Why YOU should go to Evolution 2013!

Hello all,

It's April 25th, 2013, and that means Evolution 2013 is a little less than two month away. Now, a lesser known thing about Evolution meetings is (a) you only have to submit a title unless you're trying for a special student presentation award and (b) you can view everyone's submission as they submit on a public website:

 Evolution 2013 - Presentation Search

ALSO, the organizers have extended presentation deadlines, you still have until TOMORROW (April 26th) to submit your presentation! Still on the fence about whether to go? Well, here's one (cough) short list of reasons why you should go.

Once upon a time, I remember some people who told me I probably wouldn't enjoy my time at Evolution: that the majority of the talks involved genetic evolution. (And I work on an extinct group so...) Well look down and tell me if that's true in 2013.

If you have any interests in paleontology, phylogenetics or macroevolution, you'll find something below of interest, I guarantee it. This is an amazing time to be a young scientist working in this area. Also, we really need to see more paleontology at Evolution! Note well though that many of the Evolution talks given by paleontologists aren't even listed under paleontology: many of us are giving macroevolution, phylogenetics, biogeography or community ecology and evolution.



Here's the list:

A generalized kappa statistic for estimating phylogenetic signal from multivariate data
Dean Adams
http://evo2013.evolutionmeeting.org/engine/search/index.php?func=detail&aid=454

A genomic approach to understanding allopatric speciation in tropical montane birds
Ben Winger and John Bates
http://evo2013.evolutionmeeting.org/engine/search/index.php?func=detail&aid=62

A linear-time algorithm for Gaussian and non-Gaussian trait evolution models.
Ho, Lam; Ane, Cecile
http://evo2013.evolutionmeeting.org/engine/search/index.php?func=detail&aid=51
   
An artifact caused by undersampling optimal trees in supermatrix analyses of locally sampled characters
Pitkin Simmons, Mark; Goloboff, Pablo.
http://evo2013.evolutionmeeting.org/engine/search/index.php?func=detail&aid=98

A new birth-death model recovers the K-Pg mass-extinction event in mammals.
Hoehna, Sebastian
http://evo2013.evolutionmeeting.org/engine/search/index.php?func=detail&aid=1206

Arbor: Comparative Analysis Workflows for the Tree of Life
Harmon, Luke, Baumes, Jeff, Hughes, Charlie, Soberon, Jorge, Specht, Chelsea, Thacker, Robert, Turner, Wes, Lisle, Curtis
http://evo2013.evolutionmeeting.org/engine/search/index.php?func=detail&aid=668

A simple index of the strength of convergent evolution.
Arbuckle, Kevin
http://evo2013.evolutionmeeting.org/engine/search/index.php?func=detail&aid=823

Assembly & early diversification of modern reef fishes.
Price, Samantha, Wainwright, Peter
http://evo2013.evolutionmeeting.org/engine/search/index.php?func=detail&aid=249

Association between colony life-history and polymorphism in Cheilostome br.
Carl Simpson
http://evo2013.evolutionmeeting.org/engine/search/index.php?func=detail&aid=659

A variable rates approach to quantifying the processes underlying trait co-variation.
Smaers, Jeroen
http://evo2013.evolutionmeeting.org/engine/search/index.php?func=detail&aid=654

Bayesian inference of biogeographical histories for hundreds of discrete areas
Landis, Michael; Matzke, Nicholas; Moore, Brian; Huelsenbeck, John
http://evo2013.evolutionmeeting.org/engine/search/index.php?func=detail&aid=194

Bayesian inference of phylogeny from partitioned data
Moore, Brian, Fredrik, Ronquist, McGuire, Jim, Huelsenbeck, John
http://evo2013.evolutionmeeting.org/engine/search/index.php?func=detail&aid=1176

Better interpretation of patterns of trait evolution using a novel reversible-jump method of detecting adaptive regimes from phylogenetic comparative data
Josef Uyeda and Luke Harmon
http://evo2013.evolutionmeeting.org/engine/search/index.php?func=detail&aid=601

