Anthropology.net

Both Razib and John Lynch, of Science Blogs, have pulled a fast one on us about an interesting new study published recently in PNAS. The paper is titled, “Hotspots for copy number variation in chimpanzees and humans ” and it comes from some people at ASU’s School of Human Evolution and Social Change. The abstract reads,

“Copy number variation is surprisingly common among humans and can be involved in phenotypic diversity and variable susceptibility to complex diseases, but little is known of the extent of copy number variation in nonhuman primates. We have used two array-based comparative genomic hybridization platforms to identify a total of 355 copy number variants (CNVs) in the genomes of 20 wild-born chimpanzees (Pan troglodytes) and have compared the identified chimpanzee CNVs to known human CNVs from previous studies. Many CNVs were observed in the corresponding regions in both chimpanzees and humans; especially those CNVs of higher frequency. Strikingly, these loci are enriched 20-fold for ancestral segmental duplications, which may facilitate CNV formation through nonallelic homologous recombination mechanisms. Therefore, some of these regions may be unstable “hotspots ” for the genesis of copy number variation, with recurrent duplications and deletions occurring across and within species. “

Which basically means that “hotspots ” are most likely a key feature in the evolution of genetically determined morphology and behavioral characteristics of chimps. Hotspots are places in the genome of an organism that show signs of lots of work, like duplications and deletions. In studying the chimpanzee genome, Perry et. al., has found these hotspots but they call them a super scientific term also known as copy number variants. Here’s what George Perry has to say about his findings,

“We found that chimpanzees have many copy number variants, [actually... ] 355 copy number variants among the genomes of these 20 unrelated chimpanzees… and found that the overall chimpanzee genetic diversity may be more extensive than was previously thought — duplications or deletions of large segments of DNA — in the same regions of the genome as do humans. What this suggests is that some regions of the genomes are inherently unstable in both humans and chimpanzees… This is a relatively new area of research and this is the first time this has been investigated on a genome-wide scale in a population sample of nonhuman primates. These copy number variants may be very significant from an evolutionary perspective, and they’re important to study and understand.

We talk about genetic diseases and cures, but first you have to find out that genetic differences such as copy number variants are there. And then you can study what they’re involved in and what they mean from a morphological variation and disease standpoint.

Ultimately, we can use information about within-a-species variation to identify unusual patterns between species. This may highlight copy number differences between humans and chimpanzees that were somehow involved in the evolution of human-specific traits. This study is an important first step, not the ultimate answer, but an exciting first step in studying the evolution of copy number variant regions and their downstream implications for disease and phenotypic variation. “

I will try to get my grubby hands on the article tomorrow, where I have access potentially to PNAS.

This maybe a little to late to announce, but I just flipped on my PBS channel here in Northern California, after my friend Andrew clued me in, and low and behold there’s a special on that group of siblings who walk on all fours. So far the NOVA special has outlined the origins of bipedalism and is now opening into a discussion on genetic mutation, genes that pattern and diversify the body. If you have a moment, turn it on! I’m sure there will be reruns.

I’ll do some liveblogging on it. The hypothesis, as was mentioned before, is that there’s some sort of genetic mutation that affected their brain development. Clearly they have some neurological disorders. The team comes across some interesting cultural clashes when beginning to study, such as the distaste to evolutionary theory and how these people will be compared against non-human animals. Also, there seems to be some disdain from one of the family members as she goes under the MRI for a brain scan.

The scientists find out the cerebellum, an ‘ancient’ part of the brain that controls movement, balance, and basic bodily functions are damaged in the bipedal siblings. The other quadrupedal siblings are now questioned, as is that hypothesis. They get Svante Paabo to throw some words in there too. After doing some primarily sample collection and testing, no genetic mutations in known brain development genes, such as ASPM were found.

The question whether culture had a role in their development is raised… and whether we can reverse any behavioral traits that the siblings were grown up with. I really appreciated the commentary that much of our behaviors are not genetic, and that our genes interact with environmental cues such as social and physical ones. The mother of the kids describes how the four siblings crawled at a normal age but exhibited a “bear crawl” different from a traditional crawl and never progressed out of the crawl. Could this be due to the mother’s lack of pressure to put her children on twos? Who knows. And at that point the analysis seemed to end.

Rather, some rehabilitation came into play, after the psychologist heading the study begins to become frustrated and overwhelmed with the lack of analysis. So the local physical therapist comes over, does some check ups, and installed some parallel bars and brought a walker for the impoverish family. The children began to use it and around 1 year later, they are progressing exponentially.

The documentary wraps up with a warm and fuzzy take on how humans are adaptable and can overcome some of the most debilitating developmental disorders. In general it was an excellent overview of this problem, and the multiple paths one can go to analyze and fix the problem. I appreciated the heavy emphasis on anthropology of movement and the genetic development of the brain.

