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This has been split off from the 500 scientists threads to keep the technical issues away from the political.
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mv Wrote:I recall seeing a paper (well, a report of a paper) a few months ago that stated that the mutation rate is not constant and species building came in clusters.

Mutations occur when DNA polymerase makes an error at DNA replication. It would seem that this is a random event, but in reality, some regions of DNA are more likely for DNA polymerase to make an error.

Not to mention of course, that the way of life also influences mutation rate. Salt and UV light, for example. So definitively, mutation rate is not constant. The choice of DNA sequences for calibrating "molecular clock" is never easy. However, for closely related species almost any stretch of DNA will do.

mv Wrote:COS,

What is your area approximately, if I may ask?
(I'm coming across some interesting issues with one specie. connected to genetics, and wondering if you may be somewhere close enough to comment.)

Microbiology, microbial genetics, population genetics, biotechnology, bioinformatics. Our university programs are never too specialised.

About chimp-human differences (at the DNA level). A draft of complete chimp genome was released last year. Accompanied paper from Science (2005, Vol 437: 69-87) sets divergence between human and chimp to be 1.23% (genome wide average, 2.4 Gb).
COS Wrote:
mv Wrote:I recall seeing a paper (well, a report of a paper) a few months ago that stated that the mutation rate is not constant and species building came in clusters.

Mutations occur when DNA polymerase makes an error at DNA replication. It would seem that this is a random event, but in reality, some regions of DNA are more likely for DNA polymerase to make an error.

Yes, I know this.
Sorry for being unclear. I was referring to the big picture. A suddenly large number of mutations within a species causing greater differentiation and formation of new species. Say, 1m years of low rate which accomplishes nothing, then a burst due to reasons unclear. (and if true, one would think of an increase in solar activity or something like this as the cause).

Quote:
mv Wrote:COS,

What is your area approximately, if I may ask?
(I'm coming across some interesting issues with one specie. connected to genetics, and wondering if you may be somewhere close enough to comment.)

Microbiology, microbial genetics, population genetics, biotechnology, bioinformatics. Our university programs are never too specialised.

I'm having a serious case of obsession with the Pangio cluster (and related species). Some of the strange things I'm having trouble understanding link to genetics. One thing that is fascinating about Pangio is the apparent instability around melanin production gene(s); it feels like there are several mutations in it that cause different effects, including melanin redistribution in an adult individual (I've seen this happening -- weird). More crazy stuff is the fact that some closely related species are polyploid (what does a polyploid animal really mean? -- plants are clear, but animals?); but it is not known if Pangio is (off hand guess -- no, polyploids should not be so unstable). And then there is the question of just how many species are out there (pop. genetics).

This kind of stuff. Of course it cannot be done on the high level since nobody will bother with decyphering Pangio genome for the next few centuries, but hopefully at least something can be understood without the heavy machinery.
mv Wrote:Sorry for being unclear. I was referring to the big picture. A suddenly large number of mutations within a species causing greater differentiation and formation of new species. Say, 1m years of low rate which accomplishes nothing, then a burst due to reasons unclear.
Well... One of the main problems in the big picture is to define what a species is. But I will not touch this topic at the moment.

The problem is, that it is impossible to say how many mutations is enough for a divergence of one species into two. Sometimes, one mutation is enough to make a strong reproduction barrier (for example fusion of 2 chromosomes into one as was probably the case of chimp vs. human), and sometimes, thousands of mutations and geographical distance are not enough (lions and tigers have fertile hybrids). So how many years, how many mutations does it take to form a new species? This is a question that can only be answered from case to case.

mv Wrote:I'm having a serious case of obsession with the Pangio cluster (and related species).
Ah, you are one of those cyprinid guys. I am more in salmonides, don't know about this melanin expression. Fish, especially freshwater fish seem to speciate pretty fast, presumably because each of several drainages works in the same way as islands separated by oceans. So, a solid geographic barrier that works as a good start for speciation.

