Anthropology.net

So far National Geographic and the BBC News are running some amazing archaeological news coming out from Cambodia’s Angkor Wat.

“…Jungle-penetrating radar has revealed traces of vast suburban sprawl surrounding the many temples and the walled central city of Angkor Thom.

Extensive waterworks threaded through the low-density development, channeling the flow of three rivers through agricultural fields, homes, and local temples.

In the end, residents of greater Angkor likely struggled with the ecological consequences of transforming the landscape.

The new survey found breached spillways and canals clogged with silt, suggesting that environmental degradation made the infrastructure increasingly difficult to maintain…

…At more than 3,000 square kilometers (1,160 square miles) it is the largest settlement ever found from the preindustrial world, the authors say.

“The scale is really unlike anything else,” said archaeologist William Saturno of Boston University, noting that it dwarfs the large Mesoamerican cities that are the subject of his own work.”

This should be an interesting read, the largest preindustrial settlement ever found is quite a claim. I can see that. 3,000 sq. km is a lot of area. Damian Evans of the University of Sydney, is the lead author of this finding, and the work will be published in PNAS soon. Until the paper comes out, I’ll leave ya with some other archaeological discoveries made using satellite imagery:

• Archaeology with Google
• Another example of using Google Earth to survey for archaeological sites

The headline making some buzz today, “Gene regulation, not just genes, is what sets humans apart,” isn’t the most Earth shattering of a statement the press is making it out to be. Most biologists and physical anthropologists have been holding, for a long time, the opinion that gene regulation is the key reason as to why humans differentiated from our other primate relatives. So the impact of gene regulation in human evolution, is actually pretty common knowledge… it even came up in a discussion on our other blog, Primatology.net way back in March of this year.

Even though we held these thoughts, the findings behind the headline are still important. Just published in Nature Genetics, the findings confirm what we’ve been thinking of all along. The paper, “Promoter regions of many neural- and nutrition-related genes have experienced positive selection during human evolution,” comes from Ralph Haygood, a post-doctoral fellow in Gregory Wray’s laboratory over at Duke University’s Biology department.

“His group looked at the regulatory sequences immediately adjacent to 6,280 genes on the DNA of chimps, humans and the rhesus macaque, a more distant primate relative that has 88 percent the same genes as humans. These regulatory stretches of DNA are where proteins bind to the genome to initiate a gene’s function. And it is here that evolution has apparently fine-tuned the performance of genes, Wray said, resulting in the dramatic differences in the human brain.

Though many studies have looked for significant differences in the coding regions of genes relating to neural system development and failed to find any, the Duke team believes this is the first study to take a genome-wide look at the evolution of regulatory sequences in different organisms.

Other studies have found significant differences between these species in the coding regions… as far back as 1975 when Mary-Claire King and Allan Wilson first said humans and chimps were 99 percent the same genetically, they had offered the suggestion that greater differences might be found in the regulatory regions.

The type of analysis performed by the Duke team couldn’t be done until the macaque genome was published in 2005 because they needed a third, closely related relative to compare the regulatory sequences…

To do a genome-wide analysis of regulatory regions, Haygood and post-doctoral fellow Olivier Fedrigo had to adapt some of the statistical tools used for genome-wide analysis of coding regions. To be sure their results would be robust, they focused on just the most reliably accurate published DNA sequences in common between the three animals, discarding two-thirds of the genome to ensure accuracy. “With only three species, we had to be very stringent about quality,” Fedrigo said.

The researchers don’t think these findings will be of any help resolving questions about how and when the ancestors of humans and chimps diverged on the tree of life…”

With more and more primate genomes being sequenced, experiments like this comparative genomic study, give us evolutionary insights that we couldn’t make from analyzing fossils, behaviors, and artifacts alone. Sometimes these experiments help identify novel genes, and sometimes they confirm what we’ve been thinking all along. In this case, it was the later. Since most primates share at least 90% of the same genetic sequences, it is in the ways genes are activated, regulated, the patterns of their expression and ultimately how and when they play out throughout development, that drive  forward most differences we see in primates.

Press photos of the Ilert skull and maxilla have come out. The calvaria is very small, as mentioned in the paper and the maxilla is still very fractured.

In light of all the physical anthropology I’ve barraged upon you this last week, balancing it out with some cultural issues seems fitting.

From Kamangir, I found about a new website called Kurdish Rights. The Kurds, as you may know, are an ethic group lodged between Iran, Iraq, Turkey, and some parts of Syria. They are the world’s largest ethnic group without their own country, roughly 30 million people. The Kurds have been struggling for a long time to keep their identity, culture, and lifestyle autonomous. Far too often has this struggle resulted in mass executions, such as Saddam’s ‘Bloody Friday’ in March of 1988. For more information on the Kurds, check out this 7 minute video.

