Article: Giving Voice to Proto-Indo-European

Reconstructing Proto-Indo-European

This is an interesting article on how linguistists are now working to reconstruct Proto-Indo-European not just as written words but actually spoken language.

Genetic Hybrids: Tales of 3 Lost Peoples Who Were Our Ancestors

This post is something I wrote for some friends:

As most of you know, one of my hobbies is my own take on genealogy:  the growing body of literature coming out of genetics studies that tell us about human prehistory.  There lately have been a bunch of new studies that I thought I'd put together for your reading pleasure:

Genetic Hybrids:  Tales of 3 Lost Peoples Who Were Our Ancestors:  New genetic evidence suggests that we modern humans are a hybrid species of sorts.  Most of our genome derives from our Homo sapien ancestors who evolved in Africa.  When the first modern humans left Africa, they encountered two other hominid species:  Neanderthals in western Asia and Europe; and Denisovans in Asia.  The discovery of the Denisovans was only announced in a 2010 paper after geneticists were stunned to find a finger bone and a few teeth -thought to be Neanderthal fossils- actually were a completely different yet related species.  Denisovans are named for the Denisova Cave in which these fossils were discovered.  This cave is in the Altai Mountains in Siberia.

Genetic evidence points to some interbreeding of Homo sapiens with Neanderthals and Denisovans.  2-6% of the DNA of non-Africans today appear to come from Neanderthals.  Indigenous sub-Saharan Africans usually do not show any Neanderthal DNA in their genomes.  It appears Homo sapiens' immune systems benefited from genes from our Neanderthal ancestors.   

One part of the diaspora out of Africa likely spread along the shores of the Indian Ocean from Africa to Arabia -> India -> Indonesia/Melanesia and finally Australia.  This group appears to have encountered the Denisovans because Melanesians have the highest percentage of Denisovan DNA in their genome (up to 6%).  Later settlers into Asia do not show much Denisovan ancestry. So the Denisovans either blended into a larger Homo sapiens population or died out before the next waves of Africans moved into Asia.  A 2013 study now suggests that Homo sapiens encountered the Denisovans not in Asia but in New Guinea or Australia after both groups successfully navigated the Indonesian sea barrier called Wallace's Line.

Finally, last year some geneticists published the results of a study of the DNA of various sub-Saharan African hunter-gatherer populations.  In their analysis they found evidence of an unknown third ancestral hominid who appears to have interbred with Homo sapiens.  Just as most Africans do not have Neanderthal or Denisovan ancestry, this mysterious third hominid species' DNA has so far only been found among these hunter-gatherer peoples in Africa. 

There are no fossil records for this 3rd species.  It doesn't even have a name yet.  One Stanford geneticist argues that the DNA doesn't point to a lost 3rd hominid people but reflects the DNA of our earliest Homo sapien ancestors.  For most African and all non-African humans, mutations have obliterated this original DNA.  So figuring out the answer to this is ongoing.

For Christmas I had my full genome analyzed (some people buy guns or handbags...I buy genetic tests...go figure).  My results came back last week and apparently my genome is 1.6% Neanderthal and an additional 1.6% Denisovan.  I was tickled to have a little bit of the rare Denisovan in me but a bit sad I wasn't more Neanderthal. :(

Some Factoids About Sunflowers

1. A recent genetic study -which I forgot to save- points to the sunflower being domesticated in a river environment in eastern North America.  The probable location is what is today Arkansas.  The new study points to a single site of domestication.  The alternative theories have the sunflower being domesticated in Mexico and spreading north or being domesticated twice:  once in Mexico and once in the eastern US. 

Arkansas' state flower though is the apple blossom. Maybe Arkansas should switch to its homegrown glory, the sunflower!

2. Sunflowers have been shown to absorb radioactive cesium from the soil.  They were planted around Chernobyl and now 10,000s are being planted around Fukashima, Japan.

Article: Dmanisi Skull May Point to Diversity within a Single Species

Unique Skull Find Rebuts Theories On Species Diversity in Early Humans

While not a genetic study, the Lordkipanidze article has an interesting angle to study of the most complete ancient skull of its age, the Dmanisi skull.  The researchers point out that there is considerable diversity to shape to the various skulls found in the cave.  Some have interpreted this as evidence of different hominid species living in the same cave over time, but the researchers in this article find that the Dmanisi skulls have no greater variability than comparing the skulls of a sample of humans living today.

