human origin

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#173 Nov 16, 2013
Centromeres were introduced into the chimp at the positions of the centromeres in the human chromosomes. An additional centromere was introduced in Chromosome 2B (formerly PTR13) at the site of the 30 kb of alpha-satellite. Finally, nine documented/known human inversions (Yunis 1982) were introduced into the ordering as was the fusion of human chromosome 2 from chimpanzee chromosomes 2A and 2B (formerly PTR12 and PTR13).

http://psycnet.apa.org/psycinfo/2005-10982-00...
pan troglodytes
Initial sequence of the chimpanzee genome and comparison with the human genome.

Mikkelsen, Tarjei S.; Hillier, LaDeana W.; Eichler, Evan E.; Zody, Michael C.; Jaffe, David B.; Yang, Shiaw-Pyng; Enard, Wolfgang; Hellmann, Ines; Lindblad-Toh, Kerstin; Altheide, Tasha K.; Archidiacono, Nicoletta; Bork, Peer; Butler, Jonathan; Chang, Jean L.; Cheng, Ze; Chinwalla, Asif T.; de Jong, Pieter; Delehaunty, Kimberley D.; Fronick, Catrina C.; Fulton, Lucinda L.; Gilad, Yoav; Glusman, Gustavo; Gnerre, Sante; Graves, Tina A.; Hayakawa, Toshiyuki; Hayden, Karen E.; Huang, Xiaoqiu; Ji, Hongkai; Kent, W. James; King, Mary-Claire; Kulbokasl II, Edward J.; Lee, Ming K.; Liu, Ge; Lopez-Otin, Carlos; Makova, Kateryna D.; Man, Orna; Mardis, Elaine R.; Mauceli, Evan; Miner, Tracie L.; Nash, William E.; Nelson, Joanne O.; Pääbo, Svante; Patterson, Nick J.; Pohl, Craig S.; Pollard, Katherine S.; Prüfer, Kay; Puente, Xose S.; Reich, David; Rocchi, Mariano; Rosenbloom, Kate; Ruvolo, Maryellen; Richter, Daniel J.; Schaffner, Stephen F.; Smit, Arian F. A.; Smith, Scott M.; Suyama, Mikita; Taylor, James; Torrents, David; Tuzun, Eray; Varki, Ajit; Velasco, Gloria; Ventura, Mario; Wallis, John W.; Wendl, Michael C.; Wilson, Richard K.; Lander, Eric S.; Waterston, Robert H.

Nature, Vol 437(7055), Sep 2005, 69-87. doi: 10.1038/nature04072

Best read together with:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1...
Additional regions that also appear to be hotspots for gene duplication are the sites of lineage-specific chromosomal rearrangements. Among the most evolutionarily dynamic of these is the chromosome 2 (chr 2) fusion region, the site at which two ancestral ape chromosomes fused to produce human chr 2 (IJdo et al. 1991). Only the human genome exhibits this fusion on chr 2, and some of the most extreme lineage-specific copy number expansions we detect appear to have occurred in this region. For example, the largest gene copy number expansion in the Pan lineage (chimp and bonobo) compared to human was found at the chr 2 fusion region and includes copies of the PGM5 gene (Cheng et al. 2005), which also maps to the pericentric region of chr 9 and is involved in synthesis and breakdown of glucose (Edwards et al. 1995).

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#174 Nov 16, 2013
Supplement
http://www.nature.com/nature/journal/v437/n70...

Full text of the comparison pan troglodytes and human genomes.
http://www.nature.com/nature/journal/v437/n70...

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#175 Nov 16, 2013
http://www.sciencedaily.com/releases/1998/09/...

Difference Between Humans And Apes Linked To A Missing Oxygen Atom

Sep. 29, 1998 — The differences between humans and apes are physically and functionally apparent, but genetically humans are extraordinarily similar to apes, especially to the chimpanzee and the bonobo (pygmy chimpanzee).

