Hennig 30, July 29-August 2, 2011, Sao José do Rio Preto, Sao Paulo, Brazil

Just a week ago I was at the 30th meeting of the Willi Hennig Society (my third in four years! :D). It was in Sao José do Rio Preto, an small city in the state of Sao Paulo, Brazil. There is a lot of people! (More than 200! most of them are students!). Here I will try to give an small review of the whole meeting :) [In the same way as I do in previous ones ;)]

July 29

This was the day of the welcome party, I meet with some good old friends and new people. Also, I'm very tired after a long trip from Campinas to Sao Jose xD.

July 30

The real meeting starts here, with an small presentation of the presidency of the Willi Hennig (by Rudolf Meier) and the organization committee (Dalton Amorim and Fernando Noll). Then a talk by Mario Viaro about the evolution of the prepositión “ate.” It is nice to see some strong similarities between cladistics and linguistics! But I think that most of the talk is based on more or less informed speculation, I hope that new quantitative approaches (like the one show by Ward Wheeler) will invigorate the field!

The first symposium was about bioinformatic tools for the analysis of diseases. Dan Janies, comment of a new way to dealt with they web services of SupraMap, and how it evolves from a monolithic application, to a more piecemeal approach (as unix/linux users know it), it will be more flexible and then more useful (And as a developer, a lot easier to maintain!). If you are curious, its new web site is GisBank.

Then Julián Villabona, a long time friend, give a review of the different tools to understand the geographic spreading of dengue, based on his own previous and current work. I think that the nice lesson is the importance of using new quantitative approaches from historical biogeography, in this clearly phylogeographic framework.

There are two more talks on this symposium, but they are more orientated in bioinformatic questions (data mining, and so), a subject that I do not really feel, so I can take anything about it :P.

The second symposium is on Phylogenetics and conservation. The first talk, of course, was by Dan Faith, that review his PD measure, that I think is the best way to take phylogeny into account in a diversity framework. He shows some way to expand the measure to complementarity, I personally do not like that approach, as it miss one of the most robust things of the PD measure: that is independent of the sampling.

I skip Roseli Pellens talk, but I see the talk of Ronald Clouse about Schizomida of Micronesia, both in terms of phylogeny of the group and at population levels. He found some particular things about its distribution, as it seems that the explanation of its distribution is based on long dispersal, but they are very well separated even inside the small islands. I will be looking forward for his publication on this particular data set :D!

There is a poster season here, but there were a lot of posters, and most of them on very technical issues of particular groups, which is wonderful :D (I love to see biodiversity research) but I'm very ignorant on most of that groups :P

July 31

The third symposium was on biogeography, specially, neotropics. Dalton Amorim shows how the “relationships” among areas shows that there are different historical components on the neotropics, each with different times. Although I don't like the methodology of his work (I'm anti “cladistic biogeography”), I guess that their own study shows that looking for hierarchical patterns in biogeography is not the right route!

Eduardo Almeida talks about the breakup of Gondwana, and the alternatives. I feel he gives much weight to the “expanding earth” hypothesis. It is important to note that this is a fringe hypothesis in geology, in fact, it is almost never mentioned in books on tectonics :P. Actual plate tectonics is one of the our most powerful theories, so the expanding earth require a more compressive mechanism set. Sadly all the discussion on the expanding earth eclipsed the most interesting part of his talk, that is about the biogeographic patterns of Colletidae bees.

To end the symposium, Juan Morrone gives a review of some of the american transition zones, in Mexico and in Patagonia. This prompt an interesting discussion, and I feel, like in the talk of Amorim, that their own research shows that the hierarchic classification in biogeography is not feasible.

Then contributing papers season start. I was very afraid (there is a lot of people xD), but fortunatelly all the discussion on Juan's talk gives me a nice time to keep my mind and provide a nice starting point for my talk ;).

Then Cyrille D'Haese talk about the relationships of a beauty group of colorful and “giant” collembolans of New Caledonia and South west Asia. Fernando Dagosta discuss the relationships of a characid group of fishes (I guess that you can ask Marcos about this talk :P jejeje). Jerome Murienne talk was about niche modelling, and how to integrate them into a phylogenetic framework. I think that this is a very difficult topic, and I was gland that Jerome was very cautions on its presentation ;) as more approaches to integrete phylogeny and distribution modelling are brutally ad-hoc. Denis Machado talk was about the phylogeny of freshwater stingray's tapeworms.

