By Dai Cooper, via my grad student listserv.

Click here to view the embedded video.

Svante Pääbo’s group at the Max Plank Institute have a paper coming out in the February issue of Cell Biology. In it, they describe sequencing a complete early human mitochondrial genome from the Markina Gora specimen from the Kostenki 14 site in Russia. The remains date to around 30,000 years ago, not the oldest human sequence, but interesting nonetheless because the authors have identified new ways to determine if ancient DNA sequences are genuine vs. contamination.  This is especially important for more anatomically modern human fossils, who may have similar sequences to extant populations.

For Neandertal mtDNA, identifying contamination is relatively simple, because their mtDNA sequences fall outside the range of variation found in modern humans. Not so for more recent fossils.  So how can researchers identify true archaic sequences?

fragment length, deamination-induced sequence errors at ends of molecules, and purine-associated fragmentation represent features by which endogenous and contaminating populations of DNA molecules can be distinguished in at least some late Pleistocene specimens (1).

So, fragments sequenced from ancient samples are typically shorter than modern contaminants.  In many cases, the fragments are shorter than what can be amplified using PCR, meaning high-throughput direct sequencing methods are required to analyze these ancient samples.  In addition, the cytosine bases at the 5′ ends of ancient DNA fragments are susceptible to deamination (removal of an -NH₃ group), causing those bases to be misread as thymine. The 3′ ends of ancient sequences have a commensurate increase in G-A errors. Finally, fragmentation of ancient sequences occurs more frequently at purine bases (guanine and adenine).

With these criteria in mind, the researchers determined that the Markina Gora sequence belongs to mitochondrial haplogroup U2, a haplogroup still present in Europe today.

Figure 3D from Krause et al. (2010) - with the EMH sequence highlighted in red.

The authors determine that it is unlikely that this sequence is the result of modern contamination, because the nucleotide difference between the Markina Gora specimen and the ancestral U sequence is much shorter than than seen between the root and modern sequences, which have accumulated many more mutations over time.  Their results also support the hypothesis of pre-agricultural genetic continuity in Europe, so that genetic lineages which were present on the continent prior to the Neolithic transition can still be found in modern European populations.

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Krause J, Briggs AW, Kircher M, Maricic T, Zwyns N, Derevianko A, & Pääbo S (2009). A Complete mtDNA Genome of an Early Modern Human from Kostenki, Russia. Current biology : CB PMID: 20045327

Holly Dunsworth, a physical anthropologist at Penn State, wrote an essay for NPR’s This I Believe project titled I Am Evolution. You can read it, or listen to Holly read it, from NPR’s site. Holly says, in part:

If our beliefs are important enough, we live our lives in service to them. That’s how I feel about evolution. My role as a female Homo sapiens is to return each summer to Kenya, dig up fossils, and piece together our evolutionary history. Scanning the ground for weeks, hoping to find a single molar, or gouging out the side of a hill, one bucket of dirt at a time, I’m always in search of answers to questions shared by the whole human species. The experience deepens my understanding not just about what drives my life, but all our lives, where we came from.

That’s why I’m an anthropologist, and I would imagine most of my labmates feel the same way.

PLoS ONE has a article this month titled The Phylogeny of the Four Pan-American mtDNA Haplogroups: Implications for Evolutionary and Disease Studies. There are several points of interest:

1. The authors make use of data that is publicly available, either through GenBank or other DNA databases.
2. Complete mtDNA sequences (ie., all 16568 bases) were used for phylogenetic reconstruction.
3. Among 265 “novel” mtDNA sequences reported among Hispanics and African Americans in a recent addition to GenBank, 101 were of Native American origin.
4. All four Native American founder lineages (A2, B2, C1, D1) date to between 18,000-24,000 years ago.

Their results suggest that human expansion into the Americas coincided with the decline of the Last Glacial Maximum (Ice Age), knocking another hole in the “Clovis-first” hypothesis. Given that all four lineages give similar coalescent times, this study may also contribute to the “waves of migration” debate.

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Achilli A, Perego UA, Bravi CM, Coble MD, Kong QP, Woodward SR, Salas A, Torroni A, & Bandelt HJ (2008). The phylogeny of the four pan-American MtDNA haplogroups: implications for evolutionary and disease studies. PloS one, 3 (3) PMID: 18335039

Just a couple of quick items that popped up this week. First, from Ironic Sans, scientist themed Valentine’s cards. The Darwin one is my personal favorite.

And from the “Love in the Animal Kingdom” files, researchers from the Wildlife Conservation Society and the Max Planck Institute for Evolutionary Anthropology published the first documented proof that wild gorillas, like humans and bonobos, occasionally mate face-to-face.

This suggests that gorillas might use sex, not just for reproduction, but also to reinforce social bonds. An interesting sidenote, the female, Leah, is the same female that was documented using tools.

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Image credit: ©Thomas Breuer – WCS/MPI-EVA

Friedlaender et al. have a recent article in PLos Genetics. Titled The Genetic Structure of Pacific Islanders, the study used 687 microsatellite and 203 indel loci in nearly 1000 individuals from 41 populations in and around Oceania, in order to determine the genetic origins of these populations.

