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Author Topic:   Definition of Species
Wounded King
Member (Idle past 2381 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 256 of 450 (614607)
05-05-2011 11:17 AM
Reply to: Message 253 by Big_Al35
05-05-2011 10:40 AM


It would be interesting to discover how many genes are different between humans and chimps and what fraction of the entire genome this represents?

There is already quite a bit of information on this from the human and chimpanzee genome projects. Some highlights from an overview from NIH's Genome.gov site ...

At the protein level, 29 percent of genes code for the same amino sequences in chimps and humans.

In fact, the typical human protein has accumulated just one unique change since chimps and humans diverged from a common ancestor about 6 million years ago.

the number of genetic differences between a human and a chimp is about 10 times more than between any two humans.

More than 50 genes present in the human genome are missing or partially deleted from the chimp genome.

The researchers found six regions in the human genome that have strong signatures of selective sweeps over the past 250,000 years.

A slightly more recent paper from 2007 (Hahn et al.) looks at rates of gene loss and gene gain in the primate lineage and notes unusual expansions in neural related genes in the human lineage.

This ties in to studies of what are called Human accelerated Regions, regions which are conserved amongst mammals generally but show significant differences in humans ( Prabhakar et al, 2006; Katzman et al., 2010).

As a fraction of the genome these regions are all pretty tiny, ~50 missing genes, 50 human accelerated regions. Even as a proportion of the difference between chimps and humans, and allowing the same again for the chimp lineage, they are still likely to be a very small proportion, especially when there are some single insertion-deletion events which account for megabases of sequence at a time. Small but possibly very important in terms of the actual functional changes which account for the differences between humans and chimpanzees.

TTFN,

WK


This message is a reply to:
 Message 253 by Big_Al35, posted 05-05-2011 10:40 AM Big_Al35 has not yet responded

    
Percy
Member
Posts: 18872
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.4


Message 257 of 450 (614683)
05-05-2011 9:17 PM
Reply to: Message 253 by Big_Al35
05-05-2011 10:40 AM


Big_Al35 writes:

Percy writes:

everything I said in Message 241 about gene sets being unique to species is still accurate. And WK agrees


Thats very interesting given that we share 98% of our entire genome with chimpanzees and yet only 2-3% of the genome consists of genes!

It is the gene sets that are unique. Different species can share many of the same genes, but the complete set of genes are unique for each species. The more closely related two species are the more genes they are likely to share, but if they are in reality two different species then one or both will have genes the other does not have. And if you discovered a new species that shared all the same genes as an existing species, guess what? It's not a new species!

It would be interesting to discover how many genes are different between humans and chimps and what fraction of the entire genome this represents?

Yes it would. Looking over the Wikipedia article on the Chimpanzee genome project it appears that we don't really know. Maybe WK can confirm, but I get the impression that while we might know a great deal about some genes, the majority are vague and amorphous and possibly only known to exist by some gross estimation process.

--Percy


This message is a reply to:
 Message 253 by Big_Al35, posted 05-05-2011 10:40 AM Big_Al35 has responded

Replies to this message:
 Message 258 by Big_Al35, posted 05-06-2011 6:46 AM Percy has responded
 Message 260 by Wounded King, posted 05-06-2011 7:16 AM Percy has responded

    
Big_Al35
Member
Posts: 384
Joined: 06-02-2010


Message 258 of 450 (614703)
05-06-2011 6:46 AM
Reply to: Message 257 by Percy
05-05-2011 9:17 PM


Percy writes:

It is the gene sets that are unique. Different species can share many of the same genes, but the complete set of genes are unique for each species.

Let me get this right, 97% of our genome (maybe 98%) consists of apparent junk (no function identified as of yet) and yet 98% of our genome is shared with chimpanzees.

So really the vast bulk of DNA that is shared across the species is junk and in the case of chimpanzees our genes are actually 70% different?

Do biologists deliberately set out to mislead?


