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Monday, November 24, 2008

Cryptic Variation and Ice Man

This fortnight’s Current Biology has some interesting articles, two of which caught my attention. First is a “Quick Guide” to cryptic variation, which is genetic variation that goes unnoticed under most circumstances. Also published is the mtDNA sequence of the 5,000 year old Tyrolean Ice Man (a.k.a. Ötzi; this paper actually came out right before Halloween, so I suppose I was too excited about the holiday to write about it then).

First, “cryptic variation.” The authors describe cryptic variation as, “unexpressed, bottled-up genetic potential. … expressed under abnormal conditions such as in a new environment or a different genetic background” (Gibson and Reed 2008). Sounds impossible, because one quickly asks, how can we study ‘cryptic variation’ if it refers to something that is phenotypically unexpressed? But it has been documented in plants and Drosophila, the work-horse-fly of biology. As an example, the authors cite the condition of Antennapedia in Drosophila, in which a mutation causing legs to grow in place of flies’ antennae. When placed into the genomes of different species of Drosophila, this mutation produces different phenotypes. This indicates that variation can be affected by interactions among genes, a phenomenon known as epistasis.

A related phenomenon is ‘canalization,’ which is the evolution of phenotypic ‘buffering’ that prevents variation from arising during development. [For a good synthesis of the concept of canalization, evidence for it, and an application in anthropology, check out Hallgrimsson et al.’s Yearbook paper (Hallgrímsson et al. 2002)] Basically, it seems that enough stabilizing selection can ensure that an individual’s phenotype will develop to a given form in spite of various environmental or internal stresses (i.e. climate and the external environment, or the genetic environment of an organism). This suppression of phenotypic variation can allow ‘cryptic’ genetic variation to accumulate, to be suddenly expressed in a future generation because of certain circumstances. The authors point out that this is possibly problematic because this is not how genes are supposed to work, as far as we know. I think this is an interesting, and potentially very important, avenue of paleoanthropological research, specifically regarding the possibility of hybridization. I’ve written elsewhere, as have others, about the possibility and implications of hybridization on human evolution. Could hybridizing hominin lineages have ‘released’ some type of cryptic variation? An interesting idea, but as always it’s fairly pointless unless it can be tested. And at the moment I cannot think of a way, but I’ll work on it…

In the mean time, researchers have sequenced the mtDNA of the Tyrolean Ice Man. This poor chap, unfortunately for him but fortunately for science, died and ended up in a glacier between Italy and Austria that preserved his soft-tissue very well, some 5000 years ago. What did the study find? Turns out Ice Man’s mtDNA is part of haplogroup K, but has two specific mutations that make his unlike any living mtDNA haplogroup. I seem to remember reading recently about another ancient mtDNA sequence that is unlike anything modern known in modern humans… Oh yes, the 38 ky old Neandertal from Vindija (Green et al. 2008)! If a 5,000 year-old Italian could have belonged to an extinct mtDNA lineage, what does this mean for a similarly ‘extinct’ 38ky old Neandertal? Not a whole lot, but it does underscore how easily mitochondrial lineages can be lost, and it cautions against using the single Neandertal’s mtDNA to argue against their contribution to the modern Homo sapiens gene pool.

Additionally it highlights some of the limitations of genetic studies. Genetic studies like this are limited to the current database of sequences. Ötzi was compared to a sample of some 2000 individuals’ genomes. But there’s always a chance that Ötzi’s ‘extinct’ mitochondrial haplogroup is present but has not yet been sampled. This reminds me of a recent Q&A in Nature entitled, “The pitfalls of tracing your ancestry.” Here, Charmaine Royal of Duke University described issues that arise when people try to trace their ancestry with genetic testing. Here’s what Royal said that has bearing on Otzi, and other ancient genomes:

“The general limitation, I'd say, of all of these tests, is that they can't pinpoint with 100% accuracy who your ancestors may or may not be. Some people are concerned that the biogeographical ancestry test reifies the notion of race. This is the notion that there are four or five parental groups from which we all came and there are discrete boundaries between these groups. But our genetic research has shown that those boundaries don't exist.

In lineage testing, where someone is wanting to know which tribe or region in Africa they came from, the information that's given is based on the present day populations. The names of those groups and those locations have changed over time and so people getting that information about present day Africans and extrapolating to who their pre-middle-passage ancestors may have been — that may not necessarily be accurate. So, those limitations need to be clarified.

