The effect of domestication of wheat on its genetic diversity

Molecular Biology and Evolution, doi:10.1093/molbev/msm077

Grinding up Wheat: a Massive Loss of Nucleotide Diversity Since Domestication

A Haudry et al.

Several demographic and selective events occurred during the domestication of wheat from the allotetraploid wild emmer (Triticum turgidum ssp. dicoccoides). Cultivated wheat has since been affected by other historical events. We analysed nucleotide diversity at 21 loci in a sample of 101 individuals representing four taxa corresponding to representative steps in the recent evolution of wheat (wild, domesticated, cultivated durum and bread wheats), to unravel the evolutionary history of cultivated wheats and to quantify its impact on genetic diversity. Sequence relationships are consistent with a single domestication event and identify two genetically different groups of bread wheat. The wild group is not highly polymorphic, with only 212 polymorphic sites among the 21,720 bp sequenced, and, during domestication, diversity was further reduced in cultivated forms — by 69% in bread wheat and 84% in durum wheat — with considerable differences between loci, some retaining no polymorphism at all. Coalescent simulations were performed and compared with our data, to estimate the intensity of the bottlenecks associated with domestication and subsequent selection. Based on our 21-locus analysis, the average intensity of domestication bottleneck was estimated at about 3 — giving a population size for the domesticated form about one third that of wild dicoccoides. The most severe bottleneck, with an intensity of about 6, occurred in the evolution of durum wheat. We investigated whether some of the genes departed from the empirical distribution of most loci, suggesting that they might have been selected during domestication or breeding. We detected a departure from the null model of demographic bottleneck for the hypothetical gene HgA. However, the atypical pattern of polymorphism at this locus might reveal selection on the linked locus Gsp1A, which may affect grain softness — an important trait for end-use quality in wheat.

Link

Modern human origins in Australia

Homo (in press)

Modern human origins in Australasia: Testing the predictions of competing models

D. Curnoe

Abstract

The evolutionary background to the emergence of modern humans remains controversial. Four models have been proposed to explain this process and each has clearly definable and testable predictions about the geographical origins of early Australians and their possible biological interaction with other Pleistocene populations. The present study considers the phenetic affinities of early Australians from Kow Swamp (KS 1 and KS 5) and Keilor to Pleistocene Africans and Asians from calvarial dimensions. The study includes analyses employing log-transformed and size-corrected (Mosimann variables) data. The strongest signals to emerge are as follows: (1) a phenetic pattern in which Australians are most like each other, (2) all three crania possess a mosaic of archaic and modern features, (3) Kow Swamp crania also show strong affinities to archaic remains, (4) Keilor is more modern than KS 1 and KS 5 and (5) Keilor shows affinities to Pleistocene East Asian modern crania (Liujiang and Upper Cave 101) providing evidence for a broad regional morphology. The results refute the predictions of multi-species replacement models for early Australians but are consistent with single-species models. Combined with published evidence from DNA, the present study indicates that the Assimilation model presently offers the best explanation for the origins of Pleistocene Australians.

Link

Physical anthropology and ethnicity in Asia

J Physiol Anthropol. 2007 Mar;26(2):77-82.

Physical Anthropology and Ethnicity in Asia: The Transition from Anthropometry to Genome-based Studies.

Bittles H, Black ML, Wang W.

Initial physical anthropology studies into ethnic diversity were largely dependent on comparative whole body and craniometric measurements, and through time assessments of ethnic diversity based on these measures exhibited increasing statistical sophistication. Since the 1990s, in Asia as elsewhere in the world, human diversity studies have increasingly utilized DNA-based analyses, with Y-chromosome and mtDNA markers providing complementary perspectives on the origins and gene pool structures of different ethnic groups. This approach is illustrated in a study of population genetic structure in PR China, in which DNA samples from the Han majority and eight ethnic minorities were analyzed. The Y-chromosome and mtDNA data showed multiple paternal geographical and ethnic origins but restricted maternal ancestries. However, interpretive problems were apparent in the definition of a number of the ethnic study populations, which appear to reflect political as well as genetic influences. In all anthropological studies, whether based on anthropometry or genomic analysis, unambiguous and appropriate community identification is a prerequisite.