This message is a reply to:
 Message 257 by Percy, posted 05-05-2011 9:17 PM Percy has responded

Replies to this message:
 Message 259 by Percy, posted 05-06-2011 6:57 AM Big_Al35 has not yet responded
 Message 262 by Wounded King, posted 05-06-2011 8:36 AM Big_Al35 has responded

    
Percy
Member
Posts: 18872
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.4


Message 259 of 450 (614706)
05-06-2011 6:57 AM
Reply to: Message 258 by Big_Al35
05-06-2011 6:46 AM


Hi Al,

You'll have to provide the source for your figures. There were no such figures in my post, nor in the Wikipedia article I referenced, so maybe it came from some posts earlier in the discussion, or from links mentioned in those posts? Let me know.

--Percy


This message is a reply to:
 Message 258 by Big_Al35, posted 05-06-2011 6:46 AM Big_Al35 has not yet responded

    
Wounded King
Member (Idle past 2381 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 260 of 450 (614711)
05-06-2011 7:16 AM
Reply to: Message 257 by Percy
05-05-2011 9:17 PM


It is the gene sets that are unique. Different species can share many of the same genes, but the complete set of genes are unique for each species. The more closely related two species are the more genes they are likely to share, but if they are in reality two different species then one or both will have genes the other does not have. And if you discovered a new species that shared all the same genes as an existing species, guess what? It's not a new species!

Hey Percy, now its you that is either using genes in a funny way or getting the biology mixed up. Alternatively you may be using yet another species concept.

If we go by the biological species concept of interbreeding potential as the criteria for distinct species then it is quite possible to produce reproductively isolated species without changing the Gene sets in terms of the broader conception of a gene, i.e. a specific genetic locus which is associated with a heritable trait rather than any particular exact sequence of nucleotides at that locus.

At base as few as 2 SNPs might be sufficient to establish reproductive isolation between two populations. We could envision an initial isolation event followed by subsequent evolution leading to the origination and fixation of these SNPs, either in one population or split between them. Alternatively they may already be extant in one population but the presence of other genetic variants allows sufficient gene flow to keep them within one species if subsequently the mediating genetic variations are lost from the population you have potential sympatric speciation.

Maybe WK can confirm, but I get the impression that while we might know a great deal about some genes, the majority are vague and amorphous and possibly only known to exist by some gross estimation process.

Again it all comes down to what we mean by a "gene". In terms of the traditional protein coding sequence conception of a gene we have things pretty tied up, open reading frame (ORF) detection is a pretty mature technology and error checking approaches have been set up to screen out false positives (a few years ago about 5,000 putative coding sequences were scrubbed (Clamp et al., 2007)) although thorough annotation is still lacking in most genomes outside of mouse, human and chimp. Also there is still quite a bit of work to be done tidying up the multiple isoforms of proteins that many genes produce. Where there is considerably more doubt is in the areas of regulatory sequences and non-coding RNAs, areas that while not matching the conception of a gene as a protein coding sequence match the more traditional Mendelian idea of a gene as a discrete heritable genetic locus with variants associated with a trait/phenotype.

Another study estimated that between them humans and chimps have 6% of their genes different through loss or gain (1,418 of 22,000 genes) (Demuth et al., 2007), but there is some reason to think that they overestimate the numbers one comment on the article describes several possible artefactual problems with their approach.

TTFN,

WK


This message is a reply to:
 Message 257 by Percy, posted 05-05-2011 9:17 PM Percy has responded

Replies to this message:
 Message 261 by Percy, posted 05-06-2011 8:09 AM Wounded King has responded

    
Percy
Member
Posts: 18872
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.4


Message 261 of 450 (614715)
05-06-2011 8:09 AM
Reply to: Message 260 by Wounded King
05-06-2011 7:16 AM


Wounded King writes:

Hey Percy, now its you that is either using genes in a funny way or getting the biology mixed up. Alternatively you may be using yet another species concept.

We've run into this issue before. My approach of starting simply and gradually adding complexity often draws objections from you. The species divisions getting attention in this thread, such as between chimp and human, include differences in gene sets, even in chromosomes because of the fusion of 2-into-1 possessed by humans.

It is possible to project a better understanding onto replies than is actual there in reality, encouraging one to continue the discussion at what can become for many an inaccessible level, especially when long familiarity with complex details causes some simple but important things to go unsaid.

