jim sims

Human diversity on the Indian subcontinent

In a recent Nature paper by Lalji Singh et al., they found genetic evidence for three ancestral migrations into India (fig 4 from the paper).  The oldest being out of Africa and represented today by the Onge people of the Andaman Islands, followed by introgression of the ancestors of the modern South Indian (ASI)  populations today followed much later by introgression of the ancestors of the North Indian (ANI) populations.

They further note that almost all Indians today are admixed from the ANI and ASI ancestral populations.  

They also find evidence for many founder events took place followed by population expansion without much gene flow between groups.

Today's South Indians often speak a Dravidian language while the North Indians often speak an Indo-European language.

There is a free Nature podcast with a segment devoted to this paper.  Skip to about 24:45 for the 6.75 minute segment.

Ref:  Vol 461|24 September 2009|doi:10.1038/nature08365

Genes and geography in Europe

At left is a principle component analysis of European genetic variability as described in a recent paper by Carlos Bustamenta et al. in the British journal Nature.  The paper describes the genotyping of 3,192 Europeans at 500,568 single nucleotide (SNP) polymorphisms using the Affymetrix 500K chip. The authors say that they focused on 197,146 SNPs from 1,387 individuals that met their criteria of high confidence that included having four grandparents born nearby the location in Europe sampled.

The principle component analysis looks very much like the map of Europe, suggesting more population structure than may have been previously appreciated. It remains to be seen if these kinds of analyzes will be useful for families that left Europe between three and four hundred years ago.  Only time will tell if we can say with some certainty that this part of this chromosome came from England, this part from France, this from Spain, etc.

Ref:  Carlos D. Bustamente et al., a letter in Nature doi:10.1038/nature07331, 2008; listen to an interview with two of the authors featured on the Nature: 04 Sep 2008 podcast, skip to 1:20 to begin the segment.

Mike Hammer speaks on human origins

There is an excellent lecture on the current scientific consensus view of the origins of modern humans.  The speaker is Mike Hammer, Ph.D. currently at the University of Arizona.  I have personally heard Dr. Hammer speak on two different occasions at Family Tree DNA surname project administrator conferences.  His one hour and five minute lecture is available on the iTunes web store as a free video podcast in the iTunes University section.   This lecture is aimed at an educated lay audience.  This talk summarizes what we think we know as we put together the archaeological, anthropological and molecular genetic lines of evidence.  This podcast is part of a lecture series Evolution:  Our World and Ourselves at the University of Arizona.

Climate consensus update

The Intergovernmental Panel on Climate Change released its updated consensus on climate change in February 2007.  The Summary for Policy Makers is available now at the IPPC web site, with the full report to follow.  Because this is a consensus document, it should be considered a conservative estimate on climate change.

"Global atmospheric concentrations of carbon dioxide, methane and nitrous oxide have increased markedly as a result of human activities since 1750 and now far exceed pre-industrial values determined from ice cores spanning many thousands of years (see Figure SPM-1). The global increases in carbon dioxide concentration are due primarily to fossil fuel use and land-use change, while those of methane and nitrous oxide are primarily due to agriculture...Warming of the climate system is unequivocal, as is now evident from observations of increases in global average air and ocean temperatures, widespread melting of snow and ice, and rising global average sea level (see Figure SPM-3).

Commentary:
Ira Flatow of Science Friday interviewed one of the authors, Kevin E. Trenberth, in a podcast dated 02 Feb 2007. I have a copy, but can't seem to find the link now on the web.

Scientific American magazine 07 Feb 2007 has a story in the first 00:14:35 of a podcast interview of one of the editors covering the climate change meeting, available at the iTunes web store (free).

Earliest solar observatory in Americas

In the news of late is a claim to the earliest solar observatory in the Americas built around 2,300 years ago in a very arid coastal area in Peru.  A building complex and a line of 13 towers on a mountain ridge were used to observe the sun and mark the passing of time. "It is uncontroversial to postulate direct observations of the annual movement of the rising or setting Sun along the horizon for the purposes of regulating seasonal events such as religious festivals or for maintaining a seasonal calendar. Nonetheless, it is not simple to evaluate the nature of the observations made and the social and ritualistic context within which they operated and derived their relevance."

References:
New York Times report (free registration required)
Listen to the first story on this Science Magazine podcast (free at iTunes store)
News in Science (free)
Ivan Ghezzi and Clive Ruggles in (Science, paid subscription required) pdf

Purple sea urchin sequenced

The purple sea urchin, Strongylocentrotus purpuratus, has been sequenced and is reported on in this week's issue of the journal Science.  The sea urchin as been a model specie for the study of embryology for more than a century.

Despite intense study, the genomic DNA sequence appears to provide valuable new insights regarding this specie. For example, the sea urchin has orthologs of genes for  hearing, balance, vision and chemosensation that are present in vertebrate animals like humans.  Also, the sea urchin contains some genes that were thought to be specific to chordates, that is animals with backbones, something the sea urchin definitely lacks.  Scientists may need to rethink our current notions of perception in light of these findings.

Sea urchins and the lineage on the tree of life leading to modern humans had a most recent common genetic ancestor about 450 million years ago.

Listen:  Skip to 10:27 and listen to 8 minutes of the Science podcast for Nov 10, 2006 that is an  interview with Eric Davidson, Ph.D., of Cal Tech, one of the authors who reports on the complete sequence of the purple sea urchin in the Nov 10, 2006 issue of the journal Science. 

Sean B. Carroll, Ph.D., interviewed

Sean B. Carroll, Ph.D. was interviewed by Ira Flatow on Science Friday, a weekly syndicated radio show carried on many PBS radio stations, but not mine, here in the USA. You can listen to the 24 minute interview as a podcast dated 10/20/2006 posted on the iTunes store (free).  They discuss Carroll's new book The Making of the Fittest: DNA and the Ultimate Forensic Record of Evolution, currently in hardback.  I've not read the book yet, but was intrigued by how taken Ira was with the clear language of the book.

Here is a book review published last week in the scientific journal Nature.

I'm a little behind on listening to Science Friday.  BTW, I don't make any money on this blog by linking to Amazon.com or others.  Links like this are provided as a convenience to the reader.

Honeybee genome sequenced

Last week, The Honeybee Genome Sequencing Consortium published the honeybee genome in the British scientific journal Nature.  The honeybee, Apis millifera, is an important agricultural and ecosystem insect because of its role in flower pollination, and it is a model specie to study social behavior and the co-evolution of insects and plants. 

It seems the honeybee has more genes for odor detection and fewer genes for taste than does the fruit fly, Drosophila melanogaster, another model insect genome that was sequenced back in 1999.  It looks like the honeybee lives by its "nose", so to speak.

With the honeybee sequence in hand, a large number of SNPs (single nucleotide polymorphisms) were used to look at the population relationships of ten subspecies of A. mellifera.  From the Consortium's analysis it appears that A. m. scutellata, better known to us as the African Killer Bee, is much older than our western and northern European Apis millifera millifera bees.  Like humans, it looks like our western honeybees of today have their genetic roots in Africa.  The authors suggest at least two separate migrations of A. mellifera into Eurasia: one into Europe via the Iberian Peninsula that expanded into central Europe and Russia, and one or more migrations into Asia and eastern Europe south of the Alps.

References: Nature News; Nature podcast—skip to time 5:30 and listen to the 4:30 long interview with one of the authors; Editorial in Nature; News and Views in Nature by Edward O. Wilson; The Honeybee Genome Sequencing Consortium, Insights into social insects from the genome of the honeybee Apis mellifera, Nature 443: 931-949 (2006).