Hennig XXXI (23-27 Jun 2012) Riverside, California, USA

This year, the Hennig meeting was held at Riverside, California, and I'm fortunate enough to be able to be there (in great part thanks to the Kurt Pickett award, given by the Willi Hennig Society). As in previous occasions, I will try to give a short review of many of talks!

23 jun

I want to remark the excellent reception given by the organizers, and the opportunity to meet some wonderful heteropteran researchers [which is huge for an heteroptera aficionado! :)]

24 Jun

The meeting start up with a plenary talk given by Quentin Wheeler, with the title of Cladistic cosmology. Basically it is about of building a “Hubble like” project for taxonomy, specifically the description of new species, and facilities to make access to museum specimens across the web, both as metadata, but using some form of virtual specimens (e.g. scans of herbaria types, 3d scans of specimens, etc.). I like his point, but I think he miss the point of sampling: we not only need better understanding of current museum data, but also, we need to go to the field and look for never seen before specimens!

The first symposium was organized by Ward Wheeler about linguistics. The first talk, was a video-conf given by Peter Whitely about  the phonetic character definition used for an analysis of Uto-Aztec languages. The actual analysis was presented by Ward, that shows some of the particularities of using phonetic characters in comparison with DNA data, such as having 121 letters (against 4) and short strings (against long sequence fragments). Peter Forster talks about the using of phylogenetic networks for language data, and how it can be associated with what we know about the history inferred from mitochondrial molecular markers. You can found his program here. Joanna Nichols also uses phylogenetics networks with emphasis of using different sources of cognate data. To finish the season, John Wenzel shows a reanalysis of some previous indo-european analysis, showing some problems with the character coding, and how much of the current resolution was a by product of the errors in the codings, and the method used. I do not know much about the state of the field of phylogenetic linguistics (although I like the use of these techniques in linguistics!), I found a nice blog that usually talk about phylogenetics in linguistics here.

The next session was on phylogenomics, and was organized by Gonzalo Giribet, so are heavily biased towards invertebrates, but for a frustrated entomologist like me, it was wonderful :D! First Gonzalo talks about how new advances in sequencing technology has increased the amount of available data for phylogenetics, and how the problem was shifted from phylogenetic analysis to orthology recognition among this huge amount of new sequences. Then Torsten Struck shows how the selection of outgroups affects the position of one most mysterious group of annelids, the Myzostomida. Sebastian Kvist, explores the genomics of the blood feeding proteins used by Hirudinid leeches, and the realtionships of their host bacteria, a group related with nitrogen-fixing bacteria found in plants! Kevin Kocot was interested on orthology detection using phylogenetic trees, so he implement a program to detect the best possible set of ortholog sequences. Björn von Reumont talks about the pancrustacean phylogenomics, and how the acquisition of newer data from Remipedia is key in the problem and that results shows than remipedians are more closely related to hexapodans than to more traditional crustaceas, he also hints the existence of some apomorphies for such group based on nervous system. Vanessa González talks about the relationships among Bivalbia, that as many molluscan taxa, seems to be well known, but their phylogenetic relationships are just barely explored.

Then the poster season starts, most of the posters present a lot of entomological work on heteropterans (specially reduviids), so that makes me so happy, I like most the poster from Michael Forthman as he works with Ectrichodiins the group that I see for an small [very small!] amount of time xD, so hopefully he will construct a nice phylogeny of the group! :) The winning poster was given by Guayang Zhang and it is about the elongation of the front legs in harpactorines.

25 Jun

Students day! Most of students talks where given this day, so it will allow the judges to give the student awards with a complete overview of all the material presented by students.

