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Author Topic:   Neanderthals and Cro-Magnon
Mammuthus
Member (Idle past 6475 days)
Posts: 3085
From: Munich, Germany
Joined: 08-09-2002


Message 16 of 87 (40734)
05-20-2003 10:12 AM
Reply to: Message 14 by Quetzal
05-20-2003 8:50 AM


Uhhh...thanks for the retina damage Quetzal...he looks like the Abraham Lincoln of the Australopithecines...

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Mammuthus
Member (Idle past 6475 days)
Posts: 3085
From: Munich, Germany
Joined: 08-09-2002


Message 17 of 87 (40741)
05-20-2003 10:42 AM
Reply to: Message 14 by Quetzal
05-20-2003 8:50 AM


{I've taken the liberty to remove the content, which was yet another jab at Salty - Adminnemooseus}
Now, people, how about the real topic?
Adminnemooseus
[This message has been edited by Adminnemooseus, 05-20-2003]

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Mammuthus
Member (Idle past 6475 days)
Posts: 3085
From: Munich, Germany
Joined: 08-09-2002


Message 18 of 87 (40754)
05-20-2003 11:37 AM
Reply to: Message 17 by Mammuthus
05-20-2003 10:42 AM


Okay Moose Okay ...I will attempt to refrain from salty jabs
and swerving back on topic...did not get the entire article but the abstract sounds interesting..will try to order the paper.
this is more along the lines of what Alan Tempelton has argued...it is also great to see someone trying to REDUCE the number of designated species rather than calling every new find a new species
Homo 2003;53(3):201-24 Related Articles, Links
Number of ancestral human species: a molecular perspective.
Curnoe D, Thorne A.
Department of Archaeology and Natural History, Research School of Pacific and Asian Studies, Australian National University, Canberra ACT 0200, Australia. d.curnoe@unsw.edu.au
Despite the remarkable developments in molecular biology over the past three decades, anthropological genetics has had only limited impact on systematics in human evolution. Genetics offers the opportunity to objectively test taxonomies based on morphology and may be used to supplement conventional approaches to hominid systematics. Our analyses, examining chromosomes and 46 estimates of genetic distance, indicate there may have been only around 4 species on the direct line to modern humans and 5 species in total. This contrasts with current taxonomies recognising up to 23 species. The genetic proximity of humans and chimpanzees has been used to suggest these species are congeneric. Our analysis of genetic distances between them is consistent with this proposal. It is time that chimpanzees, living humans and all fossil humans be classified in Homo. The creation of new genera can no longer be a solution to the complexities of fossil morphologies. Published genetic distances between common chimpanzees and bonobos, along with evidence for interbreeding, suggest they should be assigned to a single species. The short distance between humans and chimpanzees also places a strict limit on the number of possible evolutionary 'side branches' that might be recognised on the human lineage. All fossil taxa were genetically very close to each other and likely to have been below congeneric genetic distances seen for many mammals. Our estimates of genetic divergence suggest that periods of around 2 million years are required to produce sufficient genetic distance to represent speciation. Therefore, Neanderthals and so-called H. erectus were genetically so close to contemporary H. sapiens they were unlikely to have been separate species. Thus, it is likely there was only one species of human (H. sapiens) for most of the last 2 million years. We estimate the divergence time of H. sapiens from 16 genetic distances to be around 1.7 Ma which is consistent with evidence for the earliest migration out of Africa. These findings call into question the mitochondrial "African Eve" hypothesis based on a far more recent origin for H. sapiens and show that humans did not go through a bottleneck in their recent evolutionary history. Given the large offset in evolutionary rates of molecules and morphology seen in human evolution, Homo species are likely to be characterised by high levels of morphological variation and low levels of genetic variability. Thus, molecular data suggest the limits for intraspecific morphological variation used by many palaeoanthropologists have been set too low. The role of phenotypic plasticity has been greatly underestimated in human evolution. We call into question the use of mtDNA for studies of human evolution. This DNA is under strong selection, which violates the assumption of selective neutrality. This issue should be addressed by geneticists, including a reassessment of its use for molecular clocks. There is a need for greater cooperation between palaeoanthropologists and anthropological geneticists to better understand human evolution and to bring palaeoanthropology into the mainstream of evolutionary biology.

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 Message 19 by Quetzal, posted 05-20-2003 11:54 AM Mammuthus has replied

  
Quetzal
Member (Idle past 5872 days)
Posts: 3228
Joined: 01-09-2002


Message 19 of 87 (40757)
05-20-2003 11:54 AM
Reply to: Message 18 by Mammuthus
05-20-2003 11:37 AM


This ought to light some fires! Everybody from taxonomists (Pan into Homo), to anthropologists with their favorite subspecies/species, to fundies with the "I ain't related to no monkey". Whee! Fun times were had by all...
I personally always thought that chimps should have been in the same genus as humans, but of course no one ever listens to me...