Polyploid fish are very common, especially when it comes to hybridization of closely related species (hybrid sturgeons can have 400+ chromosomes). Anyway, fish have small chromosomes and lots of them, so presumably they also have a different mechanism to pull them around during meiosis. And unlike in higher animals, they don't seem to care if one or several of them are in multiple copies. As long as there is at least one complete set.
I just remembered, a classic speciation problem and a good example of unclear definition of species.

Two subspecies or two species? They hybridized in certain areas, but never in the other areas where they live together (sympatry).

http://www.santarosa.edu/lifesciences2/ensatina2.htm

Quote:What is most interesting about this species of salamander, is that the two southern most subspecies, eschscholtzi and klauberi, meet in several locations. Near Mount Palomar, these two subspecies meet in a very narrow zone and hybridize infrequently. (Brown, 1974) To the south near Cuyamaca State Park, klauberi and eschscholtzi meet and apparently fail to interbreed under natural conditions even though they are narrowly sympatric. In fact, by analyzing electrophoretic separations of selected enzymes and studying DNA patterns, the two subspecies klauberi and eschscholtzi are different species by every definition. (Wake, Yanev and Brown, 1986) This poses a very interesting problem. Should the species Ensatina eschscholtzi be split into two or more species, or be considered a single species? If the species is to be split, where does one draw the line?
COS Wrote:One of the main problems in the big picture is to define what a species is. But I will not touch this topic at the moment.

Yes, of course. It is also one of the more interesting problems around.

Quote:So how many years, how many mutations does it take to form a new species? This is a question that can only be answered from case to case.
Do we have a single case which has been fully answered.

Quote:
mv Wrote:I'm having a serious case of obsession with the Pangio cluster (and related species).
Ah, you are one of those cyprinid guys.
Worse than this, in two ways. I'm really only interested in Cobitinae and around, and these are not "mainstream" cyprinids. Secondly, I'm not a biologist of any kind (I did work on some bio- projects, although, so I'm not totally ignorant, but I'm not up to date on most literature).


Quote: I am more in salmonides, don't know about this melanin expression.
I'm quite tempted to run one guess by you anyway; I think you know more than enough to shut it down, if it a bad one, without knowing much about melanin. OK?

Quote:Fish, especially freshwater fish seem to speciate pretty fast, presumably because each of several drainages works in the same way as islands separated by oceans. So, a solid geographic barrier that works as a good start for speciation.
Yes, if it is truly solid, and if we have good data about the species (cluster) geographic distribution. Not the case with Pangios.

Your analogy with islands is an excellent one. I always thought that there is a parallel between the original Darwin's birds case study and the freshwater fish, but the second group is much richer in examples.

Quote:Polyploid fish are very common, especially when it comes to hybridization of closely related species (hybrid sturgeons can have 400+ chromosomes). Anyway, fish have small chromosomes and lots of them, so presumably they also have a different mechanism to pull them around during meiosis. And unlike in higher animals, they don't seem to care if one or several of them are in multiple copies. As long as there is at least one complete set.

This is about as much as I know about this. TBA, I was really shocked to learn about this; a very different mechanism is required. I wonder if anyone looked at the overall picture here: there ought to be some nice correlations between the # of chromosome sets and (1) size of fish (2) frequency of mutations being expressed.
COS Wrote:I just remembered, a classic speciation problem and a good example of unclear definition of species.

....

Will read carefully, thank you for the link.

In Pangio (Specifically, around P.myersi and P.semicincta) the current state of "science" is that there are two species. Everything that satisfies about 4 criteria is one, everything else is another, including specimens that satisfy 3 criteria. Which is a total insanity since the "species" of the rejects (semicincta) occupies a large geographical area and is full of variations (species?).
mv Wrote:This is about as much as I know about this. TBA, I was really shocked to learn about this; a very different mechanism is required. I wonder if anyone looked at the overall picture here: there ought to be some nice correlations between the # of chromosome sets and (1) size of fish (2) frequency of mutations being expressed.

OK, now I understand what you mean.

