Phylogenetics discussion

[mauriciodelamaza]

Nandus wrote:

My only problem with DNA being the last word on the subject is the evolutionary plasticity cichlids posses. It is known that cichlids evolve faster that most other groups of fish and other animals for that matter.

Dear Nandus,

While I mostly agree with you on the genetic plasticity of cichlids, I have also noticed in this forum that sometimes molecular studies have been “frowned upon” basically on the (sound) argument that inferring the whole evolutionary history of a determined taxon based on only one or two (out of millions of) genetic loci may be (and most certainly is) misleading.

However, let us not forget that Systematics is in essence the Science of identifying, naming and most important, establishing evolutionary relationships amongst different taxa. This last activity or discipline is called Phylogenetics.

Phylogenetics on the other hand is in essence the Science of discerning synapomorphies and uncovering through those the evolutionary paths of taxa…... In other words, it is about identifying characteristics which are homologous (shared by all members of a particular taxon e.g. presence of a dorsal fin in the Cichlidae) and which ideally show some degree of variation or states (e.g. in the number of spines and soft rays present) which may reflect e.g. genetic mutations that happened somewhere along the parental line of descent, and which may allow us to draw conclusions as to the evolutive relations of taxa within a taxon (e.g. Thoricthys, Vieja and Herichthys within Cichlidae). As a general rule of thumb, the more of these homologous-variant-characters or attributes (also called character-states) are found and taken into account, the more likely the true evolutionary paths of a particular taxon and its relation to others may by discerned.

The fundamental problem becomes distinguishing which characteristics may be homologous, that is have been inherited along the line of descent from a common ancestor that “first developed it”, and which characters are analogous, that is, are the product of convergent evolution.

In some cases this may be a rather straight forward task……. For example: while dolphins and cichlids both have dorsal fins, it becomes obvious that such structure is analogous and not homologous. The trait was not inherited down the line from a common ancestor, but is the product of convergent evolution consequence of mammals returning to the sea. Therefore, it cannot be deduced that cichlids and dolphins are related based on the possession of a dorsal fin, as it is obvious that dolphins are not cichlids.

In other cases discerning whether a single “characteristic” on itself –be it colour, shape, number of spines, patterns of behaviour, or a sequence of bases that conform a gene- is homologous or analogous becomes extremely difficult…… For example: The breeding dress of Amphilophus macracanthus and the Herichthys cyanoguttatus complex. Is its “apparent state” consequence of a common ancestor inheriting such trait down the line, or an adaptation acquired through a convergent evolutionary process?

The diagnosis of Cichlasoma scitulum for example is based on a series of character-states which, to mention one C. scitulum differs from C. fecetum in having 8-9 anal-fin spines vs. 6-7. In this case, both species are identical in so many “relevant” characters that it can be demonstrated that both species are indeed very close, and that the meristic differences are probably the product of a set of states (6-7 and 8-9 spines) within a homologous structure (anal fin) that appeared in an ancestor –probably due to mutation- which inherited them down its line of descent diverging into a separate lineage (species).

From the above it may be concluded that any attribute –including a gene locus- may be a “good” or a “bad” phylogenetic character depending upon whether its “existence” is the product of convergence, or of it being inherited in a particular new form (state) down the line of descent.

As you well state, the apparent genetic plasticity of cichlids does not help in this matter. However, it is my opinion that the value of molecular characters is as good a character as any other meristhic, morphometric or qualitative character, as long as it represents a synapomorphy, and may be qualitatively expressed in terms of clear-cut and preferably discontinuous states......... But that is another story.

Saludos

Mauricio De La Maza

[Willem Heijns]

very well spoken, Mauricio

BTW, is genetic plasticity a well defined term? I have never heard of it

[Don Hiatt]

Hi mauriciodelamaza,
You presented your information in a very clear manner and thanks for your time to address this matter.

Hi Willem,
I believe I first heard the term "Morphological Plasticity" in a paper on Anolis lizards from Central America. I have heard the term used for cichlids too. Evolutionary plasticity is another term that is in use.

[mauriciodelamaza]

Thanks Nandus and Willem

Hello Willem,

Is genetic plasticity a well defined term? I have never heard of it

You really had me thinking, and I am not sure the term “genetic plasticity” is a well defined term..... However, I guess that, in the context of this thread the terms “Evolutionary Plasticity” and “Morphologic Plasticity” that Nandus mention could be substituted by the term “genetic plasticity” on the grounds that morphologic changes and evolution at the population level are the manifestation of changes at the genetic level, although it becomes clear that the three concepts are not exactly synonyms.