Link

IQ and Wealth

Intelligence (Article in Press)

Do you have to be smart to be rich? The impact of IQ on wealth, income and financial distress

Jay L. Zagorskya et al.

Abstract

How important is intelligence to financial success? Using the NLSY79, which tracks a large group of young U.S. baby boomers, this research shows that each point increase in IQ test scores raises income by between $234 and $616 per year after holding a variety of factors constant. Regression results suggest no statistically distinguishable relationship between IQ scores and wealth. Financial distress, such as problems paying bills, going bankrupt or reaching credit card limits, is related to IQ scores not linearly but instead in a quadratic relationship. This means higher IQ scores sometimes increase the probability of being in financial difficulty.

Link

New YHRD release

The Y-chromosome Haplotype Reference Database (YHRD) has a new release:

Release 21 is out with 51,253 haplotypes in 447 populations. 49,396 haplotypes of these are completely typed for 9 and 23,075 for 11 loci. Fifty-nine populations were added today: from Macedonia, from three regions in Venezuela (Maracaibo, Isla Toas, San Jose Heras) and three Venezuelan Amerindian tribes (Bari, Wayuu, Yukpa), from 10 provinces at the Pacific and Caribbean coast in Colombia: Valle de Cauca, Cauca, Narino, Bolivar, Guajira, Magdalena, Cesar, Cordoba, Sucre and Atlantico, from Ecuador (Quito), from Germany (Stuttgart), from Southern Poland (Nowy Sacz, Nowy Targ, Limanowa, Zakopane), from the following districts of the Russian Federation: Archangelsk, Brjansk, Ivanowo, Lipezk, Novgorod, Orel, Pensa, Rjasan, Smolensk, Tambov, Tver and Vologda, from Sweden (updates of the already existing samples), from Rio de Janeiro (Brazilians of European and African ancestry), from Nicaragua, from Slovakia (Bratislava), from Belarus (Homiel, Hrodna, Mahiliou, Viciebsk), from the following prefectures in Japan: Tokyo, Aomori, Chiba, Ehime, Fukuoka, Gunma, Hiroshima, Hokkaido, Hyogo, Mie, Miyagi, Nagasaki, Nara, Okayama, Shizuoka, Toyama, Wakayama, Yamaguchi and Yamanashi, from the USA (European, African, Hispanic and Asian American). We would like to thank the following colleagues for submissions and updates: Zlatko Jakovski and his group (Macedonia), Lisbeth Borjas and Tatiana Pardo (Venezuela), Sandra Avila and Elena Romero (Colombia), Eduardo Arroyo and his group (Ecuador), Gerhard Baessler and his group (Stuttgart), Marcin Wozniak and his group (Poland), the groups in Berlin (Carmen Krueger, Lutz Roewer) and Leipzig (Ivan Nasidze) for the Russians, Gunilla Holmlund and her group (Sweden), Elizeu Fagundes de Carvalho and his group (Rio den Janeiro), Fabricio Gonzalez (Nicaragua), Krzysztof Rebala and his coworkers (Slovakia, Belarus), Natsuko Mizuno and her group (Japan) and Amy Decker and her group at NIST for the US data.

Y chromosomes of South Siberia

No abstract to this paper. An excerpt:

Archeological and paleontological evidence suggests that South Siberia is an area where the most ancient contacts occurred between the members of Caucasoid and Mongoloid peoples. These contacts have substantially affected the racial type of most populations of Eurasia. Analysis of mitochondrial DNA (mtDNA) inherited without recombination in the maternal line has shown that Southern Siberian populations have developed on a heterogeneous genetic basis. This is a result of not only the diversity of Mongoloid components that were either indigenous to the gene pools of Siberian populations since the Paleolithic Age or introduced in different periods of time from Central Europe and East Asia, but also the presence of the Caucasoid component expressed in different degrees in most populations that have contributed into this heterogeneity [1, 2]. The nonrecombining portion of the Y chromosome inherited in the paternal line is another genetic system widely used for studying the population genetic history. The Y chromosome polymorphism has been analyzed in a wide spectrum of Asian populations; nevertheless, the data on numerous aboriginal opulations of Southern Siberia are scanty with respect to both the number of populations and the set of loci studied. Therefore, there is no comprehensive idea as to how the gene pools of individual ethnic groups have been formed, taking into account the contributions of both paternal and maternal lineages [3, 4].

