Thursday, March 12, 2009

Evolution Claims: Lake Malawi Cichlids

I have been directed to several evolution claims, most of which I have seen before, and which fall under the category of ring species, or as I call it, “Big dog, little dog”. I have clarified this in the new side-bar titled “Challenge to Evolutionists”. I have also tried to clarify what appears to me to be characteristic of actual evolution, as it is said to have produced man out of a line leading back to a single replicator.

For now, I will take on the Lake Malawi cichlid claims, found in Proc. Natl. Acad. Sci. USA Vol. 96, pp. 5107–5110, April 1999.

To appreciate the issue, I suggest that the reader go to the link and at least read the intro and the graphics.

The Lake Malawi cichlids demonstrate set theory in action.

Cichlids are varieties of related fish that live in Lake Malawi. There are said to be more than 500 species in the lake. This study addressed rock dwellers, or “mbuna”, of which there are some 300 species. The intent of this study – short form – was to attempt to nail down DNA relationships of this population consisting of such wide variations.

The study concluded with a dendogram –tree drawing – of relationships between several varieties. While the tree appears to be firmly implied, there is some wiggle in the conclusions, for several reasons given in the text.

My conclusions follow, based on my understanding of the text, and assuming that the methodology was sound and not compromised, an assumption that is not possible to test without replication of the procedure myself (won’t happen).

First The fact that hybridization can, in fact, occur shows conclusively that there is no genetic barrier that has been created to prevent it from physically occurring. So speciation, as is defined by the tests (not the implied meaning) is said to be due to other considerations, primarily coloration of the fish, and not the salient jaw morphological differences.

Second, the population differentials are not analyzed by features gained through changes to the overall genome, they are based on features lost (missing DNA) as each group finds its own niche.

Also, cichlid speciation doesn’t include much allelic differentiation:
“The branch lengths in the tree reflect the distribution of genetic variation within and among species. Consistent with previous evidence for incomplete lineage sorting (9), the vast majority of genetic variation resides within populations. Only a small proportion of the variation is distributed among species and genera, suggesting that speciation has occurred without significant population bottlenecks. Consistent with this idea, surveys of mitochondrial DNA haplotypes (30) and microsatellite loci (13) have found high allelic diversity within most populations”
In fact four separate populations are given 100% correlation with the DNA of the entire crowd. The presumption seems to be that loss of DNA correlation means speciation, at least for purposes of the tree graph.

If the loss of correlation is accompanied by an accumulation of new genetics, not contained in the original population, say for jaw morphology, then an evolutionary event is a justified conclusion. But that is not the case, in this analysis. In this analysis only the loss of genetic comparability is presumed and documented, meaning that the original cichlids had all the DNA required to make the subsequent cichlids.

Also it is said that jaw morphology was not the defining difference; coloration was.

It is not clear how the DNA analysis was performed in terms of selecting points on the DNA molecule to compare. It appears, however, that the selection might have been random, occurring roughly every 0.5 centimorgans:

“Our data set consists of 2,247 characters derived from 11 selective primer pair combinations. This corresponds to a marker about every 0.5 centimorgans over the genome (21). Of these, 1,205 were polymorphic among the taxa studied here.”
From Biology on-line:
Genetic polymorphism Definition
noun
(1) The existence together of many forms of DNA sequences at a locus within the population.
(2) A discontinuous genetic variation that results in different forms or types of individuals among the members of a single species.

Supplement
Genetic polymorphism promotes diversity within a population. It often persists over many generations because no single form has an overall advantage or disadvantage over the others regarding natural selection. A common example is the different allelic forms that give rise to different blood types in humans.”

The impact of this is not clear. Presumably the remaining 1,047 characters were not common to the entire group, but are they common only to the original cichlids? From line length, this seems to be the case, but it is not clear. This is not enough information to make any conclusion. Especially on the nature of the characters involved. However, presuming this to be the case, the difference is still subtractive, not additive; the resulting populations are still subsets of the original until shown otherwise.

