Simulating Budding CladogeneticTrait Change

So, an important realization I just had. I think some of you who read this will find it interesting, so here you go:

Imagine you want to simulate cladogenetic trait evolution, where traits change only when a branching event occurs on a tree. (This is what we would expect if Puncuated Equilibrium is valid). For simplicity, let's say the changes act as under a Brownian motion diffusion model. Let's also assume we're looking at a species-level tree, so the branching events are also speciation events, making this also a 'speciational' model of trait evolution.

Most of the time, this is modeled in the comparative methods literature by taking a phylogeny, setting the branches all equal to one and simulating trait evolution across the branches. However, this implicitly assumes that the trait change is symmetric. What if its asymmetric? And, you might be wondering, what the heck do I mean by that?

Well, check out this figure.So what is going on here? Let's start with the first diagram. The vertical axis is time and the horizontal axis is trait space. If you're a paleontologist, you probably see diagrams like this all the time as stratophenetic hypotheses of the relationships among taxa in a group. This describes a general pattern observed in some groups in the fossil record, where we have morphotaxa that are (more or less) morphologically static, with some separation between them. The model of speciation inferred is referred to as budding cladogenesis (e.g. Foote, 1996). When speciation/branching occurs, the 'ancestral' taxon doesn't change at all, while there is considerable change leading to the daughter taxon.

Of course, we don't really know that the (generally unobserved) changes were actually that sudden and happened exactly at the same time that lineage branching (cladogenesis/speciation), occurred, because the fossil record is under-sampled. The important thing is that budding cladogenesis is a possible interpretation of how morphotaxa are related in the fossil record.

In this example, which is meant to represent a simulated dataset of evolution under budding cladogenesis, we have a dataset of four taxa, where A is ancestral to taxa B, C and D. A remained static through the cladogenesis events that led to those four taxa. The second diagram is a time-scaled phylogeny describing the relationships among the populations present at the first occurrence of these four taxa. (If the taxa are static in a model of budding-cladogenesis, then simulating things to their first appearance datum should be okay.)

The problem with the budding cladogenesis model and simulating trait change in this scenario is that its asymmetric: only one of the lineages sees any change at speciation events. I realized this earlier this week when I was using the function simFossilTaxa and taxa2phylo from my paleotree library. taxa2phylo converts taxon ranges into a phylogeny, as depicted by the second diagram above. I was simulating clades under budding cladogenesis (as above), converting the datasets to phylogenies, then simulating trait evolution using standard Brownian Motion (BM) simulations on phylogenies (like rtraitcont or fastBM in the ape and phytools packages, respectively). To simulate cladogenetic trait change, I set all the branches in the second diagram to 1 and simulated BM.

But this was wrong! If I did this for the example above, the trait value of taxa B would be just a function of the trait value of A above and a single speciation event. That's what's we want (look at the first diagram). But for C and D, their trait values also become a function of trait evolution which occurred at previous nodes in the tree, when their trait values should actually be independent of those events: i.e. the values of C and D should simulated just like B, only being a function of their ancestor (A) and single trait value change.

I have another function in paleotree which translates a 'taxa' matrix from simFossilTaxa into a cladogram of nested relationships (assuming that systematic characters don't vary over morphotaxon ranges). However, this is just as useless in this situation, as there are no nested relationships in the four taxa above, so they just form one big polytomy. If you try simulating BM on that using standard methods, the trait values of all the taxa will equally depend on some ancestor (which is not inferred to be A). Yeesh!

Note that if the changes were symmetric in the model (as in a bifurcating cladogenesis model) than all would be fine and dandy: species traits always shift after speciation; there is none of this static ancestor stuff. But for the asymmetric case, you need to have information about which branch experienced the change. One could always just randomly pick one, if all a user had was a topology, but that isn't the case here. I'd like the changes to match to the budding pattern in the simulation I've already done! (Who knows how sampling of morphotaxa in time could affect these things...)