Beyond the lower-bound: the fossil record can provide empirically-informed prior distributions on node ages in poorly-sampled groups
Graeme Lloyd, Matt Friedman and Mark Bell
http://evo2013.evolutionmeeting.org/engine/search/index.php?func=detail&aid=1134

Coevolution, diversification, and biogeography of a specialized insect-plant pollination mutualism on oceanic islands
David Hembry
http://evo2013.evolutionmeeting.org/engine/search/index.php?func=detail&aid=553

Constraints on mammalian forelimb development: Insights from developmental disparity
Ross, Darcy; Marcot, Jonathan; Betteridge, Keith; Nascone-Yoder, Nanette; Bailey, Scott; Sears, Karen
http://evo2013.evolutionmeeting.org/engine/search/index.php?func=detail&aid=794

Deflating trees: improving Bayesian branch-length estimates using informed priors
Nelson, Brad, Andersen, John, Brown, Jeremy
http://evo2013.evolutionmeeting.org/engine/search/index.php?func=detail&aid=674

Detecting Genomic Introgression at the Phylogenetic Scale
Eaton, Deren; Ree, Richard
http://evo2013.evolutionmeeting.org/engine/search/index.php?func=detail&aid=538

Distance-based phylogenetic algorithms around a polytomy
Davidson, Ruth; Sullivant, Seth
http://evo2013.evolutionmeeting.org/engine/search/index.php?func=detail&aid=472

Diversification of a diverse lineage of Neotropical rodents (Caviomorpha: Octodontoidea): integrating DNA sequences, fossils, and species traits
Nate Upham and Bruce Patterson
http://evo2013.evolutionmeeting.org/engine/search/index.php?func=detail&aid=406

Duplicate gene evolution on the Y-chromosome: insights from ampliconic genes of Indonesian macaques
Hermina Ghenu, Ben Bolker and Ben Evans
http://evo2013.evolutionmeeting.org/engine/search/index.php?func=detail&aid=875

Dynamic variation in rates of body mass evolution in birds
McEntee, Jay P; Ruhfel, Brad; Burleigh, J. Gordon
http://evo2013.evolutionmeeting.org/engine/search/index.php?func=detail&aid=754

Estimating Phylogeny from microRNA Data: A Critical Appraisal
Thomson, Robert; Plachetzki, David; Mahler, D. Luke; Moore, Brian
http://evo2013.evolutionmeeting.org/engine/search/index.php?func=detail&aid=1203

Evo-devo to Everest: travels with the trilobite time lords
Nigel Hughes
http://evo2013.evolutionmeeting.org/engine/search/index.php?func=detail&aid=571

Evolution and the Levels of Lineage
Matt Haber
http://evo2013.evolutionmeeting.org/engine/search/index.php?func=detail&aid=862

Evolution of desert biotas
John Wiens
http://evo2013.evolutionmeeting.org/engine/search/index.php?func=detail&aid=908

Expeditionary Science in Deep Time: Motor for Paradigm Change
Paul Sereno
http://evo2013.evolutionmeeting.org/engine/search/index.php?func=detail&aid=1104

Experience with maximum likelihood morphometric methods that use phylogenies
Joe Felsenstein
http://evo2013.evolutionmeeting.org/engine/search/index.php?func=detail&aid=229

Exploring Divergence and Convergence in the Hyperdiverse Myrmicine Ants
Ward, Philip; Schultz, Ted; Fisher, Brian; Brady, Sean
http://evo2013.evolutionmeeting.org/engine/search/index.php?func=detail&aid=1287

Exploring the pelagic abyss
Karen Osborn
http://evo2013.evolutionmeeting.org/engine/search/index.php?func=detail&aid=458

Founder-event speciation dramatically improves likelihoods and alters parameter inference in Dispersal-Extinction-Cladogenesis (DEC) analyses
Nicholas Matzke
http://evo2013.evolutionmeeting.org/engine/search/index.php?func=detail&aid=1242

Fossils as terminals: a total-evidence analysis to estimate angiosperm divergence date
Magallon, Susana, Doyle, James
http://evo2013.evolutionmeeting.org/engine/search/index.php?func=detail&aid=852