In that sense, I will try to produce an ad hoc definition for the term “genetic plasticity” and what I meant by it:

Genetic plasticity is the capacity of a given taxon to express, suppress and/or mutate genes, which reflects upon the degree of easiness and speed with which it may evolve in terms of shape (morph), behaviour, conduct and/or any other attribute, thus adapting to new environments.

Any thoughts are highly welcome

Saludos

Mauricio De La Maza

[Don Hiatt]

Mauricio,
Well, I think the term "genetic plasticity" is not too far off. As we all know, cichlids are very diverse and prone to change. I think the term actually fits quite well.

I also Google'd the term and I got 10 pages of genetic plasticity.

I was about to congratulate you for coining a new term. lol.

[mauriciodelamaza]

Thanks Nandus ,

After reading your post I googled for the word myself……. While the definitions that I found of “genetic plasticity” are mostly in the context of the “malleability” or capacity of the DNA molecule to assume various shapes under certain physical-chemical conditions; there seems to be a lot of papers in which the term is used in exactly the same semantic context that I did. Therefore, even though I could not find an explicit definition in such context (within my no more than two minutes search) it becomes clear that the term has indeed been used before.... I also agree with you that the "plastic" metaphor fits quite well .

Saludos

Mauricio

[kercheznee]

it seems that there are two schools to me:
one that frowns upon gene markers in developing an evolutionary tree
and one that frowns upon morphology as the determiner of the evolutionary history within a clade.
is science currently in a, "one or the other" situation, concerning the evolutionary relationships within the family cichlidae. or is there a combination of both. it seems that they are intrinsically linked. morphology is determined by genetics isn't it? i have read some papers where there is only the DNA method used and it seems to have many contradictions and anomalies (for example the one nandus posted in which several species appear on different branches). however from a strictly morphological standpoint, there also seems to be many errors and oversights. i read a post in which michi tobler seemed to equate the two methods for determining the phylogenetics of cichlids, is this being practiced? sorry if any of the terminology is incorrect, i am only in my first year of undergrad biology and haven't gotten everything nailed down.

[mauriciodelamaza]

Dear Kercheznee,

I think you touched a very interesting, but rather complex topic here, so I will try to pose my opinion in that respect, hoping not to be oversimplistic:

Concerning molecular markers, I believe that the “frowning upon” the use of molecular markers in phylogenetics has more to do with the still limited availability of techniques and statistical tools to researchers, than with the “right” or “wrong” of using one or the other. Let us remember that phenotypes reflect genotypes, and in essence it is genetic differences that separate species from one another.

I think that most of the critics of using molecular markers, as I expressed in my previous posts, centre on the number and type of genetic markers being used, and not on their use in itself…… Let us take another example: Take a white (the type with pink eyes) farm rabbit and a cave Astyanax. Imagine the rather dumb and hypothetical case in which a researcher performed a “blind” parsimony analysis based solely upon the genetic material (not bothering to acquaint himself with the species it came from) using the gene that codes for “albinism”as a marker. Could he conclude that white rabbits and cave Astyanax are more related to each other than let’s say Astyanax to Myleus (pacus) in an analogous way to concluding that dolphins are cichlids based on the possession of a dorsal fin?

On the other hand as you assert, systematists, especially those in the cladistic school frown upon the use of morphometry in the determination of evolutionary history. Some prominent Scientists indeed state that continuous variables, which morphometric characters are in essence, are not useful at all in phylogenetic analysis because precisely of their continuous nature. That based on the fundament that speciation occurs at the individual level and not at the population level, and that statistical methods like Principal Components represent pooled aggregates of samples and not individual members of species.

Another school affirms that ONLY SOME morphometric characters are OK as long as they do not overlap and therefore can be coded into states in a qualitative manner that may be used in the statistic models available e.g. short sized head, medium sized head, large size head.

Yet another school, especially amongst Botanists, accept and have developed what are called Character-Coding-Techniques which attempt to “break” continuous morphometric characters into qualitative states that may be “fed” into parsimony analysis…..the technical and fundamental issues of these which have been strongly criticized by some and accepted by others I prefer not to get into…….

As you can see, the problem of Morphometrics is basically a problem of how to deal with variables that have infinite states, especially when there are no empty gaps between the extreme members of a population and the extreme members of the contiguous one.

Just to round up another example:

Imagine that we have two sets of cichlids in two contiguous bodies of water. Body A has red cichlids ( R) and Body B has blue cichlids (B). Since colour is a continuous variable, as it is the reflection of infinite possibilities of wavelengths, the first school of thought would automatically reject such character. The second and third schools would codify it into qualitative Red vs. Blue no mattering which tone of red or blue respectively the members of each body of water have.

