domingo, agosto 07, 2011

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.


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!

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

domingo, febrero 13, 2011

¿Quien es un cladista?

Hace algún tiempo, alguien me preguntó en que se diferenciaba la cladística de los otros métodos filogenéticos. Para mucha gente, la respuesta es simple: un cladista es el que usa parsimonia (e.g. [1][2]).

Yo creo que la parsimonia es muy importante para los cladistas, pero no creo que uno sea cladista solo cuando usa parsimonia. Hay muchos artículos de autores que usan parsimonia, pero que no creo que sean artículos cladísticos. También hay trabajos de autores que no usan parsimonia, pero que están claramente dentro del marco cladístico (Pienso en los autores lejendarios: Hennig, Brundin, Wygodzinsky etc., todos ellos cladistas, pero ninguno uso parsimonia, al menos de una manera explícita [=numérica]).

Entonces, si no es un algoritmo ¿donde esta la diferencia? ¿cuando uno es un cladista?

Una parte escencial del pensamiento cladístico es la monofilia, pero actualmente la monofilia se entiende como un termino topologico (esto es, solo la relación representada en el árbol), pero creo que este pasaje de Hennig [3] es claro:
“La suposición de que dos o más especies están más cercanamente relacionadas entre si que con cualquier otra especie, y por ello forman un grupo monofilética, solo puede ser confirmada demostrando la presencia en común de un carácter derivado (“sinapomorfía”). Cuando ese carácter se a demostrado, entonces la suposición ha confirmado que lo han heredado del ancestro común únicamente para esas especies que muestran el carácter.”
Entonces, para un cladista, la monofilia no es solo la relación, sino los caracteres que apoyan esa relación. Cuando un cladista responde a la pregunta “¿es este grupo monofilético?” el /ella no muestra únicamente un árbol, sino además los caracteres que apoyan ese agrupamiento.

Entonces, la cladística no es sobre el algoritmo en particular usado para inferir las relaciones, sino sobre los caracteres que apoyan esos grupos. No es extraño entonces que la mayor parte de los cladistas usen morfología en sus análisis. Aún así, usando solo datos moleculares, se puede ser un cladista, cuando al referirse a calda clado, se discute también las sinapomorfías de dicho clado (sean moleculares y/o morfologicas). Después de eso, uno puede preferir cierto algoritmo sobre otro.

Aquí va un ejemplo, estos dos artículos, uno es de Wiens et al. [4] sobre la filogenia de los Escamados, y el otro es de Beutel et al. [5] sobre la filogenía de Holometabola. Ambos artículos usan parsimonia y análisis bayesiano de sus datos, y ambos parecen preferir los resultados del árbol del análisis bayesiano. Ambos artículos tienen más o menos el mismo tamaño (en cuanto a páginas), discuten las relaciones de grupos de gran diversidad y usan conjuntos de datos morfológicos y moleculares. Uno es claramente un trabajo cladístico, y el otro no.

Si uno mira el artículo de Beutel et al., uno se encuentra con un montón de discusión sobre los caracteres que apoyan cada clado. Para ellos, el apoyo no es solo el valor del apoyo de Bremer, la frequencia de Jackknife o la probabilidad Bayesiana, todo eso es importante por su puesto, pero no tiene sentido sin una referencia explicita a los caracteres que en el nodo. Entonces, así ellos prefieran el análisis bayesiano, ellos continúan siendo cladístas.

Del otro lado, esta el artículo de Wiens et al. Para estos autores, lo único importante son las relaciones, ellos discuten grupos y probabilidades bayesianas, pero nunca discuten ningún carácter de manera explicita para ningún grupo. Entonces, incluso si Wiens et al. solo hubieran usado parsimonia, ellos no son cladistas: los caracteres no son importantes para ellos.

Un cladista no es que escribe un artículo con las ultimas estrategías de búsqueda, o las medidas de apoyo, o la mayor cantidad de nuevos datos moleculares, o usa parsimonia. Todo eso es de gran importancia. Pero en un artículo cladístico, lo importante son los caracteres que apoyan la filogenía. Un buen artículo cladístico es un artículo sobre los caracteres.