Freeloader to free-living: lineage diversification and morphological evolution of the megadiverse marine bivalve clade Galeommatoidea
Li, Jingchun; Ó Foighil, Diarmaid; Strong, Ellen
http://evo2013.evolutionmeeting.org/engine/search/index.php?func=detail&aid=182

From 'Bigmessidae' to Merulinidae: integrating molecules and morphology to resolve the systematics of scleractinian corals.
Huang, Danwei; Smith, Nathan; Budd, Nancy
http://evo2013.evolutionmeeting.org/engine/search/index.php?func=detail&aid=74

Genetic correlates of morphological diversity in Costa Rican army ants
Winston, Max; Moreau, Corrie
http://evo2013.evolutionmeeting.org/engine/search/index.php?func=detail&aid=35

Geometric morphometrics for analysis of any type of symmetry: Methods and biological applications
Savriama, Yoland; Klingenberg, Christian Peter; Neustupa, Jiří; Gómez, José María; Francisco, Perfectti
http://evo2013.evolutionmeeting.org/engine/search/index.php?func=detail&aid=952

How clades expand in size/shape space: integrating fossil and Recent data to evaluate the role of clade age, species richness and position in morphospace
Shan Huang and David Jablonski
http://evo2013.evolutionmeeting.org/engine/search/index.php?func=detail&aid=803

How cryptic is cryptic diversity? Machine learning approaches to fine scale variation in the morphology of Emys marmorata.
Smits, Peter D; Angielczyk, Kenneth D; Parham, James F
http://evo2013.evolutionmeeting.org/engine/search/index.php?func=detail&aid=425

How do measures of "signal" relate to patterns of traits distributed on a phylogenetic tree?
Forrestel, Elisabeth J.; Donoghue, Michael 
http://evo2013.evolutionmeeting.org/engine/search/index.php?func=detail&aid=1241

How good is good enough? - Taxonomy and phylogeny in evolutionary analyses.
Laura Soul, Graeme Lloyd and Matt Friedman
http://evo2013.evolutionmeeting.org/engine/search/index.php?func=detail&aid=825

How to quantify the magnitude and significance of convergent evolution
C. Tristan Stayton
http://evo2013.evolutionmeeting.org/engine/search/index.php?func=detail&aid=957

Identifying hidden rate changes in the evolution of a binary morphological character: the evolution of plant habit in campanulid angiosperms
Beaulieu, Jeremy; O'Meara, Brian C.; Donoghue, Michael 
http://evo2013.evolutionmeeting.org/engine/search/index.php?func=detail&aid=1127

Indirect defensive traits and lineage diversification rates in plants
Weber, Marjorie; Agrawal, Anurag
http://evo2013.evolutionmeeting.org/engine/search/index.php?func=detail&aid=36

Integrating Phylogeny, Climatic Niche, and Biogeographic History to Explain Growth Form Evolution in the Spine-shield Euphorbias (E. sect. Euphorbia, Euphorbiaceae)
Dorsey, Brian; Berry, Paul
http://evo2013.evolutionmeeting.org/engine/search/index.php?func=detail&aid=115

Late Quaternary climate velocity, contemporary environmental gradients, and marine biodiversity patterns on coral reefs
Sbrocco, Elizabeth J.
http://evo2013.evolutionmeeting.org/engine/search/index.php?func=detail&aid=716

Losing to the Red Queen I: a tale of two rates.
Quental, Tiago Bosisio; Marshall, Charles
http://evo2013.evolutionmeeting.org/engine/search/index.php?func=detail&aid=504

Losing to the Red Queen II:  when non-equlibrial processes trump diversity dependence
Marshall, Charles; Quental, Tiago Bosisio
http://evo2013.evolutionmeeting.org/engine/search/index.php?func=detail&aid=1108

Lung evolution in Amniotes
Colleen Farmer
http://evo2013.evolutionmeeting.org/engine/search/index.php?func=detail&aid=1210

Lying through your teeth: saturation and non independence in morphological data, and what to do about it
Davalos, Liliana M; Velazco, Paul M; Warsi, Omar M; Smits, Peter D; Simmons, Nancy B
http://evo2013.evolutionmeeting.org/engine/search/index.php?func=detail&aid=646

