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Hans-Peter Uerpmann of the University of Tubingen has lead a team excavating the Jebel Faya site in the United Arab Emirates, right near the Straits of Hormuz. They’ve found 125,000 year old stone tools that look like early modern human tools from East Africa around the same time. They’ve published their findings in today’s Science, under the title, “The Southern Route “Out of Africa”: Evidence for an Early Expansion of Modern Humans into Arabia.”

The current understanding is what we know as anatomically modern humans (AMH) originated in Africa about 250,000 years ago. The oldest Home sapiens, known as H. sapiens idaltu, was found to be 160,000 years old, found at the Middle Awash site in Ethiopia. Then between 80k-100k years ago, modern humans began appearing in the middle east, as remains from sites like the Qafzeh cave in Israel have yielded. Most agree that AMH stayed in Africa and about 140,000 years ago they began migrating out. There was an exception, a colonization remained or failed in Israel about 100,000 years ago.

One of the hand axes from Jebel Faya, UAE (Photograph courtesy Science/AAAS)

These hand axes, pictured above, show a pattern of flaking distinct from that made by Neandertals and also dissimilar to those by ~100,000 year old Israeli tools. They are two sided and very similar to stone tools seen only in early Africa.

What this means is early humans left Africa 20,000 years earlier than thought. Just how did they do it? 130,000 years ago, there was a window of climate change. They figured this out by using luminescence dating to determine the age of sand grains buried with the stone tools. Luminescence dating is a technique that measures naturally occurring radiation stored in the sand. The data showed that 130,000 years ago, the Arabian Peninsula was relatively more warm which caused more rainfall, turning it into a series of lush habitable land. During this period the southern Red Sea’s levels dropped and was only 2.5 miles or 4 km wide. This offered a brief window of time for humans to easily cross the sea and cross the Peninsula to opposing sites like Jebel Faya.

Does this study tell us that modern humans left Africa, into Arabia and out from there? It is most certainly a possibility. However, these axes could be of an abandoned migration like the site in Israel I’ve mentioned. I say that because no genetic clade, be it from mitochondrial, Y-chromosome, or somatic genome, shows an earlier divergence of modern humans from Africa earlier than 60,000 years ago. At the very minimum a find like this tells us humans left Africa a bit sooner than we thought, but does not really tell us that these were the humans that helped seed the Eurasia.

Armitage, S., Jasim, S., Marks, A., Parker, A., Usik, V., & Uerpmann, H. (2011). The Southern Route “Out of Africa”: Evidence for an Early Expansion of Modern Humans into Arabia Science, 331 (6016), 453-456 DOI: 10.1126/science.1199113

The Phoenician Alphabet

The Phoenician civilization is understood to be the dominant maritime trading culture between the period of 1550 BC to 300 BC. While they were based out of the Levant, their city-states were spread all across the Mediterranean. The golden age of Phoenician culture and seapower is usually placed around 1200–800 BC. When Cyrus the Great conquered Phoenicia in 539 BC, he divided the Phoenicians into four vassal kingdoms by the Persians: Sidon, Tyre, Arwad, and Byblos. Each flourished, building fleets for the Persians against the Greeks. But their autonomy as distinctly Phoenician people declined after this. The lasting and most important cultural legacy of Phoenicians on modernity is their alphabet. It is generally thought that their alphabet is the ancestor of most modern alphabets.

Okay enough of a history lesson, a team of researchers developed a set of algorithms to detect the subtle genetic impact of historical population migrations. They’ve tested out their formulas on 1,330 men in hopes that they’ll be able reveal the genetic legacy of the Phoenicians. Specifically, they have made a new set of tests that seek out patterns in genetic signatures of modern men. They’ve published their research in the the American Journal of Human Genetics under the title, “Identifying Genetic Traces of Historical Expansions: Phoenician Footprints in the Mediterranean.”

The team sampled Y chromosomes of men from historic Phoenician trading centers in the Mediterranean regions of Syria, Palestine, Tunisia, Morocco, Cyprus, and Malta. After genotyping them, they compared them on 11 STRs and 58 Y-SNPs markers. They weeded out background variation from previous Neolithic migrations, and singled out more widespread Greek colonization events from isolated Phoenician expansions, such as the Phoenician colonization of Tunisia.

