Many links for the past articles of your blog are broken. I want to read the articles. Can you fix them?

[CZ: Happy to fix broken links. But I'll need to know which ones aren't working. There are too many to test them all out.]

Thanks! And a hat-tip to the several who gave thoughtful responses to the interesting questions and comments on the thread…!

http://www.jpost.com/servlet/Satellite?cid=1176152801536&pagename=JPost%2FJPArticle%2FShowFull
http://www.pnas.org/cgi/content/short/104/16/6568

http://www.eurekalert.org/pub_releases/2007-03/nyu-med032307.php
http://www.sciencemag.org/cgi/content/summary/316/5821/27c?ck=nck

I have always heard that the Celera Genome is all Craig Venter’s DNA. In fact, based on conversations I’ve had with researchers who should know what they’re talking about, I believe that to be the case. However, before I made my original comment (#6), I tried to do some fact checking via Google to make sure I could provide a reference for that assertion if one were demanded.

During this quick search, I couldn’t find a source of irreproachable evidence for the claim that Celera is 100% Venter, and I found a few places that mentioned that the Celera genome was actually built from 5 individuals, only one of which was Venter. So, in the interests of honesty, I decided to go with the “watered down” number instead of just posting what I have heard for years but can’t back up with proof, which is that the Celera Genome is 100% Craig Venter.

If anyone has a source that settles the question, please post it. I’m now interested in which account is the truth. I’m sure it will come up again at some point and I’d prefer to have a definitive answer.

I’m not sure why you quoted me, but I re-read the section of my comment you quoted, then I re-read my entire comment (#6). I can’t find any place in which I implied that rhesus monkeys are “lower” animals. I didn’t even use the word “lower”.

Like most people working in evolution, I don’t usually deal in lower-higher distinctions. As you are probably aware, those sorts of distinctions rarely have useful meanings in the context of biology. The terms “ancestral” and “derived” come up much more often when we try to explain if a characteristic is more similar to the way we think it was in the common ancestor or if it has been changed significantly since then.

Now, you may occasionally hear scientists, including me, use the term “lower”, but I’d argue that those instances are more conversational laziness than an actual misunderstanding of the facts on the part of the speaker. I would completely agree, however, that such laziness should be kept out of classrooms, papers, and public talks because it gives those unfamiliar with evolution the wrong idea about the picture of life that the field is showing us.

As for the number of species within the genus, Pan, that’s always going to be a tough nut to crack. Anytime you deal with the question of how many species are in a certain genus, you have to consider exactly which one of the several different species definitions you’re going to use to make your groupings. And, while the species definition arugment is always a lively and thought-provoking discussion to have, my experience has told me that there really is no “one right way” to do species determinations. It just depends on what seems to most reflect the biology of the things you’re studying. But, there’s almost always a robust case to be made that you should have chosen a different species definition and, therefore, that the number of species in your genus should change.

The publishing of the rhesus genome is bad news for monkeys, as even more will be demanded by ever-hungry monkey labs.

Why care if more moneys are bred and experimented on? See:
http://www.madisonmonkeys.com/monkeys.htm

The phylogeny showing the relationships between the various species of macaques is not completely resolved (I believe), but being that they’re all in the same genus (Macaca), it’s not likely to be very much divergence. Possibly less than that between humans and chimpanzees.

Why are they “lower” animals?
‘Cause Man’s so vain.

Else the genus Pan might have another species.

http://ostol.blogspot.com
http://ostol.blogspot.com
http://ostol.blogspot.com
http://ostol.blogspot.com

“Given that a slower rate of variability at the single-nucleotide level in the X chromosome compared with autosomes has been interpreted as support for speciation models, this difference is worthy of further investigation.” [Citation omitted.]

This appears near the bottom of the right-hand column on page 224 of the article at the following link: http://www.sciencemag.org/cgi/reprint/316/5822/222.pdf

The answer to your second question is “yes”. Each individual of a species will have differences at the nucleotide level from each other individual. So, in that sense, each individual has his or her own unique genome. However, the value of a complete genome sequence like this comes from knowing where all the parts are and what they’re likely to be. Most of the differences between individuals will be very minor — a nucleotide here, a mobile element insertion there. And those individual differences, when compared to the full sequence can give lots of insights into what makes individuals different, which loci might be involved in a disease mechanism, or what sort of structure may be present within and between populations of individuals.

I can’t answer your third question precisely because I don’t have the figures. But, I can guarantee that any two human genomes will likely be well over 99% similar. In fact, since there are two fully sequenced human genomes (the public one and the Celera one). The percent similarity between different macaque species will largely depend on how far in the past they diverged from one another. The phylogeny showing the relationships between the various species of macaques is not completely resolved (I believe), but being that they’re all in the same genus (Macaca), it’s not likely to be very much divergence. Possibly less than that between humans and chimpanzees.

Your final quesiton is a good one. The way the two human genomes were sequenced involved using sequence from several individuals. We don’t really know who is the “humans” for the public human genome project. That’s kept secret. Though, it has been reported that the lion’s share of the DNA for that project came from one individual from New York due to the good quality that those samples yeilded. The Celera project, which is a privately funded complete human genome that was published at the same time as the public one, used five indivudals, one of which is the president and founder of Celera, Craig Venter.

There are other projects ongoing, such as the International HapMap Project, that are busily trying to get partial and/or complete genomes from a wide diversity of humans from various ethnic groups in order to help us determine what genetic differences there may be between human subpopulations. Having the complete reference sequences from the public genome and Celera’s genome, however, are absolutely critical to these other efforts.

Hope this helped.

There are 22 species of macaque in the world”

First – If there are 22 species, doesn’t each specie (singular of species?) have a different genome?
Second – Don’t any two individuals of the same species also have different genomes, though to a lesser degree?
Third – If the human genome is 93% the same as the macaque genome, and 94% the same as the chimpanzee genome, what percent the same are any two human genomes, or the genomes of different macaque species?
And, finally, depending on the answer to #3,if two humans have different genomes, how does one decide which is “the” human genome?