Macroevolutionary dynamics of diversification across extant bats
Shi, Jeff; Badgley, Catherine; Rabosky, Daniel
http://evo2013.evolutionmeeting.org/engine/search/index.php?func=detail&aid=217

Macroevolutionary patterns of trait diversification in social insects: a phylogenetic analysis of caste evolution using turtle ants
Scott Powell
http://evo2013.evolutionmeeting.org/engine/search/index.php?func=detail&aid=834

MCDUSA: A Monte Carlo method for more reliable detection of lineage-specific rates of diversification
Michael May and Brian Moore
http://evo2013.evolutionmeeting.org/engine/search/index.php?func=detail&aid=1140

Missing data lead to holes in the tree of life
Cabezas, Patricia; Drew, Bryan; Gazis, Romina; Swithers, Kristen; Deng, Jiabin; Rodriguez, Roseanna; Katz, Laura; Crandall, Keith; Hibbett, David; Soltis, Douglas
http://evo2013.evolutionmeeting.org/engine/search/index.php?func=detail&aid=512

Models of species diversification and the age-richness relationship paradigm
Sánchez-Reyes, Luna Luisa; Magallón, Susana
http://evo2013.evolutionmeeting.org/engine/search/index.php?func=detail&aid=417

Morphology and exploitation in ray-finned fishes using crowdsourced data
Jonathan Chang, Dan Rabosky, Mike Alfaro
http://evo2013.evolutionmeeting.org/engine/search/index.php?func=detail&aid=1293

Multi-Dimensional Optimization - A Mathematic Model For Evolution
Leng, Xuguang
http://evo2013.evolutionmeeting.org/engine/search/index.php?func=detail&aid=87

New graphical methods for visualizing comparative data on phylogenies
Liam Revell
http://evo2013.evolutionmeeting.org/engine/search/index.php?func=detail&aid=954

Node-based analysis of clade distribution
Catherine Graham
http://evo2013.evolutionmeeting.org/engine/search/index.php?func=detail&aid=1179

Open Tree of Life: large-scale phylogenetic data synthesis
Karen Cranston
http://evo2013.evolutionmeeting.org/engine/search/index.php?func=detail&aid=586

Patterns of phenotypic correlations and integration in animals and plants
Conner, Jeffrey K; Cooper, Idelle; La Rosa, Raffica; Perez, Samuel; Royer, Anne
http://evo2013.evolutionmeeting.org/engine/search/index.php?func=detail&aid=323

Phylogenetic ANCOVA: The study of adaptation and phenotypic radiation when combining continuous and categorical traits
Fuentes, Jesualdo; Martins, Emilia
http://evo2013.evolutionmeeting.org/engine/search/index.php?func=detail&aid=740

Phylogenomics offers insights into hemichordate evolution
Cannon, Johanna; Kocot, Kevin; Santos, Scott; Swalla, Billie; Halanych, Ken
http://evo2013.evolutionmeeting.org/engine/search/index.php?func=detail&aid=1014

Sexual dichromatism and speciation rate in birds
HUANG, HUATENG; Rabosky, Daniel
http://evo2013.evolutionmeeting.org/engine/search/index.php?func=detail&aid=488

Tempo of diversification across a 900-species muroid-rodent phylogeny; what do different methods tell us?
Schenk, John, Steppan, Scott
http://evo2013.evolutionmeeting.org/engine/search/index.php?func=detail&aid=234

Testing irreversibility/Dollo's law using ancestral state reconstruction: How hard is it?
David Swofford
http://evo2013.evolutionmeeting.org/engine/search/index.php?func=detail&aid=1130

Testing the strength of evolutionary correlations between dental morphology and diet in extant Carnivora
Sam Hopkins and Sam Price
http://evo2013.evolutionmeeting.org/engine/search/index.php?func=detail&aid=1285

The discovery and documentation of convergent evolution in the morphology and mechanics of turtle shells
C. Tristan Stayton
http://evo2013.evolutionmeeting.org/engine/search/index.php?func=detail&aid=645

