Dear Students!
Our next speaker will be Ed Green from UC Santa Cruz and he will be talking about recent human evolution "as revealed by Neanderthals" !
The paper you need to read for this seminar is called "A Draft Sequence of the Neanderthal Genome" by R.E. Green (and a hundred thousand others) from 2010!
Looking forward!
Julia
I’m not sure where this paper fits in to the overall hypothesis of the class. I feel like I understand the conclusion but I am just having some difficulties with contextualizing it into the class narrative because it is very technical and my understanding is more conceptual. I would really appreciate it if we could just take a moment in class to just kind of assess where we are in the course’s overall trajectory and discuss where we’ve been and where we are going so that I am not so confused!
ReplyDeleteI’m thinking back to the paper that discussed language as pre-dating the split between Neandertals and modern humans. If, as this current paper asserts, Eurasians interbred with Neandertals and Africans did not (or had no detectable gene flow anyways,) does this lead us to believe that there may have been some cultural interchange? What do we know about Neandertal culture that could have affected the development in these other areas? The paper discusses doing more research to look at functional differences, and I’m interested what kinds of differences these might be. Since we are talking about the co-evolution of brain, language, and culture, I’d like to see these get put together because I’m not really sure what the implications are.
Also, I don’t understand what (in reference to HAR positions) an ancestral version and a derived version are. It’s probably a simple concept but I’m unfamiliar so if someone could explain it to me I’d appreciate it as it seems to be important. Thanks!
I think the main question that have about this article is: How exactly is it proving what it's saying? And what are some of the more nuanced conclusions reached by the authors? I mean, I think I understand the conclusions at the end of most of the sections, but I don't think I have ever been so lost when reading a scientific article. What exactly are the methods they're using to determine all of this? Can someone explain them in a language that is more understandable to the uninitiated? Also, what exactly is "gene flow"? Is it just the general flow of gene mutations down a specific lineage? How is that exactly measured?
ReplyDeleteThe paper offers genetic and evolutionary evidence for the phylogenetic relationship between modern humans and Neandertals. While my knowledge in this particular area of research is extremely limited, I have two questions that are hopefully at least on the right track. The first, methodological, question concerns the manner in which the DNA was gathered and tested. For instance, the authors noted that the three test bones were from three different individuals (two most likely related along maternal lines and one non-relative), the Neandertal genes were successfully distinguished from the microbial DNA that took over large parts of the bones in the subsequent years after the three subjects had died, and lab conditions allowed for limited transference of nuclear contamination. With research projects such as the Human Genome Project and several cited studies on developing testing practices in mind, what are some key developments that have allowed us to develop the Neandertal genome project to the level it is currently at?
ReplyDeleteSecond, and a bit more theoretical, are there specific components of this project that would offer support for one side in the debates about gene-centric vs. group-centric accounts of evolution? In other words, the main question in my mind, here, concerns the driving force of evolution, particularly in light of why we are producing models of genomes in the first place. To echo Nick's question in slightly different terms, how could we relate the hypothesis of evo-devo and the rich interplay of genes, brain, body, and world in human development with a genome project in general?
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ReplyDeleteI might have misunderstood but from what I understand I was little confused about some part of the paper.
ReplyDeleteBriefly speaking, are authors arguing that Neandertals are closer to chimpanzee or humans? In page 712, “ In the second strategy, we take advantage of the fact that sites where present-day humans carry a high frequency of a derived allele (not seen in chimpanzee) while Neandertals carry a high frequency of the ancestral allele (matching the chimpanzee) provide information about the extent of contamination. To implement this idea, we identified sites where five present-day humans that we sequenced all differ from the chimpanzee genome by a transversion.” At the end of this paragraph, authors of the paper concluded that “all three measurements of human mtDNA contamination produce estimates of less than 1% contamination. Thus, the vast majority of these data represent bona fide Neandertal DNA sequneces.” When reading only this part, I thought that authors may be arguing that Neandertals are more like chimpanzee because they were certain that their data was less likely to be contaminated. However, in the next page, it is said that “ Neandertals from across a great part of their range in western Eurasia are equally related to present-day humans.” This seemingly contradictory statement made me confused understanding what the authors are arguing.
Also, I would like to hear more about what the finding in this paper that Neandertals are close to non-African than African would imply and what/how this finding would affect the research area of anthropology.
The main thing this article seemed to do was demonstrate that it is possible to extract material from ancient bones in order to model the neandertal genome. It seemed to me that the questions concerning the relationship between modern humans and neandertals was of secondary importance. So I’m wondering first why we chose this article in particular given the course themes.
ReplyDeleteSecond, I’m wondering about sample sizes. Is genetic material extracted from three bones enough provide a base for claims about the neandertal genome in general? Likewise, can you take a DNA sample from one person from Africa and make claims about all people from Africa? To my eye this looks weird, but is this how genetic science works? I guess I need some very basic things explained here.
In this extensive study, one of their findings is a gene flow from Neandertals into modern humans but no reciprocal gene flow from modern humans into Neandertals. Is that right that the time human and Neandertals live together, even though there are people whose father is Neandertalss, but no human exists whose mother is Neandertals? Taken together, why gene flow from modern human into Neandertals had not happened? We can assume that appears of female Neandertals are not sexually attractive at all?
ReplyDeleteI guess I have a methodological question. They mentioned that they were only able to extract about 200 endogenous base pairs from the Neanderthal gene sequence. The filled in the rest of the critical parts of the sequence with the genomes of other organism (if I've understood correctly). My question is: how could they know how to replace the missing sequences? I know that many areas of the genome, especially those HOX genes, remain fairly stable across species. But even so, it must involve conjecture to some degree. I don't think that this is a problem for their work, really; I'm just fascinated by how we might expect to know or predict something like that.
ReplyDeleteMy question is that when the researchers found the bones in the sites, how do they know they were Neandertals rather than ancient chimpanzees or other kinds of animals? Were the chimpanzees genomes used in the paper modern chimpanzees’ genomes?
ReplyDeleteAt the end of the paper, the authors stated that autism is associated with mutations in several genes, so I wonder if autism is more of a nature than a nurture issue?
I found this article interesting. While I agree with some of the earlier post that I need a little more to go on for this notion, it does seem a reasonable assertion. Genetics is a bit like a different language and I need a little more decoding. However, if we did indeed interbreed with Neanderthals at some point, what selection pressures led to such? Also, when did this really take place and for how long? It is interesting that the similarities in the genome that have been found thus far were closer in relation to non-African humans, in particular Eurasian decent, than those of African decent.
ReplyDelete