The thing is that in most cases polyploidy occurs at hybridization. Not always, but often. And in some cases, hybrids have some characteristics (like size) that are even more expresed than in parents (called heterosis or hybrid vigor). This effect is lost in next generation. So the question in this particular issue is weather size of fish is really influenced by hybridization effect as I described or is a result of more chromosome sets and impact on size is kept in all next generations. A quick google search revealed that heterosis and polyploidy are often studied together, but I am not competent to comment the connection in more details.

This heterosis has a economic impact. Corn on the fields is mostly hybrid (and polyploid). I was told that the same can be done in pigs without polyploidity. First generation hybrids between different breeds result in superior first generation hybrid. The problem is that in most cases it is not worth to keep two herds of parental breeds to produce a third hybrid herd.
COS,

OK, we are on the same wavelength now.

The plants and economy connection is what made me think in this direction.

The polyploid-hybridization link is not certain, at least for Botias. Barbs interbreed left and right, so maybe. But Botia macracanthus (now renamed to Chromobotia) is a very stable species showing little variation which generally does not breed outside of the wild -- still, it is tetraploid. Of course, it can be a result of a hybridization in the remote past,...I kind of doubt this.

Do you happen to know if there is a table or listing of # of sets for different species? (preferably cyprinids). Maybe I can just take a quick look and see how it feels.
mv Wrote:Do you happen to know if there is a table or listing of # of sets for different species? (preferably cyprinids). Maybe I can just take a quick look and see how it feels.

Can't find a list, but this paper might be a good starting point for Botiinae.

Quote:Mol Phylogenet Evol. 2005 Dec 5; [Epub ahead of print]

Molecular phylogeny of the Southeast Asian freshwater fish family Botiidae (Teleostei: Cobitoidea) and the origin of polyploidy in their evolution.

Slechtova V, Bohlen J, Freyhof J, Rab P.

Institute of Animal Physiology and Genetics of the Academy of Sciences of the Czech Republic, Rumburska 89, 277 21 Libechov, Czech Republic; Department of Zoology, Faculty of Biological Sciences, University of South Bohemia, Branisovska 31, 370 05 Ceske Budejovice, Czech Republic.

The freshwater fish family Botiidae is represented by seven genera on the Indian subcontinent and in East and Southeast Asia and includes diploid as well as evolutionary tetraploid species. We present a phylogeny of Botiidae including 33 species representing all described genera using the mitochondrial cytochrome b and 12s rRNA genes to reconstruct the phylogenetic relationships among the genera and to estimate the number of polyploidisation events during their evolution. Our results show two major lineages, the subfamilies Leptobotiinae with the genera Leptobotia and Parabotia and Botiinae with the genera Botia, Chromobotia, Sinibotia, Syncrossus, and Yasuhikotakia. Our results suggest that two species that were traditionally placed into the genus Yasuhikotakia form a monophyletic lineage with the species of Sinibotia. A review of the data on the ploidy level of the included species shows all diploid species to belong to Leptobotiinae and all tetraploid species to Botiinae. A single polyploidisation event can therefore be hypothesised to have occurred in the ancestral lineage leading to the Botiinae.
This is more than just a starting point, it is a great find...makes me jump.

Unfortunately for me it seems that they did not cover pangio (nobody cares about pangio), but the way they drew the line between 2x and 4x species already should be telling. What I wrote in the PM makes me feel that Pangios are duploid too.

All right, I have to figure out how to get this paper, even the abstract is very telling.

(Funny that Googling on Leptobotiinae -- not the usual spelling -- results in another Czech paper on botias).

Thank you very very much!!!
Quote:A single polyploidisation event can therefore be hypothesised to have occurred in the ancestral lineage leading to the Botiinae.

This is imho the hardest thing to believe about evolution. This is even worse than the example with the change of sex determination mechanism we talked about once before.
Quote:A single polyploidisation event can therefore be hypothesised to have occurred in the ancestral lineage leading to the Botiinae.

This hypothesis is the simplest explanation for tetraploidity of extant species within Botiinae. Parsimony at its finest.
It suffers from the same problem as the sex determination: lets assume that a random event created one 4x individual. Is he going to be able to mate with any 2x's around?