Wei Song Hwang gives a talk about the phylogeny of Reduviidae (specifically Reduviinae subfamily, a non-monophyletic assemblage). It was a terrific talk, on a group that requires an extensive revision although I will prefer more morphological data to be coupled with the molecular data. Anyway, I love this talk. [Side note, I guess it helps that bugs are theo only group that I was on the verge to work with it xD]

Marcos Mirande shows its update of its phylogeny of Characidae--there is a lot of characid papers in this meeting! :)--with new characters, new taxa, and molecular sequences. Owen Davies, who I meet in South Africa, study a group of small african birds of the genus Cisticola, and how old taxonomic revision was good and also wrong, I like this appreciations for old works :D. To close the season, Guanyang Zhang talk about the phylogeny of Harpactorini, a tribe of neotropical Harpactorinae, another grouop of assassin bugs, that, if you live in south America, you can see waiting on leaves with their front legs raised into the air: they have some stiky glands to capture prey, and that was Guanyong main subject.

Another poster season, I just have few time to check it out the other posters :-/, as I have my own, and I was very busy there: I have a pair of very good discussions ;).

August 1

There is another symposium, this one about techniques for molecular phylogenetics. Lone Aagesen explore some different weighting schemes to dealt with full genomic data and explore some groupings detected under different gene duplications among angiosperms. Torsten Dikow about the effects on combining morphology and molecules in Asilidae, as in many cases morphological data set produce an excellent retrieval of actual classification, whereas combined data does not.

Then Ross Mounce give a great talk about how ILD was abused in the literature, and why the way in it was presented in publications made most of the results difficult to repeat--If you read Ross's blog, you will know that he is, rightfully ;), obsessed with result reproduction!--He also shows how there are several ways to extract information on the results of this test, beyond the probability of the test.

As I mentioned before, Ward uses the dynamic homology framework to explore the phylogenetic relationships among uto-aztec languages, I think that this approach provides a real improvement on the analysis of linguistic data, and I am waiting for its publication :D!

Then Mario DePinna gives a talk about ontogeny and rooting. I guess that this talk is most on the same line of the works Nelson and Platnick, that I despise, and I thing are hot topic about 20 years ago, but not now.

Pedro Romano was interested on the use of ordered and unordered multistate characters, and how that decision is not usually well explored in most phylogenetic works. Then Apurva Narechania shows a methodology called “Radical” to explore the data concatenation. I think that his approach can be expanded in several ways, for example, looking for stability after adding taxa (instead of characters), that I feel, is a unexplored field.

Tim Crowe compare the evidence value of nuclear vs. mitochondrial molecular data, and show how their behavior is just not as usually supposed (mitochondria work well on tips, nuclear data work well on deep nodes) in his extensive data set of Galliformes.

Herbert Ferrarezzi explore a way to code polymorphic taxa, instead of using single specimen molecular sequences. Jaime Rodriguez present gives a talk about the use of spectral firms to identify insects, he tries to link it with phylogenies, but I really do not understand how this was done.

The talk of Claudia Szumik was about new character systems used in the classification of Embioptera. I like her work as it is a clear example that in many groups, the “lack” of informative morphological characters, rest on traditional grounds (i.e. taxonomic research centered on some particular character systems), rather than in a really uninformative morphology.

To end the day, Gustavo Hermes speak about a difficult wasp group, the Eumeninae.

The banquet!

This day was the banquet, in a place with a lot of food of several sources: fish, shrimps, sushi, meat (a lot!). It was great ;). And of course there are the Banquet speech (about “addiction on cladistics,” an excellent talk given by John Wenzel), and the Society awards for students, both the travel grants (Marie Stoppes) and the Don Rosen award for the best poster (to Rafaela Lopes), the Lars Brundin award for the second student talk (to Gustavo Hermes), and the Willi Hennig award for the best student talk (to me! I was pretty surprised :D, and really happy! :D). Congrats to the winners :), I'm proud of be in such nice company :D!