Stephen Juan, an anthropologist from the University of Sydney answers Lee Staniforth of Manchester, UK question, “Do humans have a compass in their nose?” He writes about some scientists at California Institute of Technology discovered that humans possess a tiny, shiny crystal of magnetite in the ethmoid bone (pink bone to the image on your right), located between your eyes, just behind the nose… but doesn’t give us any clue as to where the research was published.

In other species of animals, magnetite, a magnetic mineral, is present in homing pigeons, migratory salmon, dolphins, honeybees, and bats. Even some bacteria even contain strands of magnetite that function, according to Charles Walcott of the Cornell Laboratory of Ornithology in Ithaca, New York,

“as tiny compass needles, allowing them [the bacteria] to orient themselves in the earth’s magnetic field and swim down to their happy home in the mud.”

Magnetite helps orientation and direction finding in animals. It no doubtingly helps migratory species migrate successfully by allowing them to draw upon the earth’s magnetic fields. In the case, when it comes to humans, magnetite makes the ethmoid bone sensitive to the earth’s magnetic field and helps one’s sense of direction. Some have even suggested that this “compass” was helpful in human evolution as it made migration and hunting easier.

Again, I don’t have much evidence to support this, other than Juan’s comments but I wonder then does the presence of magentite support the out of africa theory more than multiregional? I would assume the magentite would have to innervate with the bone and wonder if it is closer to the Crista galli (top out cropping on the pink bone on your right)? Also, I wonder if anyone will do or has done a comparative study to see if other primates have it. I hypothesize they don’t because no primate migrates as much as humans. It would be interesting to see if the presence of magentite was an example of independent convergent evolution.

I’d like to share news on how archaeology is growing to use non-traditional tools like Google Earth to find sites. See nearly one year ago, I passed on the news that an Italian man accidentally discovered the outline of an ancient Roman villa while looking at his house on Google Earth. Since then, UNC-Chapel Hill archaeologist Scott Madry has confirmed the free service’s promise as a research tool.

Here’s an excerpt from the news article reporting this all,

Madry looks for things that are difficult to see on the ground, usually from airplanes or in aerial photographs. Altered ground can preserve the outlines of things people built centuries ago.

For 25 years, Madry has scrutinized such details to explore how a Celtic people called the Aedui lived in France for about three centuries starting about 300 B.C. It is hard to find new clues.

After reading about the Italian man’s good luck, Madry got out his laptop, fired up Google Earth and looked over lands in Burgundy near his research area. Google Earth displays that area in particularly good resolution. Immediately he spotted features that, to his trained eye, resembled outlines of Iron Age, Bronze Age, ancient Roman and medieval residences, forts, roads and monuments.

“I’ve spent 25 years in this region of France,” Madry said. “In the whole time, I’ve found a handful of archaeological sites. I found more in the first five, six, seven hours than I’ve found in years of traditional field surveys and aerial archaeology.”

Also, “in all, he recorded 101 possible ancient sites along with their longitudes and latitudes.” This is good news for me, I always like hearing about how technology is being adapted for anthropology.

I’m even more happy to report that Madry has reported his preliminary findings at the international Computer Applications and Quantitative Methods in Archaeology conference this spring. It caught the attention of a lot of other archaeologists as a tool to do preliminary aerial surveying research… It seems especially useful for archaeologists who work in countries where aerial photographs are forbidden or restricted for security reasons are particularly curious. I wonder if we are gonna hear more of archaeological success stories like this with Google Earth?

Madry was encouraged to teach the technique at next spring’s gathering, but I think that’s too far off. It’s not that hard everyone, Google Earth is free and easy to use!

PNAS has released a one-two sucker punch of information regarding Neandertal and human evolution. The first piece of information came from an anatomical and carbon dating reanalysis of ‘early modern humans’ from Pestera Muierii. Erik Trinkaus conducted this research, and here is the DOI link to the paper. The second piece of information comes from Bruce Lahn’s lab at Howard Hughes Medical Institute, and that paper is titled, “Evidence that the adaptive allele of the brain size gene microcephalin introgressed into Homo sapiens from an archaic Homo lineage.” This just came out this week and it supplements the previous anatomical analysis with comparative genomic analysis.

Before I get into the details, as you may know I haven’t yet commented on this all. Instead, I’ve taken a step back, this week or so, to watch everyone blog about it and throw in their two cents, because these two papers really change a lot. I guess you can say it all started in May-July of this year, when Razib commented or rather schooled me on what Bruce Lahn now knows… actually if you trace back all the posts and what not, I must have been oblivious to not see this coming. In my post, I wondered if Lahn had not read Paabo’s PLoS paper, “No Evidence of Neandertal mtDNA Contribution to Early Modern Humans?” Razib told me,

“Lahn knows about the mtDNA work of Paabo, but, he has information about other loci that you do not.”