In a paper published in the September 28 issue of the Proceedings of the National Academy of Sciences, Varki and a team of researchers from UCSD, the San Diego Veterans Affairs Medical Center, the Living Links Center of the Yerkes Primate Center, the Howard Hughes Medical Institute at Emory University, and Baylor College of Medicine describe a missing enzymatic action resulting from a mutated gene in humans that is the basis for the lack of a single oxygen atom in an otherwise identical sialic acid molecule.

In PNAS, the team reports cloning the human and chimpanzee hydroxylase cDNAs, and identifying a mutation in the coding region of the human cDNA that regulates hydroxylase activity. The same gene in apes codes for a hydroxylase enzyme which adds this atom to the sialic acid molecule, but due to a mutation at some point in human evolution, the human gene lacks this coding section, accounting for the structural difference in the molecule.

Similar findings in humans were recently reported by a group of Japanese scientists based at the Tokyo Metropolitan Institute, but Varki's team includes a complete cDNA sequence of both humans and chimpanzees which clearly establishes that the genetic mutation occurred after the lineage leading to modern humans diverged from the common ancestor with the chimpanzee and bonobo.

These findings and their implications are also discussed in the October 1 publication of the American Journal of Physical Anthropology, co-authored by Varki, Elaine Muchmore and Sandra Diaz, all of the UCSD Cancer Center and Cellular and Molecular Medicine program of the University of California, San Diego and the San Diego Veterans Affairs Medical Center.

"It...remains to be seen if this loss of expression of a common gene product can explain any of the major changes that occurred during hominid evolution, and thus any of the morphological and functional differences between humans and great apes," they write in the AJPA paper. "...Apart from altering interactions with extrinsic microbial agents, can the loss of Neu5Gc explain intrinsic differences between humans and the great apes?...(T)he biological situation resulting from the loss of sialic acid hydroxylation may be very complex, and could affect the growth, development and function of multiple systems."

In both papers, the authors urge further comparative work on the biochemical differences between the great apes and humans, in order to better understand the molecular basis for human evolution.

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#176 Nov 16, 2013
Gorilla genome sequenced 2012
What Have We Got in Common With a Gorilla? Insight Into Human Evolution from Gorilla Genome Sequence

Mar. 7, 2012 — Researchers have just completed the genome sequence for the gorilla -- the last genus of the living great apes to have its genome decoded. While confirming that our closest relative is the chimpanzee, the team show that much of the human genome more closely resembles the gorilla than it does the chimpanzee genome.

http://www.sciencedaily.com/releases/2012/06/...
Bonobo Genome Completed: The Final Great Ape to Be Sequenced

June 13, 2012 — In a project led by the Max Planck Institute for Evolutionary Anthropology in Leipzig, an international team of scientists has completed the sequencing and analysis of the genome of the last great ape, the bonobo. Bonobos, which together with chimpanzees are the closest living relatives of humans, are known for their peaceful, playful and sexual behaviour that contrasts with the more aggressive behaviour of chimpanzees. The genome sequence provides insights into the evolutionary relationships between the great apes and may help us to understand the genetic basis of these traits

http://www.sciencedaily.com/articles/h/homini...
Hominidae
The hominids are the members of the biological family Hominidae (the great apes), which includes humans, chimpanzees, gorillas, and orangutans.

Also:
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DNA Demands Chimps Be Grouped In The Human Genus, Say Wayne State Researchers (May 21, 2003)— Proposed changes in the primate order are stirring up evolutionary debate. Humans and chimpanzees should be grouped in the same genus, Homo, according to WSU researchers in a May 19 article (#2172)... > read more

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#177 Nov 16, 2013
http://www.sciencedaily.com/releases/2012/03/...
Gorilla, what do we have in common...Genome sequenced.

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#178 Nov 17, 2013
Some on hominini continued in the start of life, biochemistry and geochemistry.

http://www.topix.com/forum/news/evolution/T9Q...