Instea,d we'll need a specialized function that simulates trait evolution using the taxa matrix itself, since that's the only place where we have the data on the ancestor-descendant relationships and the stasis of particular lineages. Using Liam Revell's excellent description (also here and here) of how he constructed fastBM for his phytools package, I was able to cobble together a little function for simulating cladogenetic trait evolution on the output from simFossilTaxa. Here it is (this will be included in the next release of paleotree):

cladogeneticTraitCont<-function(taxa,rate=1,meanChange=0,rootTrait=0){
#simulate speciational trait evolution for datasets from simFossilTaxa
#idiot proofing
taxa<-taxa[order(taxa[,1]),]
if(any(taxa[-1,2]>=taxa[-1,1])){stop("Ancestors have higher IDs than Descendants?")}
anctaxa<-sapply(taxa[-1,2],function(x) which(x==taxa[,1]))
traits<-rootTrait
for(i in 2:nrow(taxa)){
traits[i]<-traits[anctaxa[i-1]]+rnorm(1,mean=meanChange,sd=sqrt(rate))
}
names(traits)<-paste("t",taxa[,1],sep="")
return(traits)
}

We can use plotTraitgram to see what the evolutionary pattern would like, under a model where we infer ancestral traits via time-dependent BM (so not cladogenetic/speciational). Obviously, that ain't true for our simulated data, but we wouldn't know that a priori for most datasets so let's do it anyway.

library(paleotree)
set.seed(444)
taxa<-simFossilTaxa(0.1,0.1,mintaxa=100,plot=T)
trait<-cladogeneticTraitCont(taxa)
tree<-taxa2phylo(taxa)
plotTraitgram(trait,tree,conf.int=F)

And we get:

Presenting: paleotree v1.2

Hello all,
After more than month of having my library up on CRAN and finally feeling satisfied that I've worked out enough of the bugs, I'd like to introduce you to my R library, paleotree! It does many things, but if you like phylogenetics, fossils and particularly the overlap of those two, you may find something in interest! With paleotree, you can time-scale cladograms of fossil taxa, estimate sampling rates from the ranges of fossil taxa, plot diversity curves and simulate diversification and sampling in the fossil record. So, go download version 1.2 and check it out! The entire library will be described in a paper I submitted a week and a half ago to Methods in Ecology and Evolution and apparently is now in review. I'll add a citation file to paleotree when that gets more definite. Until then, cite Bapst, D. (in review)!

http://cran.r-project.org/web/packages/paleotree/index.html

Now, I would like to note that some of the included functions, such as the sampling-rate conditioned time-scaling methods, are not described yet in the primary literature. The methods are included in the current release and you can use them if you wish, but Buyer Beware and all that. The algorithm behind these methods will be described in more detail in a future. For the moment, I would actually suggest you use the more typical time-scaling methods, applicable with timePaleoPhy and bin_timePaleoPhy.

Let me know if you run into any bugs! You can find my email address in the help files for R if you don't know it already. Also, I have tried to be very meticulous with regards to the help files and tried to make them as clear as possible, but I am sure my general muddled-ness will show through. So, if you don't understand anything, let me know so I can clarify the help files in the next release!

So far, in terms of potential errors and bugs in version 1.2, I have discovered that simFossilTaxa can enter an infinite loop under some parameter choices if you try a pure-birth model. I don't know why you'd want to do a pure-birth simulation of the fossil record, but this will be fixed in the next release. Then you can simulate your extinction-less fossil record to your heart's content!

Finally, let me know if you get any good ideas of what I could add that would make analyses in phylogenetic paleobiology easier for you!

Cheers,
-Dave B.

Model-based Phylogenetics and Morphology

Hello listeners,

(Sorry for the long hiatus; I'm not much for soapboxes.)