...

In general, our results suggest a significant genetic differentiation between the ethnic groups of Baikal and Altai–Sayan regions, which is mainly accounted for by
different contributions of the Central/East Asian and East European components into the gene pools of South Siberian ethnic groups.

Haplogroup distribution:

Doklady Biological Sciences, 2006, Vol. 411, pp. 466–470

The Diversity of Y-Chromosome Lineages in Indigenous Population of South Siberia

M. V. Derenko et al.

Y chromosome lineages in Sao Tome and Principe

Am J Hum Biol. 2007 Apr 9;19(3):422-428 [Epub ahead of print]

Y-chromosome lineages in Sao Tome e Principe islands: Evidence of European influence.

Goncalves R, Spinola H, Brehm A.

The Y-chromosome haplogroup composition of the population of Sao Tome e Principe (STP) archipelago was analyzed using 25 biallelic markers and compared with populations of different origins from Europe, Africa, and the Middle East. Two main Y-chromosome haplogroups were found: E3a, very common among sub-Saharans accounts for 84.2% of the paternal lineages and R1b, typical of West Eurasia, represents 8.7% of the overall male population. Nevertheless, we detected in the population of STP a significant heterogeneous distribution of R1b among the two main ethnic groups of the archipelago: Forros (10.3%) and Angolares (6.6%). Together, haplogroups known to be prevalent in West Eurasia reach 12.5% of the chromosomes analyzed unequally distributed among the two groups: Forros present 17.7% while Angolares display only 8.2% of west Eurasian haplogroups. Our findings suggest that, despite its sub-Saharan genetic background, a relevant contribution of European paternal lineages is present in nowadays STP population. This influence has shown to be stronger in Forros than in Angolares, which could be explained by the social isolation that these have last experienced through their history.

Link

Genetic affinities of Uttar Pradesh populations

BMC Genet. 2007 Apr 7;8(1):12 [Epub ahead of print]

Genetic affinities between endogamous and inbreeding populations of Uttar Pradesh.


Khan F, Pandey AK, Tripathi M, Talwar S, Bisen PS, Borkar M, Agrawal S.

ABSTRACT: BACKGROUND: India has experienced several waves of migration since the Middle Paleolithic. It is believed that the initial demic movement into India was from Africa along the southern coastal route, approximately 60,000-85,000 years before present (ybp). It has also been reported that there were two other major colonizations which included eastward diffusion of Neolithic farmers (Elamo Dravidians) from Middle East sometime between 10,000 and 7,000 ybp and a southern dispersal of Indo Europeans from Central Asia 3,000 ybp. Mongol entry during the thirteenth century A.D. as well as some possible minor incursions from South China 50,000 to 60,000 ybp may have also contributed to cultural, linguistic and genetic diversity in India. Therefore, the genetic affinity and relationship of Indians with other world populations and also within India are often contested. In the present study, we have attempted to offer a fresh and immaculate interpretation on the genetic relationships of different North Indian populations with other Indian and other world populations. RESULTS: We have first genotyped 20 tetra-nucleotide STR markers among 1800 north Indian samples of nine endogamous populations belonging to three different socio-cultural strata. Genetic distances (Neis DA and Reynolds Fst) were calculated among the nine studied populations, Caucasians and East Asians. This analysis was based upon the allelic profile of 20 STR markers to assess the genetic similarity and differences of the north Indian populations. North Indians showed a stronger genetic relationship with the Europeans (DA 0.0341 and Fst 0.0119) as compared to the Asians (DA 0.1694 and Fst - 0.0718). The upper caste Brahmins and Muslims were closest to Caucasians while middle caste populations were closer to Asians. Finally, three phylogenetic assessments based on two different NJ and ML phylogenetic methods and PC plot analysis were carried out using the same panel of 20 STR markers and 20 geo-ethnic populations. The three phylogenetic assessments revealed that north Indians are clustering with Caucasians. CONCLUSIONS: The genetic affinities of Indians and that of different caste groups towards Caucasians or East Asians is distributed in a cline where geographically north Indians and socially both upper caste and Muslim populations are genetically closer to the Caucasians.