----

Q: do you have more of that paper by chance?
Sorry for late response. Flu.

mv Wrote:It suffers from the same problem as the sex determination: lets assume that a random event created one 4x individual. Is he going to be able to mate with any 2x's around?

Impossible to be 100% certain for ancestral taxa. It works with present day sturgeons and prussian silver carps.

mv Wrote:Q: do you have more of that paper by chance?

Published ahead of print found on sciencedirect

I am not sure if it can be accessed from any computer, universities most likely have access to it. If you can't get it and really, really want it, PM me your email or provide a place on the web where I can temporarily place it.
COS,

Thanks a lot! -- I hope you feel better.

On ploidy: I found a seemingly very related article in the same database:
Ploidy status of progeny from the crosses between tetraploid males and diploid females in mud loach (Misgurnus mizolepis)
I'll read this later, but it looks like the title already provides the answer (and supplements the Czech article with another loach in an interesting way).

I can access the article from the univ. without any problems (reading it right now.... very interesting). The only problem is that they don't cover Pangio and there seems to be no hits on Pangio in the database. Most likely reason is that no one ever looked at Pangio's...or perhaps I'm not doing the right kind of search.
Darn. You were right, cannot read it from home.

The paper was *very interesting* and confirmed another conjecture we had (existence of two species rather than one of another botia). The dojo papers nicely supplement it---seems like there was another poly event in the dojo group (which is closely related to the mainstream botias covered by the paper). Thanks a lot!

If I may ask you one more favor: you are experienced with these databases, unlike me: could you run a search on
Pangio and Genetics
or
Pangio and Genome
just to see if there is anything there? Perhaps "Acanthophthalmus" instead of "Pangio" would work better?

I drew blanks, but this may be because I'm not used to the system.
mv Wrote:If I may ask you one more favor: you are experienced with these databases, unlike me: could you run a search on
Pangio and Genetics
or
Pangio and Genome
just to see if there is anything there? Perhaps "Acanthophthalmus" instead of "Pangio" would work better?

Checked. Not many hits. It seems that Pangio fish are studied more from species description view, but only one genetic study so far (not about polyploidity). My guess is that this is something you should be asking people who work with this fish. Two papers (and I could only find 5) were written or cowritten by Singaporean researcher named Lim KKP (Natl Univ Singapore, Raffles Museum Biodivers REs, Dept Biol Sci, Singapore, 119260 Singapore). Try to google it and find some emails, he/she seems to be the right person for your questions.
COS,

Thanks a lot.

I'll try to find the genetic study you mentioned, anything about these guys is interesting to me. species description is total crap in this case, they sampled the species in a few places, defined two species on the basis of the sample (after a few decades of going back and forth) and failed to realize that most of the population has a mix of two characteristics.

Yes, I think I know who Lim is.

I managed to see a live Leptobotiinae (usual sp. Leptobotia) today...this is the alleged 2x ancestor of the current 4x species. Interestingly, it actually looks very similar to Misgurnus --- gen. outside of the Czech study asacr, but the one which is known to have individuals with different ploidi. Of course, a visual comparison is not the way to conclude anything, but still I wonder a little if they did not miss something essential here.

Let me reread the paper carefully tomorrow.
COS,

Do you per chance have access to JSTOR? -- apparently we have only partial, and I could get only the first page of the paper.

Sorry to bother you, but you opened a pandora box by showing me where to look... :oops:

Systematics of the Acanthophthalmus kuhlii Complex (Teleostei: Cobitidae), with the Description of a New Species from Sarawak and Brunei
Mary E. Burridge
Copeia, Vol. 1992, No. 1 (Feb. 3, 1992) , pp. 172-186

Online link seems to be
http://links.jstor.org/sici?sici=0045-85...size=LARGE
mv Wrote:Do you per chance have access to JSTOR? -- apparently we have only partial, and I could get only the first page of the paper.

Sorry, no access. I doubt that 1992 paper is online anyway.
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