Neanderthals

Hi Ned,
There are also some serious problems with the neandertal work (and with ancient DNA from humans and their relatives in general). First, the neandertal mtDNA gives you absolutely no insight as to what the nuclear DNA composition of neandertals were. We only see the maternal line via mtDNA. This is a technical limitation as nuclear sequences from aDNA are difficult to retrieve and have only been done so reproducibly from mammoths and giant ground sloths.A more serious problem (and one that Svante Paabo and Alan Cooper recently shot themselves in the foot with) is what constitutes an "acceptable" neandertal or cro magnon sequence for example? Paabo made the argument with neandertals but more recently with Cro magnon that if a sequence is retrieved from either and looks modern, there is no way to distinguish it from a modern contaminant. Thus, only divergent sequences are accepted as bona fide neandertal or cro magnon. What the hell kind of science is that then? I know researchers who have pulled out very modern looking sequences from neandertal fossils. The one published Cro magnon sequence is identical (for the portion sequenced) to the first full mtDNA genome published by Anderson and colleagues i.e. plain old normal human mtDNA. These sequences are called into question or outright rejected as valid. So if you can only a priori accept that divergent neandertal or cro magnon (no H. erectus sequence claims have yet been made) sequences are valid the you will a priori determine that they were either a separate species or radically divergent from modern humans...that is just not good science. This was pointed out to Paabo and Cooper by the Italian group that did the Cro magnon sequencing.My overall point is that one should take the claims made by the ancient DNA community and the human evolution community in general with a grain of salt. They argue as badly as creationists sometimes.

That is fine but then when a sequence comes out like the one from Cro magnon the same group screams it is a contaminant, dont accept it. I know almost all of the people who worked on the various neandertals personally. There were some specimens that gave modern looking sequences i.e. non-divergent. They were dropped because they could not be distingished from contamination. How is that science if you exclude any data that does not fit your hypothesis i.e. humans and neandertals or humans and cro magnon were divergent? It does not matter how many times you verify the divergent samples if you exclude samples that give a different result. I am not claiming that the sequences for the neandertals were incorrect, though a few positions have come into question as DNA damage rather than polymorphism. I am questioning whether it is even possible to do the science at all if you cannot distinguish less divergent sequences from contamination...

Hi sfs,
I completely agree with your assessment. And I personally don't care whether multi-regionalism or out of Africa is correct or whether or not neandertals and H. sapiens interbred. But I do object to Paabo and Cooper's attack on the cro magnon work as being a contaminant since it is identical to modern human and their suggestion that only divergent sequences can be accepted. That is just not good science. If it really is a technical limitation then at this current juncture, studies of ancient human remains just should not be done . Otherwise no conclusions about human evolution can be drawn at all. My opinion is that this is exactly the stage aDNA is at....another reason why I work on mammoths and ancient muskoxen...pretty easy to identify human contamination I am also horrible at remembering names unless they are amusing....like the sales rep I met whose last name was Fartmann...

The issue is in distinguishing a sequence that is endogenous to the bone from one or many which come from environmental contamination say, the curator who touched the bone. Over time DNA degrades once the organism is dead so that after thousands of years (if there is any DNA left) there are many times as much DNA in the skin cells you shed doing the experiment than remain in the bone. In addition, the contaminating DNA will always be in better shape than ancient DNA. So, you extract DNA from a neandertal, all controls are clean, and the sequence falls right in the middle of the range of modern human...Paabo and Cooper scream contamination and discount the data. That is what they did with cro magnon which fell exactly in the middle of human mtDNA diversity (well for europe at least). Paabo and Cooper, and others then go on to claim that neandertals were genetidfcally divergent from modern humans and no cro magnon sequences that are acceptable exist. If you cannot accept sequences that look like modern then any "accepted" sequence will a priori have to be divergent and a priori assumes the conclusion that we are different. This is not scientific. Accepting the data that supports your pet hypothesis and ignoring or claiming any data that goes against it is invalid is what creationists do.

Hi Nosy,
As Speel-yi pointed out, your last sentence is what I mean. Samples are rejected if the sequence obtained from them look modern but are accepted if they look divergent. Culling the samples that give results you don't like is not good science...I am not questioning that validity of the published neandertal sequences. There were clearly neandertals that were divergent relative to modern mtDNA sequences. However, we don't really know what ancient human mtDNA diversity looked like and there is evidence that H. sapiens has been subjected to genetic bottlenecks so that our current mtDNA diversity may not be representative of the overall historical diversity. For example, the Mungo Lake sample from Australia which was modern human but a fairly old sample had a very divergent sequence....and guess who showed up to claim it must be a contaminant? Cooper...so if it is too modern like it is a contaminant, if it is to divergent it is a contaminant.I have a real problem with a lot of the human molecular evolutionists because of crap like this...I think one should be extremely sceptical of broad claims about human ancestry based on a couple of sequences from fossils reported by scientific camps that hate each other.

I agree completely though the idea that humans were present earlier than 12 kya is starting to gain support though tentative. There are also south American sites that are really old.I see some of the same logic applied to extinction i.e. mammoths and other Pleistocene megafauna. It is assumed widely that a small number of humans went Rambo and killed every last mammoth, giant sloth, cave bear, sabre-tooth, etc. in about 1000 years, left the buffalo alone and then became relatively ecologically minded native Americans. All this with about a total of 12 confirmed mammoth kill sites in hand as evidence. But it sounds cool to think that it happened this way so it is probably the most accepted idea out there replacing climate change...and ignoring what I am interested in which is the potential for disease to mediate extinction.

