Saturday, May 31, 2008

Monogamy and Eusociality

Is high relatedness a cause or effect of eusociality? In this paper that just came out in Science, they find through some phylogenetic analyses and mating data among social insects that monogamy (which maximizes relatedness) is ancestral for all lineages, meaning that kin selection is likely a cause of eusociality (I have no idea of the details of how they did this). It's somewhat disappointing and surprising that they make no mention of humans or the paper by Bowles which hints at the relationship between monogamy (reproductive leveling), relatedness and kin selection and group selection, although in a different way.

Ancestral Monogamy Shows Kin Selection Is Key to the Evolution of Eusociality
William O. H. Hughes, Benjamin P. Oldroyd, Madeleine Beekman, Francis L. W. Ratnieks
Science 30 May 2008: Vol. 320. no. 5880, pp. 1213 - 1216
Abstract: Close relatedness has long been considered crucial to the evolution of eusociality. However, it has recently been suggested that close relatedness may be a consequence, rather than a cause, of eusociality. We tested this idea with a comparative analysis of female mating frequencies in 267 species of eusocial bees, wasps, and ants. We found that mating with a single male, which maximizes relatedness, is ancestral for all eight independent eusocial lineages that we investigated. Mating with multiple males is always derived. Furthermore, we found that high polyandry (>2 effective mates) occurs only in lineages whose workers have lost reproductive totipotency. These results provide the first evidence that monogamy was critical in the evolution of eusociality, strongly supporting the prediction of inclusive fitness theory.

Tuesday, May 27, 2008

Is human quadrupedalism due directly to genetic factors?

This paper that I blogged about a couple months ago about the possible genetic basis for quadrupedalism (walking on all fours) among a family in Turkey finally came out in PNAS and elicited a couple of letters in the same issue of PNAS (here, here) criticizing the interpretation of what they find. They bring up families in Iraq and among the Hutterites who are quadrupedal yet don't have the same mutation, or have the same mutation but aren't quadrupedal. Both of these letters suggest that quadrupedalism is not due directly to genetic factors but is "epiphenomenal" in that it's a way of compensating for balance problems caused by cerebellar hypoplasia, and due to a lack of "supportive therapy".

Friday, May 23, 2008

Sharing of chromosomal segments to analyze human colonization

via Dienekes, an interesting looking paper that includes some "fun" movies that describe the results of their modeling of the spread of humans around the globe.

Inferring Human Colonization History Using a Copying Model

Garrett Hellenthal, Adam Auton, Daniel Falush
PLoS Genetics 4(5): e1000078
Abstract: Genome-wide scans of genetic variation can potentially provide detailed information on how modern humans colonized the world but require new methods of analysis. We introduce a statistical approach that uses Single Nucleotide Polymorphism (SNP) data to identify sharing of chromosomal segments between populations and uses the pattern of sharing to reconstruct a detailed colonization scenario. We apply our model to the SNP data for the 53 populations of the Human Genome Diversity Project described in Conrad et al. (Nature Genetics 38,1251-60, 2006). Our results are consistent with the consensus view of a single “Out-of-Africa” bottleneck and serial dilution of diversity during global colonization, including a prominent East Asian bottleneck. They also suggest novel details including: (1) the most northerly East Asian population in the sample (Yakut) has received a significant genetic contribution from the ancestors of the most northerly European one (Orcadian). (2) Native South Americans have received ancestry from a source closely related to modern North-East Asians (Mongolians and Oroquen) that is distinct from the sources for native North Americans, implying multiple waves of migration into the Americas. A detailed depiction of the peopling of the world is available in animated form.

mtDNA diversity in Southeast Asia and rising sea levels

In this paper, the authors look at mtDNA diversity in Island Southeast Asia and propose that haplogroup E arose "in situ" 35 Kya ago and then there was a dispersal of the haplogroup around the time that the area broke up into islands due to rising sea levels.

Climate Change and Postglacial Human Dispersals in Southeast Asia
Pedro Soares et al.
Molecular Biology and Evolution 2008 25(6):1209-1218
Abstract: Modern humans have been living in Island Southeast Asia (ISEA) for at least 50,000 years. Largely because of the influence of linguistic studies, however, which have a shallow time depth, the attention of archaeologists and geneticists has usually been focused on the last 6,000 years—in particular, on a proposed Neolithic dispersal from China and Taiwan. Here we use complete mitochondrial DNA (mtDNA) genome sequencing to spotlight some earlier processes that clearly had a major role in the demographic history of the region but have hitherto been unrecognized. We show that haplogroup E, an important component of mtDNA diversity in the region, evolved in situ over the last 35,000 years and expanded dramatically throughout ISEA around the beginning of the Holocene, at the time when the ancient continent of Sundaland was being broken up into the present-day archipelago by rising sea levels. It reached Taiwan and Near Oceania more recently, within the last 8,000 years. This suggests that global warming and sea-level rises at the end of the Ice Age, 15,000–7,000 years ago, were the main forces shaping modern human diversity in the region.

Saturday, May 17, 2008

New pigmentation loci found

IRF4 and SLC24A4, according to this GWAS among people of European ancestry.

A Genome-Wide Association Study Identifies Novel Alleles Associated with Hair Color and Skin Pigmentation
Jiali Han et al.
PLoS Genet 4(5): e1000074
Abstract: We conducted a multi-stage genome-wide association study of natural hair color in more than 10,000 men and women of European ancestry from the United States and Australia. An initial analysis of 528,173 single nucleotide polymorphisms (SNPs) genotyped on 2,287 women identified IRF4 and SLC24A4 as loci highly associated with hair color, along with three other regions encompassing known pigmentation genes. We confirmed these associations in 7,028 individuals from three additional studies. Across these four studies, SLC24A4 rs12896399 and IRF4 rs12203592 showed strong associations with hair color, with p = 6.0×10−62 and p = 7.46×10−127, respectively. The IRF4 SNP was also associated with skin color (p = 6.2×10−14), eye color (p = 6.1×10−13), and skin tanning response to sunlight (p = 3.9×10−89). A multivariable analysis pooling data from the initial GWAS and an additional 1,440 individuals suggested that the association between rs12203592 and hair color was independent of rs1540771, a SNP between the IRF4 and EXOC2 genes previously found to be associated with hair color. After adjustment for rs12203592, the association between rs1540771 and hair color was not significant (p = 0.52). One variant in the MATP gene was associated with hair color. A variant in the HERC2 gene upstream of the OCA2 gene showed the strongest and independent association with hair color compared with other SNPs in this region, including three previously reported SNPs. The signals detected in a region around the MC1R gene were explained by MC1R red hair color alleles. Our results suggest that the IRF4 and SLC24A4 loci are associated with human hair color and skin pigmentation.
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