August 2

I must admit that I was pretty tired after two days of brazilian joy ;) so, I just barely play attention to several of this talks :P, and loss the talks from Phillippe Grandcolas and Nobuhiro Minaka.

Hilton Japyssu talk about how to codify different behavior patterns, in particular grooming on rodents. They produce a very well supported phylogeny with a lot of this rutines, congruent with several other data sources. Then Carlos Alberts, on the same line work with behavior patterns of Arini parrots.

Later, Santiago Catalano present his method about landmark alignment, and how it produces better results than alignments that not take into account the phylogeny. Another hit for the dynamic homology approach.

One of the talks I want to hear, is the one by Jan DeLaet on character weighting. He was very interested on implied weighting approaches, but it seems that he prefers linear functions instead of concave ones, so he present some properties for a particular function schema that he call, “self calibrated.”

To finish the meeting there is a symposium on theoretical and phylosophical aspects on cladistics. The first talk was by Pablo Goloboff about some improvements to implied weights, that is, to use different weighting functions among different characters, and the possibility to weight blocks of characters instead individual characters (that is mostly for molecular data).

James Carpenter gives a talk about the meaning of homology vs. synapomorphy. Of course, synapomorphy is not homology, as you can also have homology in symplesiomorphy! In the same line Kevin Nixon (who was not there, but send a video of his talk) was on the same line. This might be an old fashion discussion, but given that there is a lot of recent publications by people like Malte Ebach, David Williams and company (they publish a book, and have several papers in journals like zootaxa) it is important to recall this arguments again.

Andy Brower, tries to show how really most of objections on parsimony are not so strong, and that actually, parsimony is not as bad as their criticizers argue: the results are nearly identical with alternative methods. There are several topics I agree with Andy, but there are others that not, mostly he uses some sociological explanations in some cases, but ignore them in others (and of course, I'm very realist :P ejeje, but that is my own problem xD).

The second talk of Jan was about the topics touched on its 2005 paper, that is, about the use of gaps weighting and how they are related to dynamic homology, and of course, why really using everything in 1, is not really a straight forward consequence of using parsimony.

To finish, Steve Farris criticize the most recent attempts of users of 2 taxon analysis approach (already mentioned: Ebach, Williams, Nelson, Platnick), and how they change their own words when new criticisms where made.

Overview

A very long piece here :P! It was a very nice meeting. With a lot of students, that as great, and I think the most important objective of the WHS: to bring students into phylogenetics. But there is disappointment, apart from brazilian students there are few from other countries. I guess that it is a consequence of recent economic downside, as there are just few US students (3 or 4), and just one European students (just Ross). It is shocking when you see such small representation from first world countries. Representation from latinamerica is also scarce: just one from Argentina (were was everybody?), and nobody from other latin American countries. Of course, there are some colombians working on Brazil, but they count as Brazilian students (as its fundings are given by brazilian institutions). I don't know what happens, it is not lack of publicity: there is the same amount as in any other Hennig meeting. It is not the price, after all, this is one of the cheapest international meetings out there!

Nevertheless, that is not a problem of the organization, so I just can tell that the meeting was great, a lot of students, a nice people, and several interesting talks and posters :) Now, it is time to think on the next one, which will be somewhere in the U.S., hopefully I can made it :D!

Acknowledgments

Of course, a lot of fundings is required to do this trip, and I want to acknowledge the support given by the FONCyT, CONICET and the INSUE, and the Willi Hennig Society that gives me a Marie Stoppes award, and the Organization committee that give us a discount rate at the hotel, and everyday lunch ;)! Obrigado! :D

We can't get characters, but we can get states

Another piece for the seminaries, this time, about phylogenetics

Ramírez, M. J. 2007. Homology as a parsimony problem: a dynamic homology approach for morphological data. Claditics 23: 588-612. DOI: 10.1111/j.1096-0031.2007.00162.x

I read it few time after it was posted early on line, and I don't want to talk about it, but as it was proposed for the seminar, I put my own view about the paper.