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#180 Nov 18, 2013
MAAT wrote:
More criticism on ENCODE's too broad a definition of 'function'.
Interesting: some creatonists have claimed 'junk-DNA'to be god.
Plus the strange (to me)dichotomy made between biology and chemistry.(bio-chemistry..hmm! )
Includes a scatching paper.
http://blogs.scientificamerican.com/the-curio...
Hey Maat. Interesting article. I am going to have to save finishing it for later if I want to get through the threads, but thanks for posting the link.

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Jesus probably rode dinosaurs!

#181 Nov 18, 2013
MAAT wrote:
The ability to metabolize alcohol...booze-gene
(That denizovans lack, but that seems to have been a later development.)
http://www.dailymail.co.uk/sciencetech/articl...
It would be interesting to find the actual scientific article.
Maat, I believe this may be the paper.

http://www.ffame.org/pubs/BennerPub12_Carriga...

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#182 Nov 18, 2013
MAAT wrote:
http://www.plosgenetics.org/ar ticle/info%3Adoi%2F10.1371%2Fj ournal.pgen.1003295?utm_source =feedburner&utm_medium=fee d&utm_campaign=Feed%3A+plo sgenetics%2FNewArticles+%28Amb ra+-+Genetics+New+Articles%29
Epigenetics and additive genetic effects.
As in why the 'bad' stuff is still beneficial for the 'good' stuff, as well as to track the latter with greater accuracy.
I have been attending lectures when I can and trying to teach myself epigenetics.

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#183 Nov 19, 2013

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#184 Nov 19, 2013
DanFromSmithville wrote:
<quoted text>I have been attending lectures when I can and trying to teach myself epigenetics.
Bound to be a project of a lifetime given all the developments.
I found keeping handy an up to date Collins dictionary of biology helpfull.

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#185 Nov 19, 2013
DanFromSmithville wrote:
<quoted text>Maat, I believe this may be the paper.
http://www.ffame.org/pubs/BennerPub12_Carriga...
Makes a nice set on methodology with the plos one.

A net dictionary:
http://groups.molbiosci.northwestern.edu/holm...

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Orlando

#186 Nov 19, 2013
Pertinent to this thread, I believe:

http://phys.org/news/2013-11-virus-dna-neande...

Virus DNA first found in Neanderthal genome identified in modern humans
November 19th, 2013 in Biology / Biotechnology

( Phys.org )—An ancient retrovirus that altered the DNA of Neanderthals and Denisovans has now been found to have left alterations in modern human DNA as well—in some cancer patients. The team of researchers from the U.K. that made this startling discovery has written about what they've uncovered in a paper published in the journal Current Biology.

Scientists have known for many years that some viruses can impact not just the general biology of animals (and humans) but can make their way into their genome, causing changes to strands of DNA. Those changes can then be passed on to offspring. To date, no such strands have ever been found to cause ailments in humans, however.

In June of 2012, another team of researchers discovered changes that had come about in Neanderthal and Denisovan DNA due to an ancient retrovirus. The virus left evidence of its existence in a parts of the genome known as "junk" sequences—so named because they don't hold any information related to creating proteins—they don't appear to do anything. That team found 14 unique instances of such virus evidence. Intrigued, the team then looked to see if any of the 14 existed in modern human DNA. Their cursory inspection didn't find any matches.

In this new research, the team in Britain took a much closer look, and in doing so, found 7 matches—but only in cancer patients. More specifically, they took DNA samples from 67 people, all of whom had some form of cancer. In studying the samples, the researchers found that every single one of the cancer patients had seven of the virus sequences that matched those found in Neanderthal and Denisovan DNA last year.

The findings by the team suggest that there might be a link between people with the ancient virus information stored in their junk sequences and a tendency to get cancer. The researchers suggest that because of what they've found, it seems likely that the other seven retroviruses found by the team last year in Neanderthal and Denisovan DNA exist in the genomes of other people alive today. That could mean that such people have a higher incidence of other unknown medical problems. More research will have to be conducted, though the team acknowledges it could take a lot of time as the process could potentially involve examining the genomes of groups of people afflicted with any number of ailments.