A while ago I found myself in discussions relating to how one should do phylogenetics. Now, one could have arguments for many lifetimes on all the details of how to make a tree, many of which I have no opinion on. One that I do feel strongly about is that more people should at least consider using model-based phylogenetics in morphological systematics; this is in contrast to the more classic use of parsimony-based phylogenetics. For those of you unfamiliar with this distinction, all you need to know that there are different ways biologists use to reconstruct phylogenies based on data about the characters that are shared or differ between lineages. Maximum parsimony just tries to find the tree(s) that have the fewest character changes along the branches (the most parsimonious tree; it infers the least complicated scenario of evolution). Model-based methods take some model of how a trait should change over time and calculates the likelihood/posterior probability of the characters being at their observed states, given a phylogenetic hypothesis. This is commonly in either a maximum likelihood or Bayesian analysis and more commonly with molecular character (ex. DNA) than morphological characters (distinct features of bones/shells/etc). Of course, if you're a paleontologist, you probably deal with morphological characters.

Now, I should point out that even the most simple model of evolution for morphological characteristics has only been around in the published literature for about ten years. This model is Lewis's (2001) Mkv model, which is a description of the number of changes we expect to see in all characters where we see any change at all.

Now, I could (and have) given long arguments about why we should use model-based approaches in morphological phylogenetics, even if they are relatively simple models. But I don't really care and anyway its mostly my opinion versus someone else's opinion. So who cares?

I'd rather talk about something with data. A particular point that came up a month or two ago in a discussion, where a friend claimed that although models of morphological phylogenetics existed, no one used them. I thought he was mostly right at the time. Later, I decided to go see just how many papers I could find where a morphological dataset had been analyzed with model-based phylogenetics. The answer? I found about 50 papers. That's way more than I expected. I also happily saw that a number of them applied them to paleontological datasets. Of course, this would be insignificant compared to the number of parsimony-based morphological studies over the past 10 years, which surely in the hundreds, if not a few thousand.

I sent this list of papers that use the Mkv model or a variant for morphological phylogenetics to a few people but recently decided that people might find it useful in general, so here it is below!