D. Lordkipanidze, M. S. Ponce de Leon, A. Margvelashvili, Y. Rak, G. P. Rightmire, A. Vekua, C. P. E. Zollikofer. A Complete Skull from Dmanisi, Georgia, and the Evolutionary Biology of Early Homo. Science, 2013; 342 (6156): 326 DOI: 10.1126/science.1238484 

A. Margvelashvili, C. P. E. Zollikofer, D. Lordkipanidze, T. Peltomaki, M. S. Ponce de Leon. Tooth wear and dentoalveolar remodeling are key factors of morphological variation in the Dmanisi mandibles. Proceedings of the National Academy of Sciences, 2013; DOI: 10.1073/pnas.1316052110

Article: The Teeth Say the LCA of Modern Humans and Neanderthals Is Farther in the Past

Dental Study Takes Last Common Ancestor of Neanderthals and Homo Sapiens Back to 1 Million Years Ago

No Known Hominin Is Common Ancestor of Neanderthals and Modern Humans, Study Suggests

This study focuses on comparison of hominid teeth rather than genetics.  It argues the last common ancestor of Neanderthals and Homo sapiens lived at a much earlier date than currently postulated -closer to one million years ago.

Aida Gómez-Robles, José María Bermúdez de Castro, Juan-Luis Arsuaga, Eudald Carbonell, and P. David Polly. No known hominin species matches the expected dental morphology of the last common ancestor of Neanderthals and modern humans. PNAS, October 21, 2013 DOI: 10.1073/pnas.1302653110

Article: Using Herpes to Track Human Migrations

Hitchhiking Virus Confirms Saga of Ancient Human Migration

Aaron W. Kolb, Cécile Ané, Curtis R. Brandt. Using HSV-1 Genome Phylogenetics to Track Past Human Migrations. PLoS ONE, 2013; 8 (10): e76267 DOI: 10.1371/journal.pone.0076267

Article and Discussion: Four Key Migratory Events Shape the European Gene Pool

As you all know, I am intrigued by the stories genetics is adding to human history.  The journal Science has a very interesting article that I will summarize and contextualize for folks.

By about 600,000 years ago, the hominid ancestor of Neanderthals leaves Africa and eventually settles Europe.  This ancient relative of modern humans will evolve into Neanderthals.

~40,000 years ago:  The first modern humans, Cro-Magnons, enter Europe -probably via Greece and the Danube Valley.  They encounter Neanderthals, and genetics point to some limited interbreeding.

~30,000 to ~25,000 years ago:  The last full Neanderthals die out.  The last skeleton of Neanderthals found to date is from a cave in Gibraltar.  

~28,000 to ~14,000 years ago:  The last Ice Age drives human and Neanderthal populations south to four refuges in a) Iberia, b) Italy, c) the Balkans, and d) the Ukraine.  A mutation arises in the population living in Iberia.  This mutation gives rise to the Rhesus negative factor in human blood (A-, B-, O-, and AB-).  Today  about 50% of Basque people carry this mutation with the frequency of the mutation dwindling the farther you get from the Pyrenees.  

~8,000 years ago:  agriculture arrives in Europe -again with people moving up the Danube Valley- via farmers immigrating from Turkey (Anatolia) and the Fertile Crescent.  These first European farmers appear genetically to be similar to modern Sardinians, residents of a large, relatively isolated island that is now part of Italy.  The genetics of Ötzi, the Ice Man whose body was found in a glacier on the Austrian-Italian border, places him as belonging to this group of Neolithic farmers.  The T and J mitochondrial haplogroups are also associated with these first farmers.  Note:  Ötzi and I are both in the T haplogroup.

~7,500 years ago:  Among the new Neolithic farmers in the Danube Valley a mutation occurs that will allow most Europeans to have lactose persistence, or the ability to digest dairy products after childhood.  