This message is a reply to:
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 Message 20 by Mammuthus, posted 05-20-2003 12:13 PM Quetzal has not replied
 Message 25 by Andya Primanda, posted 05-21-2003 5:24 AM Quetzal has not replied

  
Mammuthus
Member (Idle past 6475 days)
Posts: 3085
From: Munich, Germany
Joined: 08-09-2002


Message 20 of 87 (40761)
05-20-2003 12:13 PM
Reply to: Message 19 by Quetzal
05-20-2003 11:54 AM


Nobody listens to me either
But more to the topic...todays New Scientist is reporting that a study by Morris Goodman's group (if you are out there SLPx maybe you can confirm this?) suggest that humans are about 99.4% similar to chimps in coding sequences. A recent study by Roy Britten suggested a 5% difference. The discrepancy between the two is that Goodman focused on coding sequences and Britten included non-coding.
Thus Goodman calls for the inclusion of P. troglodytes and P. panicus in the genus Homo with us...
Well, why not..I have met plenty of people who are hairier and less literate than a chimp and they are still Homo
I saw an argument by a poster at internet infidels that I thought was also relevant...he argues it does not matter how you classify other primates..the creationists will turn it around and say ok, chimps descended from humans and represent the fall of man...

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 Message 21 by derwood, posted 05-20-2003 12:21 PM Mammuthus has replied

  
derwood
Member (Idle past 1876 days)
Posts: 1457
Joined: 12-27-2001


Message 21 of 87 (40762)
05-20-2003 12:21 PM
Reply to: Message 20 by Mammuthus
05-20-2003 12:13 PM


ah, yes...
quote:
But more to the topic...todays New Scientist is reporting that a study by Morris Goodman's group (if you are out there SLPx maybe you can confirm this?) suggest that humans are about 99.4% similar to chimps in coding sequences. A recent study by Roy Britten suggested a 5% difference. The discrepancy between the two is that Goodman focused on coding sequences and Britten included non-coding.
Britten also includes the number of estimated sites in insertions and deletions. For example, the 'old way' would count a 100 base deletion as a single difference (since with rare exceptions, such deletions/insertions would have been one-time events). Britten's method would count a 100 base deletion as 100 differences.
So, applying Britten's methoid universally would simply make everything more gentically distant from everything else, and thus not really impact the relative differences at all.
quote:
Thus Goodman calls for the inclusion of P. troglodytes and P. panicus in the genus Homo with us...
He has suggesting this for years, in our 2001 paper, we suggest this.
quote:
Well, why not..I have met plenty of people who are hairier and less literate than a chimp and they are still Homo
I saw an argument by a poster at internet infidels that I thought was also relevant...he argues it does not matter how you classify other primates..the creationists will turn it around and say ok, chimps descended from humans and represent the fall of man...
Interesting.. Creationists say the wackiest things. Like evolution has stopped, or humans were the 'target' of directed evolution...

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Replies to this message:
 Message 22 by Mammuthus, posted 05-20-2003 12:25 PM derwood has replied

  
Mammuthus
Member (Idle past 6475 days)
Posts: 3085
From: Munich, Germany
Joined: 08-09-2002


Message 22 of 87 (40763)
05-20-2003 12:25 PM
Reply to: Message 21 by derwood
05-20-2003 12:21 PM


Re: ah, yes...
quote:
Britten also includes the number of estimated sites in insertions and deletions. For example, the 'old way' would count a 100 base deletion as a single difference (since with rare exceptions, such deletions/insertions would have been one-time events). Britten's method would count a 100 base deletion as 100 differences.
So, applying Britten's methoid universally would simply make everything more gentically distant from everything else, and thus not really impact the relative differences at all.
I don't know how you feel about this but I think this would tend to greatly overestimate differences if every single base difference was counted as a discrete event.
quote:
Interesting.. Creationists say the wackiest things. Like evolution has stopped, or humans were the 'target' of directed evolution...
Or GUToB, non-random mutation, pop gen has nothing to do with evolution, semi-meiosis...the list could become rather substantial

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 Message 23 by derwood, posted 05-20-2003 2:00 PM Mammuthus has replied

  
derwood
Member (Idle past 1876 days)
Posts: 1457
Joined: 12-27-2001


Message 23 of 87 (40767)
05-20-2003 2:00 PM
Reply to: Message 22 by Mammuthus
05-20-2003 12:25 PM


Re: ah, yes...
quote:
I don't know how you feel about this but I think this would tend to greatly overestimate differences if every single base difference was counted as a discrete event.
Indeed, I agree. I think thisd may be why Britten's method has sort of become a non-starter.