The evolution of cichlid craniofacial diversity
Matthew McGee, Sam Borstein, Peter Wainwright
http://evo2013.evolutionmeeting.org/engine/search/index.php?func=detail&aid=1233

The evolution of ecological specialization in birds
Oswald, Jessica A.; Burleigh, J. Gordon
http://evo2013.evolutionmeeting.org/engine/search/index.php?func=detail&aid=298

The evolution of neopilionid harvestmen and a new, putative Gondwanan relic from New Caledonia
Krentzel, Dallas; Cokendolpher, James
http://evo2013.evolutionmeeting.org/engine/search/index.php?func=detail&aid=660

The Fossilized Birth-Death Process: A Coherent Model of Fossil Calibration for Bayesian Divergence Time Estimation
Tracy Heath, John Huelsenbeck and Tanja Stadler
http://evo2013.evolutionmeeting.org/engine/search/index.php?func=detail&aid=193

The Genomic Nature of Linnaean Genera
Masalia, Rishi R.; Barker, Michael
http://evo2013.evolutionmeeting.org/engine/search/index.php?func=detail&aid=339

The genome of the big-eyed arboreal ant Pseudomyrmex gracilis
Ben Rubin and Corrie Moreau
http://evo2013.evolutionmeeting.org/engine/search/index.php?func=detail&aid=524

The Impact of Time-Scaling Methods on Phylogenetic Comparative Methods in the Fossil Record
David Bapst
http://evo2013.evolutionmeeting.org/engine/search/index.php?func=detail&aid=149

The inference of basal snake phylogenetic relationships: The importance of combining molecular, morphological, and fossil data
Harrington, Sean
http://evo2013.evolutionmeeting.org/engine/search/index.php?func=detail&aid=1150

The major features of plant trait evolution, or: how I learned to stop worrying and love the model
Pennell, Matthew; Cornwell, William; Harmon, Luke
http://evo2013.evolutionmeeting.org/engine/search/index.php?func=detail&aid=935

The Signal and the Noise: Why we're still searching for resolution of deep phylogenies
Showers Corneli, Patrice
http://evo2013.evolutionmeeting.org/engine/search/index.php?func=detail&aid=17

Tracking the evolution of fur color patterns in the short-tailed opossum (Monodelphis: Didelphidae): common ancestry or independent evolution?
Pavan, Silvia; Jansa, Sharon; Voss, Rob
http://evo2013.evolutionmeeting.org/engine/search/index.php?func=detail&aid=559

When are missing data problematic for phylogenetic estimation from phenotypic data sets?
April Wright and David Hillis
http://evo2013.evolutionmeeting.org/engine/search/index.php?func=detail&aid=231

Why do species not adapt but go extinct?
Bokma, Folmer
http://evo2013.evolutionmeeting.org/engine/search/index.php?func=detail&aid=1187

Wing shape evolution in social wasps and phylogenetic signal.
Perrard, Adrien, Baylac, Michel, Carpenter, James M., Villemant, Claire
http://evo2013.evolutionmeeting.org/engine/search/index.php?func=detail&aid=326


............................

... And last but not least, the three presidential speeches:

The dechronization of E. coli:  A 25-year love story
Richard Lenski
http://evo2013.evolutionmeeting.org/engine/search/index.php?func=detail&aid=847

Speciation and latitude
Dolph Schluter
http://evo2013.evolutionmeeting.org/engine/search/index.php?func=detail&aid=1142

Systematic biology two decades after Snowbird 1993 and w(h)ither the species tree?
Jack Sullivan
http://evo2013.evolutionmeeting.org/engine/search/index.php?func=detail&aid=1212


.......................

Okay guys, now tell me about all the amazing talk submissions I missed, cause I know I must have missed a bunch!

Also, go submit your own talk title! Go make the list above out-dated in the next 24 hours! Get to it!

-Dave

How to Find a Paleontological Phylogeny (For Those With a Rapidly Approaching Deadline)

Hello all! Recently I got some email requests about where to find paleontological phylogenies, particularly for invertebrate groups. I wrote some responses and then asked if I could post my answer to them here, as I expect they aren't the only ones to have such issues. I mainly got the sense these individuals wanted trees for use with comparative analyses (macroevolutionary analyses) and found me through my authorship of paleotree, the predominant function of which is to prepare a phylogenetic dataset for such evolutionary analyses.

