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Author Topic:   Definition of Species
Wounded King
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Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 267 of 450 (614878)
05-08-2011 9:02 AM
Reply to: Message 266 by Big_Al35
05-08-2011 7:10 AM


Essentially this means that humans and chimps share exactly the same genes making a nonsense of Percy's previous comments.
No, it doesn't. Those figures apply when you have a stretch which you can align. What Percy is pointing out is that there are certain genes which are unique to each lineage. In the case of protein coding genes these could either be genes where specific sequences required for the production of the protein have been lost, such as the motifs marking the transcriptional start site or it could be the result of a deletion event removing a whole gene from one lineage, it could even be a mutation giving rise to an entire novel coding sequence de novo although such events are considered vanishingly rare, (Knowles and McLysaght, 2009).
Even with these unique sequences bringing it down the overall similarity throughout the genome is still in the 95-98% range.
The figure of 70% different was a question as you will note.
Sure, but presumably it wasn't a figure you just pulled out of thin air. All we are doing is asking you what you were basing that figure on since it is so divergent from any commonly used figure?
TTFN,
WK
Edited by Wounded King, : No reason given.

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Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


(1)
Message 272 of 450 (614888)
05-08-2011 1:50 PM
Reply to: Message 271 by Big_Al35
05-08-2011 12:29 PM


The article has a link at the bottom to the new research article on CNVs it is discussing (Perry et al., 2008) and also the previous initial comparison between chimp /human genomes from Nature (The Chimpanzee Sequencing and Analysis Consortium, 2005).
The data related to the specific genes APOL1, APOL4, CARD18, IL1F7, IL1F8 are from the original Nature paper, in fact there is a table (S.42) in the supplementary data (Word Doc) for that paper which lists about 35 genes which appear to have been completely deleted from the Chimp genome.
The way they distinguish a deletion which occurred in the chimp lineage is also by looking at other species. If a gene is only present in humans then it is probably a human innovation, if it is present in humans, gorillas and macaques and absent in chimps then it was probably lost in the chimp lineage. In this case the other species were non-primates like mouse and rat on which we already had a lot of genetic data.
There is no evidence in the article about that fact however. The article goes on to suggest that regulation must be provided by other means in chimps but again no evidence given.
The evidence is that chimpanzes have functional inflammatory responses despite not having these specific genes.
Sorry but I can't take this article seriously.
You should take this article seriously, it is essentially a slightly modified press release from the Sanger Centre one of the premier institutes of genetic research in the world, if you can't then perhaps it is because you lack the tools to effectively evaluate the quality of the information you are presented with.
As an aside to Percy, if you are trying to argue that differences in gene complement are indicative of distinct species then CNVs are so not the way to go, considering that they show there are differences in gene complement within species.
TTFN,
WK

This message is a reply to:
 Message 271 by Big_Al35, posted 05-08-2011 12:29 PM Big_Al35 has replied

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Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


(1)
Message 280 of 450 (614927)
05-09-2011 6:29 AM
Reply to: Message 277 by Big_Al35
05-08-2011 6:57 PM


You make the assumption I guess on the basis that you have assumed a closer relationship between humans and chimps than other primates. Whilst some DNA might suggest a closer relationship, APOL1 suggests a more distant relationship.
It isn't 'some' DNA which suggests a closer relationship, it is the overwhelming majority of the DNA, based on cross species comparisons between multiple different species.
If you can present a more parsimonious explanation of all the genetic data than humans and chimps being each other's closest extant relative then go ahead, but you can't simply cherry pick a single gene and argue chimps and humans are more distantly related from that single data point.
TTFN,
WK

This message is a reply to:
 Message 277 by Big_Al35, posted 05-08-2011 6:57 PM Big_Al35 has replied

Replies to this message:
 Message 281 by Big_Al35, posted 05-09-2011 11:00 AM Wounded King has replied

  
Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


(1)
Message 284 of 450 (614955)
05-09-2011 11:50 AM
Reply to: Message 281 by Big_Al35
05-09-2011 11:00 AM


Hardly, when chimps and gorillas have a 97% correlation and humans and gorillas have a 97% correlation while chimps and humans have a 98% correlation
Well again, this is one of the times when some source or context for your numbers would be helpful. Have we not just finished discussing a whole lot of different things that such % values can represent, from nucleotide level substitutions, through indels and up to entire gene deletions?
Even so, I'm not sure what point you think you are making. I made a specific claim, that in the overwhelming majority of genetic sequences chimp and human are each other's closest relative. You aren't countering that claim by pointing out that they are both less closely related to gorillas, you are just agreeing with me in a highly idiosyncratic manner.
I didn't say that the degree by which chimps and humans were more related was overwhelming. I said that the extent of the genome over which this was the case was overwhelming, i..e the vast majority of the genome coding and non-coding, as opposed to the one gene comparison you were trying to use to argue against it. I'm quite happy to stipulate that there are probably many more genes where humans and gorillas or chimps and gorillas will tree out more closely, but that isn't the case for the vast majority of sequences.
You seem to be moving farther and farther away from trying to have a genuine discussion. By dismissing Dr. A's point so cavalierly you are essentially dismissing maximum parsimony, one of the key methods used in phylogenetics, with nothing more than a wave of your hand.
All you seem to be bringing to this discussion is contrariness.
TTFN,
WK