More information: Neanderthal and Denisovan retroviruses in modern humans, Current Biology, Volume 23, Issue 22, R994-R995, 18 November 2013. DOI: 10.1016/j.cub.2013.10.028

Abstract
In the June 5th 2012 issue of Current Biology, Agoni et al. reported finding 14 endogenous retrovirus (ERV) loci in the genome sequences of Neanderthal and/or Denisovan fossils (both &#8764;40,000 years old) that are not found in the human reference genome sequence. The authors [1] concluded that these retroviruses were infecting the germline of these archaic hominins at or subsequent to their divergence from modern humans (&#8764;400,000 years ago). However, in our search for unfixed ERVs in the modern human population, we have found most of these loci. We explain this apparent contradiction using population genetic theory and suggest that it illustrates an important phenomenon for the study of transposable elements such as ERVs.

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#188 Nov 19, 2013
http://www.nature.com/nrg/journal/v8/n10/box/...
cont. for comparison
Cancer->RAD 51

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#189 Nov 19, 2013
Similar conclusions were drawn by Adam Eyre-Walker and his colleagues at Sussex University, from statistical analysis of “homeoplasies,” common mutations in mitochondrial proteins that occur in seemingly distinct lineages around the world. Assuming maternal inheritance only of mtDNA, these were thought to be “hypervariable” sites where mutations occurred with high frequency. Review of some European and African mtDNA sequences by Eyre-Walker et al., however, show no evidence that these sites are particularly variable over all lineages. Most of these mutations were found in only a limited geographic area, suggesting they occurred rarely and then spread locally by recombination, which appears a far more likely cause of the homeoplasies.

Such findings, if upheld, seriously complicate the basis of using mtDNA to provide straightforward genetic lines, such as assumed in the Mitochondrial Eve hypothesis. The surprising homogeneity in the mtDNA of modern humans interpreted, in the Mitochondrial Eve hypothesis, as resulting from a recent common ancestor, may simply show the dilution of mutations caused by the recombination of mtDNA.''
---
Sofar they have not been upheld
Though it might be a solution for dating issues.

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#190 Nov 19, 2013
cont. from
http://en.wikipedia.org/wiki/Paternal_mtDNA_t...

http://www.wormbook.org/downloads/textpresso/...
see mitogenetics

The multi-regional hypothesis has its merits; especially in terms of paleoanthropology. However, the main problem with it is that it doesn't adequately explain the modern global distribution pattern of mtDNA lineages.

Haplogroup L3 is the Eurasian Eve, the parent clade to all maternal lineages found today outside of Africa. On its face, this supports an early dispersal model from Africa for anatomically modern humans... unless it can be shown that L3 itself originated outside of the continent. Researchers claim that this hasn't yet been demonstrated. This assumption, however, hinges on the notion that the various L3 samples found today in Europe and Asia stem from relatively recent admixture with L3 carriers from Africa. This may not actually be the case, though. At least some of those clades may instead have been in Eurasia for several thousand years. The actual situation will be made clearer once more old human specimens are sampled for ancient DNA/aDNA. That's what it will all come down to in the end i.e. actual testing.


Multiregionalists raise several points about DNA here:

(a) The reliability of the molecular clock hypothesis (MCH).
(b) mtDNA transmission.
(c) Recombination.

Firstly (a) is challenged by the fact the nature of dating DNA is incredibly complicated by mutation rates. In the 1990's an age around 400,000 years was given for “Eve”. Moving ahead to 2004, Eve became 200,000 years old, while as of today, the figure 100,000 - 150,000 commonly appears in literature. There is no accurate "molecular clock" because mutation rates vary.