Link

Nicholas Wade on human sexuality

Nicholas Wade has a very interesting article on recent advances in human sexuality in the New York Times. Some excerpts:

It is no surprise that the male and female versions of the human brain operate in distinct patterns, despite the heavy influence of culture. The male brain is sexually oriented toward women as an object of desire. The most direct evidence comes from a handful of cases, some of them circumcision accidents, in which boy babies have lost their penises and been reared as female. Despite every social inducement to the opposite, they grow up desiring women as partners, not men.

...

Presumably the masculinization of the brain shapes some neural circuit that makes women desirable. If so, this circuitry is wired differently in gay men. In experiments in which subjects are shown photographs of desirable men or women, straight men are aroused by women, gay men by men.

Such experiments do not show the same clear divide with women. Whether women describe themselves as straight or lesbian, “Their sexual arousal seems to be relatively indiscriminate — they get aroused by both male and female images,” Dr. Bailey said. “I’m not even sure females have a sexual orientation. But they have sexual preferences. Women are very picky, and most choose to have sex with men.”

...

Sexual orientation, at least for men, seems to be settled before birth. “I think most of the scientists working on these questions are convinced that the antecedents of sexual orientation in males are happening early in life, probably before birth,” Dr. Breedlove said, “whereas for females, some are probably born to become gay, but clearly some get there quite late in life.”

...

Several profound consequences follow from the fact that men have only one copy of the many X-related brain genes and women two. One is that many neurological diseases are more common in men because women are unlikely to suffer mutations in both copies of a gene.

Another is that men, as a group, “will have more variable brain phenotypes,” Dr. Arnold writes, because women’s second copy of every gene dampens the effects of mutations that arise in the other.

Happy Easter

Neolithic Near Eastern Origin of domesticated cattle

Proc Biol Sci. 2007 Apr 3; [Epub ahead of print]

Mitochondrial DNA analysis shows a Near Eastern Neolithic origin for domestic cattle and no indication of domestication of European aurochs.

Edwards CJ et al.

The extinct aurochs (Bos primigenius primigenius) was a large type of cattle that ranged over almost the whole Eurasian continent. The aurochs is the wild progenitor of modern cattle, but it is unclear whether European aurochs contributed to this process. To provide new insights into the demographic history of aurochs and domestic cattle, we have generated high-confidence mitochondrial DNA sequences from 59 archaeological skeletal finds, which were attributed to wild European cattle populations based on their chronological date and/or morphology. All pre-Neolithic aurochs belonged to the previously designated P haplogroup, indicating that this represents the Late Glacial Central European signature. We also report one new and highly divergent haplotype in a Neolithic aurochs sample from Germany, which points to greater variability during the Pleistocene. Furthermore, the Neolithic and Bronze Age samples that were classified with confidence as European aurochs using morphological criteria all carry P haplotype mitochondrial DNA, suggesting continuity of Late Glacial and Early Holocene aurochs populations in Europe. Bayesian analysis indicates that recent population growth gives a significantly better fit to our data than a constant-sized population, an observation consistent with a postglacial expansion scenario, possibly from a single European refugial population. Previous work has shown that most ancient and modern European domestic cattle carry haplotypes previously designated T. This, in combination with our new finding of a T haplotype in a very Early Neolithic site in Syria, lends persuasive support to a scenario whereby gracile Near Eastern domestic populations, carrying predominantly T haplotypes, replaced P haplotype-carrying robust autochthonous aurochs populations in Europe, from the Early Neolithic onward. During the period of coexistence, it appears that domestic cattle were kept separate from wild aurochs and introgression was extremely rare.