Cheers!
-Dave

Morphological Phylogenetic Analyses that Used the Mkv model or a variant:
Ayache, N. C., and T. J. Near. 2009. The Utility of Morphological Data in Resolving Phylogenetic Relationships of Darters as Exemplified with Etheostoma (Teleostei: Percidae). Bulletin of the Peabody Museum of Natural History 50(2):327-346.
Bergmann, P. J., and A. P. Russell. 2007. Systematics and biogeography of the widespread Neotropical gekkonid genus Thecadactylus (Squamata), with the description of a new cryptic species. Zoological Journal of the Linnean Society 149(3):339-370.
Bergsten, J., and K. B. Miller. 2007. Phylogeny of Diving Beetles Reveals a Coevolutionary Arms Race between the Sexes. PLoS ONE 2(6):e522.
Beutel, R. G., F. Friedrich, T. Hörnschemeyer, H. Pohl, F. Hünefeld, F. Beckmann, R. Meier, B. Misof, M. F. Whiting, and L. Vilhelmsen. 2011. Morphological and molecular evidence converge upon a robust phylogeny of the megadiverse Holometabola. Cladistics 27(4):341-355.
Brandley, M. C., and K. d. Queiroz. 2004. Phylogeny, Ecomorphological Evolution, and Historical Biogeography of the Anolis cristatellus Series. Herpetological Monographs 18:90-126.
Bybee, S. M., T. H. Ogden, M. A. Branham, and M. F. Whiting. 2008. Molecules, morphology and fossils: a comprehensive approach to odonate phylogeny and the evolution of the odonate wing. Cladistics 24(4):477-514.
Cabrero-Sanudo, F. J. 2007. The phylogeny of Iberian Aphodiini species (Coleoptera, Scarabaeoidea, Scarabaeidae, Aphodiinae) based on morphology. Systematic Entomology 32(1):156-175.
Cabrero-Sañudo, F.-J., and R. Zardoya. 2004. Phylogenetic relationships of Iberian Aphodiini (Coleoptera: Scarabaeidae) based on morphological and molecular data. Molecular Phylogenetics and Evolution 31(3):1084-1100.
Ceotto, P., and T. Bourgoin. 2008. Insights into the phylogenetic relationships within Cixiidae (Hemiptera: Fulgoromorpha): cladistic analysis of a morphological dataset. Systematic Entomology 33(3):484-500.
Clarke, J. A., and K. M. Middleton. 2008. Mosaicism, Modules, and the Evolution of Birds: Results from a Bayesian Approach to the Study of Morphological Evolution Using Discrete Character Data. Systematic Biology 57(2):185-201.
Druckenmiller, P. S., and A. P. Russell. 2008. A phylogeny of Plesiosauria (Sauropterygia) and its bearing on the systematic status of Leptocleidus Andrews, 1922. Zootaxa 1863:1–120.
Egge, J. J. D., and A. M. Simons. 2009. Molecules, morphology, missing data and the phylogenetic position of a recently extinct madtom catfish (Actinopterygii: Ictaluridae). Zoological Journal of the Linnean Society 155(1):60-75.
Eklöf, J., F. Pleijel, and P. Sundberg. 2007. Phylogeny of benthic Phyllodocidae (Polychaeta) based on morphological and molecular data. Molecular Phylogenetics and Evolution 45(1):261-271.
Feng, C.-M., S. R. Manchester, and Q.-Y. Xiang. 2009. Phylogeny and biogeography of Alangiaceae (Cornales) inferred from DNA sequences, morphology, and fossils. Molecular Phylogenetics and Evolution 51(2):201-214.
Friedrich, F., B. D. Farrell, and R. G. Beutel. 2009. The thoracic morphology of Archostemata and the relationships of the extant suborders of Coleoptera (Hexapoda). Cladistics 25(1):1-37.
Fröbisch, N. B., and R. R. Schoch. 2009. Testing the Impact of Miniaturization on Phylogeny: Paleozoic Dissorophoid Amphibians. Systematic Biology 58(3):312-327.
Gernandt, D. S., S. Magallon, G. Geada Lopez, O. Zeron Flores, A. Willyard, and A. Liston. 2008. Use of Simultaneous Analyses to Guide Fossil-Based Calibrations of Pinaceae Phylogeny. International Journal of Plant Sciences 169(8):1086-1099.
Giusti, F., V. Fiorentino, A. Benocci, and G. Manganelli. 2011. A Survey of Vitrinid Land Snails (Gastropoda: Pulmonata: Limacoidea). Malacologia 53(2):279-363.
Glenner, H., A. J. Hansen, M. V. Sørensen, F. Ronquist, J. P. Huelsenbeck, and E. Willerslev. 2004. Bayesian Inference of the Metazoan Phylogeny: A Combined Molecular and Morphological Approach. Current Biology 14(18):1644-1649.
Heikkilä, M., L. Kaila, M. Mutanen, C. Peña, and N. Wahlberg. 2011. Cretaceous origin and repeated tertiary diversification of the redefined butterflies. Proceedings of the Royal Society B: Biological Sciences.
Hultgren, K. M., and J. E. Duffy. 2011. Multi-Locus Phylogeny of Sponge-Dwelling Snapping Shrimp (Caridea: Alpheidae: Synalpheus) Supports Morphology-Based Species Concepts. Journal of Crustacean Biology 31(2):352-360.
Jenner, R., C. Dhubhghaill, M. Ferla, and M. Wills. 2009. Eumalacostracan phylogeny and total evidence: limitations of the usual suspects. BMC Evolutionary Biology 9(1):21.
Keck, B. P., and T. J. Near. 2008. Assessing phylogenetic resolution among mitochondrial, nuclear, and morphological datasets in Nothonotus darters (Teleostei: Percidae). Molecular Phylogenetics and Evolution 46(2):708-720.
Lee, M. S. Y., and A. B. Camens. 2009. Strong morphological support for the molecular evolutionary tree of placental mammals. Journal of Evolutionary Biology 22(11):2243-2257.
Lee, M. S. Y., A. F. Hugall, R. Lawson, and J. D. Scanlon. 2007. Phylogeny of snakes (Serpentes): combining morphological and molecular data in likelihood, Bayesian and parsimony analyses. Systematics and Biodiversity 5(04):371-389.
Lee, M. S. Y., and T. H. Worthy. In Press. Likelihood reinstates Archaeopteryx as a primitive bird. Biology Letters.
Muller, J., and R. R. Reisz. 2006. The Phylogeny of Early Eureptiles: Comparing Parsimony and Bayesian Approaches in the Investigation of a Basal Fossil Clade. Systematic Biology 55(3):503-511.
Near, T. J. 2009. Conflict and resolution between phylogenies inferred from molecular and phenotypic data sets for hagfish, lampreys, and gnathostomes. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution 312B(7):749-761.
Nylander, J. A. A., F. Ronquist, J. P. Huelsenbeck, and J. Nieves-Aldrey. 2004. Bayesian Phylogenetic Analysis of Combined Data. Systematic Biology 53(1):47-67.
Ogden, T. H., J. L. Gattolliat, M. Sartori, A. H. Staniczek, T. SoldÁN, and M. F. Whiting. 2009. Towards a new paradigm in mayfly phylogeny (Ephemeroptera): combined analysis of morphological and molecular data. Systematic Entomology 34(4):616-634.
Organ, C., C. L. Nunn, Z. Machanda, and R. W. Wrangham. 2011. Phylogenetic rate shifts in feeding time during the evolution of Homo. Proceedings of the National Academy of Sciences 108(35):14555-14559.
Pérez-Losada, M., M. Harp, J. T. Høeg, Y. Achituv, D. Jones, H. Watanabe, and K. A. Crandall. 2008. The tempo and mode of barnacle evolution. Molecular Phylogenetics and Evolution 46(1):328-346.
Pollitt, J. R., R. A. Fortey, and M. A. Wills. 2005. Systematics of the trilobite families Lichidae Hawle & Corda, 1847 and Lichakephalidae Tripp, 1957: The application of bayesian inference to morphological data. Journal of Systematic Palaeontology 3(3):225-241.
Pyron, R. A. 2011. Divergence Time Estimation Using Fossils as Terminal Taxa and the Origins of Lissamphibia. Systematic Biology 60(4):466-481.
Ravara, A., H. Wiklund, M. R. Cunha, and F. Pleijel. 2010. Phylogenetic relationships within Nephtyidae (Polychaeta, Annelida). Zoologica Scripta 39(4):394-405.
Robovský, J., V. ŘIčánková, and J. Zrzavý. 2008. Phylogeny of Arvicolinae (Mammalia, Cricetidae): utility of morphological and molecular data sets in a recently radiating clade. Zoologica Scripta 37(6):571-590.
Schneider, H., A. R. Smith, and K. M. Pryer. 2009. Is Morphology Really at Odds with Molecules in Estimating Fern Phylogeny? Systematic Botany 34(3):455-475.
Schneider, S. A., and J. S. LaPolla. 2011. Systematics of the mealybug tribe Xenococcini (Hemiptera: Coccoidea: Pseudococcidae), with a discussion of trophobiotic associations with Acropyga Roger ants. Systematic Entomology 36(1):57-82.
Shimizu, A., M. Wasbauer, and Y. Takami. 2010. Phylogeny and the evolution of nesting behaviour in the tribe Ageniellini (Insecta: Hymenoptera: Pompilidae). Zoological Journal of the Linnean Society 160(1):88-117.
Sikes, D. S., R. B. Madge, and S. T. Trumbo. 2006. Revision of Nicrophorus in part: new species and inferred phylogeny of the nepalensis-group based on evidence from morphology and mitochondrial DNA (Coleoptera : Silphidae :Â