The main stream press hasn’t been giving them a fair shot, ignorantly choosing what the rest of the world considers genocide. And now with Kurdish blogs and sites being blocked by middle eastern ISPs, their voices are even further silenced.

Kurdish Rights, the website I linked above, aims,

“…to prevent Kurdish blogs and sites from being blocked by Middle Eastern ISPs. Throughout our history, Kurds were never given a powerful voice in the mainstream media, and we believe that new technology can effectively change that. However, for that to happen, we first need to allow bloggers and administrators to blog safely and without any censorship.”

Check out this video they made, the music and the message are awesome :

They’ve setup a petition that demands that Internet Service Providers (ISPs) within the Middle East unblock Kurdish blogs and websites in order to ensure the rights to freedom of speech and freedom of information for all Middle Easterners. They will this petition to the send to the Ministries of Information and ISP companies of Turkey, Iran, and Syria once they reach 10,000 signatures.

Knowing how stubborn the governments of Turkey, Iran, and Syria are, I don’t know what good the petitions will do as far as coaxing them to unblock the blogs. If these regimes really gave a rats ass about freedom of speech and information, we wouldn’t being seeing half the problems we see come out of that area of the world. Nonetheless, it is a worthy cause, and I implore you to sign — I can’t rain on the determination this organization has already shown, and I see nothing but good things come out of spreading awareness about the situation of the Kurds.

As far as anthropology goes, the plight of the Kurdish ethnic population is something that will always occupy the cannon. For as long as people try to forcibly wipe out ethnic minorities there will always be those of us that do something to resist.

Afarensis has chimed in on the Ilert fossils, as well as Ann Gibbons of Science. Please check out both their pieces on these two fossils.

To make this a more complete post, I’m also shamelessly plucking a well-illustrated diagram of hominin evolution from Afarensis’ post. I don’t know where he got it from… But, I’m using it to make a point that if anyone ever thought that paleoanthropologists propose that human evolution is entirely anagenetic, then they are wrong.

Of course, one branch of human evolution was ultimately anagenetic — hell, it led to us, H. sapiens! However, as Afarensis mentions, both cladogenesis and anagensis have played a role throughout human evolution. It really is a matter on how narrow you want to view the scope down in on… and at the point it comes down to says H. erectus versus H. habilis, then I consider it futile even foolish to debate one or the other.

Elizabeth Culotta’s news focus on the Liang Bua conference got trapped by my radar as I checked the RSS headlines this morning, but because the gods have not blessed me with easy access to Science, I couldn’t report on the one sentence teaser Science gives us. Thankfully, John Hawks has. A disclosure, since I don’t have the article, what I’ll be sharing with you is a third hand account.

Hawks nails the paedomorphosis theory being brought up by Christoph Zollikofer. For those not in the know, paedomorphosis is biological term for the retention of traits, previously seen only in juveniles, in full grown adult organisms. An example of paedomorphosis is some salamanders retain the gills, which in most amphibians, are lost upon reaching adulthood. Zollikofer suggests that LB 1, what we call the Flores hominin, really is a paedomorphic Homo erectus. Hawks lays down some of the anatomy that tells us otherwise.

Also,

“Morwood is now arguing for descent from early pre-erectine Homo or Australopithecus, while there is some discussion about whether Dmanisi is a plausible ancestor. These are all attempts to minimize the amount of evolutionary change on Flores; I think that is misguided. If the island really generated a highly derived lineage, then let it be highly derived!”

The article seems pretty thorough, even getting into some discussion on the archaeology recovered from Liang Bua. And since it has been a while since we last heard from the great island of Flores and the Liang Bua cave, it is a welcome little news clip.

Earlier today, I shared the news that two of the Leakeys published their Ilert Homo fossil findings in the latest Nature. The paper is out now, under the title, “Implications of new early Homo fossils from Ileret, east of Lake Turkana, Kenya.” Here is the abstract, I’m bolding what I think are the most important parts,

“Sites in eastern Africa have shed light on the emergence and early evolution of the genus Homo. The best known early hominin species, H. habilis and H. erectus, have often been interpreted as time-successive segments of a single anagenetic evolutionary lineage. The case for this was strengthened by the discovery of small early Pleistocene hominin crania from Dmanisi in Georgia that apparently provide evidence of morphological continuity between the two taxa. Here we describe two new cranial fossils from the Koobi Fora Formation, east of Lake Turkana in Kenya, that have bearing on the relationship between species of early Homo. A partial maxilla assigned to H. habilis reliably demonstrates that this species survived until later than previously recognized, making an anagenetic relationship with H. erectus unlikely. The discovery of a particularly small calvaria of H. erectus indicates that this taxon overlapped in size with H. habilis, and may have shown marked sexual dimorphism. The new fossils confirm the distinctiveness of H. habilis and H. erectus, independently of overall cranial size, and suggest that these two early taxa were living broadly sympatrically in the same lake basin for almost half a million years.“

I’ve read the paper and for a two page report on the fossils, they spend a remarkable majority of it making the case that these two fossils indicate the co-occurrence of H. habilis and H. erectus. Instead of describing and documenting the fossils they focus almost entirely on the claim that these two hominins occupied the same evolutionary time frame and ecology.