The Phoenician Genetic Footprint In the Mediterrenean

The authors were able to detect a half dozen haplotypes and they call them Phoenician Colonization Signals (PCS). PCS3+ is calculated to be the strongest Phoenician-colonization candidate. It is tightly associated with the SNP haplogroup E3b, but it does not show the wide geographic coverage that the other PCS+s demonstrate. Both PCS1+ and PCS2+ score well, although not as strongly as PCS3+. The excess of haplogroup J2, and PC1+ to PS3+ in coastal Tunisia, the site of Carthage, compared to inland Tunisian populations is exceptionally significant, and suggests that the Roman destruction of Carthage did not eliminate the Carthaginian gene pool. So the presence of these seven related genetic lineages in places around the Mediterranean Sea, tell us that where Phoenicians had lived and persisted genetically.

These lineages suggest that the Phoenicians contributed their genes to at least six percent of modern populations of historic Phoenician trading outposts. In fact, one boy in each school class from Cyprus to Tunis may be a direct male-line descendant of the Phoenician traders.

Of course, since this is only a Y-chromosome test, we’re only getting part of the genealogical history. If a Phoenician man fathers only daughters, his Y-chromosome lineage dies out. That means tests likes these can only say something when there’s an unbroken male line in that area. It is certainly possible that more people from Cyprus to Tunis have a Phoenician heritage. Dienekes, a Greek, has a scathing criticism of the paper. This paper explicitly says they didn’t try to seek out Greek expansion but Dienekes outlines six shortcomings, related to Greek expansions, that the paper didn’t factor that would affect these conclusions — he ends his post saying,

“Is there anything of value in this paper? Well, it’s a good idea to try to correlate Y-chromosome distribution with historical rather than pre-historical events. Too bad the authors botched the job, but their paper can at least serve as a reference point for how not to go about doing it.”

Pierre A. Zalloua, Daniel E. Platt, Mirvat El Sibai, Jade Khalife, Nadine Makhoul, Marc Haber, Yali Xue, Hassan Izaabel, Elena Bosch, Susan M. Adams, Eduardo Arroyo, Ana María López-Parra, Mercedes Aler, Antònia Picornell, Misericordia Ramon, Mark A. Jobling, David Comas, Jaume Bertranpetit, R. Spencer Wells, Chris Tyler-Smith, The Genographic Consortium (2008) American Journal of Human Genetics. DOI: 10.1016/j.ajhg.2008.10.012

The other day Dienekes pointed out a paper on ancestral human population dynamics within Africa before the out of Africa migrations. The paper is very similar to one I reviewed in April, which also focuses on the diversity of the mitochondrial haplogroup L — one of the oldest mtDNA haplogroups out there.

The new paper, “Bayesian coalescent inference of major human mitochondrial DNA haplogroup expansions in Africa,” published in the Proceedings of the Royal Society B, uses coalescent theory to investigate past population sizes of each of the four major African mtDNA haplogroups (L0-L3). 224 different mitochondrial genomes were analyzed and the comparison yielded some similar results to the previous paper I mentioned. But remember, the last paper investigated the time of the emergence of each haplogroup. This paper focuses on effective population sizes.

Anyways, for starters, the results show that three distinct demographic histories can be seen from the underlying the four haplogroups. Two of the oldest haplogroups, L0 and L1, show exponential growth from 213,000 to 156,000 years ago. The previous paper suggested that the L0 and L1 split about 200,000 years ago. Soon after this split, one of the the paleoafrican branches L0 established what we now consider sub-Saharan Khoisan peoples.

L1 split up into the L2 and L3 branches sometime around 127,000 to 72,000 years ago, again consistent with the previous paper. The L2 and L3 branches show two exponential growth periods, one around 86,000 to 61,000 years ago and another around 20,000 to 12,000 years ago. The authors observed a distinct expansion of the L3 branch around 12,000 to 8,000 years ago. They suggest that,

“L3 did not simply spill over into Eurasia, but was driven as part of an expansion that had begun in sub-Saharan Africa thousands of years earlier.”