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Personally, I don't see why we shouldn't treat the extinction of large mammals when humans were introduced in the same manner that we can look at the virtual extinction of most new-world races with the introduction of Europeans. It wasn't due to a single factor, but instead was due to *many* factors. Westerners brought disease, guns, and competition over resources, to name a few. No one factor brought them down.

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However, to study it we have to be able to isolate factors where we can gather evidence. I for one have worked on (and still have some largely languishing side projects) on looking for pathogens in extinct megafaunal remains. The idea being to do a time series and see if some pathogens appear in megafauna at the same time as humans and their commensals arrive. Given that normal ancient DNA work on megafauna is a royal pain in the ass, you can probably imagine the world of hurt pathogen studies are from such lousy material. But it is still in principle something you can test. The same goes for climate change though there are problems with climate change as a singular cause. Overkill sounds nice but there is very little evidence for it.Sure it is probably a combination of factors. For example, mammoths presumably like other elephantids had a tremendous impact on their envirnoment. In Africa when elephants disappear from a region, the flora changes dramatically. This would open up the area to competition from other animals which could in turn cause the extinction of other species.

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One shouldn't get too comfy with the idea of natives as being "ecologically benign people", and that environmental destruction as being a relatively new concept. The desertification caused by the Anasazi, or the complete deforestation of Easter Island are striking examples of this. Westerners have only caused the extinction of one large mammal species in the New World (although a number of subspecies have been destroyed as well); the extinctions from the Native Americans (albeit, over a much longer period of time) astoundingly dwarf our record on this front.

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One should not get too comfortable with the idea that the early migrants into Asia and across Beringia were able to slaughter everything in a short span of time either. Native Americans would not have to have been particularly peaceful or ecological minded. But it is telling that the end Pleistocene saw the extirpation of about 70% megafauna and then from 10kya on that ratio flipped even though there still were megafaunal species in abundance and the hunting tool kit progressed during that time. I doubt it was because the Native Americans suddenly decided overkill was a bad idea. Given the paltry evidence for overkill I just don't think it is a reasonable scenario as the mitigating factor even though I do think humans hunted megafauna...though I would like to know who would think it is a good idea to eat a mylodon? The have thick ossicles in their skin..probably lousy meat like modern sloths. Also the energy requirments for hunting a mammoth would outweigh the calories you get in return for killing it..though you could make a lot of wigs and impress the neighbors.

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I do, however, think that you underestimate the value to a society of a megafauna kill. I don't have figures for mammoths, but after watching a show about the Donner party and cannibalism, they mention that the average adult male human has about 4.5 lbs of protein, enough for 60 people for one day. Assuming a 180lb human and a 8 ton mammoth, with simply scaling these figures up by body mass, we're looking at about 400 lbs of protein, feeding a whopping 5,400 people for a day (or more realistically, a smaller number for notably longer). Do you have more precise figures (also addressing things like calorie consumption)?

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I do have a book written by Gingerich (read it 7 years ago so have to dig it up) on the subject where he did do a calorie expenditure versus calorie gain calculation based on traditional hunting of African elephants. Also because of the thickness of the skin and the high muscle to fat ratio the meat of an elephant is not as good as other large herbivores. This still does not address the extreme lack of kill sites.

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Also, where did you get that sloth meat is bad? It's eaten in some parts of South America.

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Aside from the fungi that live on Choloepus, I can hardly imagine anyone subsisting on sloth meat..but I could be wrong. In any case, Mylodon, Nothrotheriops to a lesser extent, was full of ossicles throughout the skin and probably not so easy to kill. It is at least not thought that the giant ground sloths were as slow moving and defenseless as tree sloths.

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I would argue that the reason some of North America's large mammals survived is that a steady state was reached before extinction. Early humans were no more migratory than many other predators, especially without horses. If left in a fairly stable environment for long enough, most species tend toward equilibrium. Not only do the buffalo, for example, adapt, but also do the social values of the native tribes. They are selected apon - through natural selection - based on their ability to not kill off all of the food supply in the area.

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This assumes that the immigrants practiced a more non-economical form of subsistance i.e. killing more than you need in the lands they came from. I don't know that there is any evidence for this. That there was social adaptation and adaptive behavior of the animals in North America say, probably also occurred. One other point, the end Pleistocene was anythig but stable. With the mass extinction of predominantly megafauna, both the flora and fauna would have been in transition for some time following their disappearance.cheers,
M

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I really have a tough time with the pathogen hypothesis as well. We see very diverse species all disappearing at the same time. What it's going to take is a species by species evaluation of what happened and then we have to consider what effect each species has on the ecosystem as a whole

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However, this ignores several modern viruses which jump species boundaries and cause mass mortality. The problem we have had in trying to detect viruses in ancient samples is that they are mostly RNA viruses and it is hard enough getting DNA from such samples, RNA is impossible. In any case, if you have populations separated for extended periods of time i.e. North American megafauna, and pathogens then are introduced from another location, mass mortality could ensue and knock the populations down to a level where they cannot recover and then become extinct from other simultaneous pressure such as environment change and novel predators...not much different than the effect of the Spanish bringing european disease to South America except on a much greater times scale with regard to population separation...and as you point out, it would only require that several keystone species become extinct to completely change the environment for other species which could result in extinction of animals that were dependent on the effects of the key species.Note: If you and Rei are interested in discussing extinction in more detail, should I make a separate thread? We are drifting off of the topic but I think the discussion is interesting and am up for it.[This message has been edited by Mammuthus, 10-15-2003]

Great! I will start a topic in the Misc. Topics forum called
Overkill, Overchill, Overill? Megafaunal extinction causes.