Link

Y chromosomes across the Himalayas

American Journal of Human Genetics (online early)

The Himalayas as a Directional Barrier to Gene Flow

Tenzin Gayden et al.

High-resolution Y-chromosome haplogroup analyses coupled with Y–short tandem repeat (STR) haplotypes were used to (1) investigate the genetic affinities of three populations from Nepal—including Newar, Tamang, and people from cosmopolitan Kathmandu (referred to as "Kathmandu" subsequently)—as well as a collection from Tibet and (2) evaluate whether the Himalayan mountain range represents a geographic barrier for gene flow between the Tibetan plateau and the South Asian subcontinent. The results suggest that the Tibetans and Nepalese are in part descendants of Tibeto-Burman–speaking groups originating from Northeast Asia. All four populations are represented predominantly by haplogroup O3a5-M134–derived chromosomes, whose Y-STR–based age (±SE) was estimated at 8.1 ± 2.9 thousand years ago (KYA), more recent than its Southeast Asian counterpart. The most pronounced difference between the two regions is reflected in the opposing high-frequency distributions of haplogroups D in Tibet and R in Nepal. With the exception of Tamang, both Newar and Kathmandu exhibit considerable similarities to the Indian Y-haplogroup distribution, particularly in their haplogroup R and H composition. These results indicate gene flow from the Indian subcontinent and, in the case of haplogroup R, from Eurasia as well, a conclusion that is also supported by the admixture analysis. In contrast, whereas haplogroup D is completely absent in Nepal, it accounts for 50.6% of the Tibetan Y-chromosome gene pool. Coalescent analyses suggest that the expansion of haplogroup D derivatives—namely, D1-M15 and D3-P47 in Tibet—involved two different demographic events (5.1 ± 1.8 and 11.3 ± 3.7 KYA, respectively) that are more recent than those of D2-M55 representatives common in Japan. Low frequencies, relative to Nepal, of haplogroup J and R lineages in Tibet are also consistent with restricted gene flow from the subcontinent. Yet the presence of haplogroup O3a5-M134 representatives in Nepal indicates that the Himalayas have been permeable to dispersals from the east. These genetic patterns suggest that this cordillera has been a biased bidirectional barrier.

Link

Nicholas Wade on Etruscan Origins

Nicholas Wade has an article in the New York Times summarizing the recent research ib Etruscan origins (click on the label below for more) and giving some interesting background on the dispute between 'indigenist' and 'migrationist' views of Etruscan origins:

“The overwhelming proportion of archaeologists would regard the evidence for eastern origins of the Etruscans as negligible,” said Anthony Tuck, an archaeologist at the University of Massachusetts Center for Etruscan Studies.

Because Italians take pride in the Roman empire and the Etruscan state that preceded it, asserting a foreign origin for the Etruscans has long been politically controversial in Italy. Massimo Pallottino, the dean of modern Etruscan studies in Italy who died in 1995, held that because no one questioned that the French, say, developed in France, the same assumption should be made about the Etruscans. “Someone who had a different position didn’t get a job in archaeology,” said Antonio Torroni, a geneticist at the University of Pavia.

...

In Tuscany as a whole, part of the ancient Etruscan region of Etruria, the Torroni team found 11 minor mitochondrial DNA lineages that occur nowhere else in Europe and are shared only with Near Eastern people. These findings, the teams says, “support a direct and rather recent genetic input from the Near East, a scenario in agreement with the Lydian origin of the Etruscans.”

Dr. Torroni said he had data awaiting publication that are based on Y chromosomes and point to the same conclusion.

40,000 year old human from China

From EurekAlert:

Researchers at Washington University in St. Louis and the Institute of Vertebrate Paleontology and Paleoanthropology (IVPP) in Beijing have been studying a 40,000-year-old early modern human skeleton found in China and have determined that the "out of Africa" dispersal of modern humans may not have been as simple as once thought.