[1] Felsenstein, J. 2001. The troubled growth of statistical phylogenetics. Syst. Biol. 50: 465-467. Doi: 10.1080/10635150119297 [disponible gratis en el sitio de Syst. Biol.]
[2] Williams, D.M., Ebach, M.C. 2007. Foundations of systematics and biogeography. Springer, New York (USA).
[3] Hennig, W. 1965. Phylogenetic systematics. Ann. Rev. Entomol. 10: 97-116. Doi: 10.1146/annurev.en.10.010165.000525 [disponible gratis aquí]
[4] Wiens, J.J. et al. 2010. Combining phylogenomics and fossils in higher-level squamate reptile phylogeny: molecular data change the placement of fossil taxa. Syst. Biol. 59: 674-658. doi: 10.1093/sysbio/syq048 [disponible gratis en el sitio de Syst. Biol.]
[5] Beutel, R.G. et al. In press. Morphological and molecular evidence converge upon a robust phylogeny of the megadiverse Holometabola. Cladistics. Doi:10.1111/j.1096-0031.2010.00338.x [disponible gratis en el sitio de Cladistics]

sábado, febrero 12, 2011

Who is a cladist?

Some time ago, someone ask me about which makes cladistics different from other phylogenetic approaches. For most people the answer is straightforward: a cladist is the one that uses parsimony (e.g. [1][2]).

I think parsimony is very important for cladists, but I do not think that you are only a cladists when use parsimony. There is a lot of papers from author that use parsimony, but which I'm not think that are cladistic papers. Also there are a lot of works form author that do not use parsimony, but they are clearly under the cladistic framework (I think on the old one authors: Hennig, Brundin, Wydodzinsky, etc., all of them are cladists, but no one uses parsimony, at least in an explicit [=numerical] way).

So, if it is not an algorithm, where is the difference? When are you a cladists?

A key part of cladistic thinking is monophyly, but monophyly actually is usually understood as a topological term (i.e. just the relationships depicted on a tree), but I think this passage from Hennig [3] is clear:
“The supposition that two or more species are more closely related to one another than to any other species, and that, together they form a monophyletic group, can only be confirmed by demonstrating their common possession of derivative characters (“synapomorphy”). When such character have been demonstrated, then the supposition has been confirmed that they have been inherited from an ancestral species common only to the species showing these characters.”
Then, for a cladist, monophyly is not just about the relationship, but the characters that support such relationship. When a cladist answer the question “Is this group monophyletic?” he/she not only shows a tree, he/she also shows the characters that support such grouping.

Then cladistics is not about the particular algorithm used to infer the relationships, but about the characters that support such groups. It is not estrange then that most cladists used morphology in their analyzes. But even, using just molecular data, you can be a cladist, when referring to each clade you are also discussing the synapomorphies of that clade (either molecular and/or morphological). Then also, you might prefer some particular algorithm over another.

Here is an example, there are two papers, one by Wiens et al. [4] about the phylogeny of Squamates, and other from Beutel et al. [5] on the phylogeny of Holometabola. Both papers use parsimony and bayesian analysis on their data, and both seems to prefer the tree resulting from the bayesian analysis. Both are about the same size (in pages), and discuss highl level relationships of a largely diverse group using both molecular and morphological data sets. One of this works is clearly a cladistic work, and the other not.

If you look to Beutel et al. paper, you will find a lot of discussion about the characters that support each clade. For them, support is not just the Bremer' support value, jackknife frequency or Bayesian probability, they are important of course, but they are meaningless without an explicit reference to the characters on the node. So, even if they prefer Bayesian analysis, they continue to be cladistis.

On the other hand, you have de Wiens et al. paper. For that authors, just the relationships are important, they discuss groupings and bayesian probabilies, but no discussion on any explicit character for any group is made. Then, even in the case of Wiens et al. only use the results of parsimony, they are not cladists: characters are not important for them.

A cladist is not the one which write a paper with the more up-to-date search strategies, or support measures, or larges amounts of new molecular data, or parsimony analysis. All of that things are important. But in a cladistic paper, the important think are the characters that support the phylogeny. A good cladistic paper is a paper about the characters.

[1] Felsenstein, J. 2001. The troubled growth of statistical phylogenetics. Syst. Biol. 50: 465-467. Doi: 10.1080/10635150119297 [available free at Syst. Biol. site]
[2] Williams, D.M., Ebach, M.C. 2007. Foundations of systematics and biogeography. Springer, New York (USA).
[3] Hennig, W. 1965. Phylogenetic systematics. Ann. Rev. Entomol. 10: 97-116. Doi: 10.1146/annurev.en.10.010165.000525 [available free here]
[4] Wiens, J.J. et al. 2010. Combining phylogenomics and fossils in higher-level squamate reptile phylogeny: molecular data change the placement of fossil taxa. Syst. Biol. 59: 674-658. doi: 10.1093/sysbio/syq048 [available free at Syst. Biol. site]
[5] Beutel, R.G. et al. In press. Morphological and molecular evidence converge upon a robust phylogeny of the megadiverse Holometabola. Cladistics. Doi:10.1111/j.1096-0031.2010.00338.x [available free at Cladistics site]