Now imagine the same bodies of water having (A) blue cichlids and (B) green cichlids. While the character being analysed is still the same one in essence: colour, or reflection of a particular wavelength, the second school of thought would probably reject this character as a valid-phylogenietic-one based on the overlapping of both colours at their extreme ends. Where does blue turn green and green turn blue? They may ask, and stress the impossibility of discerning true gaps, unlike the previous example, between the populations. In this case, the third school says that the appropriate statistic techniques should be applied to arbitrarily, but logically break the character into qualitative states (green and blue).

Which school is correct? It is my opinion that the three of them have strong sound arguments, but that since the world is so colourful and complex, and not simple, black and white, we should attempt to make sense of it with the material and techniques available according tour resources in our particular moment in space and time, and keep on tuning as technology is developed that may allow us to get a better picture with a better resolution of the world around us.

Saludos

Mauricio

[mauriciodelamaza]

Just to clarify that while colour is not a morphometric character, it is a continuous variable (if seen from a wavelength reflected perspective) which illustrates the problems that these types of variables create for phylogenetic analysis…….. Switch the attribute Colour for e.g. Anal Fin Base Length, and there is an example applied to morphometry.

[Willem Heijns]

this is becoming a very interesting thread indeed

I'm a little amazed at some of the posts. mind you, I am not a trained biologist, so I can only use my common sense. as I understood, morphological plasticity of a chacarter renders the character less useful for phyogenetical studies because it can vary within the organism (the individual) through it's lifetime. the development of pharyngeal teeth is a good example (feed a cichlid snails and it will develop molariform teeth). Axel Meyer has done a lot of work on this.

I don't believe the same can be said for DNA. an organism simply cannot change it's DNA (genome) in it's lifetime.

I get even more confused if the term evolutionary plasticity is applied. and the two terms are combined into one.

the mistake might be that the term plasticity is used where variabilty is really what one is talking about. if that is correct I can understand the discussion of a high rate of evolution in cichlids and the rest.

but then, I'm only a layman

[mauriciodelamaza]

Hi Willem

I agree with you, this is becoming a very interesting thread .... I also concur with you in your interpretation of the term morphological pasticity, which is why I stated, and I quote:

......in the context of this thread the terms “Evolutionary Plasticity” and “Morphologic Plasticity” that Nandus mention could be substituted by the term “genetic plasticity” on the grounds that morphologic changes and evolution at the population level are the manifestation of changes at the genetic level, although it becomes clear that the three concepts are not exactly synonyms.

I think the problem here is semantics-related, and arises from the use of the "plastic-metaphore" to highlight the phenomenon of "easiness of change" at the "x" level.

In the above sense, I think we all concur in that cichlids seem to have a greater ability to transform their shape than other taxa. As you well state, environmental factors can, and do have tremendous influence upon the individual, molding characters -like plastic- such as lip-metrics or teeth development to an extent that the character becomes worthless in a phylogenetics context; and as you well state "individuals cannot change their genome in their life time"

Nevertheless, some individuals can and in some cases will drastically modify their shape through physiological or even behavioural induced events that may trigger the expression or supresson of certain genes -without modifying their genome- throughout their life time leading to phenomena like allometry; or in extreme cases metamorphosis e.g. the change of catterpillars into butterflies or tadpoles to frogs. Some Amphibians, e.g. some salamanders can even remain in their larval stage (mud-puppies) throughour their whole life. It is for the above reason that I included in my definition the phrase ".......capacity of a given taxon to express, suppress and/or mutate genes...."

It is because of the above that I state that morphometric changes at the individual level can be environmentally induced as in the case of the development of pharyngeal teeth, or physiologically induced as in the case of the development of nuchal hump or an alfa colouration- through the expression and/or supression of genes; and at the population level by the same previous factors plus mutation.............The problem becomes descerning one factor from the other.

On the other hand, could "evolutionary plasticity" be more related to the "easiness" with which a taxon can radiate adapting to new environments through genomic changes that manifest in the phenotype, and consequently in the shapes that may arise from it?

From my point of view, it is my opinion that as you point out, the three terms are different. However they are related, and could be interchanged within certain contexts, especially if we keep in mind that it is a metaphore, and not an absolute term that is being employed.

Saludos

Mauricio

[Tom Lorenz]

Hopefully I can simplify this. You cant 'change' your genes, so they aren't plastic in and of themselves.