Nicrophorinae). Invertebrate Systematics 20(3):305-365.
Sikes, D. S., S. M. Vamosi, S. T. Trumbo, M. Ricketts, and C. Venables. 2008. Molecular systematics and biogeography of Nicrophorus in part—The investigator species group (Coleoptera: Silphidae) using mixture model MCMC. Molecular Phylogenetics and Evolution 48(2):646-666.
Snively, E., A. P. Russell, and G. L. Powell. 2004. Evolutionary morphology of the coelurosaurian arctometatarsus: descriptive, morphometric and phylogenetic approaches. Zoological Journal of the Linnean Society 142(4):525-553.
Straka, J., and P. Bogusch. 2007. Phylogeny of the bees of the family Apidae based on larval characters with focus on the origin of cleptoparasitism (Hymenoptera: Apiformes). Systematic Entomology 32(4):700-711.
Tippery, N. P., C. T. Philbrick, C. P. Bove, and D. H. Les. 2011. Systematics and Phylogeny of Neotropical Riverweeds (Podostemaceae: Podostemoideae). Systematic Botany 36(1):105-118.
Torres-Carvajal, O. 2007. Phylogeny and biogeography of a large radiation of Andean lizards (Iguania, Stenocercus). Zoologica Scripta 36(4):311-326.
Voss, R. S., and S. A. Jansa. 2009. Phylogenetic Relationships and Classification of Didelphid Marsupials, an Extant Radiation of New World Metatherian Mammals. Bulletin of the American Museum of Natural History:1-177.
Wahlberg, N., M. F. Braby, A. V. Z. Brower, R. de Jong, M.-M. Lee, S. Nylin, N. E. Pierce, F. A. H. Sperling, R. Vila, A. D. Warren, and E. Zakharov. 2005. Synergistic effects of combining morphological and molecular data in resolving the phylogeny of butterflies and skippers. Proceedings of the Royal Society B: Biological Sciences 272(1572):1577-1586.
Wiens, J. J., C. A. Kuczynski, T. Townsend, T. W. Reeder, D. G. Mulcahy, and J. W. Sites. 2010. Combining Phylogenomics and Fossils in Higher-Level Squamate Reptile Phylogeny: Molecular Data Change the Placement of Fossil Taxa. Systematic Biology 59(6):674-688.
Winterton, S. L., N. B. Hardy, and B. M. Wiegmann. 2010. On wings of lace: phylogeny and Bayesian divergence time estimates of Neuropterida (Insecta) based on morphological and molecular data. Systematic Entomology 35(3):349-378.
Zaldivar-Riverón, A., M. Mori, and D. L. J. Quicke. 2006. Systematics of the cyclostome subfamilies of braconid parasitic wasps (Hymenoptera: Ichneumonoidea): A simultaneous molecular and morphological Bayesian approach. Molecular Phylogenetics and Evolution 38(1):130-145.