This message is a reply to:
 Message 281 by Big_Al35, posted 05-09-2011 11:00 AM Big_Al35 has not replied

  
Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 285 of 450 (614958)
05-09-2011 12:04 PM
Reply to: Message 283 by Percy
05-09-2011 11:22 AM


Re: Gene Deletion
Hi Percy,
Just to be clear, while they did perform alignments of mouse and rat with the human and chimp genomes, that doesn't mean that all of the chimp deleted sequences were present in mouse and rat.
For example the APOL gene cluster, including APOL1, seems to be primate specific.
Sorry if what I wrote was misleading.
TTFN,
WK

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Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 288 of 450 (615031)
05-09-2011 6:27 PM
Reply to: Message 286 by Big_Al35
05-09-2011 5:23 PM


Re: Gene Deletion
Can you come up with anything?
Olfactory Receptor genes, lots of them (Gilad et al., 2005). This paper covers both cases where genes have lost their functionality, pseudogenisation, and also those where the basis seems to be lineage specific expansion of a gene family.
TTFN,
WK

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Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


(2)
Message 303 of 450 (615196)
05-11-2011 9:44 AM
Reply to: Message 300 by Big_Al35
05-11-2011 8:13 AM


Re: Gene Deletion/pseudogenisation
The evidence suggest it is a pseudogene in humans but an active gene in chimps. For some further human specific pseudogenes (HSPs) which have become fixed in the human population see Kim et al. (2010). This paper identifies 38 distinct human specific pseudogenes 25 of which are Olfactory Receptor (OR) genes. Some of the non-OR pseudogenes are CMAH, GLRA4, MBL1, MHY16, SIGLEC-13, TDH and KRT41 (for the full list see here. The authors used a more stringent approach than the original human-chimp comparison paper which had identified 120 putative HSPs, the supplementary table I linked to in the last sentence also includes the criteria they used to gategorise many of these as non-authentic HSPs.
Hopefully having established to any reasonable person's satisfaction that chimps have some functional genes humans don't and humans have some functional genes chimps don't why not now relate this back to the topic at hand, the definition of species?
TTFN,
WK

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 Message 300 by Big_Al35, posted 05-11-2011 8:13 AM Big_Al35 has not replied

Replies to this message:
 Message 304 by Percy, posted 05-11-2011 10:11 AM Wounded King has replied

  
Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 306 of 450 (615201)
05-11-2011 11:03 AM
Reply to: Message 304 by Percy
05-11-2011 10:11 AM


My bad
You are right it may be a chimp specific expansion rather than a human pseudogenisation event. I was trying to find the actual sequences in the Human Olfactory Data Explorer (HORDE) but unfortunately none of the terms there correspond to the nomenclature in the paper, I took human OR4C10P, which is a pseudogene, to be the orthologue of the chimp sequence, but now I'm doubtful if that is correct.
From the figure itself there is no way to tell the functional genes (intact) from the pseudogenes, quite why they didn't bother to do this is beyond me since they go on to say how many there are of each. Given this omission there is not actually enough information to tell which orthologous pairs are both intact or in which one or both members are pseudogenised. I suppose since the point of the figure was simply the expansions this is understandable, but it would have been nice information to have.
TTFN,
WK

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Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 316 of 450 (615315)
05-12-2011 8:06 AM
Reply to: Message 311 by Big_Al35
05-11-2011 2:39 PM


Re: Gene Deletion
Well we've had a few examples of gene names eg
APOL1, APOL4, CARD18
To be precise those aren't actually gene names, they are gene symbols. The gene names are Apolipoprotein L1, Apolipoprotein L4 and Caspase recruitment domain-containing protein 18.
Human Gene symbols are unique identifiers which are assigned to genes by the HUGO gene nomenclature committee. Gene names are usually a matter of choice of the initial discoverers although it varies depending on the organism, some species have more rigid gene nomenclature than others and many genes end up with various synonyms, for instance CARD18 was previously known as Iceberg.
Unfortunately the designations given to the OR genes in the Gilad paper do not seem to correspond to those on the HORDE database that the sequences came from. To take the OR4C subfamily as an example the HORDE database does have 10 intact genes and 10 pseudogenes, but it has properly assigned gene nomenclature where pseudogenes are designated with a P suffix, i.e. olfactory receptor, family 7, subfamily E, member 18 pseudogene has the symbol OR7E18P.
I'm not sure why the paper uses their own idiosyncratic nomenclature, it is understandable for the chimp sequences they derived de novo through their analysis but not for the human ones, especially since in a subsequent table they use the standard nomenclature. It has the very unfortunate side effect of effectively anonymising all of the actual sequences in the tree.
If I find myself at a loose end I might try Blasting the sequences for the 4c subfamily against the chimpanzee genome and see if I can recover any sort of similar tree.
TTFN,
WK
Edited by Wounded King, : Messed up link fixed