Another limitation is that the outcomes of ancestry tests are very much dependent on what is already in a database — who a client's DNA can be matched to. If a database is not comprehensive some potential matches will be missing, and nobody has a complete database. That's a major limitation, probably one of the biggest.”

Royal also discusses some interesting issues of when genome testing goes wrong—that is, when people’s genetic results about their identity don’t conform to what they’d expected, how they identify themselves. The piece does a good job illustrating the complex nature of cultural identity and genetic affinity. In the same vein, paternity testing creates the same issues: how one’s social identity/reality can be ripped asunder by a genetic test. So, while genetics and genomics are incredibly valuable scientific avenues, it’s always fun to point out their limitations and adverse effects. Anyway, paleogenomics and cryptic variation are interesting topics that will hopefully continue to be developed and incorporated into Anthropology in the coming years.

References
Gibson G, and Reed LK. 2008. Cryptic genetic variation. Current Biology 18(21):R989-R990.
Green RE, Malaspinas A-S, Krause J, Briggs AW, Johnson PLF, Uhler C, Meyer M, Good JM, Maricic T, Stenzel U and others. 2008. A Complete Neandertal Mitochondrial Genome Sequence Determined by High-Throughput Sequencing. Cell 134(3):416-426.
Hallgrímsson B, Willmore K, and Hall BK. 2002. Canalization, developmental stability, and morphological integration in primate limbs. American Journal of Physical Anthropology 119(S35):131-158.

Sunday, November 16, 2008

Busidima female pelvis

Yay! A female, mostly complete, Homo erectus pelvis has been found (Simpson et al 2008)! I say “yay” because female pelves are the best way to learn about the effects of birthing on pelvic morphology, despite the numerous studies that claim to glean this knowledge from male pelves (I’m basing this mainly on Neandertal examples as I am admittedly not as well versed with H erectus papers).

Quick summary of the facts: Found in Gona, Ethiopia, BSN49/P27a-d (a.k.a. the Busidima pelvis) consists of both os coxae (hipbones) and the upper part of the sacrum of what has been identified as an adult female Homo erectus dated to 0.9 to 1.4 Ma. The hipbones are mostly complete, except for portions of the ilium missing on both sides and portions of the ischial tuberosities. Overall, the pelvis has been reconstructed so that measurements can be taken (see image below, taken from the Simpson et al 2008 article).


Why I’m excited: Since this fossil is female and has the first complete early Pleistocene pubis, and thus the first complete pelvic inlet, it means legitimate inferences about birthing can be made. The initial paper addresses this by exploring neonate (i.e. infant at birth) head sizes compared to inlet dimensions. The authors found that Busidima would have been capable of birthing infants 30% larger than predicted based on the Homo erectus pelvis KNM-WT 15000 (male subadult). Already this find is showing why making assumptions about birth based on male specimens is flawed! Yay!!

Why I’m concerned: The authors draw conclusions about the width of the trunk based on the bi-iliac breadth. As the picture shows, the ilia are largely reconstructed, making any measurement between the widest points on the iliac crest dubious. I’m not saying it’s a bad reconstruction; in fact it looks reasonable to me. I just believe caution must be used when drawing conclusions based on reconstructed measurements. Especially since I cannot find details on how the ilia were reconstructed (if I’ve missed something in my reading of the online supporting material, please, someone correct me). Given that this is the case, it seems extreme to use incomplete ilia as evidence against an endurance running hypothesis and as evidence for what type of environment this specimen lived in.

What others are saying: Hawks goes into more anatomical detail in his blog post about the article. He discusses questions raised by the study and points out that you really have to read the supporting stuff to get the full picture as the Science article is “superficial”. Beast Ape’s blog post discusses the bi-iliac interpretation and what it means. For a multilingual look, Mundo Neandertal also discusses the article, and based on my imperfect Spanish capabilities, I think they discuss the infant head size findings. Finally, New Scientist describes the findings in a newsy way, detailing the bigger birth canal (compared to WT 15000) and the squat proportions of Busidima. Enjoy!

References:
Simpson et al. 2008 A Female Homo erectus Pelvis from Gona, Ethiopia. Science 322: 1089-1092.

