Neanderthals had same version of FOXP2 "language gene" as modern humans

Via National Geographic:

A team of European researchers tested Neandertal bones recovered from a Spanish cave for a certain gene, called FOXP2, that has been dubbed "the speech and language gene."

It's the only gene known so far that plays a key role in language. When mutated, the gene primarily affects language without affecting other abilities.

The new study suggests that Neandertals (often spelled Neanderthals) had the same version of this gene that modern humans share—a different version than is found in chimpanzees and other apes.

"From the point of this gene, there is no reason to think that Neandertals did not have language as we do," said the study's lead author, Johannes Krause of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany.

"Of course many genes are involved in language, so we can't say from this result alone that Neandertals spoke just as modern humans do," Krause added.

Genome-wide detection of positive selection

Nature 449, 913-918 (18 October 2007) | doi:10.1038/nature06250; Received 8 August 2007; Accepted 13 September 2007

Genome-wide detection and characterization of positive selection in human populations

Pardis C. Sabeti et al.

With the advent of dense maps of human genetic variation, it is now possible to detect positive natural selection across the human genome. Here we report an analysis of over 3 million polymorphisms from the International HapMap Project Phase 2 (HapMap2)1. We used 'long-range haplotype' methods, which were developed to identify alleles segregating in a population that have undergone recent selection2, and we also developed new methods that are based on cross-population comparisons to discover alleles that have swept to near-fixation within a population. The analysis reveals more than 300 strong candidate regions. Focusing on the strongest 22 regions, we develop a heuristic for scrutinizing these regions to identify candidate targets of selection. In a complementary analysis, we identify 26 non-synonymous, coding, single nucleotide polymorphisms showing regional evidence of positive selection. Examination of these candidates highlights three cases in which two genes in a common biological process have apparently undergone positive selection in the same population:LARGE and DMD, both related to infection by the Lassa virus3, in West Africa;SLC24A5 and SLC45A2, both involved in skin pigmentation4, 5, in Europe; and EDAR and EDA2R, both involved in development of hair follicles6, in Asia.

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Conservation of frequently used words in Indo-European languages

I wonder what implications -if any- this finding has on attempts to date the PIE language before the dispersal of its speakers. After all, PIE is constructed based on words found in several (at least two) daughter languages, and thus will tend to use words that are conserved more (since they have survived in more than one language). The implication of this article is that conserved words are replaced at a slower rate. Hence, it is important to take into account the rates of evolution of different terms when trying to figure out how long ago two languages shared a common ancestor.

Nature 449, 717-720 (11 October 2007) | doi:10.1038/nature06176; Received 30 April 2007; Accepted 17 August 2007

Frequency of word-use predicts rates of lexical evolution throughout Indo-European history

Mark Pagel et al.

Greek speakers say "ουρα", Germans "schwanz" and the French "queue" to describe what English speakers call a 'tail', but all of these languages use a related form of 'two' to describe the number after one. Among more than 100 Indo-European languages and dialects, the words for some meanings (such as 'tail') evolve rapidly, being expressed across languages by dozens of unrelated words, while others evolve much more slowly—such as the number 'two', for which all Indo-European language speakers use the same related word-form1. No general linguistic mechanism has been advanced to explain this striking variation in rates of lexical replacement among meanings. Here we use four large and divergent language corpora (English2, Spanish3, Russian4 and Greek5) and a comparative database of 200 fundamental vocabulary meanings in 87 Indo-European languages6 to show that the frequency with which these words are used in modern language predicts their rate of replacement over thousands of years of Indo-European language evolution. Across all 200 meanings, frequently used words evolve at slower rates and infrequently used words evolve more rapidly. This relationship holds separately and identically across parts of speech for each of the four language corpora, and accounts for approximately 50% of the variation in historical rates of lexical replacement. We propose that the frequency with which specific words are used in everyday language exerts a general and law-like influence on their rates of evolution. Our findings are consistent with social models of word change that emphasize the role of selection, and suggest that owing to the ways that humans use language, some words will evolve slowly and others rapidly across all languages.