While this date is a bit later than the one suggested in the previous paper, both indicate that there were deep African migrations within Africa. The later expansions of L2 and L3, coincide with environmental and cultural changes, such as the greening of the Sahara and emergence of pastoralism. The authors write that,

“The timing of the L3 expansion-8-12kyr prior to the emergence of the first non-African mtDNA lineages-together with high L3 diversity in eastern Africa, strongly supports the proposal that the human exodus from Africa and subsequent colonization of the globe was prefaced by a major expansion within Africa, perhaps driven by some form of cultural innovation.”

Quentin D. Atkinson, Russell D. Gray, Alexei J. Drummond (2008). Bayesian coalescent inference of major human mitochondrial DNA haplogroup expansions in Africa Proceedings of the Royal Society B: Biological Sciences, -1 (-1), -1–1 DOI: 10.1098/rspb.2008.0785

The Sahul is the Australia-New Guinea continent, which is exposed during glacial maximums. If one were to take a satellite photograph of the Sahul during an ice age, you’d see more or less a complete island in the picture, one that spans from New Guinea to Australia and Tasmania. Kind of like the one to your right. Understanding the peopling of the Sahul is critical to understand human migrations and the peopling of Australia.

In the late ’70′s to the late ’80′s, most archaeologists thought that the Sahul was occupied by Late Pleistocene humans, somewhere around 45,000 years ago. A bit of a shake-up spurred about the exact timing of the occupation when older sites like the Devil’s Lair, Lake Mungo, Nauwalabila, Malakunanja, and Huon Peninsula were discovered.

Predictably, two camps emerged. One camp asserted that the Sahul was peopled around 60,000 years ago. The other camp held on the later date, contesting that their dates are based upon more reliable dating techniques, such as radiocarbon, luminescence, and uranium-thorium dating methods. They also contest that 45,000 year old artifacts better resemble the Out of Africa “package” that is represented elsewhere.

A new paper in the Journal of Human Evolution looks at the archaeological “package” from the earlier sites. The authors of the paper compare this archaeological record to the record of other Middle Stone Age sites in Africa, Europe, and Asia. Similar to genes, the displacement of artifacts occurs when new technologies and cultures influence existing ones. It can happen under different tempos — there can be a slow, gradual change of material culture or there can be rapid and punctual changes. There can even a mix of the two. In places like Europe, we see rather fast changes, as pre-existing populations like Neandertals were replaced by humans during the Middle to Upper Paleolithic transition.

To see whether or not the Sahul represents a slower change, Phillip Habgooda and Natalie Franklin have looked at the archaeological record of the Sahul. They’ve published their findings under the title, “The revolution that didn’t arrive: A review of Pleistocene Sahul.” I figure you can extract the main conclusion from this concise title. But I won’t stop there because Habgooda and Franklin have written up a rather thorough study. They specifically timed the rate of change in exchange networks, mining & quarrying, beads, ochre, art, burials, shellfish middens, grindstones, modified bone, and new lithic techniques.

For the section on exchange networks, they review the archaeological record of 20 sites. The trade of exotic materials for symbolic reasons, especially over long-distances, is understood to be a relatively modern behavioral trait. 40,000 years ago, the people who occupied the Sahul were moving shells and other materials long distances — in some cases 300 kilometers and in other cases to places like the little islands in the Bismarck Sea, which is north of Papau New Guinea.

Related to trade networks, mining and quarrying, also represents a modern trait as people specifically sought out certain rocks to fashion into tools and adornments. The record for mining emerges at a much more recent date: around 24,000 years ago. Take note of the discontinuity between these dates, because a rapid displacement of the Sahul should share similar dates among the different parts of the package looked at.

I shouldn’t really need to define why we consider personal adornments like beads, as modern. And in the Sahul, they are seen as 42,000 years ago. But other pieces of adornments, such as this limestone plaque from the Devil’s Lair appear only as early as 25,000 years ago. The role of ochre in art, rituals, and personal hygiene is also looked at. Similar to bead usage, ochre usage is seen as early as 42,000 years ago but not in an artistic and elaborate burial context until 2,000 years later. Complex rock art and symbolic burials are traits of modern humans and for them to not sync up with ochre usage and adornments make me wonder what was going on?