Ansel Payne gives a wonderful talk about the general relationships of Hymenopteran superfamilies. Rebecca Dikow explores a huge data set (in term of characters) using bacterial genomes, so her trees have brutal lengths over 37 millions of steps! Ross Mounce talks about measuring support using supertrees, he also remind us about the importance of using machine readable data for phylogenetics, and that he thinks that using svg files will be great for publishing data, as you can include a lot of non-published metadata inside the files. Julieta Gallego presents a talk about the stability of molecular clocks (as I am a co-author of the talk, maybe I will talk about this in other time!). John Denton gives a talk about the usage of iterative alignments to improve the searches under likelihood approaches. Greame Oatley speaks about a cool group of birds [give me a passeriform, and I will love it ;)], and their species limits, in a work in part phylogeographic, in part taxonomic. Juanita Rodriguez (from Colombia! But she is working in Utah), talks about the phylogeny and biogeography of a group of Pompilid wasps. Fernando Gelin talks about Polybia, a wasp genus. Federico López (another colombian! And old friend of my from undergrad days! He is now at Vermont) gives a talk about the phylogenetics of a group of Vespids. To finish the first student season, I give my own talk about biogeography of amphibians.

In between student talks, there is an interesting symposium about the species problem. I'm personally no see so much in that problem, but is nice to see a lot of talk about that. Fortunatelly, I guess, although the problem is recognized, most taxonomists and systematist can continue to work, and work well, even if there is no consensus in what an species is. Brent Mischler spokes about the phylogenetic (topologic-monophyletic) species concept. Rudolf Meier talks whats about the problem of discussing the topic, and how most people skip the problem at all, and why he thinks it is important to discuss the subject. For me, this is the best talk of the symposium. Finally Kipling Will talks about the influence of the species definition in alpha-taxonomy, specifically how it is affected by some recent approaches, like bar-coding. Then a nice discussion (which includes Quentin Wheeler) was given by the four panelists of the symposium.

The second student seasson begin with a talk given by Christine Hayes about the the phylogenetic relationships of a group of phorid flies. Anna Dal Molin explore several techniques to visualize large groups of trees. Pei-Luen Li talks about a worldwide distributed (but concentrated in Hawai'i) group of asparagales, and Cecilia Waichert explore some adaptation hypothesis about nesting behavior using a phylogeny of Pomipilid wasps.

26 Jun

Pablo Goloboff, gives his talk about the implementation of Iter-PCR, focusing on the effects of changing the ingenuous algorithms, with the use of algorithms that take previous information into account, and makes feasible the use of iter-PCR in TNT. Jean DeLaet, gives an insight on his future program for phylogenetic analysis, Anagallis, that will include his algorithms for dealing with non-applicable data! I'm very curious about it [hopefully it will be open source!]. Nico Franz speaks about using taxonomy ontologies, although I think that kind of work is nice to discover some particular things, I guess that the missing thing is that they at the moment are no using character data, and I think that the key for this kind of databases will be both explicit references, and explicit data supporting each taxonomic affirmation. Lenka Drabkova talks about the plant cytokinins. Claudia Szumik shows the results of a the search of areas of endemism, using also phylogenetic information, with a huge data set of mammals. Then Santiago Catalano presents GB-to-TNT a user friendly program to build huge matrices, and also some nice taxonomy mapping tools found in the newer version of TNT. Daniel Janies, shows that super-trees are not a real solution to the uses of super-matrices, as they fails to produce approximate results of a super-matrix. In one of the most controversial talks Donald Buth argues that mitochondrial data, as non intrinsic source of data, and susceptible of the host-parasite interactions, must not be used for phylogenetic analysis. Personally I do not agree with him, but a friend of me, tells me that the same concerns have been raised in population genetics (a.k.a. Phylogeography) literature. So maybe, mitochondrial data is not good for small taxonomic levels, by the same reason of gene vs species trees, but at large levels, it will provide a nice source of evidence (as the difference between gene and species trees at this levels are no so important). This is an intriguing line of though, as it is precisely the opposite to the most received view, from at least five years ago. John Wiens gives a review of all of his papers about the use of phylogenies for study ancestral ecology. I was too tired after Jon talk, so I miss the next ones. Later Santiago gives a nice talk about  the usage of morphometric data on several and different kinds of studies. Tim Crowe talks about the results of a whole life dedicated to study guinea fowls at different taxonomic levels. Dalton Amorim, shows a new analysis of phorid flies based on morphology, one of the few talks using explicit morphological data! Continuing with morphological data, and dipterans, Torsten Dikow shows its phylogenetic analysis Mydidae, he also shows interest on detecting unstable terminals. Efraín de Luna, talks about the use of morphometric data in phylogenetics. To finish the day, Nico Franz gives a talk about how his analysis of some particular group of curculionids evolve in time from the initial data matrix to the definitive one. I think this is a nice exercise, but ultimately, it is difficult to extract some information about it, except from the anecdotal experience.