Homology for some morphological structures is, sometimes, straightforward within a group, but, as we move to more inclusive scopes, the interpretation becomes blurred. For example, we know well that the legs from insects are all the same legs, also we know that the joint-legs are homolog within all arthropoda, but which is the equivalent for the pair-2 of insect legs in myriapoda? In vertebrates, the homology of cranial bones is nearly direct in each 'class', but comparison of cranial bones in fishes (specially the fossil ones) with the cranial bones is fairly complicated.

So Matín [Ramírez] give us two-step ways to deal with such cases. The first step, is a formalization of the classic way to deal with characters, a comparison with the possibles states, and its implications, but he puts under lights that the whole decision would be made in a context that evaluates several possible alternatives, and set an specific cost to each one, as a way to chose among the possible alternatives, the most parsimonious one is preferred. In this vein, their work is very similar to Agnarsson and Coddington [1], and in my opinion more easy to grasp.

But in [1] you make the chose and then, go to the standard cladistic analysis. Martín does not make the decision, he wants that the simultaneous analysis, selects the best possible arrangements, in a framework directly derived from molecular 'dynamic homology' [2, 3]. Under an strict dynamic framework each topology would indicate an specific arrangement for the morphology, but as Martín notes, in a direct difference among DNA, not all arrangement can be valid. Then he limits their scope to a set of previously defined morphological 'alignments' and choose the most parsimonious one.

Although Martín description of the problem is more adequate than [1], Agnasson and Coddigton are far better in leaving homology decisions and parsimony analysis separated. When choosing homologous characters, the main objective is to found characters that are the same, you can use several tools of the morphological analysis to do it. If there are some doubts, then it seems better to leave potential unions separated, or fused but with a lesser weight than the other, well established characters [4]. You can use a particular weighting schema to found the homologs, but it is not necessary to use the same in the construction of the cladogram.

As is seen in every character discussion, you can have a plenty of reasons to decide about a character (sometimes, such discussion includes what happens with alternative codings), but claiming that the choose was made because it fits with the best cladogram found... it seems not to be a good reason.

And it is not a good reason! Why? Because a character claim based solely on the cladogram, is just like homoplasy, you can only spoke about it because of the cladogram, then it is an ad hoc hypothesis [5]. 'Dynamic homology' in the molecular sense, or in the morphological one proposed by Ramírez are both ad hoc. It is not a coincidence that Martín found that under his method, the justification of parsimony of minimization of ad hoc hypothesis is not easily followed, and then, methods based directly on homoplasy, like implied weights [6] produce estrange results.

I think that the paper have a great value for its first part, and can be integrated with the proposal of [1]. But as most of the justifications of 'dynamic homology', Martín trades a fully coherent minimization of ad hoc hypothesis of homoplasy [5] with 'minimization of steps' .

[1] Argarsson, I., Coddington, J.A. 2007. Quantitative tests of primary homology. Cladistics 24: 51-61, DOI: 10.1111/j.1096-0031.2007.00168.x
[2] Wheeler, W.C. 1996. Optimization alignment: the end of multiple sequence alignment in phylogenetics? Cladistics 12: 1-9. DOI: 10.1111/j.1096-0031.1996.tb00189.x
[3] Wheeler, W.C. et al. 2006. Dynamic homology and phylogenetic systematics: an unified approach using POY. AMNH, New York. Freely available: http://research.amnh.org/scicomp/pdfs/wheeler/Wheeler_etal2006b.pdf
[4] Neff, N. 1986. A rational basis for a priori character weighting. Syst. Zool. 35: 110-123. JSTOR link: http://www.jstor.org/pss/2413295
[5] Farris, J.S. 1983. The logical basis pf phylogenetic analysis. In: Advances in Cladistics, vol. 2 (Platnick, N.I., Funk, V.A., Eds.). Columbia, New York vol 2. Pp. 7-36.
[6] Goloboff, P.A. 1993. Estimating character weights during tree search. Cladistics 9: 83-91. DOI: 10.1111/j.1096-0031.1993.tb00209.x

Addendum
Of course I do not deny the role of previous analyses and the checking of different alternative codings. That forms part of the tools from which morphologist made their homology desitions.

Homology and parsimony

Today is a transaltion day ;). This post is a translation of my previous post in spanish about the subject.