Secondly (b) mtDNA transmission may not be strictly from the mother. This may surprise many, but recent papers have shown paternal mtDNA transmission in numerous species, including humans. This is obviously a serious blow to the "Eve" theory, which strictly relies on mtDNA to be maternal and then attempts to date it through a constant mutation rate (which is flawed anyway).

Third (c) random DNA recombination, which can imitate common descent or invent lineages that don't exist. As an example:

''Now such evidence appears to have been found in a mtDNA research project led by Erika Hagelberg on the tiny island of Nguna, in the archipelago of Vanuatu in Melanesia (west of Polynesia including the Solomon Islands and Fiji). Studying human migrations, Hagelberg and her colleagues were analyzing hundreds of people from Papua-New Guinea and Melanesia. MtDNA samples on Nguna Island showed, as expected, three main population groups from colonizations over thousands of years. But in all three there also occurred a single mutation previously only known from one northern European. Hagenberg and her colleagues (1999) think it highly improbable for such a rare mutation event to occur repeatedly in such an isolated location. A more likely explanation would be recombination between different mitochondrial DNA types.

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#194 Nov 19, 2013
One could copy it for googling and remove the break.(full tet and comments by f.i. Svante Paäbo.
or
http://whyevolutionistrue.wordpress.com/2012/...
9 studies have come out on the topic. a.o.:
'Ewen' Callaway Studies Slow the Human DNA Clock NATURE vol. 489 no. 7416 September 20, 2012 page 343
Ann Gibbons Turning Back the Clock: Slowing the Pace of Prehistory SCIENCE vol. 338 no. 6104 October 12, 2012 page 189
Fossils do not equal a correct molecular genetic clock, since change onset happens earlier.(Except for cases where we have enough material.

Commented on, in:
http://dienekes.blogspot.nl/2012/10/ann-gibbo...

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#196 Nov 19, 2013
More magic life and dead tricks with mitochondria:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2...
Adaptation of topoisomerase I paralogs to nuclear and mitochondrial DNA

Ilaria Dalla Rosa,1 Steffi Goffart,2 Melanie Wurm,3 Constanze Wiek,3 Frank Essmann,4 Stefan Sobek,1 Peter Schroeder,5 Hongliang Zhang,6 Jean Krutmann,5 Helmut Hanenberg,3 Klaus Schulze-Osthoff,4 Christian Mielke,1 Yves Pommier,6 Fritz Boege,1,* and Morten O. Christensen1,*

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#197 Nov 19, 2013
hmmm...gorilla's first.

See Discussion
A Model-Based Analysis of GC-Biased Gene Conversion in the Human and Chimpanzee Genomes
John A. Capra , Melissa J. Hubisz , Dennis Kostka,
Katherine S. Pollard , Adam Siepel.

The different time scales associated with crossover-based recombination maps and our predicted gBGC tracts are particularly well illustrated by the region of the chromosome 2 fusion in human (Figure S6). Consistent with its location near a centromere in the human genome, this region displays no elevation of crossover rates in human populations, while the orthologous regions of the chimpanzee genome show elevated crossover rates typical of telomeres. Accordingly, this region exhibits little W&#8594;S DAF skew in human, but a clear skew in chimpanzee. However, the density of predicted gBGC tracts in this region is elevated in both species, only slightly more so in chimpanzee than human, suggesting that this region was telomeric for most of the approximately 6 million years during which human-specific recombination-associated substitutions could have occurred. Thus, our observations indicate that the fusion event is fairly old relative to intraspecies coalescence times but young relative to the human/chimpanzee divergence time. They are qualitatively consistent with Dreszer et al.'s [15] estimate of 0.74 Mya (95% confidence interval: 0–2.81 Mya) for the date of the fusion event and inconsistent with the argument that this event contributed to the initial speciation of humans and chimpanzees [44].

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#198 Nov 19, 2013
Which made me scroll back.
(Melanesians were closer to Denisovans and still different. puzzling.)
Various threads on the mystery hominid.
As well as one on Denisovans pg 3
news:
http://www.topix.com/search/article...

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