I do understand that biology is whatever works and that the many simple rules we wish were hard and fast are not, but there are still general principles that are true in a broad or general sense and that are understandable to most. As ring species helpfully make clear for the biological layperson, species is a actually a very fuzzy boundary, but the concept itself of an well-delineated interbreeding population is very clear and very helpful in discussion. Equally helpful is the concept of genetic uniqueness of a species, a point made most simply by assuming that each species has a unique gene set. Once that point is made and understood one can move on and say that even just allele differences can divide species.

I'd like to be more a help than a hindrance in your discussion with Al, I'll do my best.

--Percy


This message is a reply to:
 Message 260 by Wounded King, posted 05-06-2011 7:16 AM Wounded King has responded

Replies to this message:
 Message 263 by Wounded King, posted 05-06-2011 8:49 AM Percy has acknowledged this reply

    
Wounded King
Member (Idle past 2381 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


(1)
Message 262 of 450 (614718)
05-06-2011 8:36 AM
Reply to: Message 258 by Big_Al35
05-06-2011 6:46 AM


Let me get this right, 97% of our genome (maybe 98%) consists of apparent junk (no function identified as of yet)

I think you are mixing up a whole lot of things here. About 2% of the human genome consists of protein coding genes. Junk DNA is not simply everything that isn't a protein coding gene, that is a very naive conception such as one might find in a newspaper science article. Even in the 70s when the term was coined there were already a number of known functions for non-coding stretches of DNA, there are structural elements like telomeres and centromeres which have very clear roles in mitosis and chromosome stability, there are regulatory sequences where transcription factors bind which mediate the timing and extent of expression of specific genes and there are genes for non-coding RNAs which form part of the machineries of protein synthesis. Since the 70s we have discovered more functional elements, such as non-coding RNAs which have regulatory roles.

There are still however large regions with no readily apparent function. These include large amounts of repetitive DNA, some simply the same 2 or 3 nucleotides repeated multiple times, others longer sequences between 10 and 60 bps. This sort of repetitive DNA makes up around 40% of the genome and overlaps to some extent with the other major class of sequences which make up most of the rest. This other class is retrotransposons, most retrotransposons in the human genome are no longer active but they make up ~42% of the human genome, these are mostly variants on 2 types of sequence LINE (Long interspersed elements) and Sines (Short interspersed elements). Another class of sequence usually considered junk are pseudogenes which are the normally non-functional remnants of genes and gene duplicates. Some neo-functionalised pseudogenes have been identified but only a handful.

So really the vast bulk of DNA that is shared across the species is junk

Not necessarily, the vast majority of DNA is shared between Humans and chimpanzees, including that in 'Junk' DNA. Some biologists do argue that the vast majority of DNA is junk, in which case you would be right, and that its conservation across species is strong evidence in favour of common ancestry.

in the case of chimpanzees our genes are actually 70% different?

I assume you get this figure from when I quoted ...

www.genome.gov writes:

At the protein level, 29 percent of genes code for the same amino sequences in chimps and humans.

... if so then I apologise for not clarifying the statement from the article. When they say the sequences are "the same" they mean they are 100% identical at the amino acid level as opposed to the other genes which vary in a few amino acids, but not so many as to bring the typical amino acid divergence above 1 per protein.

I hope that clears things up, no one is trying to mislead you.

TTFN,

WK

Edited by Wounded King, : No reason given.


This message is a reply to:
 Message 258 by Big_Al35, posted 05-06-2011 6:46 AM Big_Al35 has responded

Replies to this message:
 Message 264 by Big_Al35, posted 05-07-2011 8:13 AM Wounded King has responded

    
Wounded King
Member (Idle past 2381 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 263 of 450 (614720)
05-06-2011 8:49 AM
Reply to: Message 261 by Percy
05-06-2011 8:09 AM


My approach of starting simply and gradually adding complexity often draws objections from you. The species divisions getting attention in this thread, such as between chimp and human, include differences in gene sets, even in chromosomes because of the fusion of 2-into-1 possessed by humans.