As mentioned, how they are expressed can change. The correct term here is phenotypic plasticity. Looking up that term will help a lot.

There are other problems with using genes but their plasticity is not a question. Which genes you examine could be a much better question.

[Tom Lorenz]

I'm not big on just using genetics but the reverse argument can me made against morphology. Just using morphological characters can make for a mess BECAUSE there is phenotypic plasticity. An example is cichlid teeth which were used for taxonomy before until it was found that they weren't the best characters to use (they change in an individual's life time).

All said, both morphology and molecular biology are necessary to flesh out the picture.

[mauriciodelamaza]

This is truly getting complicated.

Dear Pliosaur,

I guess it all depends on at which level –individual vs. population- we are talking about, and what is meant by the term “plasticity”.

I suppose that while a component of “morphologic plasticity” is indeed a component of phenotypical plasticity, and within certain contexts the terms could be interchangeable, I am sure that again the fact that they are not synonyms would produce a (genuine) critical reaction on some, if it were claimed that they may be in absolute terms “combined into one.”

Morphology or shape is a component of Phenotype, just as any other trait (qualitative, behavioural, physiological, etc.) which is the consequence of gene interactions, manifestations or suppressions within a genotype which physically manifests itself in what makes the essence of any living creature.

You wrote:

You cant 'change' your genes, so they aren't plastic in and of themselves.

Again it depends upon what is meant by the term “plasticity”. The Webster´s New World Dictionary defines Plasticity as “that can be molded or shaped”, and it is to that definition that I will adhere for purposes of this debate.

Both individuals and populations can and sometimes “reshape their genotype” through a phenomenon called “mutation”. Mutation is one if not the major factor that triggers Evolution. There are two types of Mutations: Chromosome Aberrations e.g. polyploidy in Plants-; and Point Mutations which occur at the nucleotide level. While it is logical to think that every gene and every chromosome in every living creature has the same probability to mutate, the fact is that that is a false statement. Just look at the evolution of Crocodiles which shape has remained almost unaltered for tenths of millions of years, and the adaptive radiations that some cichlids show in lapses shorter than 10,000 years.

Deletions, duplications, translocations and inversions of chromosomes are all Chromosome Aberrations, and therefore are Mutations which can, and do change genotypes and consequently phenotypes both in species and in populations; and consequently they also trigger evolution…... Since sections of chromosomes play a very important role in the “remolding” of genetic material which alters size, colour, physiology, and behaviour amongst other traits, the frequency with which certain genes contained within sections of chromosomes mutate depends on the physical location of them within a chromosome,and in some instances (few cases) such aberrations are neutral and can be passed on to the next generations without affecting their reproductive viability, then the genetics of individuals and populations can be said to be plastic.

Saludos

Mauricio

[mauriciodelamaza]

Just one more comment: for mutations to remain within a population they must be either “good”, neutral or recessive and must happen at the germoplasm level, that is within reproductive cells……. Somatic cell mutations are normally detected and eliminated by the immune system of the organism, otherwise they may become a serious health problem e.g. some cancers.

[Willem Heijns]

Both individuals and populations can and sometimes “reshape their genotype” through a phenomenon called “mutation”.

I'm afraid I have to disagree with you here, Mauricio. Individuals cannot "reshape their genotype". in sexually reproducing species mutations can only occur between one generation and the next, i.e. in reproduction. furthermore the term genotype is usally applied to species and/or higher taxa. so an individual cannot change it's genes wheras a species can change it's genotype through time. and that's where variability comes into play. and cichlids are well known for their high ability to develop mutations that get fixed in the genotype.

so if genetic plasticity refers to this ability I can understand what is meant by that. I still reject the term evolutionary plasticity though. if genotypes weren't "plastic" evolution wouldn't even occur.

[mauriciodelamaza]

Hi Willem,

While I must say that I concur with you in that only mutations that occur at the reproductive-cell level in sexually reproducing species can pass on to the next generation(s), the above does not mean that mutations cannot occur within individuals at the somatic level, or that a single individual cannot receive a “piece” of mutated DNA from one of its parent’s reproductive cells without necessarily changing the whole genotype of the entire population or taxon.

Willem wrote:

………the term genotype is usally applied to species and/or higher taxa.

I am afraid here I cannot concur with you. According to Warwick and Legates,“Breeding and Improving of Farm Animals” of which I admit that I have a rather old edition, 1980, Genotype is defined as “The Genetic constitution of an Individual.” Kimball, Biology, Fourth Edition defines genotype in exactly that same manner. Winchester in "Genetics: A survey of the Principles of Heredity" goes even further down a level and defines Genotype as “the genetic constitution of the somatic cells of an organism”.

