West African Chromosome studies?

[Chromedome]

Hey, is anyone out there aware of mtDNA analysis of any West African species groups? This science has been around for a while now, and I've seen very good data on Killifish from SA and Africa, some on livebearing fish, and more recently some very interesting studies on Central American Cichlids. There are some being done within certain groups of Malawian Cichlids, but who cares? :tongue:

Anyway, I've not heard of any such work with West African groups. Certainly this science could help fill out some information on the Pelvicachromis species, especially taeniatus. One risk is that some people consider this to be the final answer, but I'd take that risk to see some data.

 

[aquaticclarity]

I know that Dr. Lamboj has started the ball rolling in Pelvicachromis (Ted and I sent him fin clips from 80+ wild specimens that I had). I don't know how far along things are with the work though. It all takes time and $$$. Not to mention the desire to do the work!

Jeff

 

[tjudy]

In the greater scheme of things molecular data is one small piece of evidence that can be used along with other classification tools. Molecular comparisons are being used with Pelvicachromis, as Jeff mentioned, and also Hemichromis. It is pretty mich standard practice today to take tissue samples when possible even if there are no immediate plans to have them analyzed.

Molecular comparisons have been used heavily in the investigation of evolutionary relationships between crater lake cichlids and the cichlids of surrounding river systems. Most notably Lake Barombi Mbo.

 

[tjudy]

In the greater scheme of things molecular data is one small piece of evidence that can be used along with other classification tools. Molecular comparisons are being used with Pelvicachromis, as Jeff mentioned, and also Hemichromis. It is pretty mich standard practice today to take tissue samples when possible even if there are no immediate plans to have them analyzed.

Molecular comparisons have been used heavily in the investigation of evolutionary relationships between crater lake cichlids and the cichlids of surrounding river systems. Most notably Lake Barombi Mbo.

 

[ed seeley]

To add to Ted's reply the results you get also depend on which section of DNA you look at. While at Uni I did some work on Tangyikan cichlids at looked at the D-loop of their mitochondrial DNA. This is a slowly and steadily evolving section of non-coding DNA that was suggested could be used as a molecular clock. As it is mitochondrial it is only passed down the maternal line too.

Other sections of DNA will change differently and be swapped and mixed up during the process of meiosis and sex and, if they are sections that code for proteins, there are then different selection pressures on them compared to other non-coding sections (which may also have selection pressures on them but different and probably less 'intense' than the coding sections which will more likely have phenotypic consequences if they are changed by mutation).

A phylogenetic tree generated from different sections of DNA will probably give different results to each other. The bootstrap program and phylogenetic consensus will also give different results too! This is why it is important that DNA studies should be done on multiple sections of DNA (not that this happenes very often as each lab or person tends to use a set of primers and a section of DNA they are familiar with and stick to it partly as the primers aren't cheap and once you know they work you're halfway to being done!) and compared with other non-molecular data.

The important thing IMHO, in both molecular and non-molecular data is that you try to look for common characters or DNA that does not have heavy selective pressure on it as these are the features that selection will be working hardest on to change them rapidly (just think of the teeth of some mbuna and Victorian cichlids that have changed in two or three generations in captivity) or keep them the same for long periods of time. What you need to look at are the characteristics (hard to so with these) or DNA areas that are allowed to drift and change as their alterations have no effect upon the organism.

More to the point one DNA study will not provide a definitive answer to anything, just more, different information to add to the collective whole.

 

[Nebraska_cichlids]

Ed,

with the recent advent and now widespread availability of high-throughput sequencers (454, ABI, Solexa) many of your concerns are easy to address for a molecular biologist. Any of these machines would give you the (mt)DNA sequence of the entire genome of a species in one single run. Price tag as low as $1500 per analytical run.