Now for where the paper starts off:

Geneticists and historians wondered if the first farmers assimilated the original Cro-Magnon hunter-gatherers, killed them off, or diluted their genetic contributions by filling Europe with larger families supported by agriculture. Instead, the researchers -Brandt et al.-  found some really unexpected and fascinating things by comparing modern European populations' DNA with the DNA from skeletons found in central Germany.  These German skeletons cover 4,000 years of history from the first farmers to about 3,500 years ago during the Bronze Age.  What did they find?

a. For 2,000 years after the Neolithic farmers arrived, there appears to have been limited interbreeding between the farmers and the hunter-gatherers.  The farmers appear to have been successful with their numbers steadily growing.  It is interesting to ponder what social mechanisms kept two populations from intermarrying for two millennia.  

b. ~7000 years ago:  About a 1,000 years after the farmers arrived, their overall percentage in the gene pool appears to decline and the hunter-gatherers and their genes make a comeback.  This may have resulted from climate change or disease.  Adapting Near Eastern plants and farming to cooler Europe surely must have entailed crop failures and setbacks.  The rapid spread of the lactose persistence gene points to the importance of dairy.  The ability to digest it conferred survival when those without it starved.  Moreover, most infectious diseases in humans arise from pathogens that jump the species boundary and are more likely to infect people living with livestock.  

c. ~4,800 years ago:  A new migration of people from the Russian steppes arrives.  These people have horses and carts.  They decorate their pottery in a distinctive design giving them the name the Corded Ware people.  They likely are the first proto-Indo-European speakers, and thus are the linguistic ancestors of almost every European language spoken today except Basque, Hungarian and Finnish.

d. ~4,500 years ago:  A fourth migration starts in Portugal around modern Lisbon.  These people, the Bell-Beaker people, work copper and appear to have a culture built around trade.  They make pottery in the shape of wide-lipped, upside-down bells and build megalithic stone monuments.  At first they spread along the Atlantic and Mediterranean coasts.  These first maritime settlements include modern Brittany in northwest France.  From there the traders appear to follow existing, ancient trading routes up the valley of the Seine to the Rhine and then into the heart of Germany.  In Germany the Bell-Beaker traders mix with the a) hunter-gatherers, b) farmers, and c) Indo-European speakers.  They bring with them the H mtDNA haplogroup, the most common maternal lineage in Europe today.

The authors say Europeans' -and European-Americans'- DNA is a more complex story than Neolithic farmers simply replacing Paleolithic hunter-gatherers.  Instead, today's European gene pool appears to be a mix of these four migrations plus a little Neanderthal, Denisovan, and some later additions from outside Europe.

Guido Brandt, Wolfgang Haak, Christina J. Adler, Christina Roth, Anna Szécsényi-Nagy, Sarah Karimnia, Sabine Möller-Rieker, Harald Meller, Robert Ganslmeier, Susanne Friederich, Veit Dresely, Nicole Nicklisch, Joseph K. Pickrell, Frank Sirocko, David Reich, Alan Cooper, Kurt W. Alt, the Genographic Consortium. Ancient DNA Reveals Key Stages in the Formation of Central European Mitochondrial Genetic Diversity. Science, 2013 DOI: 10.1126/science.1241844

Article: Was There a Paleolithic Population Boom?

Genetic Study Pushes Back Timeline for First Significant Human Population Expansion

This article discusses some recent genetic research that argues the Homo sapien population expanded rapidly during the Paleolithic 60,000-80,000 years ago.  In those areas that saw the most expansion, a second Neolithic expansion occurred more robustly about 10,000 years ago with the invention of agriculture.

Article: Denisovans East of Wallace's Line?

Did Homo sapiens encounter the mysterious Denisovans east of Wallace's Line?

Mysterious Ancient Human Crossed Wallace's Line

Wallace's Line represents a water boundary separating the southeast Asian part of Indonesia from the western part of the Indonesian archipelago, New Guinea, and Australia.  The above Science Daily article summarizes the work of Cooper and Stringer who argue that early modern humans -Homo sapiens- met and interbred with Denisovans, a related hominid species, east of Wallace's Line.  Having the interbreeding take place in this area would help explain why Denisovan DNA is found in the highest concentrations among the aboriginal peoples of New Guinea and Australia, but it would also mean the Denisovans also managed to cross the watery Wallace's Line and thus likely had boats.

One intriguing remark in this article is the statement that it appears Denisovan males mated with Homo sapien females.  Were there no Homo sapien males mating with Denisovan females?  

A. Cooper, C. B. Stringer. Did the Denisovans Cross Wallace's Line? Science, 2013; 342 (6156): 321 DOI:10.1126/science.1244869

Welcome!

Welcome to my blog on human genetics and prehistory.  I use this blog as a way to collect and share my interest in how genetics is opening a doorway into human migrations and geography.