Later this day was the banquet, that as is a tradition in the hennig meetings was free for students! The banquet speech was given by Dennis Stevenson, the current editor of the journal of the society (Cladistics), and it was funny, although it was somewhat small!

The winners of the awards? Ok, there is a lot of Marie Stoppes and Kurt Pickett awards for traveling students. The Don Rosen award for the best poster was given to Guayang Zhang, as I tell you before. Cecilia Waichert receives the Lars Brundin award, for the second best talk, and John Denton receives the Willi Hennig award for the best student talk! Congratulation to the winners, all are well deserved, and I think the judge have a difficult time selecting these three, because there are a lot of great talks given by students :)!

27 Jun

I think this is the most difficult day to give a talk: everyone is tired of the amount of talks in previous days, as it is the day after the banquet, a lot of people are dehydrated and overtighted, and as it is the last day, you have to check-out from the hotel...

Here this is the last symposium, this one, about molecular clocks organized by Sean Brady, who discuss several sources of error. Tracy Heath talks about how to model dating in bayesian analysis, and Elizabeth Murray has a more concrete talk on the dating of some group of Hymenoptera.

Robert Sansom presents some differences between results using hard and soft anatomy in vertebrates, and the implications for the fossil record, that is only based on hard parts. Mark Simmons shows some problems from using multiple matrices, with small overlap. He present a lot of interesting results for some particular examples, so it is important to known how general they are. Mari Källersjö gives one of the most beautiful talks of the meeting, about a working project of a particular group of plants. Everyone loves his talk :D. Veronica Pereyra talks about thysanopterans, but unfortunately I have to make the check out, so I lost it :-(. Ronald Clouse talks about the phylogeography of an opilion that lives in southeastern US, that is a remaining of a gondwanian clade (as Florida was long time ago, part of African plate!). Ulf Jondelius, talks about the acoelan worms, a poorly known taxon, that he was sampled across the world. To finish the meeting Steve Farris talks about the recent surge of the three taxon statements authors (Ebach, Williams, etc.).

General overview

The meeting was very well organized by John Hartley and Christiane Weirauch, that move around all the time to make sure everything is right. They have a full group of students that are helping with everything, so it was huge :).

On the meeting itself, it has a lot of students, with several very nice talks, and a lot of discussion, that is always welcomed :D. One of the things that I note, is in the same line of previous meetings in which few morphology is used, here I see that although most studies only use molecules for phylogenetic analysis, people is more interested in link several of their findings with well detailed morphological data, hopefully, in the next few years, fully integrative, genomic and morphological data will be used in conjunction in almost every work!

The next year, the meeting will be held in Rostock, Germany, a city on the coast of the baltic sea. Hopefully I will be able to make it, and several of my cladistists ends will be there :D Also, if any one reading this blog interested in phylogenetics, and living somewhere in Europe, I encourage you to go, even if you don't work with parsimony! [In fact, a lot of people that does not use parsimony analysis shows their results at the meeting! And nobody complains about it, at much, someone as why do you not use parsimony, but just that] So! See you there :)!


Acknowledgments
I receive a lot of funding support from several institutions that make this trip possible: CONICET, FONCyT, GBIF (well, this one in the future) provides monetary funding, whereas INSUE allows me to work at their facilities. I receive a Kurt Pickett travel award from the Willi Hennig Society. At personal level, my advisors (Pablo and Claudia) provides me a lot of support, Julí convince me to go, Santí helps me with the trip logistics, and they, with Ross, they are excellent room-mates :)!

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

Who is a cladist?

Versión en español

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.

References

[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]

The behemot! for free! / El behemot gratuito!