Introducing or examining aspects of Mkv:
Lewis, P. O. 2001. A Likelihood Approach to Estimating Phylogeny from Discrete Morphological Character Data. Systematic Biology 50(6):913-925.
Allman, E. S., M. T. Holder, and J. A. Rhodes. 2010. Estimating trees from filtered data: Identifiability of models for morphological phylogenetics. Journal of Theoretical Biology 263(1):108-119.
Springer, M. S., A. Burk-Herrick, R. Meredith, E. Eizirik, E. Teeling, S. J. O'Brien, and W. J. Murphy. 2007. The Adequacy of Morphology for Reconstructing the Early History of Placental Mammals. Systematic Biology 56(4):673-684.

On the Use of Terms 'Phylogenetic Comparative Methods' and 'Neontologist'

Some boring discussion of terminology.

I've heard the phrase "Phylogenetic Comparative Methods" or "Comparative Methods" get used for everything from just analyses for assessing evolutionary correlations (independent contrasts or phylogenetic general least squares), to all phylogeny-based analyses of trait evolution, to even include birth-death modelling of lineage diversification and phylogenetic community analyses. I'm actually a bit surprised that things in the past, like Pete Wagner's work on evolutionary rates, hasn't been subsumed under this phrase yet. I think using this phrase so vaguely, to refer to anything in which a phylogeny is somehow involved, contributes to some confusion among newcomers and increasingly removes any ability of ours to refer to a cohesive distinction among analytical methods.

It would be better and clearer if we used PCM to only refer to studies of evolutionary correlation. That's what comparative methods meant, prior to Felsenstein (1985), from what I understand. If I can be so forward, why not the term 'macroevolutionary analysis'? Of course, that term would also include many of the analyses done in evolutionary paleobiology, but well, as I was stating earlier, these methods largely differ in data used, not the question addressed. Maybe we can differentiate with 'phylogenetic macroevolutionary analysis' if we really want.