Sure I get that, I just thought that you were making some pretty bald statements there that simply aren't backed up by the biology.

It is possible to project a better understanding onto replies than is actual there in reality, encouraging one to continue the discussion at what can become for many an inaccessible level, especially when long familiarity with complex details causes some simple but important things to go unsaid.

Yeah, I get that a lot. To some extent I blame the Creationist/IDists since so many of them come in insisting that they know exactly what they are talking about.

Equally helpful is the concept of genetic uniqueness of a species, a point made most simply by assuming that each species has a unique gene set. Once that point is made and understood one can move on and say that even just allele differences can divide species.

I agree, I just think that the fact that it is an assumption for the purposes of demonstration needs to be in there somewhere rather than presenting it as a fact of biology that each species has a unique set of genes.

TTFN,

WK


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 Message 261 by Percy, posted 05-06-2011 8:09 AM Percy has acknowledged this reply

    
Big_Al35
Member
Posts: 384
Joined: 06-02-2010


Message 264 of 450 (614823)
05-07-2011 8:13 AM
Reply to: Message 262 by Wounded King
05-06-2011 8:36 AM


WK writes:

Junk DNA is not simply everything that isn't a protein coding gene

Thanks for clearing that up. Your information is most helpful. I don't work in genetics or biology so bear with me as I am discussing this purely as a lay person.

I haven't added references for my figures because I didn't want to get bogged down in an argument about who had the most reliable source or to be quibbling over 1-2% figures. I usually round up or down anyway and my figures are usually based on not one source but an average of several sources.


This message is a reply to:
 Message 262 by Wounded King, posted 05-06-2011 8:36 AM Wounded King has responded

Replies to this message:
 Message 265 by Wounded King, posted 05-07-2011 4:31 PM Big_Al35 has responded

    
Wounded King
Member (Idle past 2381 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 265 of 450 (614842)
05-07-2011 4:31 PM
Reply to: Message 264 by Big_Al35
05-07-2011 8:13 AM


I usually round up or down anyway and my figures are usually based on not one source but an average of several sources.

The only figure I had an issue with was the one for ...

in the case of chimpanzees our genes are actually 70% different?

Which isn't really consistent with anything, which was why I thought you might just have misunderstood.

No one is bothered to quibble about protein sequences being 1 or 2 % identical but going from 100% identical to 30% is a pretty dramatic difference and the 30% figure isn't really supported by anything at all as far as I can tell. I'm pretty sure Percy wasn't thinking of the 97-98% figures when he asked you for a source.

TTFN,

WK


This message is a reply to:
 Message 264 by Big_Al35, posted 05-07-2011 8:13 AM Big_Al35 has responded

Replies to this message:
 Message 266 by Big_Al35, posted 05-08-2011 7:10 AM Wounded King has responded

    
Big_Al35
Member
Posts: 384
Joined: 06-02-2010


Message 266 of 450 (614874)
05-08-2011 7:10 AM
Reply to: Message 265 by Wounded King
05-07-2011 4:31 PM


in the case of chimpanzees our genes are actually 70% different?

Which isn't really consistent with anything, which was why I thought you might just have misunderstood.

If you look at any stretch of DNA code in a human and the parallel set of code in a chimp only two letters of code in every 100 are different. Ofcourse there is the fusion of the chromosome to consider to. This is where the 98% figure comes from.

Essentially this means that humans and chimps share exactly the same genes making a nonsense of Percy's previous comments.
How the foot of the a chimp grows differently to the foot of a human is still not understood well but the gene is essentially the same gene. (see [Matt Ridley 1999, Genome] Out of date maybe).

The figure of 70% different was a question as you will note.


This message is a reply to:
 Message 265 by Wounded King, posted 05-07-2011 4:31 PM Wounded King has responded

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 Message 268 by Percy, posted 05-08-2011 9:20 AM Big_Al35 has responded

    
Wounded King
Member (Idle past 2381 days)
Posts: 4149
From: Edinburgh, Scotland
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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 Message 266 by Big_Al35, posted 05-08-2011 7:10 AM Big_Al35 has not yet responded

    
Percy
Member
Posts: 18872
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.4


(1)
Message 268 of 450 (614880)
05-08-2011 9:20 AM
Reply to: Message 266 by Big_Al35
05-08-2011 7:10 AM


Big_Al35 writes:

Essentially this means that humans and chimps share exactly the same genes making a nonsense of Percy's previous comments.