In general, resource exploitation is a modern human trait and by looking at the composition of middens and the number and specialization of grindstones, we can get an idea about when people started to change their lifestyles. In the Sahul, this didn’t start happening until around 30,000 years ago. Again, remember some other modern human traits are seen as early as 42,000 years ago but economic intensification didn’t happen until much later. Furthermore, modified bone tools, a hallmark of modern human behavior, is seen around 22,000 years ago but compound stone tools like adzes are seen as early as 40,000 years ago!

Clearly, this paper shows that the Sahul was gradually influenced by the modern human expansions out of Africa. Parts of the modern human package appear at different sites, separated spatially and temporally. The authors provide us with this poignant summary as well as an image depicting their results,

“Following initial colonization of the continent, terrestrial fauna are the dominant resources exploited, but freshwater shell middens are apparent around the palaeoriver and lake systems of southeast Australia. Long-distance transport and/or exchange networks are evident, as is collection and use of ochre for ritual behaviour (burial) and rock painting. Stone assemblages are dominated by retouched and unretouched flakes, but waisted hatchets are found in Papua New Guinea at this time. By 30,000 years BP, an expansion in resource exploitation may be signified by evidence of marine exploitation on islands off the northern coast of Sahul, the (possible) appearance of grindstones, and the intensive exploitation of macropods in southwest Tasmania. Flake-based stone tool assemblages are augmented by the introduction of ground stone hatchets in northern Australia and small thumbnail scrapers in southwest Tasmania. Personal ornaments in the form of shell beads are also present in northwestern Australia at this time. By 20–18,000 years BP the variety of personal ornaments has expanded to include bone beads, pendants, and notational pieces. Although there is evidence of painting of some form by 40,000 years BP, identifiable art does not appear until around 20,000 years BP. Flint mining is evident at this time, and the flake-based stone tool assemblages are supplemented with bone points made on macropod long bones in the southeast of the continent.”

Modern human behavioral traits in the archaeological record of the Sahul, emerged over a 30,000 year period, even though modern humans clearly had an early influence. The authors consider one possibility may have been that there was not a rapid colonization of the Sahul. I’ve thought about this some and think that differences in population densities and impact of new technologies, i.e. adoption rates amongst ‘stubborn’ populations affect rates of cultural change. Hell, look how long it has taken people to switch from Windows to Macs. ;-) Somethings may not have been useful to early peoples and may have not been taken up as readily, and adopted later under different pressures and considerations. What we can figure out is that what we consider the “package” is not necessarily and all or none indicator of modern human existance.

If you’re interested in understanding the peopling of the Greater Australia area, and wanna know more about Sahul sites, I recommend reading this paper. I got a bit annoyed by the over-usage of “package.” I know even though I used the phrase in similar manner — without directly defining it. But if you mentally replace it with other synonyms that work for you, the paper is much more digestible and chock full of information about the archaeology of early Austrialia, Papau New Guinea and adjacent areas.

P HABGOOD, N FRANKLIN (2008). The revolution that didn’t arrive: A review of Pleistocene Sahul Journal of Human Evolution, 55 (2), 187-222 DOI: 10.1016/j.jhevol.2007.11.006

According to this press release, a new paper reports on the discovery of a 10,000 year old SNP on the Y-chromosomes of men from Tanzania and southern Africa. It will be appearing in PNAS‘ online early edition tomorrow (DOI: 10.1073/pnas.0801184105). The SNP is thought to have originated in eastern Africa,

“The team analyzed Y chromosomes from men in 13 populations in Tanzania in eastern Africa and in the Namibia-Botswana-Angola border region of southern Africa. They discovered a novel mutation shared by some men in both locations, which implied those men had a common ancestor. Further analysis showed the novel mutation arose in eastern Africa about 10,000 years ago and was carried by migration to southern Africa about 2,000 years ago. The mutation was not found in Bantu-speakers, suggesting that a different group – Nilotic-language speakers – first brought herds of animals to southern Africa before the Bantu migration.

This new genetic evidence correlates well with pottery, rock art and animal remains that suggest pastoralists – herders who migrated to new pasture with their flocks – first tended sheep and cattle in southern Africa around 2,000 years ago. The genetic finding also helps explain linguistic similarities between peoples in the two regions.”