This post is somewhat inspired in a discussion by Ebach and Williams in their blog systematics & biogeography (they had many post about the subject!). Here I want to show the relationship between parsimony (or cladistic analysis) and homology.

Homology

It is a long tradition of discussion about the definition of homology. I use a definition similar to the traditional one, then two structures are homologs when both are considered the same structure in different organism. There are countless arguments to acept two structures as being the same: God's plan, natural order, morphotype, or the one I endorse, by common ancestry.

If two structures are homologs, it implies that they are the same structure, and they are inherited from a common ancestor of the two examined organims. Inheritance implies several things by definition: specially from genetics and development biology. Moreover, the structures could not be highly similar, even if they are the same, because they can be strongly modified. Nevertheless both are the same, so it implies that structures change across the time, in our assumptions include several process that promote the differentiation, such as genetic interaction and population dynamics.

Cladistic analysis do not have a direct interest in these phenomena associated with homology. The process are of interest in other fields like evolutionary biology, development biology, genetics, molecular biology, population genetics, ecology, etc. But lack of interest do not imply that they could be ignored! In the character definition for a cladistic analysis (i.e selection of homolog characters) several of those factors would be taken into account to propose character limits and character codification.

Unfortunately, as process is not of direct interest for cladistics allows the erroneous idea that the process is irrelevant in character definition. The the so called pattern cladists (as Nelson and Platnick [1] and recently Pleijel [2], Brower [3] and Ebach and Williams) to think that cladistics is free of evolutionary thinking, but it is a totally wrong position: the use of homolog characters implies a framework based on origin by common ancestry, the every character--and not only its apomorphic state--are the same structure [4, 5].

But it is more, implications of evolution are big for several characters, specially if there is a well knowledge of the character, the the idea of Kluge [6] who claims that only assumption of cladistic analysis is 'descent with modification' is also wrong. When you include inheritance and evolution, many things are included in the definition of character. Of course, for some characters we only got a morphological knowledge of the character, then assuming a simple 'descent with modification' seems to be correct, but for other characters (as in many vertebrates) we got knowledge from development and genetics of the structure, in such cases the assumption are far more complex than descent with modification.

Parsimony: the algorithm

The basic principle of parsimony algorithm is fairly simple. If you want to know the character state in the node 'x', which descendants are 'y' and 'z', and we know their character states, then the character state of 'x' is the intersection between states of 'y' and 'z', if the intersection is void then the state of 'x' is the union of 'y' and 'z' states. Using an union implies a character change (a step). Of course, optimization of states is more complex, but for the present discussion we only need the basic steps.
State assignation using the parsimony algorithm: (A) and (B) the state of ancestor 'x' is equal to the intersection of descendants 'y' and 'z', i this case, white; (c) 'y' and 'z' do not share any state, then the state assigned to 'x' is the state union of his descendants.

As you see, the algorithm is 'independent' of the data used, you can use any kind of character (in computer science this problem is know as the coloring problem, and the 'characters' are colors of a map) and any kind of terminal. It is a common character of every method formalized in an algorithmic form. Then it is necessary to provide a proper justification to use the algorithm in a particular problem.

Parsimony: cladistic analysis

With the evolutive concept of homology, its union with the algorithmic parsimony is direct. If a character, no matter its state, is the same between two organisms that share a common ancestor, it implies that the character is inherited from the common ancestor, then the common ancestor would have the character.

Moreover if both organisms share the same form of the character, that is the same state, then that state would be in its common ancestor (the character is the same!), but if both organisms had different forms of the characters, we do not know which form would be present in the common ancestor, so we assume that it could be any of the both states, in that case, if both organisms really share the same character then a transformation would be happen.

This is exactly the same description of the parsimony algorithm. In cladistics the use of parsimony algorithm is justified because used characters are homologs. In this context the algorithm maximize our homology propositions when minimize transformations: this allows that most terminals with the same states would be contiguous. Then the hypothesis ad hoc of homoplasy are minimized [7].

Parsimony and homology tests

It is a common idea between cladists to say that parsimony is a test of homology: congruence. O disagree, because as I argument here the basis of parsimony is assuming from the very beginning that character are homologs! Any homology test would be previous to a rigorous cladistic analysis.