Is there any reason from this to think that new characteristics have “evolved” ? Given that the main morphological change is the mouth configuration, and that this characteristic variability is common within color-designated speciation, and given the ability to crossbreed, there is no morphological reason.

Given that the DNA variability under discussion is subtractive, not additive, there is no reason to think that the variations are not just subsets or subspecies of the main, overall species, which still exists.

Since the time frame assignments are based on differences in the number of common DNA markers seen, and there is no actual clocking mechanism involved other than this inference, there is no reason to think that this is meaningful, especially since the markers are not defined as to purpose, and might be meaningless to the presumed speciation.

To summarize: given the stated ability to cross-breed, plus the existence of members of the original population, and the lack of any reason to think that there was speciation based on new features, the conclusion follows that this is consistent with variation within a genome: subspeciation; not with evolution beyond the original genome.

If you disagree with my assessment of the information in the cichlid study article, let's discuss it.

2 comments:

Scott Hatfield . . . . said...

I admire your gumption in attempting to engage the literature I referenced. A few comments:

1) It is one thing for two related species to produce hybrids, it is another to demonstrate that such hybrids would be either reproductively viable or likely to gain a selective advantage. It is possible that hybrids show increased vigor in some area, but this vigor can only be of an advantage if the hybrid is itself able to reproduce.

2) The fact that some Malawi cichlid species can hybridize does not demonstrate that all of them can hybridize. In fact, since this study is confined to species that share similar habitats, it is to be expected that a higher percentage of them might be able to interbreed.

3) Field workers often use conventional taxonomic indicators (coloration, feeding morphologies, behavior) rather than reproductive isolation to describe 'species', and you are correct to note that this study doesn't demonstrate individual speciation events. Indeed, many of the cichlid 'species' may in the future be classified as 'sub-species'. That is the nature of systematics today, in that they are continually reevaluating one set of claims (largely traditional) with the tools of molecular biology.

4) Your inference about the differences between the populations being entirely 'subtractive' isn't supported by the study. You would need to know the genome of the putative common ancestor or ancestors to the present-day populations in order to do that comparison. The purpose of the study is to determine what pattern of selection would be consistent with both interspecific and intraspecific genetic variation in the cichlid populations studied. This in turn was limited to various markers, not an exhaustive survey of the present-day genomes of the present-day populations. Their big conclusion is that there is a lack of evidence for recent bottlenecks between these species. This suggests a wide availability of unfilled niches within the Lake Malawi environment, which is consistent with the hypothesis of rapid and recent speciation.

Stan said...

Scott, thanks for your comments.
Your points 1, 2, and 3 do not seem to contradict my conclusions in any way, but point out some unknowns that were not spelled out in the study. Interbreeding could mean either hybridization or it could mean breeding between subspecies. In either event it was observed and cannot be discounted using the information provided in the study.

Your point number 4 seems incorrect since the dendogram clearly does indicate 100% common ancestors (although based only on incomplete DNA analysis). The use of the DNA random sampling was thought sufficient to make the dendogram, so that is what must be used to look at the methodology of choosing the branches for the "tree". The branches are clearly chosen by the number of remaining DNA markers common with the preceding branch. This is very clearly subtractive. There is no indication at any point that there are beneficial added genetics that are used in the definition of the tree branches. In fact the DNA markers are unknown in terms of their utility to the fish.

"Their big conclusion is that there is a lack of evidence for recent bottlenecks between these species. This suggests a wide availability of unfilled niches within the Lake Malawi environment, which is consistent with the hypothesis of rapid and recent speciation."

This is, in fact, their conclusion; I feel that it is unsubstantiated by the evidence presented in the article, for the following reasons:

The genetic variability is said to be greater within a single genome than between genomes. If this, plus the existence of 100% ancestors, indicates subspeciation, not speciation, then the issue of bottlenecks is rendered moot. There are no bottlenecks to subspeciation.

So using "bottlenecks" as a definitive indicator for speciation oversteps the boundaries of the actual evidence that is made available in the article.