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Y chromosomes from the Gulf of Oman

European Journal of Human Genetics advance online publication 10 October 2007; doi: 10.1038/sj.ejhg.5201934

Y-chromosome diversity characterizes the Gulf of Oman

Alicia M Cadenas

Abstract

Arabia has served as a strategic crossroads for human disseminations, providing a natural connection between the distant populations of China and India in the east to the western civilizations along the Mediterranean. To explore this region's critical role in the migratory episodes leaving Africa to Eurasia and back, high-resolution Y-chromosome analysis of males from the United Arab Emirates (164), Qatar (72) and Yemen (62) was performed. The role of the Levant in the Neolithic dispersal of the E3b1-M35 sublineages is supported by the data, and the distribution and STR-based analyses of J1-M267 representatives points to their spread from the north, most likely during the Neolithic. With the exception of Yemen, southern Arabia, South Iran and South Pakistan display high diversity in their Y-haplogroup substructure possibly a result of gene flow along the coastal crescent-shaped corridor of the Gulf of Oman facilitating human dispersals. Elevated rates of consanguinity may have had an impact in Yemen and Qatar, which experience significant heterozygote deficiencies at various hypervariable autosomal STR loci.

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TEDtalk by Zeresenay Alemseged

An interesting talk (video) by a paleoanthropologist working in Ethiopia:

About this Talk

Paleoanthropologist Zeresenay Alemseged is looking for the roots of humanity in Ethiopia's badlands. Here he talks about what he has found -- including the oldest skeleton yet discovered of a hominid child -- and how Africa holds the clues to what makes us human.

About Zeresenay Alemseged

Zeresenay "Zeray" Alemseged digs in the Ethiopian desert, looking for the earliest signs of humanity. His most exciting find: the 3.3-million-year-old bones of Selam, a 3-year-old hominid child, from the species Australopithecus afarensis.

Lots more TEDtalks if you love science.

Neanderthals of the East

A new paper from Svante Paabo's team that shows that Neanderthals may have lived further to the east that can be assumed based on paleoanthropological evidence. Roughly speaking, to identify some remains as Neanderthals, anthropologists have to detect features belonging to the "constellation of features" typical of that species. However, when the material is limited in quantity, one cannot do this: most of the Neanderthal-identifying features are missing! Obviously, this is not a problem with DNA methods, since DNA can be extracted from small bone and tooth fragments.

Nature advance online publication 30 September 2007 | doi:10.1038/nature06193

Neanderthals in central Asia and Siberia

Johannes Krause et al.

Morphological traits typical of Neanderthals began to appear in European hominids at least 400,000 years ago1 and about 150,000 years ago2 in western Asia. After their initial appearance, such traits increased in frequency and the extent to which they are expressed until they disappeared shortly after 30,000 years ago. However, because most fossil hominid remains are fragmentary, it can be difficult or impossible to determine unambiguously whether a fossil is of Neanderthal origin. This limits the ability to determine when and where Neanderthals lived. To determine how far to the east Neanderthals ranged, we determined mitochondrial DNA (mtDNA) sequences from hominid remains found in Uzbekistan and in the Altai region of southern Siberia. Here we show that the DNA sequences from these fossils fall within the European Neanderthal mtDNA variation. Thus, the geographic range of Neanderthals is likely to have extended at least 2,000 km further to the east than commonly assumed.

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Greater genetic drift in East Asians than in Europeans

Nature Genetics 39, 1251 - 1255 (2007)
Published online: 9 September 2007 | doi:10.1038/ng2116

Measurement of the human allele frequency spectrum demonstrates greater genetic drift in East Asians than in Europeans

Alon Keinan et al.

Large data sets on human genetic variation have been collected recently, but their usefulness for learning about history and natural selection has been limited by biases in the ways polymorphisms were chosen. We report large subsets of SNPs from the International HapMap Project1, 2 that allow us to overcome these biases and to provide accurate measurement of a quantity of crucial importance for understanding genetic variation: the allele frequency spectrum. Our analysis shows that East Asian and northern European ancestors shared the same population bottleneck expanding out of Africa but that both also experienced more recent genetic drift, which was greater in East Asians.

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Anthropometric correlates of IQ

A reader alerted me to this study which re-examined Hooton's data on anthropometric correlates of IQ. Interestingly, sitting height correlates with IQ almost as strongly as (full) height, indicating that a long torso rather than long limbs is associated with statistically higher IQ.

Personality and Individual Differences
doi:10.1016/j.paid.2007.07.013

Head size correlates with IQ in a sample of Hooton’s criminal data

Jeremy E.C. Genovese

Abstract

Data collected by Hooton (1939) on 676 inmates held at the Concord Reformatory in Massachusetts include both anthropometric measures and IQ scores. In this study a sample (N = 238) was drawn to assess the nonparametric correlation between measures of head size and IQ. Head length (r = .13), breadth (r = .15), height (r = .14), circumference (r = .15) and calculated volume (r = .20) correlated with IQ. Two measures of body size also correlated with IQ; height (r = .22) and sitting height (r = .19).

Link

Deep voiced-men have more children

You might want to read the blog post on What is your voice pitch after reading this article.