The research result will be published in the Proceedings of the U.S. National Academy of Sciences on April 3.

Erik Trinkaus, Professor of Anthropology at Washington University in St. Louis, his colleague Hong Shang, and others at the IVPP examined the skeleton, recovered in 2003 from the Tianyuan Cave, Zhoukoudian, near Beijing City.

The skeleton dates to 42,000 to 38,500 years ago, making it the oldest securely dated modern human skeleton in China and one of the oldest modern human fossils in eastern Eurasia.

The specimen is basically a modern human, but it does have a few archaic characteristics, particularly in the teeth and hand bone. This morphological pattern implies that a simple spread of modern humans from Africa is unlikely, especially since younger specimens have been found in Eastern Eurasia with similar feature patterns.

According to Trinkaus and Shang, "the discovery promises to provide relevant paleontological data for our understanding of the emergence of modern humans in eastern Asia."

Genetic genealogists gone wild

Amy Harmon has an interesting article in the New York Times about some extreme cases of genetic genealogists going to great lengths to fill in their family trees.

Derrell Teat, 63, a wastewater coordinator, recently found herself staking out a McDonald’s. The man she believed was the last male descendant of her great-great-great grandfather’s brother had refused to give her his DNA. So she decided to get it another way.

“I was going to take his coffee cup out of the garbage can,” said Ms. Teat, who traveled to the Georgia mountains from Tampa, Fla., with her test kit. “I was willing to do whatever it took.”

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Since learning that she shares some markers with St. Luke the Evangelist, Kathy Johnston, 54, a dermatologist in Torrance, Calif., has been lobbying to have the saint’s remains more thoroughly analyzed.

She believes St. Luke’s mother was Celtic, as is her own lineage, not Syrian, as previous genetic tests on remains in Padua, Italy, have suggested. She is willing to pay for the test, but scientists at the University of Ferrara and the Roman Catholic Church have ignored her theories.

...

Bob Grieve, 55, stores a DNA kit in his refrigerator to use upon his father’s death.

After testing his own DNA at the request of a distant cousin, Mr. Grieve was shaken to discover that he did not match any of his extended family, including his first cousin, the son of his father’s brother.

That could only mean an occurrence of what genetic genealogists call a “nonpaternal event.” Either his father was not his father, or his grandfather was not his father’s father. But the elder Mr. Grieve has refused to surrender to the swab.

“I don’t put blame on anybody,” said Mr. Grieve, an engine design checker in Dearborn, Mich. “It would just be nice to know where I came from.”

Spencer Wells Interview

Via GNXP a link to an interview by Spencer Wells. The interesting bits:

The data are sent to a central database created by IBM. They supplied the server, which is sitting in the basement of National Geographic. They have given everybody laptops with biometric [i.e., fingerprint] recognition so that only the PIs can access to the database. We are working closely with their computational biology team on analyzing the data. So some of our first publications, which are starting to go into the journals now, are coming through that group.

...

We are expanding the survey of whole mitochondria genomes in Africa. We've doubled the size of that database and it's revealing interesting mitochondrial patterns. That effort has been spearheaded by Doron Behar in Haifa.

People tend to ignore what went on within Africa. There is this inherent bias in European and Asian scientists that we've “done” Africa and then things got interesting when we [humans] left, but of course there was still a lot going on within Africa. We're looking at routes people might have taken out of Africa and back migration into Africa. Information that is coming out, in part, from an expedition I organized in 2005 to the Tibesti mountains in Chad, up on the Libyan border.

...

We've gotten some fascinating results and a lot of e-mails. For example, a Hungarian woman wrote in and said, “You've got to redo my test. You told me I'm native American or Siberian, and I know my ancestors came from Hungary—I can tell you the village they were living in in the sixteenth century.” The Hungarian language, Magyar, is actually related to languages spoken in Siberia, and this is one of the first cases where we've actually seen Siberian lineages showing up in the Hungarian population. They are there at very low frequency. We now through this project have over 350 people who are of Hungarian descent and we see these [Siberian] lineages at four to five percent on both male and female sides.