There would be "only" two obstacles to this approach: (1) annotation, i.e., assigning a given sequence a location and putative function, and (2) a major computational biology effort where species comparisons would give us insights into how closely related certain species are. As for the annottaion probelm, one could use the zebrafish (a major model organism in various areas of research and DNA fully sequenced) as a reference.

Janos

 

[ed seeley]

Ed,

with the recent advent and now widespread availability of high-throughput sequencers (454, ABI, Solexa) many of your concerns are easy to address for a molecular biologist. Any of these machines would give you the (mt)DNA sequence of the entire genome of a species in one single run. Price tag as low as $1500 per analytical run.

There would be "only" two obstacles to this approach: (1) annotation, i.e., assigning a given sequence a location and putative function, and (2) a major computational biology effort where species comparisons would give us insights into how closely related certain species are. As for the annottaion probelm, one could use the zebrafish (a major model organism in various areas of research and DNA fully sequenced) as a reference.

Janos

While running the whole mtDNA sequence would solve some of the practical sequencing problems (and some other advances since I did my work on the D-loop) they still do not make the accuracy issues of using one type of DNA any better. You still have to run various phylogenetic analyses to compare the DNA sequences and they generally provide different weighting to different mutations to try and compensate for whether mutations occur is coding or non-coding areas and will therefore generate different results from each other.

Aside from the technical aspects my point was that a DNA study is not correct simply as a function of it being a DNA study. It could be as fallable as any other comparative study unless the various factors are born in mind.

 

[Chromedome]

Thanks for the input, gang. I was mostly looking for already published data, but it sounds like the investigations are just now getting underway, so that's a ways off. (Ted, where are those comparative studies on Barombi Mbo, etc., to be found? Title, authors?) As I stated, I have seen many of these already, and feel that some researchers have weighted this data far too heavily when using it for classification purposes. However, I believe that all the information - molecular, meristic, and behavioral - needs to be considered when trying to organize fish into genera and species.

When an relatively delicate species is as widespread as Pv. taeniatus, it certainly seems that adequate research is lacking. The range of this one Cichlid species covers that of several species of the Killifish Genus Chromaphyosemion - in fact, it almost matches the range of the entire genus. These were all once thought to be a single species as well, but research in the last 20 years has proven otherwise. And they are found mostly in the same habitats as taeniatus. I really don't think we've even scratched the surface yet.

One thing I would mention, however. Clippings from wild fish are only useful if you have the exact collecting location with GPS coordinates. Wild fish that were shipped in commercially are not usually dependable as to exact locations. That's why scientist and hobbyist collections are so important, TED!! :biggrin:

 

[tjudy]

The current species P. taeniatus is composed of two fish that were considered different species until lumped together in the 1960's. P. teaniatus was originally given to the fish from Nigeria (which we call the Nigerian forms today). The other species was P. kribensis, which are the varieties found in southern Cameroon (Kribi River). P. taeniatus was the older name, so that is they all became P. taeniatus.

 

[Chromedome]

Same thing happened with the Chromaphyosemion. There were about 4 species described, all synonymized by Scheel based on chromosome structures (pre-molecular studies, he was famous for them). Later analysis resurrected a couple of those species, and more detailed collections, especially in Cameroon, brought us a plethora of species. Tomas Hrbek did a collection through Cameroon, and thereby had actual accurate location data when he did his molecular analysis.

I should point out, of course, that Killinuts have always been a couple of decades ahead of the Cichlidiots!

 

[tjudy]

Why are you angling for an argument? If killi taxonomists want to justify their existence by splitting hairs and elevating fish form opposite sides of a stream to species status, then more power to them. Personally, taxonomy that takes into account the natural genetic variation within populations is more realistic.

But hey... we are a nice little hobby forum. You asked a question and we hobbyists answered it as best we know. If the cichlid taxonomists were in here I am sure that they could be more specific for you. So, DARRELL, the next time you are collecting fish in Cameroon please do not neglect to come in here and tells us all about your molecular protocols and how you name the probably dozens of new species you will personally work on.