You may know that previous research based upon archaeology, skeletal morphology, linguistics and mtDNA has suggested that prehistoric people in eastern and southern Africa were virtually isolated between 30,000 and 1,500 years ago, with only two known migrations between the regions during that time frame. One of the authors of this paper, Brenna Henn, acknowledges this over at the Spitton. She writes,

“Our new genetic study, while still supporting the archaeological record for the timing and place of the origins of pastoralism in sub-Saharan Africa, puts a new twist on the current thinking. It suggests that a small group of men actually migrated into southern Africa about 2,000 years ago. These men probably married into local hunter-gatherer populations, contributing their livestock and cultural knowledge of pastoralism.”

It is coincidental that a regular Anthropology.net commenter, Terry, just posted a comment about last year’s study on the origins of early American chicken because PNAS published a new paper on this topic today. Razib pointed out the link to the new paper, “Indo-European and Asian origins for Chilean and Pacific chickens revealed by mtDNA.” This current study challenges claims of last year’s paper, the one that suggested that chickens were first introduced into South America by way of seafaring Polynesians, before the arrival of Spanish chickens in the 15th century.

After sampling the mtDNA from 41 native Chilean chickens and comparing the sequences to over 1000 modern domestic chickens from around the world, including the previously published sequences from Polynesian and Chilean chicken bones, the researchers concluded that ancient chickens from Easter Island may represent mtDNA signatures (haplotypes 145 and 148) of early Polynesian chicken transport, but ancient Chilean chickens do not. In fact, the pre-Columbian chickens have haplotype 8, which is the single most common chicken haplotype found around the world.

This indicates that pre-Columbian chickens were not exclusive to Polynesian peoples. Alan Cooper, one of the authors of this paper and the director of the University of Adelaide’s Australian Centre for Ancient DNA, said,

“This sequence would undoubtedly have been common in the early Spanish chickens, and therefore provides no evidence of Polynesian contact. So while we can say the [haplotype 8] chicken was popular amongst early Polynesian voyagers, we certainly can’t use it as evidence for trade with South America.”

Gongora, J., Rawlence, N.J., Mobegi, V.A., Jianlin, H., Alcalde, J.A., Matus, J.T., Hanotte, O., Moran, C., Austin, J.J., Ulm, S., Anderson, A.J., Larson, G., Cooper, A. (2008). From the Cover: Indo-European and Asian origins for Chilean and Pacific chickens revealed by mtDNA. Proceedings of the National Academy of Sciences, 105(30), 10308-10313. DOI: 10.1073/pnas.0801991105

Ancient mtDNA from 22 individuals from two sites in Southern Denmark have been isolated, sequenced and analyzed. The two sites are Bøgebjerggård and Skovgaarde. On the map to your right, they are marked as B for Bøgebjerggård and S for Skovgaarde. They date to the Danish Roman Iron-Age period, or approximately 2000 to 1600 years ago. Bøgebjerggård yielded the remains 15 individuals, but only 8 were analyzed in this paper: 4 males, 3 females, and 1 individual whose sex could not be determined. Skovgaarde yielded the remains of 19 individuals, but only 14 were analyzed for this paper:  1 male, 9 females, and 4 individuals whose sex could not be determined.

The report of the ancient mtDNA analysis has been published in the American Journal of Physical Anthropology. In the paper, “Rare mtDNA Haplogroups and Genetic Differences  in Rich and Poor Danish Iron-Age Villages,” I did not read about any discussion of a sterile excavation. It seems as if the remains were removed and curated at the Institute of Forensic Medicine, in the University of Copenhagen for several decades. Owen Lovejoy and other notable phyiscal anthropologists have analyzed the remains to determine sex and the age at death.

The fact that a sterile excavation was not done and at least a half dozen analysts touched the remains, presumably with non-sterile technique, is troublesome for any accurate ancient DNA analysis. One way the authors of this paper compensated was to sample mtDNA from within teeth that were still sitting snug in the alveolus.

DNA isolation and amplification was done in a clean laboratory with the highest grade reagents. The authors mention all the precautions they took to avoid contamination. I would not expect anything otherwise! The products of the PCR were further amplified using Topo TA cloning. I do not know why.

Approximately, 340 bases of the Hyper Variable Region 1 (HVR-1) of the mitochondrial genome was amplified of from 22 individuals. In some cases isolations from three teeth were used per individual, but I can’t tell if they were combined because there was not enough DNA or if they were keep seperately as part of a validation control layer.