Since then, one of the crutches behind my argument and pretty much a lot of other people who were taught that Neandertals did not significant contribute to the evolution of modern humans, has been invalidated. mtDNA, the line of evidence to ‘seal the deal’ (at the time), that humans and Neandertals completely diverged roughly 400,000 years ago is now in jeopardy thanks to RPM of evolgen. He shared with us, African-American mitochondrial DNAs often match mtDNAs found in multiple African ethnic groups. I won’t get in the details of this invalidation, but take my word for it… The paper effectively nailed anyone for relying on mtDNA as a single line of evidence to make difinitive conclusions.

The Anatomical Evidence

Okay, so now that I’ve basically established almost everything I knew and have been taught about Neandertals and humans to be wrong, let’s fast forward to 10 days ago. Trinkaus’ and his colleagues, Soficaru and Dobos, published that anatomical reanalysis of the remains from Pester Muierii, that I mentioned above. In the paper they outline that the potential information the fossils from Pestera Muierii could provide has been really neglected in the last 50 or so years since they were dug up. The preliminary dating lead to a lot of confusion, and because of that the ‘fossils have never been integrated into paleoanthropology.’ And because there has been ‘accumulating evidence that… present[s] a variable mosaic of derived modern, archaic human, and Neandertal features,’ Soficaru, et al. turned to the Pestera Muierii fossils since they hadn’t been really analyzed.

First, Soficaru, Dobos, and Trinkaus re-carbon dated the bones. The previous carbon dating that lead to a lot of confusion was flawed because it used a mixture of samples from various bones that were most likely not from the same individual. Instead Soficaru et al. took small samples from each bone. The resulting dates were consistent to be around ~ 30 ka, and lead the authors to conclude they were probably derived from a single phase of occupation of the Pestera Muierii cave.

That being said, the morphology of the Muierii fossils was analyzed. What they had in front of them was a cranium, mandible, scapula, tibia, temporal, and fibula bones… to which they can attribute only three individuals. They made some outstanding conclusions, after comparative anatomical analyis, that these fossils have traits seen in Neandertal and human bones. For example, the occipital bun in Muierii individual 1 is very pronounced, and that is consistent in most Neandertals, and very infrequent in other species. I’ve included an image (figure 1), with an arrow to the bun. And for your own comparative test, follow the advice from this thread, feel the back bottom of your own head. You shouldn’t feel a bump as big as Muierii 1 has, it’s massive there.

Fig. 1.Lateral view of the Muierii 1 cranium. Note the massive occipital bun, identified by the red arrow. (Scale bar: centimeters.)

Muierii 1 also lacks an external occipital protuberance, a little bump seen on the occipital bone. This occipital protuberance is present in the skulls from modern day Asian populations as well as early human ancestors; but all Neandertals (expect two from Asia, not surprisingly) do not have this protuberance. I’ll stop here with the anatomical evidence but let’s recap on the conclusions. Trinkaus and crew re-dated Pestera Muierii fossil remains to fall in the Upper Paleolithic. The remains also show a ‘morphological mosiac’ of traits seen in both Neandertals and Homo sapien fossil specimens. This falls in with conclusions made by Vallois (1958); Trinkaus, et al. (2003); Trinkaus, et al. (2006); Frayer, et al.(in press); Wolpoff, et al. (2006), and Trinkaus (2005).

Now that we have anatomical evidence that establishes an admixture of Homo sapiens features in Neandertal bones, we should be asking, “Did humans and Neandertals get it on?” Bones can only tell us so much, they are merely phenotypes that are heavily variable and affected by environment, lifestyle and life history, as I outlined in bone is a dynamic tissue, remodeling with time and life. The only way to say for sure is to show some sort of recombination of DNA; i.e. some from Neandertals in modern humans… and that’s where I’ll leave you guys off at. I resume the second half of this post on Thursday.

If you think HIV is a nasty virus, then wait to you hear about the “Phoenix virus,” a fossil virus that has been dormant in the human genome. The retrovirus infected hominins for millions of years, and while this isn’t exactly anthropological in nature, this study does help us understand selective pressures of the past that helped us get to where we are now.

Retrovirii work by infecting the host cell with an RNA genome that is reverse transcribed into our own nuclear genome. At which point our cells could manufacture the components of the virus. The image to your right is an electron microscopy picture of how the Phoenix virus, when infecting human cells, forms particles at the cell membrane. Should a population of early human ancestors been seriously inflicted by this virus, then survivors would have a copy however would not have been infected to the point of dying. Offspring could then have a copy of the viral genome within their nuclear genome.

A French team decided to study the Phoenix virus and was led by Thierry Heidmann at the Institut Gustave Roussy. He decided to try to awaken the ancestor of an entire family of HERVs called HERV-K(HML2). And,

“to “correct” for mutations, the researchers took dozens of known HERV-K(HML2) sequences and aligned them to create a so-called “consensus” sequence. Then they converted this information into a complete viral genome.”

He and his team showed that the newly crated virus could infect a variety of human cell lines and replicate. But its infectivity was extremely low, perhaps because human cells have evolved resistance against such viral invaders. Thanks to John Hawks and Boing Boing.