Friday, November 14, 2008

We

I know that this website is predominantly authored by biological anthropologists. But seeing as how I am the oddball, I could not resist a little bit of election-inspired ethnography. If you take a look at this blog: http://countdowntovictory.blogspot.com/ you can see a preview of the reaction that happened at our house (and at all of the houses people at our house called, emailed, texted, shouted to across the rooftops...). It was truly an overwhelming response, and I have never felt such a connection with a political event as I did on November 4th. I would argue that almost everyone in our place got teary eyed (or cried outright) when President-Elect Obama gave his speech following Senator McCain's concession. And I would also argue that for the first time in a long time, or perhaps ever, people of my generation felt connections to the candidates and the electoral process. Why?

I think it's the result of a lot of things. First of all, whether you are happy or not about Obama's win, you probably would admit that our country is in a bad place. I am not just referring to the economy - we are involved in wars abroad, climate change is becoming more and more part of everyone's lives (although arguably it should have always been), and we are seeing the effects of some high tension conflicts in the world at large. Not only that, but there are so many other problems in the world (poverty, agricultural problems, political changes, health problems), and if you put that together with our access to 24 hour news coverage and overexposure to media...well, I'd be scared out of my mind if I were Obama right now. How do you take charge of a sinking ship? How do you steer it back on course? These are the types of staggering questions we had to ask of our candidates this time around. We are in trouble. And while there's always trouble in the world and in the United States, I think the problems we are seeing now are in some ways, unprecedented. With people losing their jobs, food prices rising, and our international conflicts reaching a climax...there was a hope and a fear so thick in the air you could probably have cut it with a knife on election day. I don't mean to single out one day (because there have been almost 2 years leading up to this election, and countless years leading up to all of the problems I have listed), but honestly...it was the day that made the decision. People cast their votes, polls closed, ballots were counted, and in pretty high numbers, this country spoke its mind.

I know that, of course, race is an issue that could not be overlooked in this election.  But in light of the insanely challenging and complex task that lies before him and our whole country, I wonder how this issue factored into the election and how it will play a role in his presidency. What does it mean? And what does it mean to different groups of people in our country and around the world? I have no idea what the answer is to that question, but I can only hope it's positive. Yes we can. Yes we can see past the color of a person's skin. Biological anthropologists these days deny that there is any biological foundation to race. But I don't think this means that "race" does not exist, at least in the minds of most people. For instance, the word is still used in biological anthropology textbooks, it's still on the pages of Newsweek and Time, the New York Times, and it's still something people identify with. What will happen to concepts of race now? Will they change? 

The United States prides itself on being a place where anyone can achieve her/his dreams. Will Barack Obama's presidency give hope to people in this country, something that we need so badly? There is so much riding on the next four years. So much of ourselves that have now been invested in the hopes of change. But Obama reminded us of something in his acceptance speech,  - "This victory does not belong to me, it belongs to you." Even his slogan - Yes we can - reminds us that it is WE who have to make change happen. Yes, we need to have someone in office who is intelligent, visionary, and not just competent, but BEYOND competent. But we also need to take this election as a time to reflect on ourselves. It takes two to tango and a nation of people to make things happen. We cannot blindly rely on someone else to do the work for us. Yes, Obama will have to do things that we simply cannot do - make decisions about really important things. But if we remember the president our Founding Fathers (and Mothers) dreamt of, it was not a king. Not someone who made all the decisions, and certainly not someone who is, on his (or her, one day) own, going to fix cure all the diseases of an ailing nation. 

Regardless of who you voted for, it is time to now stand together as one, with common goals of fixing the real problems in our country.  But I think we have to also remember we are not "one nation," we are members of a global community that is screaming out for justice. We can no longer live in a bubble and leave the problems for someone else to solve, someone older or wiser, or simply put - someone else. Our generation is going to be running this country one day, and we have to realize that it is WE who can change the world. WE who can take action. Because one day, President Obama will be a memory. But we'll still be here. What then?

Tuesday, November 4, 2008

Election Day is TODAY

That's right, and what do you have to do? THIS:

VOTE ON NOVEMBER 4th. I don't care who you vote for, just do it.

There are so many disenfranchised people around the world, and we have the privilege to vote. 
So get up, get in your car, get on your bike, put on your walking shoes tomorrow morning and go to your polling place. If you are in MI and don't know where to go: www.michigan.gov/vote and find out!!!!!!

THIS IS A MONUMENTAL ELECTION. You don't want to be the jerk who didn't vote.