Homology test could have several forms, they could be morphology arguments (usally put under 'similarity' label), anatomical position, structural organization, ontogeny, genetics, and in most cases the 'test' is a conjunction of these procedures--for these reasons defining a character implies an strong theoretical background--. After examining all of those alternatives you got a good character. Is for these reasons that homoplasy is an ad hoc hypothesis: homoplasy is only justified in realtion with the cladogram.

Of course, character revision is always welcomed, and homoplasic ones maybe demand a close examination, but it is equally valid to examine every character. It is possible that codification form some characters is dubious, in such cases it is possible to use, as an exploratory devise different codifications (similar to the proposition of Ramirez [8] for morphology, and Wheeler [9] for molecules). But beware: this codification is not supported by the cladogram, because the argument used to defend that codification is the same used for homoplasy: it is justified only in relation with the cladoogram, the the codification is an ad hoc codification. In ambiguous cases I prefer a weighting schema as proposed by Neff [10]: because we know little about the character, and we have some doubts about its coding, it is better that it has a lower weight than characters that we know better.

**
Bonus: an historical speculation

He I show homology and parsimony ideas in a separated fashion and then I fuse them. I do it in that way to clarify the argument. But historically the development is intertwined from the beginning. If you read Wagner [11] in the algorithmic pathway, and Hennig [12] from the logical point it is clear that both positions are very close. Both visions were fused in an excelent fashion by Farris and its collaborators [7, 13, 14], which ideas (especially from [14]) agree in many points exposed here. Then from the beginning cladistic analysis and the parsimony algorithm walk together.

Wagner, Hennig and Farris development their ideas from a morphology context. At the same time Dayoff [15] experiment with several algorithms for molecular sequences, which at least today, homology ideas for molecular biologist are different to the morphological concept, I do not know what homology ideas used molecular biologist form 60s, but it seems that she did not believe that two bases (in case of Dayoff, two aminoacids) equal in two organisms imply common origin, the idea of point mutations precludes the idea. It is worth to note that Dayoff never could find a way to assign states in ancestors.

References
[1] Nelson, G., Platnick, N. 1981. Systematics and biogeography. Columbia Univ., New York.
[2] Pleijel, F. 1995. On character coding for phylogeny reconstruction. Cladistics 11: 309-315.
[3] Brower, A.V.Z. 2000. Evolution is not a necessary assumption of cladistics. Cladistics 16: 143-154.
[4] Fitzhugh, K. 2006. The philosophical basis of character coding for inference of phylogenetic hypothesis. Zoologica scripta 35: 261-286.
[5] Grant, T., kluge, A.G. 2004. Transformation series as an ideographic character concept. Cladistics 20: 23-31.
[6] Kluge, A.G. 2003. On the deduction of species relationships: a précis. Cladistics 19: 233-239.
[7] Farris, J.S. 1983. The logical basis of phylogenetic systematics. In: Platnick, M., Funk, V.A. (Eds.), Advances in cladistics, vol. 2. Columbia Univ., New York, Pp. 7-36.
[8] Ramirez, M.J. 2007. Homology as a parsimony problem: a dynamic homology approach for morphological data. Cladistics 23: 588-612.
[9] Wheeler, W. 1996. Optimization alignment: the end of multiple sequence alignment in phylogenetics? Cladistics 12: 1-9.
[10] Neff, N.A. 1986. A rational basis for a priori character weighting. Systematic zoology 35: 110-123.
[11] Wagner, W.H. 1961. Problems in the classification of ferns. In: Recent advances in botany, vol. 1, Univ. Toronto, Toronto, Pp. 841-844.
[12] Hennigh, W. 1966. Phylogenetic systematics. Univ. Illinois, Urbana.
[13] Kluge, A.G., Farris, J.S. 1969. Quantitative phyletic and the evolution of anurans. Systematic zoology 18: 1-32.
[14] Farris, J.S., Kluge, A.G., Eckardt, M.J. 1970. A numerical approach to phylogenetic systematics. Systematic zoology 19: 172-189.
[15] Dayoff, M.O. 1969. Computer analysis of protein evolution. Scientific american 221: 87-95.

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