To finally shut my trap on things that Evolution 2011 has made me think about, I'd like to mention that the meeting caused me to have mixed feelings about the use of the word neontologist. I never really used it until I came to Chicago, it has become a useful addition to my lexicon to make the distinction between those using fossil data and those not using fossil data. However, biologists don't know they are 'neontologists' and in trying to explain why we would give such a label when I accidentally say it, I feel like I am just perpetuating bad feelings from several decades ago. But if neontologist is a poor word, than maybe paleontologist is too. Hrm.

Paleontology, Evolution 2012: Ottawa and the Future

So... with all that discussion about the meeting that just happened out the way, let's talk bigger picture here.

Next year, it will be a giant joint meeting in Ottawa with the European version of SSE. I think (and some other people are too) that it might be a pretty neat idea to lure as many paleontologists as possible to this meeting. Why? Well, based on what I observed at this meeting, evolutionary biologists and paleontologists are now asking essentially the same questions, just with different data and methods. How does trait diversity evolve? What controls lineage diversification? How do traits affect speciation and extinction (i.e. species selection or species sorting)? We definitely cannot afford to ignore one another!

This new interest in quantitative macroevolutionary analysis among evolutionary biologists means we that we should act to synthesize our efforts and learn from each other. The number of talks that were trying to use both sorts of data, either to compare or integrate, was striking. (Obviously) I think there's a lot that can be done by combining paleontological and biological data and methods. This is a very exciting time.

There are some hurdles, of course. I know some paleontologists remember earlier times, when biologists were not kind to the suggestion that paleontology could inform evolutionary biology and thus ignored paleontologists. I really don't think that is the case anymore; the relatively positive response I saw to Gene's talk on PuncEq suggested to me that biologists no longer remembered that a rift had even once existed. I see that a clear appreciation for deep time and historical factors is growing over there in biology, and we as paleontologists should be acting to nurture this.

Other hurdles, particularly limitations of money, are not as easy to fix. I don't have any great ideas on how to fix that one yet (Any ideas?). There's also time limitations. Many paleontologists do field work or museum work over the summer and there are also some early summer conferences around the same time. Nothing can be done about that.

Still, I think if evolutionary paleontologists can go and they are willing to do a little learning about how biologists do what they do and teach a little about how the fossil record works and what it means for evolution, I think they should go. I think its an opportunity that can't be missed.

Overall, I think some integration of the two communities needs to happen, but I admit that it isn't just about this Ottawa meeting next year. In discussion with some people, it was mentioned that maybe the annual SICB meeting might be a good bridge, as both paleontologist and evolutionary biologist communities partially attend. Also, Emily King and I are trying our best to try to get evolutionary biologists to come to GSA, where paleontologists generally go, but I do not know how successful we will be yet. (I'm keeping my fingers crossed!) In the long run, integration will require aisle-crossing from both sides, with paleo people going to bio meetings more frequently and bio-people coming to paleo meetings.

What do you guys think? Can we better unite these fields, at least meetings-wise?

(...Of course, once we get evolutionary biology and paleontology more copacetic, the next task is ecology and paleoecology... now there's a real challenge!)

A Paleontologist at Evolution 2011

This week I was lucky enough to attend Evolution 2011, this year's iteration of an annual convention held jointly between the Society for the Study of Evolution (SSE), the Society of Systematic Biologists (SSB) and the American Society of Naturalists (ASN). As one of the few paleontologists who attended, I'd like to spend some time discussing my expectations going in, my reaction to the general tone of the meeting and some talks that I thought were really neat.

Before I came to Evolution, more than a few people told me that the conference would be of little interest to a paleontologist. They said the talks were very focused on molecular tree-building, experimental evolution and genomics, and that paleo stuff was generally swept off to some isolated session that no one attends. I also expected it to be a very large conference, maybe the size of the Geological Society of America national meeting (the regular yearly meet-up for most paleontologists, particularly non-vertebrate workers, but mainly attended by geologists). I just thought there was a lot of evolutionary biologists in the world.