Biology Letters
10.1098/rsbl.2007.0410

Voice pitch predicts reproductive success in male hunter-gatherers

C.L. Apicella et al.

The validity of evolutionary explanations of vocal sexual dimorphism hinges upon whether or not individuals with more sexually dimorphic voices have higher reproductive success than individuals with less dimorphic voices. However, due to modern birth control methods, these data are rarely described, and mating success is often used as a second-rate proxy. Here, we test whether voice pitch predicts reproductive success, number of children born and child mortality in an evolutionarily relevant population of hunter-gatherers. While we find that voice pitch is not related to reproductive outcomes in women, we find that men with low voice pitch have higher reproductive success and more children born to them. However, voice pitch in men does not predict child mortality. These findings suggest that the association between voice pitch and reproductive success in men is mediated by differential access to fecund women. Furthermore, they show that there is currently selection pressure for low-pitch voices in men.

Link

YAP+ in South Asia

YAP+ defines haplogroup DE in the human Y chromosome phylogeny. Haplogroup D seems confined to a few Asian populations whereas haplogroup E is found in Africans and West Eurasians. Previous studies had determined that D is found at high frequencies among the short-statured isolated populations from the Andaman and Nicobar islands, and this new study indicates that D is also found in mainland South Asia among tribal Indians, albeit at lower frequencies.

Ann Hum Biol. 2007 Sep-Oct;34(5):582-6

YAP insertion signature in South Asia.

Chandrasekar A et al.

A total of 2169 samples from 21 tribal populations from different regions of India were scanned for the Y-chromosome Alu polymorphism. This study reports, for the first time, high frequencies (8-65%) of Y Alu polymorphic (YAP) insertion in northeast Indian tribes. All seven Jarawa samples from the Andaman and Nicobar islands had the YAP insertion, in conformity with an earlier study of Andaman Islanders. One isolated case with haplotype E* was found in Dungri Bhill, a western Indian population, while YAP insertion in northeast India and Andaman tribes was found in association with haplotype D* (M168, M174). YAP insertion frequencies reported in the mainland Indian populations are negligible, according to previous studies. Genetic drift may be the causative factor for the variable frequency of the YAP insertion in the mainland populations, while the founder effect may have resulted in the highest incidence of haplotype D among the Andaman Islanders. The results of YAP insertion and the evidence of previous mtDNA studies indicate an early out of Africa migration to the Andaman and Nicobar Islands. The findings of YAP insertion in northeast Indian tribes are very significant for understanding the evolutionary history of the region.

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Middle Eastern origin of Neolithic pigs

Via the BBC Pig DNA reveals farming history:

Between 6,800-4,000 BC, farming methods spread across Europe, but the question of how these methods spread has not been fully established.

The two competing theories are that farming spread through cultural exchange, possibly during trading or that people migrated to Europe bringing their expertise with them.

A previous study, in 2005, analysed modern pig DNA and showed that all modern pigs are descended from European wild boar. This led researchers to conclude that early Europeans domesticated pigs independently of other farming methods.

This new study, however, has discovered that the first domesticated pigs in Europe did have Near Eastern ancestry, indicating that farmers migrated to Europe, bringing their "package" of livestock and farming methods with them.

Domestic pigs of European wild boar ancestry appear soon afterwards.

Structure of genetic variation in US populations

A new AJHG preprint looks at the genetic variation in different groups of the US population.

From the paper:

A frequent claim about human population structure is that most common variation
is shared among all populations11-13. This, of course, depends on how population
boundaries are defined, but often cited to support such comments are the comparisons of SNP frequencies in pairs of populations in the HapMap data and the Perlegen data. Analyses of these data indicated that common SNPs were frequently both shared and common among populations of predominately African, Asian, and European ancestry. However, population genetic analysis was not the intended goal of either the HapMap or the Perlegen projects, and common, shared SNPs were over sampled by the ascertainment strategies used for each project.

Also an interesting view of the genetic structure of the main US population groups.

C. Stacked bar chart inferred from results of model-based cluster analysis using STRUCTURE 2.0. Each bar represents an individual, and each bar is divided according to the fraction of cluster membership. D. Triangle plot illustrating the proportion of African, Asian, and European American ancestry of each individual (dots) estimated from STRUCTURE 2.0. (PC=principal component; AfA=African American; AsA=Asian American; EA=European Americans; HA=Latino/Hispanic Americans; MAF=minor allele frequency.)

The structure of common genetic variation in U.S. populations

Stephen L. Guthery et al.