Santí noted that the "behemot"'s paper [1] is now available for free from Wiley/Blackwell web-page, this is the link:

http://www.wiley.com/bw/ecology/news/news.asp?id=286

Or you can jump directly to the paper abstract and download the pdf:

http://dx.doi.org/10.1111/j.1096-0031.2009.00255.x

If you want to look the results, Pablo post a quick guide to manage the trees and extract info from them. If you want to check you favorite group, or just play for a moment, there are no excuses ;)!

And the best of it, as they are macros, you can use for your own trees! and don't forget to check out the TNT wiki!

Santí me hizo notar que el paper donde el "behemot" vio la luz [1] se encuentra disponible de manera gratuita en el sitio de blackwell. El enlace es este:

http://www.wiley.com/bw/ecology/news/news.asp?id=286

O pueden ir directamente a la pagina del artículo y descargar el pdf:

http://dx.doi.org/10.1111/j.1096-0031.2009.00255.x

Para quienes quieran jugar con los resultados, Pablo publicó una guía rápida para manejar los árboles y poder extraer info de ellos. Así que si tienen curiosidad por ver como quedo el grupo que ustedes trabajan, o simplemente quieren pasar un rato, ya no hay excusas ;)

Y lo mejor de todo, como son macros, se pueden usar en sus propios resultados :D! No se olviden de consultar la wiki de TNT ;)

[1] Goloboff, P.A. et al. 2009. Phylogenetic analysis of 73 060 taxa corroborates major eukaryotic groups. Cladistics 25: 211-230. DOI: 10.1111/j.1096-0031.2009.00255.x

A phylogeny of 73060 eukaryotes

Versión en español

Finally, the behemoth has seen the light :). Our paper with a parsimony analysis of 73060 eukariotic species (and 7800 mol+morf characters) was just published (as “online early”) in Cladistics [doi:10.1111/j.1096-0031.2009.00255.x].


Pablo does a wonderful work optimizing every aspect of the tree-searches in TNT. And all of the guys worked really hard to manage that amount of data!

At first I was surprised with the high accuracy of the trees founded, because the data set is full of missing entries. Also, I fill happy because the inclusion of morphological data, even at this huge scale, produce better results than molecules alone!

Just few months ago, this was posted in dechronization:

He [Cassey Dunn] makes a convincing case for the idea that a revolution in analytical techniques will be needed as we enter an era during which computational capabilities will be more limiting than data availability.

I think our study shows exactly the inverse: that our actual search capabilities are good enough, but we do not have sufficient data (the largest gene set is SSU with 20000 species, and a handful of genes has more than 10000 species).

The second lesson?... We do not need super-trees!

Hennig XVII: “Live” blogging, day 4

It was difficult to get up early after la fiesta salvaje, but more difficult to not fall asleep, not because the presentation were boring, but because the whole meeting schedule catch me!

Torbjorn Ekrem try to produce “robust backbone trees” to perform phylogenetic analyses, but he uses a form of character elimination, so I don't like his idea.

Pancho Prevosti, works with a simultaneous analysis of otters, using morphology, molecules, and fossils.

Torsten Dikow shows a phylogenetic analysis of Asilidae robber flyes, into a context of disponible fossils of the group. And Johnatan Liria, uses morphometrical data, using TNT, to search the phylogeny of some particular Culicidae mosquitoes. For the moment, I feel really suspicious about the use of “warps” or “PCA” as characters!

Gabriel Ruá, explore several k values to choose a k value, and analyze a clade of Asteraceae. But I think that his use of a broad range of k values, made his inferences somewhat useless.

Tim Crowe, analyze a big data set to evaluate the position of some african quails, he shows that many identifications based solely on feather colors are plainly wrong. But I like his exposition of several song calls by these quails.

Using the large data set, Norberto Giannini examine some phylogenetic hypothesis of mammals, and found some interesting consequences! I like the way in which he present the results, and the good and problematic points of the study.

Gitte Peterson shows a weird behavior of his molecular data, and she connects it with paralogy, and mRNA edition. Although I think that there are better ways to attack the problem, I think that her exploration of the results was wonderful!

Then Kevin Nixon shows how some character codings used for the origin of seed plants, are highly problematic, because they are based on a preconception and a chain of errors in the description of some fossil material.