The two fossils used to make this case are KNM-ER 42700, a hominin calvaria and KNM-ER 42703, a right hominin maxilla fragment that were both found by their team. The photo I put up above are the respective fossils.

The second paragraph is where things become fudged up. The authors begin to justify how they classified each fossil instilling me with some doubt,

“Although [KNM-ER 2700] is closer in overall size to H. habilis we assign [it] to H. erectus.”

It is often smart to cautiously represent one’s work in journals like Nature and to use careful ways to describe what you say, but there’s something about reading that sentence that made me raise an eyebrow. It’s not like that paragraph got any better,

“A multivariate analysis of the calvarial dimensions confirms the affinities of KNM-ER 42700 with H. erectus. Some characteristics often considered diagnostic of this species (for example, a thick cranial vault and supraorbital torus, and strong occipital angulation) are lacking in KNM-ER 42700…”

I don’t get it. KNM-ER 42700 is not the same size as H. erectus nor does it have the characteristic morphology of H. erectus. They even say it themselves. So why the hell is it an erectus? Am I missing something here?

KNM-ER 42703′s classification as H. habilis is flawed too. To classify this maxilla, they get a crazy amount of detail out of these heavily cracked out teeth. I don’t understand how anyone could get measurements out of teeth so damaged. Don’t believe me, click on the photo of the teeth to your right. See how worn down some of the teeth are, like the crowns of the teeth? They even acknowledge that the teeth,

“exhibit heavy occlusal and interpromixmal wear as well as postmortem weathering. Little to no cusp morphology is present.”

Despite this, Spoor et al., decide there is enough measurements to do a principal components analysis (PCA) to determine if KNM-ER 42703 falls as erectine or habiline. A quick side note, PCA is a statistical test used to reduce multidimensional data sets to lower dimensions for analysis.

What gets me, and what should get anyone with an undergraduate education in statistics is, why they did a PCA with only two variables?! If I had to report on the measurements of these molars, I woulda done a bivariate plot if I were them. A bivariate plot graphs the relationship between two variables that have been measured on a single sample of subjects, a much more fitting test than PCA. The fact they used a PCA tells me either they don’t know what sort of tests to run or they specifically used PCA to render their analysis obscure.

I won’t get into the whole sexual dimorphism stuff they touch on. I’m really confused on how their fossils fall into the anti-angenesis camp. When I take their word choice, the quality of the teeth they decided to measure, and the statistical tests they ran, I can’t help but think that they are warping the data and observations to make it work for them. And by no means am I saying that angenesis was the way humans evolved. They could be right… but these two fossils don’t prove it to me.

I read that big study of hominin teeth that I mentioned earlier this week and it has turned out to be a let down. My disappointment lies in their systematics.

Martinón-Torres, et al. carried out both a cladistic and phenetic analysis on a lot of homin teeth, which sounds great at first. It sounds like they really wanted to carry out a thorough analysis.

In general, phenetic systematics aims to determine the relationships of organisms by measuring the amount of similarity, factoring both plesiomorphies or ancestral traits and apomorphies or derived traits equally.

Since plesiomorphies sometimes complicate things, cladisitics does away with them and factors only traits that make a clade unique. These identifying characteristics of a clade are called synapomorphies or shared, derived characters.

Thankfully for hominin teeth, there is the Arizona State University Dental Anthropology System (ASUDAS) which is currently the best determinitation of which plesiomorphic traits were present before the last common ancestor of the species group and which synapomorphic traits were present in the last common ancestor by establishing an outgroup or two. In other words, it is the industry standard.

Figure 2, their cladogram, is the only analysis that shows the European-Asian relationship — their big headliner. So when I flip back to the supplemental materials to see what traits were used in the cladistic analysis and read that they didn’t use ASUDAS defined dental traits, instead they establish their own traits especially for this study by,

“carry[ing] out a rigorous preselection of dental traits searching for those suitable for the cladistic approach and excluding those that are highly homoplasic and variable within a population,”

I begin to wonder what’s going on here?

How can this study be of any effect when they don’t apply to standards others use for their cladogram from homin teeth? What I mean is if one makes up their own system of traits to classify, in this case 9 traits, that haven’t been screened by others before, then getting the unique, interesting results (the whole Eurasian hominin dispersal conclusion) that you were looking for isn’t all too surprising.