Once the sequences were acquired, the authors performed a haplogroup comparison of the samples to a ‘private’ mtDNA database they maintain. There was not a discussion about how robust their private database is and that is very concerning. If their database was relatively small, i.e. not many samples, that would seriously hinder their ability to resolve fine differences. What is just as curious is that there was no discussion about why the authors decided to use their own database! There are large, accurate datasets out there that many people use. The authors could have also compared their sequences to these public datasets to validate their results!

Either way, the big headline find from this sequence comparison is that one individual, a male, from Bøgebjerggård carried the haplogroup R0a in his mitochondrial genome. This haplogroup is rarely found in modern Danish populations and not found in any of the other ancient Danish remains. This haplogroup is, however, found in sporadically in South Eastern Europe populations but predominately found in populations of Arab ancestry — Bedouins in the Arabian Peninsula, Yemenites and Ethiopian Jews, and Somalis.

Ask yourself is this surprising? No it is not. In April we read of archaeological evidence of Middle Eastern coins from the 7th century in Sweden. This indicates people were actively migrating back and forth between the Near East and Northern Europe, exchanging goods and probably exchanging genes.

Does this finding warrant headlines like, “Adolf Hitler’s Aryan theory rubbished by science” appearing in the newspaper the Telegraph? No, it does not. Like I said, this finding isn’t surprising nor does it mean that 1 individual in Iron-Age Denmark throws off the whole genetic composition of an entire population. The overwhelming majority of Danes do not carry this haplogroup. So, the presence of the remains of male with with the haplogroup R in his mtDNA simply suggests he is of Near Eastern descent.

Melchior, L., Gilbert, M., Kivisild, T., Lynnerup, N., Dissing, J. (2008). Rare mtDNA haplogroups and genetic differences in rich and poor Danish Iron-Age villages. American Journal of Physical Anthropology, 135(2), 206-215. DOI: 10.1002/ajpa.20721

Dienekes, Blaine, Razib, and Simon have all chimed in introducing us to a new paper from the American Journal of Human Genetics. It seems like a really interesting one, one that takes mtDNA to construct a phylogeny used to investigate what was happening to early Homo sapiens genetic diversity and populations within Africa. This study focuses on what was going on before the migrations out of Africa. The paper is titled, “The Dawn of Human Matrilineal Diversity,” and is open access. The research has already made it all the way onto some of my favorite news sources, such as Digg and Slashdot, but the big timers like CNN, BBC, the Economist, and the AFP are also carrying word.

The researchers constructed a mitochondrial phylogeny of 624 sub-Saharan individuals. They paid close attention to what’s going on with the phylogeny of the Khoisan, because previous research like Knight et al.‘s study on another loci, the Y-chromosome has shown that the Khoisan are carriers of oldest-diverging Y haplogroup, the Y-haplogroup A, indicating they may represent the deepest clade of modern humans. Recent research identified that the pygmy Khoisan populations share an ancestral and indigenous lineage of mtDNA with a neighboring population, the Bantu and this new study confirmed this.

The phylogenetic tree in this newer study is really informative. I’ve included it to the right. The researchers honed in on the mitochondrial haplogroup L, which is one of the oldest mtDNA haplogroups out there. The tree shows that early humans split into two small groups, demarcated by the L0 branch splitting from the L1’5 branch around 140,000 years ago. Based upon these two branches, the researchers were able to identify that one group was concentrated around eastern Africa (the L1’5 branch), while the other, the Khoisan’s L0 branch, in southern Africa. The sub-branches within the L1’5 clade represent all of the other L haplotypes in the entire remainder of humanity, including haplogroups of those that left Africa… further suggesting east Africa peoples were the main migrators out of Africa.

How could this happen? As populations of early humans migrated within Africa and reached southern Africa, they were cut off from the eastern African populations for a significant period of isolation to diverge into two separate clades. From ScienceDaily,

“Recent paleoclimatological data suggests that Eastern Africa went through a series of massive droughts between 135,000-90,000 years ago. It is possible that this climatological shift contributed to the population splits.”

The press is suggesting that this phenomenon indicated humans “started down the path of evolving into two separate species.” But that’s not true, they missed the part of the paper where populations came back together as a single, pan-African population about 40,000 years ago.