After lunch, Fabián Michelangeli gives a talk about a Melastomataceae clade, he uses molecular results, but also include a mapping of an initial set of morphological characters that he and his co-authors were working, and how this evidence to be added fit to the molecular results. I like the detailed working of his fruit characters! In the same line of Melastomataceae Renato Goldenberg talks about the preliminary results of a more inclusive project of this group of plants.

Pd. Although published few days after the meeting, this post was written the last day of the meeting. I not publish it before, because after the last talk, I like everyone, go out to celebrate the end ;).

Pd2. As part of the organization of the meeting, I want to thank every one for comming!! :D

Hennig XVII: “Live” blogging, day 3

Today was a highly theoretical day ;)... Most of the talks were highly methodological, with some scattered practical works.

Ward Wheeler, in a line similar to Grant and Kluge, argues that “objective support”, like Bremer support of Likelihood ratios are different to “average support”. His main argument, is that objective support is a better measure than average support, because it is based on a direct comparison of optimality criterion... I'm not agree xD.

Next, Pablo Goloboff showed that the common argument against weighting, that a character which is poor in clade is underweighted in a clade in which character has low homoplasy, is a problematic one, and that parsimony, as we know it, imply homogeneous weighting across the whole cladogram.

John Wenzel seems to be unsuccessful to show a different way to attack consensus trees. I think that agreement subtrees, the method that he defends is not as good as reduced consensus that can be found with TNT.

In an interesting talk, from philosophical, and statistical point of view, Chris Randle, showed that as actually implemented, Bayesian analysis in not bayesian, because the impossibility to implement a real definition of clade priors.

After coffee break, Steve Farris give an entertaining and clever talk about some misrepresentation of ideas of support by Grant & Kluge, and of course, re-affirms his masterful conclusion from his 1983 classic: parsimony is minimization of ad hoc hypotheses of homoplasy. I'm very happy to see the one that gives shape to actual numerical cladistics (and, I thinks, the major contributor of the theoretical development of phylogenetics in general!).

Then, a bunch of papers based on Pablo's implementation of continuous characters, using Farris' optimization, using Opiliones. But the most interesting contribution was from Santiago Catalano, who shows that landmark data can be viewed as a generalization of Sankoff's parsimony!

Afternoon starts with a presentation of the possibilities of EOL.org (Encyclopedia of Life) by Torstein Dikow, actually, apart of being as wonderful as Wikipedia, I do not see any application for EOL... (see Page's blog!)

Matthew Yoder, shows some wonderful ways to work using open source, in the development of his software for multi-author phylogenetic studies, with his sever-based Mx.

Then Rasmus Hovmoller, shows some interesting work to understand the spreading of avian influenza A, unfortunately, external problems was an obstacle to enjoy their results.

Federico López gives a talk about using conservation indexes to conservation in amazonia. I'm quite suspicious of that kind of indexes (although they are also bad, I think that Faith's PD is far better than Vane-Wright indexes!).

Norberto Giannini shows a new way to treat correlation of characters (“comparative method”) into a truly phylogenetic way. The method is excellent, and I think a real improvement in that field!

Fernando Noll, showed a beautiful work of behavioral data for Meliponini bees, that include oviposition and nest architecture.

Jeffrey Skevington use dragonflies from Fidji, and he tries to explain the origin of sexual bias on this beautiful insects. Juan Larrain shows his molecular analysis of a group of mosses, and compare his results with a preliminar set of morphological characters.

Martín Ramírez gives an excellent talk about the usefulness of ontologies for phylogenetic analysis! I feel that ontologies are an important step in the maintainability of morphological data (and their subsequent usage), but I think that although wonderful, the re-using, specially from authors extern to the original work, seems to be difficult (at least, as actually doing).

To finish the day, Johnatan Liria talks about k selection using some of my old TNT scripts xD...

Hennig XVII: “Live” blogging, day 2

Today the meeting starts with a highly molecular morning. Gonzalo Giribet present a symposium about new methods for “phylogenomics” (organized by him, Ward Wheeler, and Jirky Mouna). Three talk were about the use of gene order, inversions, recombination, in the context of phylogenetic analysis. All of the presented analysis are POY-oriented ;). It is sad that Andres Varón, a colombian working with POY, was unable to assist.

