jim sims

More evidence: earlier peopleing of the Americas

Tom D. Dillehay et al. report new analyzes of ancient hearth remains from the Monte Verde site in modern-day Chile, which indicate human presence at that site as early as 14,220 years B.P.  The analysis indicates the people of the area exploited several different ecosystems:  ocean-beach, river delta and inland locations.  In the same issue of Science is a paper by M. Thomas P. Gilbert et al. that reports on the recovery and sequencing of ancient human mtDNA from coprolites (feces) in Oregon in the Northwest of the United States.  They found mtDNA haplogroups A2 and B2. Their dating of the human samples is at least 1,000 years older than the Clovis toolkit dates.

Refs: Tom D. Dillehay et al., Monte Verde: Seaweed, Food, Medicine, and the Peopling of South America , Science 320:784-786 (2008) DOI: 10.1126/science.1156533

M. Thomas P. Gilbert, et al., DNA from Pre-Clovis Human Coprolites in Oregon, Science 320:786-788 (2008) DOI: 10.1126/science.1154116

Draft genome of platypus: an odd fellow

The draft genome of the platypus Ornithorhynchus anatinus was published this week in the British science journal Nature.  Just looking at the animal, you get the impression of part mammal, part bird and part reptile. That is in fact what is found in the DNA of this animal. Native to Australia and Tasmania, the platypus is a mammal with fur adapted to an aquatic environment that feeds its young milk, but has no nipples. Rather than bearing live young, the platypus lays eggs like a reptile. The bill on the platypus is reminiscent of a bird.  When diving for small animals to feed on, it closes its eyes, nostrils and mouth and uses electrochemical sensory apparatus in the bill that presumably allow it to locate prey.   The male platypus has venous spurs and the genes for the venom look like reptile venom, but evolved separately from those of reptiles.  Some of its genes have been conserved since the split between birds/reptiles and mammals, whereas other mammals no longer have these inherited gene segments.  The sex determination scheme for the platypus includes five X-chromosomes and five Y-chromosomes in the males, which is quite different from other mammals.

Ref: Wesley C. Warren et al., Nature 453: 175-184 (8 May 2008) doi:10.1038/nature06936

European men 101

Kalevi Wiik in a new paper in  J. Genet. Geneal. 4:35-85, 2008 attempts to summarize the scientific literature with regard to the genetic origins of European men.  The title of this post has two meanings:  first, the article is a kind of primer and the other meaning refers to the 101 maps in this lengthy article. For those without access to the scientific literature, this will be a good source of information and maps of haplogroup frequencies.

Early structure of human mtDNA tree

I have heard Doron M. Behar speak a couple of times on mtDNA and human genetic genealogy and anthropology.  In this paper with other authors including R. Spencer Wells and the Genographic Consortium report on the tree of mtDNA lineages in Africa.  They did full mtDNA sequencing of 624 individuals from Africa. The graphic with this post is a greatly scaled down version of Fig 1 in the Behar et al. paper. They show there was a very early split in the tree in Africa about 198,000 ago.  The L0 mtDNA was split off from the L1'5 lineages.  This is shown at the top of the figure with L0 to the left background light green and the other L1 related lineage with background of brown. The figure shows the L3 branch forming about 78,000 years ago and the M and N lineages (bright purple center of figure) about 76,000 years ago emerging from L.  M and N are the lineages that were the founding lines in the out of Africa peopling of the world outside of Africa. This deep early split indicates physical isolation of human groups very early.  The L0 lines are mostly South African.  The authors suggest climatic conditions may have isolated people for long periods before the more recent Bantu people expansion.

Ref: Behar et al., The Dawn of Human Matrilineal Diversity, The American Journal of Human Genetics (2008), doi:10.1016/j.ajhg.2008.04.002

Human mtDNA haplogroup V2 and me

I recently had my entire mtDNA sequenced by FamilyTree DNA, so I won't be needing anymore tests done on my mtDNA.  FamilyTree DNA had previously placed my sequence in haplogroup V, but with more data, I am now in haplogroup V2.  As we learn more about mtDNA, the tree is likely to change and, if my sequence is any clue, there are likely more sub-branches of V2 not yet described in the scientific literature.  The image with this post is part of figure B1 in the paper Palanichamy et al. Phylogeny of Mitochondrial DNA Macrohaplogroup N, Based on Complete Sequencing:  Implications for the Peopling of South Asia, Amer. J. Hum. Genet. 75:966-978, 2004. I double-checked with the staff at FamilyTree DNA and they are using this same paper as the most detailed description of this part of the human mtDNA tree. I circled the mutations relative to rCRS that separate pre-V from HV (16295,72), the mutations that separate pre-V from V (15904,4580) and the one mutation that separates V from V2 (13105).  I have all of the mutations circled in red plus all the others that are related to the fact that the rCRS is located in H2 and not at the biological root of the mtDNA tree, and  a couple others for a total of 19 mutations.