As can be inferred from the above, the term genotype applies to the genetic constitution of organisms at the “n” level which goes from the most basic unit: the cell to “gene pools” in Population Genetics.

Saludos

Mauricio De La Maza

[Tom Lorenz]

I still think this is being made more complex than necessary. The term "phenotypic plasticity" is well accepted and used in the scientific literature. A fish being different colors depending on its food shows its "phenotypic plasticity". "Genetic plasticity" I think can just indicate that a population has a variety of alleles or genes that may be adaptive for different situations.

For mutations I'd simplify things too For evolutionary purposes just think "neutral", "lethal", or "adaptive". Most mutations are lethal or neutral (kill the organism or do nothing). Sometimes they are adaptive. I think talking about inversions, deletions, etc. is not necessary here. (just my opinion!)

All of the points here are good but the complex aspects haven't even been touched yet (additive genetic variance, epistasis, molecular techniques, etc.), so it's best to be clear at this level. It is very true that individuals cant alter their genotype (unless you believe in Lamarckism). It is also true that populations can have new genes arise by mutation. Common garden experiments are the KEY to finding out if you have changes in genes or changes from plasticity. I can give some really good references if you guys want.


Cheers,

Tom

[Tom Lorenz]

And back to the topic at hand. I agree with what everyone has said about genetic characters being good, but not enough.

But morphometric characters have just as many pitfalls (phenotypic plasticity in particular). The best bet is to have as many traits (molecular AND morphological) as possible. The concept of 'species', by the way, is controversial in itself.

[mauriciodelamaza]

Tom wrote:

The term "phenotypic plasticity" is well accepted and used in the scientific literature.

I agree. All of the other terms that have been used here are also accepted and used in the Scientific Literature. And none of them are synonyms.

“Morphologic plasticity of a character” as Willem states relates to how a character may be modified by environmental factors rendering it of little use as a phylogenetic character. E.g. pharyngeal teeth and lip-metrics.

“Morphologic plasticity” refers exclusively to shape, and to the capacity of a given shape to be molded or changed by certain factors which may be of genetic or of environmental origin.

“Genotype” refers to the genetic constitution of an individual.

“Phenotype” refers to the appearance of an organism which results from the interactions between its genotype and the environment….. Morphology or shape is only one of many phenotypical components like colour, behaviour, physiology, etc.

“Phenotypical plasticity” refers to the capacity of organisms to change or mold their phenotype. It includes “morphologic plasticity” amongst other components.

Tim wrote:

"Genetic plasticity" I think can just indicate that a population has a variety of alleles or genes that may be adaptive for different situations.

“Genetic plasticity” as Willem states includes the “ability to develop mutations that get fixed in the genotype” amongst other components……… For example: “….Staphylococcus aureus is an important nosocomial and community-acquired pathogen. Its genetic plasticity has facilitated the evolution of many virulent and drug-resistant strains, presenting a major and constantly changing clinical.......” (Holden M.T.G et al, 2004, Complete genomes of two clinical Staphylococcus aureus strains: Evidence for the rapid evolution of virulence and drug...)

“Evolutionary plasticity” refers to the ability to evolve, and is a consequence of genetic plasticity as the above example shows.


Tom wrote:

I think talking about inversions, deletions, etc. is not necessary here.

I was not talking about them……I just mentioned them as the types of Chromosome aberrations that exist because understanding basic mutation theory is key to understanding evolution.

Tom wrote:

……..the complex aspects haven't even been touched yet (additive genetic variance, epistasis, molecular techniques, etc.), so it's best to be clear at this level

Since the thread has centred on the topic of phylogenetics, evolution, morphometry, and DNA markers; and not on genetics and molecular techniques, I agree that unlike the concept of mutation which I find relevant to understanding basic evolution, “it´s best to clear at this level”.


Tom wrote:

It is very true that individuals can’t alter their genotype (unless you believe in Lamarckism).

I think no one here has talked here about individuals or populations altering their genotypes in a “directed fashion” in a Lamarckean sense….. When I mentioned alteration of genotype at the individual level I thought I had made it clear that I meant either (a) somatic cell mutations which may lead to tumors and other somatic diseases which affect shape and which by definition are NOT passed along to the next generation or (b) mutations at the sexual cell level in a "normal" individual which may be inherited and lead to an aberrant individual (offspring) which odds of reproducing and inheriting such trait are very limited, leading in the majority of cases such mutation to a death end.


Saludos

Mauricio