The most interesting one, is the talk of Gonzalo who insists the usefulness of morphological data, and present some new analysis with his EST data for metazoa (published in Dunn et al. 2008), with more than 200 morphological characters for metazoans in a network of experts. His analysis show that morphology provide evidence for grouping at all levels of the tree. He was very suspicious about the “groundpland” coding. I always prefer exemplar coding, but sometimes, some useful information available from not directly analyzed terminals (for example, several developemental data) can provide an excellent source of information.

Prosanta Chakrabarty, try to test sexual selection in a group of luminous fishes, I get impressed with the diversity of that fishes, but, I think that the questions about selection preasures can not be answered in the way showed by Prosanta (or in any way!).

Next, there are two nice works on Curculionids. In the first Analía Lanteri, showed a particular group of broad nose weevils, then Adriana Marvaldi, showed his most recent advances in the understanding of the whole morphology (and phylogeny) of Curculionoidea, and how many of the sequence data recently assembled for that beetles, is highly congruent with the morphological results.

Afternoon talks are more interesting to me, because they are about biogeography ;) --I only have 3 interests: parsimony methodology, morphological phylogenetics, and REAL biogeography xD--.

In the first one, Peter Hovenkamp, shows a very interesting parallel between ideas form phytosociology and endemism, he founds that many of the implementations of Josias Braun-Blanquet (or the europoean school of phytosociology really did not implement that methods! He thinks that NDM (of Szumik and Goloboff, 2004) can be a better tool for phytosociological ecology!

Another wonderful talk was giving by Claudia Szumik, who made an analysis of endemism of northern argentina. The good thing about the study, is that it includes data taken directly from the experts of each group, with several data collected by Claudia and their co-authors!

Loló (Dolores Casagranda) present a comparison between NDM and PAE, I work on that talk, so I feel that a I will give a biased report, so I pass xD.

Erika Parada, an student from my undergrad university, talks about his analysis of northern andes, she uses tree-fitter,  a program that I do not like a bit :P, because it has several problems, I think she made a great work, but unfortunatelly results with TF are, for me, doubtful! :P

I do not like the talk from Dalton Amorim, but the discussion that follows the talk was very interesting, with James Liebherr, given several strong (and clever!) points against Dalton ideas.

Hennig XVII: “Live” blogging, day 1

Yesterday several people came to the reception, I talk with several nice people, it was a very cool afternoon :D!

Today, the meeting start in proper. The site, San Javier, is wonderful, it is atop of a mountain, just in front of Tucumán, so you can see the whole plain that extends to the east, incluing, of course, the city of Tucumán. Excellent place!

There are several talks, some of them are somewhat difficult to get (to me at least xD), but overall, they are really nice. I really, really like the talk of Cecilia Kopuchian about the phylogenetics of Furnaridae (Aves). She combines in a wonderful way the pics of his characters, with his results, so even, if you know noting about the group (like me), you learn several thinks about it, and you are always on the subject of the talk!

For paleontologist, Diego “el caco” Pol give a talk about some fossil Crocodiles from Argentina, and Africa, Mesosuchia (I hope I remember right xD) which were the last surviving taxa of non-modern Crocs.

Julián Faivovich, give a molecular talk about phylogenetics of Hylidae, and to keep the talk interesting, he tries to put his work into a some biogeographical framework (“one taxon” approach, but he tries to make some predictions with his data). I think his results can be very interesting for POY users, as he found a (manual) trick to speed up searches.

Afternoon, James Liebherr, gives a talk about Blackburnia a beetle from Hawaii, he uses live taxa, and several “semi” fossil taxa found in a cave. Jim speaks somewhat slowly, but I love the deep of his work!

Camilo Mattoni, shows the development of an Scorpion data set, from the use of some general data sets of morphology, to specific morphology of the Bothriuridae, to different molecular markers, to a simultaneous analysis.

Louise Crowley works on morphology (and mol. Secs) of a very hard group (also a literal meaning xD), such as oysters. I can believe how many chars you can found in a single shell!

And of course, Santi and Marcos talk about the redefinition of large :).

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.