The researchers found

only a modest association between language and genetic affiliation. Oceanic languages were introduced and dispersed around the islands within the last 3,300 years, but there was apparently only a small infusion of accompanying “Austronesian” ancestry that has survived…suggest[ing] that Oceanic languages were adopted by many formerly Papuan-speaking groups, while at the same time there was little genetic influence or marital exchange. At least in Near Oceania, rates of language borrowing and language adoption have been faster and more pervasive than rates of genetic admixture.

Two aspects of this study appeal to me.

1. Whole genome studies appear to be the wave of the future for anthropological genetic research, with the advent of new technologies that make these types of analyses feasible.
2. It was published in an open access journal, by well-respected members of the field. There’s an interesting discussion of open-access publishing at apophenia, in which she emphasizes the importance of tenured faculty supporting open-access.

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Friedlaender JS, Friedlaender FR, Reed FA, Kidd KK, Kidd JR, Chambers GK, Lea RA, Loo JH, Koki G, Hodgson JA, Merriwether DA, & Weber JL (2008). The genetic structure of Pacific Islanders. PLoS genetics, 4 (1) PMID: 18208337

The American Anthropological Association has created a traveling exhibit exploring the concept of race. It’s currently at Exploration Place in Wichita until January 1, 2008. For those outside of Kansas, there’s a virtual tour of the exhibit.

The Global Census activity is particularly enlightening. In the Bulgarian Census, my race is ‘Other.’

I’m starting a new series on Freethinker’s: Awesome Scientists. One of the goals of this blog is highlight the interesting research being done by scientists in different fields. The inaugural post highlights Dr. Julie Schablitsky, historical archaeologist at the University of Oregon. She was profiled last summer by Nova ScienceNOW.

University of Oregon archaeologist Julie Schablitsky examines part of a ceramic dish unearthed at the Donner dig in July 2004.

Not all archaeology is ancient. Julie’s work focuses on forgotten stories from the historical period. You know the old saw about history, the winner writes it. Dr. Schablitsky is more interested in the tales from minorities, those who lacked a voice, or whose stories have been embellished or misrepresented by tradition. Julie has worked on documenting the life of Chinese immigrants to the US in the 19th century, and a reanalysis of the Donner Party disaster.

Her research caught my attention because she was part of a research team that used genetic analysis of bones found in a hearth at the Donner Party site, and demonstrated an absence of human bones. Instead, there were bones of deer, rabbit, rodents, even the family dog. The researchers concluded that the pioneers trapped in the Sierra Nevadas that winter exhausted every available resource prior to resorting to cannibalism to survive, and that by the time it became necessary, many of them had managed to leave. The gruesome and gory account of the Donner party was not entirely accurate, and Dr. Schablitsky and her team were able to use the scientific method to debunk it.

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Image credit: Guy Tasa, University of Oregon

Washoe, one of the first chimpanzees to learn American Sign Language, died Tuesday evening at her home at Central Washington University. Raised by Beatrix and Allen Gardener, she eventually went to live with Robert Fouts, and his wife, Deborah, who together established the Chimpanzee and Human Communication Institute at CWU. Their charitable, educational organization, Friends of Washoe, posted the following:

Our beloved friend Washoe passed away Tuesday evening, October 30, at 8:00, after a brief illness. At the time of her passing she was at home at CHCI, with her family and closest friends. Washoe was 42 years old, a long life for a female chimpanzee. Most females in captivity live an average of 33.5 years. In lieu of flowers, please consider a donation in Washoe’s name to Friends of Washoe, to continue supporting her family.

Washoe was a wonderful ambassador for her species, a favorite topic in my Introduction to Physical Anthropology classes, and will be sorely missed.

James Watson issued an apology today, stating:

I can certainly understand why people, reading those words, have reacted in the ways they have. To all those who have drawn the inference from my words that Africa, as a continent, is somehow genetically inferior, I can only apologise unreservedly. That is not what I meant. More importantly from my point of view, there is no scientific basis for such a belief.

I haven’t yet been able to track down an explanation of exactly what he did mean, but it’s an apology. In the meantime, Cold Spring Harbor Laboratory issued this statement yesterday:

The comments attributed to Dr. James Watson that first appeared in the October 14, 2007 edition of The Sunday Times U.K. are his own personal statements and in no way reflect the mission, goals, or principles of Cold Spring Harbor Laboratory’s Board, administration or faculty. Dr. Watson is not the President of Cold Spring Harbor Laboratory and was not speaking on behalf of the institution.

The Board of Trustees, administration and faculty vehemently disagree with these statements and are bewildered and saddened if he indeed made such comments. Cold Spring Harbor Laboratory does not engage in any research that could even form the basis of the statements attributed to Dr. Watson.

This morning, the lab announced that they had suspended Chancellor Watson from all of his administrative duties pending “further deliberation by the Board.”