ABSTRACT

The common variant/common disease model predicts that most risk alleles underlying complex health-related traits are common and therefore old and found in multiple populations, rather than rare or population-specific. Accordingly, there is widespread interest in assessing the population structure of common alleles. However, such assessments have been confounded by analysis of datasets with bias toward ascertainment of common alleles (e.g., HapMap, Perlegen) or in which a relatively small number of genes and/or populations were sampled. The aim of this study was to examine the structure of common variation ascertained in major U.S. populations by resequencing the exons and flanking regions of 3,873 genes in 154 chromosomes from European, Latino/Hispanic, Asian, and African Americans generated by the Genaissance Resequencing Project. The frequency distributions of private and
common single nucleotide polymorphisms (SNPs) were measured, and the extent to which common SNPs were shared across populations was analyzed using several different estimators of population structure. Most SNPs that were common in one population were present in multiple populations, but SNPs common in one population were frequently not common in other populations. Moreover, SNPs that were common in two or more populations often differed significantly in frequency from one another, particularly in comparisons of African Americans versus other U.S. populations. These findings indicate that even if the bulk of alleles underlying complex health-related traits are common SNPs, geographic ancestry might well be an important predictor of whether a person carries a risk allele.

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Problems with Neanderthal genomic sequences

A new study freely available online throws into doubt the genomic sequences extracted from Neanderthal remains in two previous articles.

PLoS Genetics

Inconsistencies in Neanderthal genomic DNA sequences

Jeffrey D. Wall, Sung K. Kim

Two recently published papers describe nuclear DNA sequences that were obtained from the same Neanderthal fossil. Our reanalyses of the data from these studies show that they are not consistent with each other and point to serious problems with the data quality in one of the studies, possibly due to modern human DNA contaminants and/or a high rate of sequencing errors.

Link

Dispersal of haplogroup N from Siberia into Eastern Europe

J Hum Genet. 2007 Aug 17; [Epub ahead of print]

Y-chromosome haplogroup N dispersals from south Siberia to Europe.

Derenko M, Malyarchuk B, Denisova G, Wozniak M, Grzybowski T, Dambueva I, Zakharov I.

In order to reconstruct the history of Y-chromosome haplogroup (hg) N dispersals in north Eurasia, we have analyzed the diversity of microsatellite (STR) loci within two major hg N clades, N2 and N3, in a total sample of 1,438 males from 17 ethnic groups, mainly of Siberian and Eastern European origin. Based on STR variance analysis we observed that hg N3a is more diverse in Eastern Europe than in south Siberia. However, analysis of median networks showed that there are two STR subclusters of hg N3a, N3a1 and N3a2, that are characterized by different genetic histories. Age calculation of STR variation within subcluster N3a1 indicated that its first expansion occurred in south Siberia [approximately 10,000 years (ky)] and then this subcluster spread into Eastern Europe where its age is around 8 ky ago. Meanwhile, younger subcluster N3a2 originated in south Siberia (probably in the Baikal region) approximately 4 ky ago. Median network and variance analyses of STR haplotypes suggest that south Siberian N3a2 haplotypes spread further into Volga-Ural region undergoing serial bottlenecks. In addition, median network analysis of STR data demonstrates that haplogroup N2-A is represented by two subclusters, showing recent expansion times. The data obtained allow us to suggest Siberian origin of haplogroups N3 and N2 that are currently widespread in some populations of Eastern Europe.

Link

The new Ming the Merciless

I haven't watched the new incarnation of Flash Gordon on SCI-FI Channel, but can anyone spot a difference between the Ming character from the 1930s serial and last FG movie and the newest one?

Hypothesis about the origins of hemochromatosis

Med Hypotheses. 2007 Aug 7; [Epub ahead of print]

Hemochromatosis: A Neolithic adaptation to cereal grain diets.

Naugler C.

The Neolithic period in Europe marked the transition from a hunter-gatherer diet rich in red meat to an iron-reduced cereal grain diet. This dietary shift likely resulted in an increased incidence of iron deficiency anemia, especially in women of reproductive age. I propose that hereditary hemochromatosis and in particular the common HFE C282Y mutation may represent an adaptation to decreased dietary iron in cereal grain-based Neolithic diets. Both homozygous and heterozygous carriers of the HFE C282Y mutation have increased iron stores and therefore possessed an adaptive advantage under Neolithic conditions. An allele age estimate places the origin of the HFE C282Y mutation in the early Neolithic period in Northern Europe and is thus consistent with this hypothesis. The lower incidence of this mutation in other agrarian regions (the Mediterranean and Near East) may be due to higher dietary intakes of the iron uptake cofactor vitamin C in those regions. The HFE C282Y mutation likely only became maladaptive in the past several centuries as dietary sources of iron and vitamin C improved in Northern Europe.

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