwent changes similar to those of animals that underwent the domestication process. So, she argues that if we apply terminology consistently, we must also entertain the possibility that humans themselves are a domesticated species.
UPDATE
Here is the abstract and link to the open-access article. With "Darwinian" in the title and "Darwin's fingerprint" in one of the figures, I think that someone is having fun sticking it in to the creationism/ID crowd.
Proc. Natl. Acad. Sci. USA. (published online)
Global landscape of recent inferred Darwinian selection for Homo sapiens
Eric T. Wang et al.
By using the 1.6 million single-nucleotide polymorphism (SNP) genotype data set from Perlegen Sciences [Hinds, D. A., Stuve, L. L., Nilsen, G. B., Halperin, E., Eskin, E., Ballinger, D. G., Frazer, K. A. & Cox, D. R. (2005) Science 307, 1072-1079], a probabilistic search for the landscape exhibited by positive Darwinian selection was conducted. By sorting each high-frequency allele by homozygosity, we search for the expected decay of adjacent SNP linkage disequilibrium (LD) at recently selected alleles, eliminating the need for inferring haplotype. We designate this approach the LD decay (LDD) test. By these criteria, 1.6% of Perlegen SNPs were found to exhibit the genetic architecture of selection. These results were confirmed on an independently generated data set of 1.0 million SNP genotypes (International Human Haplotype Map Phase I freeze). Simulation studies indicate that the LDD test, at the megabase scale used, effectively distinguishes selection from other causes of extensive LD, such as inversions, population bottlenecks, and admixture. The {approx}1,800 genes identified by the LDD test were clustered according to Gene Ontology (GO) categories. Based on overrepresentation analysis, several predominant biological themes are common in these selected alleles, including host-pathogen interactions, reproduction, DNA metabolism/cell cycle, protein metabolism, and neuronal function.
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