But, something is a little fishy, because as I already indicated, the coalescence calculations in this new paper indicate the Khoisan matrilineal ancestry diverged from the rest of the human mtDNA pool about 140,000 years ago. At that time, the five additional, currently extant maternal lineages (Haplogroups L1’5) existed in Eastern Africa, before the emergence of L0 branch. Looking at the phylogenetic tree, these haplogroups are more ancestral to the haplogroup L0 branch by at around 40,000 years, implying that the Khoisan may not be the deepest clade of living humans alive. This doesn’t match the Y-chromosome data, but we know already that mtDNA and Y-chromosome coalescent times aren’t the same… but this doesn’t match scores of other studies that indicate the Khoisan are a basal group of humans based off of their linguistic and cultural traits.

What this ultimately indicates is that eastern Africa may have truly been the cradle of humanity, at least the maternal cradle of modern humans. Which matches the fossil record, since some of the oldest remains of early human remains are also found in Eastern Africa, such as BOU-VP-16/1 and Omo 1 from Ethiopia.

BEHAR, D., VILLEMS, R., SOODYALL, H., BLUESMITH, J., PEREIRA, L., METSPALU, E., SCOZZARI, R., MAKKAN, H., TZUR, S., COMAS, D. (2008). The Dawn of Human Matrilineal Diversity. The American Journal of Human Genetics DOI: 10.1016/j.ajhg.2008.04.002

KNIGHT, A. (2003). African Y Chromosome and mtDNA Divergence Provides Insight into the History of Click Languages. Current Biology, 13(6), 464-473. DOI: 10.1016/S0960-9822(03)00130-1

Quintana-Murci, L., Quach, H., Harmant, C., Luca, F., Massonnet, B., Patin, E., Sica, L., Mouguiama-Daouda, P., Comas, D., Tzur, S., Balanovsky, O., Kidd, K.K., Kidd, J.R., van der Veen, L., Hombert, J., Gessain, A., Verdu, P., Froment, A., Bahuchet, S., Heyer, E., Dausset, J., Salas, A., Behar, D.M. (2008). Maternal traces of deep common ancestry and asymmetric gene flow between Pygmy hunter-gatherers and Bantu-speaking farmers. Proceedings of the National Academy of Sciences, 105(5), 1596-1601. DOI: 10.1073/pnas.0711467105

National Geographic News has just published an article about the recent symposium in Alaska regarding a possible connection between Yeniseic languages in Siberia and Na-Dene languages in the Americas. John Roach’s article, Siberian, Native American Languages Linked — A First, highlights the recent work of Edward Vajda, who defended his connection during the February symposium. Vajda goes deeper than cognate lists in his parallels, providing several corresponding grammatical systems, particularly verb prefix structure. Ket, his primary Siberian source, is the only living Yeniseic language (which remains highly endangered) and bears some striking grammatical similarities to Navajo. Yeniseic languages have a unique verb prefix system: unique enough that Vajda could not find a corresponding system throughout Northern Asia. Na-Dene was the closest family geographically with a similar system. Johanna Nichols, a groundbreaking Historical Linguist and Linguistic Anthropologist, attended the symposium and made comment. Roach quotes:

With the exception of the Eskimo-Aleut family that straddles the Bering Strait and Aleutian Islands, this is “the first successful demonstration of any connection between a New World language and an Old World language,” Nichols said.

Vajda has not yet published his findings, so the extent of his linguistic claims is not yet clear. However, based on Roach’s summary of his discussion, there are two major points of controversy. First, Roach states that Vajda found “several dozen” cognates. Whether or not the comparative method for linguistic reconstruction was used remains to be seen. Regardless, a cognate list under 50 seems a bit thin to solidify a connection at all, let alone begin reconstruction. Furthermore, the public at this point has no access to the words to assess their status as true cognates. Without a doubt, a consistent and corresponding element of grammatical structure is a strong argument for a common ancestor, but we must consider the systems of linguistic change, particularly sound change (which requires cognates), as a central factor.