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Mammuthus
Member (Idle past 6475 days)
Posts: 3085
From: Munich, Germany
Joined: 08-09-2002


Message 24 of 87 (40863)
05-21-2003 4:33 AM
Reply to: Message 23 by derwood
05-20-2003 2:00 PM


Re: ah, yes...
Hi Scott,
It is a non-starter to a degree but it seems he is making it fashionable
Proc Natl Acad Sci U S A 2003 Apr 15;100(8):4661-5 Related Articles, Links
Majority of divergence between closely related DNA samples is due to indels.
Britten RJ, Rowen L, Williams J, Cameron RA.
California Institute of Technology, 101 Dahlia Avenue, Corona del Mar, CA 92625.
It was recently shown that indels are responsible for more than twice as many unmatched nucleotides as are base substitutions between samples of chimpanzee and human DNA. A larger sample has now been examined and the result is similar. The number of indels is approximately 1/12th of the number of base substitutions and the average length of the indels is 36 nt, including indels up to 10 kb. The ratio (R(u)) of unpaired nucleotides attributable to indels to those attributable to substitutions is 3.0 for this 2 million-nt chimp DNA sample compared with human. There is similar evidence of a large value of R(u) for sea urchins from the polymorphism of a sample of Strongylocentrotus purpuratus DNA (R(u) = 3-4). Other work indicates that similarly, per nucleotide affected, large differences are seen for indels in the DNA polymorphism of the plant Arabidopsis thaliana (R(u) = 51). For the insect Drosophila melanogaster a high value of R(u) (4.5) has been determined. For the nematode Caenorhabditis elegans the polymorphism data are incomplete but high values of R(u) are likely. Comparison of two strains of Escherichia coli O157:H7 shows a preponderance of indels. Because these six examples are from very distant systematic groups the implication is that in general, for alignments of closely related DNA, indels are responsible for many more unmatched nucleotides than are base substitutions. Human genetic evidence suggests that indels are a major source of gene defects, indicating that indels are a significant source of evolutionary change.
I don't per se object to examining non-coding DNA and considering indels, but to simply call every deleted or inserted base a discrete event is way to extreme. Your average provirus can be several kb long so if it is deleted by recombination and chimp has just a solo LTR and humans the entire virus it would be ridiculuos to call every base missing in the chimp a discrete deletion event....oh well, someone will write a paper again revising the numbers down the road.

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Andya Primanda
Inactive Member


Message 25 of 87 (40868)
05-21-2003 5:24 AM
Reply to: Message 19 by Quetzal
05-20-2003 11:54 AM


Q, count me as a taxonomist. The rule of priority demands that an earlier name would be preferred over later names.
Homo troglodytes is older. Methinks it was Big L (Linnaeus) who did it. He's a (respectable) creationist so the cre guys wouldn't mind using his opinion, wouldn't they?
Where can I find this paper on how many human species? The journal's name was... Homo? never heard of it, is it new?
[Currently looking for a postgrad opportunity, preferably in taxonomy, that comes with decent scholarship funds
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Mammuthus
Member (Idle past 6475 days)
Posts: 3085
From: Munich, Germany
Joined: 08-09-2002


Message 26 of 87 (40870)
05-21-2003 5:56 AM
Reply to: Message 25 by Andya Primanda
05-21-2003 5:24 AM


Hi Andya,
Here is a link to the journal Homo containing this article. In long form the journal is the Journal of Comparative Human Biology. It seems you need a subscription to read the articles (which I don't have) but my guess is you can purchase individual articles.
cheers,
M
Elsevier | Ein Unternehmen fr Informationsanalysen | Empowering Knowledge

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Peter
Member (Idle past 1479 days)
Posts: 2161
From: Cambridgeshire, UK.
Joined: 02-05-2002


Message 27 of 87 (41080)
05-23-2003 5:32 AM
Reply to: Message 9 by Quetzal
05-20-2003 7:39 AM


So all the data suggests (depending on how you might
choose to critique it) is that circa 40,000 ya there was
a relatively small 'european' population ????