Other factors to consider when new unestablished classification systems are used is how does one know that these new traits are or are not genetically correlated? Teeth aren’t the perfect genetic safe-box, as they authors tell us. They are the best phenotype to genetic correlator of any skeletal material that we have to work with as paleontologists. But that doesn’t make them flawless.  Teeth can vary and be modified a lot due to life history like wear.

Razib shares this sentiment,

“I do think it is important to be cautious about translating morphological continuity as clear and present evidence of genetic continuity in any preponderant fashion.”

So I wonder, as W. Henry Gilbert communicated to me,

“What would that say about the [traits] applicability to cladistic analysis?”

John Hawks isn’t completely impressed with this paper either,

“After working through the data supplements for the paper, I think that the analysis is much weaker in statistical power than it could be. In their analysis, they disregard much of the variation within these ancient samples…

The phenogram inexplicably omits Middle and Lower Pleistocene Africans entirely, and considers only australopithecines and habilines as the African sample….

There is no test of gene flow here, just an assertion.”

Could it be possible that Martinón-Torres, et al. setup a unique set of traits to push their Ceprano and Atapuerca hominids closer to the base of all humanity? Their cladogram sure shows it. SH, the nomenclature they used to group Atapuerca, lies awfully closer to H. sapiens in their cladogram that previously accepted. And Manzi, one of the co-authors, has attempted doing just this in the past. I wouldn’t be surprised if that’s the case. So very coy.

Have you been catching the paleoanthropology headliner today?

I sure have.

What I’ve gathered so far is that two of the Leakeys, along with other authors, are anouncing and describing two hominid fossils their team found, KNM-ER 42700 and KNM-ER 42703 from Ileret east of Lake Tukrana, Kenya. The image to your right is the KNM-ER 42700 calvaria. They go on to analyze and make some pretty bold conclusions. Here’s the most ballsy one,

“two ancestral human species seem to have lived cheek-by-jowl in the same area.”

I’ve rounded up links to articles that covers news of this Nature paper… the original paper should be up tomorrow:

• Twin fossil find adds twist to human evolution – News @ Nature.
• Small fossil skull has big implications for modern humans – Noble Intent.
• Fossils Challenge Linear Evolution – New York Times.
• Finds test human origins theory – BBC News.

More:

• Fossils paint new picture of human evolution – Reuters.
• Ancient skull tangles path of human evolution – CBC News.

I’ll have more on this later, in the mean time check out what Eric has to say over at Primate Diaries.

Diversity is a hot topic in anthropology, and is something that is studied culturally, archaeologically, linguistically, and biologically. I’ll be only addressing the latter of the four sub-disciplines of anthropology in this morning’s post, because examining the changes in genetic diversity of humans ultimately affects the other three fields.

The results of a mtDNA study spanning Europeans from five different periods of history, all the way back to 300 AD to the present day, has been published in Biology Letters. The title, “Ancient human mtDNA genotypes from England reveal lost variation over the last millennium,” gives you a clue as to what was concluded, the abstract gives a bit more,

“We analyzed the historical genetic diversity of human populations in Europe at the mtDNA control region for 48 ancient Britons who lived between ca AD 300 and 1000, and compared these with 6320 modern mtDNA genotypes from England and across Europe and the Middle East. We found that the historical sample shows greater genetic diversity than for modern England and other modern populations, indicating the loss of diversity over the last millennium. The pattern of haplotypic diversity was clearly European in the ancient sample, representing each of the modern haplogroups. There was also increased representation of one of the ancient haplotypes in modern populations. We consider these results in the context of possible selection or stochastic processes.”

I’ve bolded what I consider the most informative section.

So, about 1700 years ago, three out of every four individuals belonged to a different haplotype. But now in modern Europe, the number is only one in three.

Why’s that? What are stochastic processes?

Stochastic is a fancy scientific way of saying random. That ultimately trickles down to mean that the loss in genetic diversity is because of a lot of things. Makes sense, a lot has happened in Europe in the last 2,000 or so years. Epidemics like the plague, which decimated populations, are one of the many random processes that narrow down genetic diversity. Other processes, that are more cultural than biological, like wars and genocide, are definitely another factor to consider in loss in genetic diversity.

As I was reading this, this question popped in my head, “Isn’t what the researchers concluded basically what that whole “survival of the fittest” thing does?” Yes and no, selective processes like the plague weeded out people who didn’t have an allele of the gene CCR5, called “delta 32.” And the no, goes back to diversity is itself a survival trait in a population; in other words a population comes close to zeroing in on a single genotype is vulnerable.

Nonetheless, the results are intriguing and a bit Eurocentric. I guess that’s why it got published in a Royal Society journal. I wonder how will the influx of immigrants from the Middle East to Europe shake up the European gene pool? Anyone know of any studies that address the genetic impact of Middle Easterners in Europe?