I decided to go anyway, seeing that many of the sessions last year had been titled 'diversification', and I enjoy a good story based on a phylogeny as much anyone else. I also submitted a talk. I work on phylogenetic approaches to macroevolution in an extinct group, so my research falls very nicely into the current interests of evolutionary biologists.

First off, the meeting was surprisingly small, maybe a little bit larger than the paleo portion of GSA but definitely smaller than NAPC or IPC3. I hear this was a small year, but it makes the community of evolutionary biology less intimidating.

Secondly, there were very few paleontologists. (I count no more than 13.) However, the single paleo session at the meeting appeared to be well attended, although I didn't personally see giant crowds at the back like a few sessions had. As a speaker, I sat in the front and I did not glance behind me that often, so maybe I missed this. (After my talk, I got a lot of feedback and some compliments. People even tweeted about me! Yay!)

As far as specific talks of interest to the paleo-inclined, I particularly enjoyed Gene Hunt's talk on punctuated equilibrium. There was also some intriguing work being done on clam shrimp morphometrics to elucidate sex ratios in the fossil record, presented separately by Byron Brown and Timothy Astrop (both from the same research group). Earlier in the conference, Pete Wagner and David Polly gave talks on character evolution in the big symposium room.

There was also a considerable number of talks focusing on comparing and/or integrating the information from molecular phylogenies and the fossil record: Carl Simpson compared diversification histories in corals, Graham Slater discussed putting uncertain fossil ancestors on phylogenies for trait evolution and Rampal Etienne discussed a model of diversity-dependent diversification and fit it to both fossil data and molecular data. There was also a number of mentions in other talks about the increasing realization that fossil data was necessary for testing some macroevolutionary hypotheses. I think an integration of data and methods is a very promising route as we realize the limitations of each type of data. Although they are not integrating this data just yet, there were several people at the meeting from the BITS (Bivalves in Time and Space) working group, which holds considerable promise in exploring what a combined dataset might tell us.

Thirdly, and very importantly, the meeting was full to the brim of macroevolution. All those 'diversification' sessions were full of talks where some people made a tree and THEN went on to test some neat question about diversification rates or trait evolution using some of the more recent 'comparative methods': BISSE, MEDUSA, geiger, ouch, etc. I've talked to some people who have been to more Evolution meetings than I have and they tell me this really is something new, maybe starting last year at the Portland meeting.

All of this has given me some, well, perhaps radical thoughts which I will share in the next blog post.

Indicative of a field that is growing and developing, there was also a number of talks on the analytical power of specific methods (Richard FitzJohn, Cecile Ane, Matt Davis and Carl Boettiger). Boettiger's talk was particularly interesting, presenting a new method to show us the distinction in support for different models of trait evolution more clearly and he has also placed his slides online. Liam Revell also presented new methods for estimating shifts in rates of trait evolution, which he has discussed previously on his blog.

As always, there were a few talks I wish I had not missed: Joe Felsenstein, Josef Uyeda, Chris Martins, Sam Price... Oh well. We cannot see everything at a conference! Oh well... maybe next year!

A Preserved Graptolite Zooid?

It appears that scientists have finally discovered a preserved graptolite zooid! It's benthic and it's Cambrian, and its BIG (4 cm!) but the thing looks just like Rhabdopleura, just like we would expect based on phylogenetic analyses of colony structure...

http://www.cell.com/current-biology/retrieve/pii/S0960982211002776

Hou, X.-g., Richard J. Aldridge, David J. Siveter, Derek J. Siveter, M. Williams, J. Zalasiewicz, and X.-y. Ma. 2011. An Early Cambrian Hemichordate Zooid. Current Biology 21(7):612-616.

I don't quite see the fusellar banding that Hou et al. describe in the figures, but if anyone else can, let me know.

http://www2.le.ac.uk/news/blog/2011-archive/march/fossil-discovered/

An exciting time to be a graptolite worker!