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 Message 28 by Quetzal, posted 05-23-2003 6:38 AM Peter has replied

  
Quetzal
Member (Idle past 5872 days)
Posts: 3228
Joined: 01-09-2002


Message 28 of 87 (41084)
05-23-2003 6:38 AM
Reply to: Message 27 by Peter
05-23-2003 5:32 AM


Weeelll, I don't know about "all the data". Certainly a number of the references I've read seem to indicate that. As to the discussion of "European" (vs everybody else - and whatever the hell that means), I'm only going by what the authors state:
quote:
Our third-order analysis indicates that the dominant effect in our data is a collapse ca. 40,000 years ago (1,600 generations), consistent with the timing of the initial appearance of anatomically modern humans in Europe. To which population do our results refer? The ethnic composition of the DNA donors of the public human genome is not described, but genotyping of diallelelic, insertion-deletion type polymorphisms mined from the same BAC overlaps (27) suggests that the majority of these sequences represent donors of European origin. Similar patterns resulting in reduction of diversity and extension of linkage disequilibrium in European samples (26, 28-31), and reports of long invariable regions in the human genome (32) have been published. If our results indeed describe European chromosomes, then our estimated time of collapse is in good agreement with expansion time estimates from mitochondrial mismatch distributions.
Which is about all they say on the subject, actually.
Here are the references quoted in the above paragraph, in case you want to look 'em up (some of them are probably on-line):
26. Reich, D. E. , Cargill, M. , Bolk, S. , Ireland, J. , Sabeti, P. C. , Richter, D. J. , Lavery, T. , Kouyoumjian, R. , Farhadian, S. F. , Ward, R. , et al. (2001) Linkage disequilibrium in the human genome Nature 411, 199-204
27. Weber, J. L. , David, D. , Heil, J. , Fan, Y. , Zhao, C. & Marth, G. T. (2002) Human diallelic insertion/deletion polymorphisms Am. J. Hum. Genet. 71, 854-862
28. Kimmel, M. , Chakraborty, R. , King, J. P. , Bamshad, M. , Watkins, W. S. & Jorde, L. B. (1998) Signatures of Population Expansion in Microsatellite Repeat Data Genetics 148, 1921-1930
29. Pereira, L. , Dupanloup, I. , Rosser, Z. H. , Jobling, M. A. & Barbujani, G. (2001) Y-Chromosome Mismatch Distributions in Europe Mol. Biol. Evol. 18, 1259-1271
30. Goldstein, D. B. & Weale, M. E. (2001) Population genomics: linkage disequilibrium holds the key Curr. Biol. 11, R576-R579
31. Gabriel, S. B. , Schaffner, S. F. , Nguyen, H. , Moore, J. M. , Roy, J. , Blumenstiel, B. , Higgins, J. , DeFelice, M. , Lochner, A. , Faggart, M. , et al. (2002) The Structure of Haplotype Blocks in the Human Genome Science 296, 2225-2229
32. Miller, R. D. , Taillon-Miller, P. & Kwok, P. Y. (2001) Regions of low single-nucleotide polymorphism incidence in human and orangutan xq: deserts and recent coalescences Genomics 71, 78-88

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 Message 27 by Peter, posted 05-23-2003 5:32 AM Peter has replied

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Peter
Member (Idle past 1479 days)
Posts: 2161
From: Cambridgeshire, UK.
Joined: 02-05-2002


Message 29 of 87 (41086)
05-23-2003 7:30 AM
Reply to: Message 28 by Quetzal
05-23-2003 6:38 AM


It's at times like this I really miss working at a University
Thanks for the info. though.

This message is a reply to:
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Mammuthus
Member (Idle past 6475 days)
Posts: 3085
From: Munich, Germany
Joined: 08-09-2002


Message 30 of 87 (42151)
06-05-2003 9:12 AM


Ha! Even the guys doing this work admit that it is not very scientific
Nature 423, 468 (2003); doi:10.1038/423468b
Anthropologists cast doubt on human DNA evidence
from the article
quote:
But experts question whether Bertorelle, and others who are attempting similar experiments, can rule out contamination with material from modern humans. "Cro-Magnon DNA is so similar to modern human DNA that there is no way to say whether what has been seen is real," says Svante Pbo, a director at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany.
and
quote:
But such controls cannot definitively rule out contamination of the Cro-Magnon sample. Researchers such as Pbo and Cooper see no way to resolve the issue, and are now increasingly questioning the value of studies such as Bertorelle's. "We know that contamination is almost impossible to avoid," laments Cooper.
What Cooper and Pbo fail to acknowledge is that they (and everyone else) should then question whether their own neandertal work (and that of other groups) is even really science. If you only believe fossil human sequences which look different from modern human sequences are bona fide endogenous DNA and call all modern-like human sequences from fossils suspect contamination..what can you really conclude from this type of work at all? The neandertal crowd were claiming that the differences found in the 3 neandertals sequenced to date indicate that neandertals were not Homo sapiens and did not interbreed. From 3 samples they claim that humans replaced neandertals and the neandertal lineage became extinct. However, according to Paabo and Cooper, if a neandertal is ever extracted that turns out to be very similar to human mtDNA sequences, they will claim it is contamination and unreliable. So, they a priori determine that neandertals were different from modern humans because they only accept different sequences as real...what's the point of doing the experiments in the first place if you pre-determine the answer you will accept?
cheers,
M

Replies to this message:
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