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Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 318 of 450 (617931)
05-31-2011 4:47 PM
Reply to: Message 317 by Big_Al35
05-31-2011 2:32 PM


Re: Gene Deletion
Please provide evidence for your claims or alternatively retract your remark.
You have had a number of examples presented to you from a variety of papers.
You also stated that while humans and chimps share 98% of their genome it was the genes that were different.
Can you give a clear reference for this? Percy certainly did say that the gene complements were different, but I don't remember him suggesting that all or even most of the 2% divergence between chimps and humans was in genes and certainly not in differences in gene complement between the lineages.
The article referring to the olfactory genes refers to large numbers of pseudo genes differing between the two species.
And a number of these are cases where the gene has been pseudogenised only in one lineage, therefore representing a situation where the different lineages have distinct complements of intact protein coding sequences. There were also a couple of other articles referenced and there are more still out there, but it is hard to see the point in presenting them when you refuse to accept the evidence already presented to you.
TTFN,
WK
Edited by Wounded King, : No reason given.

This message is a reply to:
 Message 317 by Big_Al35, posted 05-31-2011 2:32 PM Big_Al35 has replied

Replies to this message:
 Message 320 by Big_Al35, posted 06-01-2011 1:24 PM Wounded King has replied

  
Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 322 of 450 (618148)
06-01-2011 3:52 PM
Reply to: Message 320 by Big_Al35
06-01-2011 1:24 PM


Re: Gene Deletion
You have named only one potential candidate ie C4C1001 which non of us have been able to cross reference with any other source.
This is original research, what other sources would you cross reference it to? On top of which your claim simply isn't true, I gave you references for several other genes, Message 303, which had been inactivated in the human lineage but not in chimps including CMP-Neu5Ac hydrolase (CMAH) and Myosin Heavy Chain 16 (MYH16).
Still lets give you yet another example to see how you fudge and slide your way around it; Several studies detail a variety of immune system genes that are distinct betwen humans and chimps, those absent in the human lineage include KIR2DL6, KIR2DL7, KIR2DL9, KIR3DL4 and KIR3DL5 (Moesta et al., 2009 ;Abi-Rached et al., 2010).
TTFN,
WK

This message is a reply to:
 Message 320 by Big_Al35, posted 06-01-2011 1:24 PM Big_Al35 has replied

Replies to this message:
 Message 324 by Big_Al35, posted 06-02-2011 6:22 AM Wounded King has replied

  
Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 327 of 450 (618254)
06-02-2011 1:46 PM
Reply to: Message 324 by Big_Al35
06-02-2011 6:22 AM


Re: Gene Deletion
Ahh finally we have something to work with ie MYH16.
Finally, as in 2 months ago when I first posted that information?
TTFN,
WK

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Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 329 of 450 (618386)
06-03-2011 5:01 AM
Reply to: Message 328 by Big_Al35
06-03-2011 4:03 AM


Re: Gene Deletion
Why do you care?
He cares because this is supposed to be a thread for discussing ways of defining species. If you aren't interested in that topic then you should make another thread to discuss the specific genetic differences between chimps and humans.
TTFN,
WK

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 Message 328 by Big_Al35, posted 06-03-2011 4:03 AM Big_Al35 has not replied

  
Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 335 of 450 (619598)
06-10-2011 2:39 PM
Reply to: Message 333 by Percy
06-10-2011 1:58 PM


Not Al's position as I understand it
On a more general level Al's position is that it isn't possible to use genetics to differentiate between species
I've got to say Percy, this sounds like the very opposite of Big Al's position. He has been saying since way back in Message 146 that species can be defined by distinct sets of genes, what he disputes is that we can meaningfully infer cross species ancestry and phylogeny from DNA similarities.
TTFN,
WK

This message is a reply to:
 Message 333 by Percy, posted 06-10-2011 1:58 PM Percy has replied

Replies to this message:
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Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 338 of 450 (622500)
07-04-2011 8:36 AM
Reply to: Message 337 by Big_Al35
07-04-2011 7:47 AM


Re: Gene Deletion
Surely Tesla's point is fairly well conveyed by the article he chose to cite. Several key differences between humans and chimps are not due to any human specific gains of novel genes but rather the human specific loss of particular non-coding regulatory sequences which are otherwise conserved in mammals.
As to what he thinks your point is, he himself says only a few posts later that he can't tell, along with the rest of us in fact. Perhaps you could put an end to our longstanding anticipation and actually tell us yourself what your point is.
TTFN,
WK

This message is a reply to:
 Message 337 by Big_Al35, posted 07-04-2011 7:47 AM Big_Al35 has replied

Replies to this message:
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