Chimps have genes that humans do not have, and vice versa. Apparently a great many of the gene differences are due to duplications. See the Wikipedia article on the Chimpanzee genome project that I referenced earlier:

Wikipedia writes:

Gene duplications account for most of the sequence differences between humans and chimps.

I was not able to locate any layperson-level description of the precise gene differences, and I suspect it isn't very well characterized at this point, but the important piece of information is that in general the genetic differences between species range from allele differences only all the way up to sharing very few genes (aside from the fundamental ones like hox genes). Humans and chimps are not a species that differ at only the allele level. Humans and chimps have different gene sets, though they overlap broadly.

You were arguing with WK about whether genetic differences were helpful in identifying species. I'm not sure whether your position is affected by whether chimps and humans "share exactly the same genes," so can you refresh our memory about your position on this?

--Percy


This message is a reply to:
 Message 266 by Big_Al35, posted 05-08-2011 7:10 AM Big_Al35 has responded

Replies to this message:
 Message 269 by Big_Al35, posted 05-08-2011 10:12 AM Percy has responded

    
Big_Al35
Member
Posts: 384
Joined: 06-02-2010


Message 269 of 450 (614883)
05-08-2011 10:12 AM
Reply to: Message 268 by Percy
05-08-2011 9:20 AM


Chimps have genes that humans do not have

Chimps, our nearest relative, don't talk. We do. Now scientists have pinpointed a mutation in a gene that might help explain the difference.

The mutation seems to have helped humans develop speech and language. It's probably not the only gene involved, but researchers found the gene looks and acts differently in chimps and humans, according to a study published online Wednesday by the journal Nature.

link

Even the FOXP2 is a mutation and therefore humans and chimps essentially share the same gene. If you can name a single gene that is only a chimp gene and a single gene that is only a human gene that would be helpful. Let me know your source. Your previous source wikipedia confirms that chimps and humans have the same genes.


This message is a reply to:
 Message 268 by Percy, posted 05-08-2011 9:20 AM Percy has responded

Replies to this message:
 Message 270 by Percy, posted 05-08-2011 11:56 AM Big_Al35 has responded

    
Percy
Member
Posts: 18872
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.4


(1)
Message 270 of 450 (614885)
05-08-2011 11:56 AM
Reply to: Message 269 by Big_Al35
05-08-2011 10:12 AM


Hi Al,

It appears to me that our difference of opinion comes down to interpretation of plain English about gene duplications. Let me try to put it in explicit terms.

Assume the human/chimp common ancestor had gene X. Some millions of years later the human branch experienced a duplication in gene X, call it X'. The chimp line did not experience this gene duplication. Therefore the human branch now has gene X' that the chimp branch does not.

Of course, as the Wikipedia article on the Chimpanzee genome project states, gene duplications are the source of only *most* of the sequence differences. There are other sources of gene differences. New genes can arise from insertions, for example retroviral insertions, and genes can be deleted.

If you want something completely unequivocal, this article titled DNA Chunks, Chimps And Humans: Marks Of Differences Between Human And Chimp Genomes from Science News makes an explicit statement about deletions where it quotes Dr. George Perry from Arizona State University:

Science News writes:

"For example, a surprisingly high number of genes involved in the inflammatory response - APOL1, APOL4, CARD18, IL1F7, IL1F8 - are completely deleted from chimp genome."

Hopefully this puts this issue to rest, so getting back to the original issue, can you refresh our memory on your discussion with WK about whether genetic differences are helpful in species identification.

--Percy

Edited by Percy, : Grammar.


This message is a reply to:
 Message 269 by Big_Al35, posted 05-08-2011 10:12 AM Big_Al35 has responded

Replies to this message:
 Message 271 by Big_Al35, posted 05-08-2011 12:29 PM Percy has responded

    
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