A second point of controversy is the matter of depth: how long ago does the proposed connection date back? Vajda makes no direct claims, but states that this would be the oldest known language link if it corresponds to the late Pleistocene migrations evident in the archaeological record. Unfortunately, the field of linguistics currently has no reliable absolute dating techniques, and relative dating such as glottochronology, has been widely discredited. In this case, it seems the lack of cognates would help secure this relationship as an old one. If that were indeed the case, a volume of cognates would become evident in the reconstructions of Proto-Yeniseic and Proto-Na-Dene. Whether or not Vajda has taken this into consideration remains to be seen. At any rate, Nichols is not convinced of a 10,000 year-old connection:

“I don’t think there is any reason to assume the connection is [10,000 years] old … this must surely be one late episode in a much longer and more complicated history of settlement,” she said.

At this point it is very difficult to make any generalizations. Vajda has not yet published his findings, but merely opened the door to discussion on the topic. Until he does, the foundation of our support or criticism is unknown.

Ken Aplin of Australia’s national science agency, the Commonwealth Scientific and Industrial Research Organisation, has been analyzing the mtDNA of 170 black rats from over 76 regions in 32 countries. He’s been doing so to investigate the animals’ genetic links and origins.

As you may know, the humans and rats share precarious symbioses. Actually, come to think of it, it is a misnomer to describe the relationships of rats and humans as symbiotic. It is anything but symbiotic. A more accurate term to define the relationships of humans and rats is as a parasitic relationship, where rats’ association with humans benefit them more than what we get in return.

The close association of rats to human societies have brought about many diseases. One of the more major ones is the black plague. Rats are ultimately a carrier of the primary vector (fleas) that carry the infectious pathogen of the plague, the bacterium Yersinia pestis. Millions of people in Europe died from plague in the Middle Ages, when human homes and places of work were inhabited by flea-infested rats. Since then, outbreaks of the plague still occur, the last urban plague epidemic occurred in Los Angeles in 1924-25. The image to your right documents the most recent distribution of reported plague outbreaks. Unfortunately, it’s from ten years ago.

The plague has been an extremely virulent pathogen. Even though we have strong antibiotics to treat the plague, if untreated people can die within a day or so. You can read more about the molecular biology and virulence of Yersina pestis, in this outstanding freely accessible research paper, Yersinia pestis–etiologic agent of plague.

I’m clearly digressing. Back to Aplin’s results, he and his team identified six lineages that all originated in Asia – in India and the Himalayan region, Thailand, the Mekong Delta of Vietnam, Indonesia…. These six lineages can be traced to four major episodes of global rat expansion, all associated with human migration or trade. See, about 20,000 years ago, one lineage moved from western India to the Middle East and from there to Europe. Apin hypothesizes that this expansion was probably associated with the growth of trade networks during the Neolithic and Bronze Ages . But I think Apin has his dates all mixed up, the Neolithic is thought to have sprung up about 11-8,000 years ago and Bronze Age around 5-4,000 years ago. His work then shows how the European established rat lineage then spread to Africa and the Americas with European explorers. The East Asian lineage, meanwhile, arrived in Micronesia, from Taiwan via Japan, the Philippines and Indonesia, about 3,500 years ago.

I don’t have any fancy diagrams to link you up with, nor do I have an actual paper where Apin describes these conclusions and his methodologies. He’s actually presenting his results at the Archaeological Science Conference at the Australian National University, Canberra this week. His work seems like a basic phylogenetic reconstruction of rat populations based upon mtDNA. Nothing all too novel, but it does give us a unique genetic insight to migrations of humans some 20,000 years ago. Prior to this line of evidence, one of the only ways we could trace human migratory patterns was using the archaeological record — which often doesn’t give as much resolution as the genetic evidence.

I’ve tried to do some sleuthing to see if current literature explains the migrations Aplin’s suggesting. I can’t come up with anything conclusive at this time. If other’s know of papers that document people moving from India to Europe some 20,000 years ago, I’d be interested to know because I’m doing a tangiential study on human skin genetics.

One last thing, this research reminds me of these two papers, “Traces of Human Migrations in Helicobacter pylori Populations,” and “An African origin for the intimate association between humans and Helicobacter pylori,” the latter of which I covered around this time last year. I like how these two studies investigate the genetics of organisms associated with humanity. Often times, human genetics gets muddled up in the complexities of culture and human behavior. These organisms have the potential to provide much more simplified genetics that give a better representation of large scale migrations.