So, I'll assume for this that you, dear reader, are a person in need of a phylogenetic tree of some fossil taxa, particularly invertebrate fossil taxa. Furthermore, I'll assume that the best answer doesn't apply here: that if one really wants a good, believable tree, one should go make a tree the hard way, using cladistics or other phylogeny-building methods and a morphological matrix. The main reason this may not apply is maybe you, dear reader, is if you want a tree for a class project or some other short-term goal, such as to just prove you can apply some method of interest even partially to a group. So you are looking for a tree without needing to make a completely new tree yourself.

First off, not all groups have experienced equal effort in understanding their relationships using algorithmic phylogenetics (i.e. maximum parsimony, likelihood, Bayesian, etc). The difference in relative effort to make trees using quantitative methods from morphological matrices is particularly large between vertebrate and invertebrate groups, but there is even variation about invertebrate groups. Check out this figure (below) from Neige et al. (2007). The main point of that paper was to show how little worked ammonites are using cladistics, but they also reviewed phylogenetic effort in a number of other major fossiliferous group. Some groups, such as bivalves, also have not been the focus of much analysis. In contrast, echinoderms and trilobites have been the focus of considerable cladistic work. Partly its cultural (sometimes there are just too few workers who are acquainted with cladistic methodology) and also its just because some groups, like bivalves, often don't preserve many of the important systematic characters needed for cladistic analysis. In some groups, systematic characters are dominated by continuous measurements, and there is still a lively debate about how to use those traits to determine relationships reliably.

This means if you want to work on a specific group, you may not be able to find a tree built using an explicit cladistic analysis. But let's hope this isn't the case for the moment. Where would you find such a phylogenetic hypothesis, if it existed? There's no general database for specifically paleontological phylogenies. While paleontologists were ahead of the curve by putting collection and occurrence data online in the PBDB years ago, collecting phylogenetics data has lagged behind. There are some morphological datasets and tree files on MorphBank, treeBASE and Dryad, but if you have a specific group you're interested in, particularly invertebrates, they probably don't contain it. 

EDIT (02-22-13):
Graeme Lloyd, who I knew had been keeping a number of fossil vertebrate character matrices and trees on his website, pointed out that he expanded at some point to also include invertebrate groups too! So, thanks for proving me wrong, Graeme!  (I clearly don't read Graeme's website often enough...) 

http://www.graemetlloyd.com/matr.html 

EDIT (02-24-13): Graeme has commented he doesn't currently have any invert matrices up just yet, so his lists at the moment just reflect literature where you could find matrices. Still, that's quite a service!
 
Also, I noticed a Bristol database Graeme mentioned which I was unaware of contains a number of matrices. Again though, coverage is still pretty spotty for some groups.
http://palaeo.gly.bris.ac.uk/cladestore/

So that means you'll have to turn to the primary literature to find trees to use, probably using some well chosen keywords in Google Scholar. Now, let's assume you find the tree you want, which in 99% of the cases will be some cladogram (I recommend the consensus trees...). Now, the tree itself may be offered in supplemental files or you might be able to get it by contact the authors, but let's be perfectly realistic and admit that sometimes those avenues won't work, or they may only work on very long time-scales (hard drives get fried, babies are had and emails go unanswered, etc). Instead, you'll probably need to use what's actually at hand: the tree as printed on the page. I've done this myself quite a bit, and there are some handy programs out there that automate this, but I've always just copied the tree out by hand. 

For small trees, the simplest way to do this is to copy trees out as Newick string. Newick is just a quick way to write relationships among taxa as a series of nested parentheses, with sister lineages seperated by commas (sometimes also called 'phylip' format). A quick example of Newick format for ctenophore, man, graptolite, fly and brachiopod genera: (Pleurobranchia,((Homo,Nemagraptus)(Drosophila,Terebratula))) You can read that into the programming language R as a text file using read.tree() in library ape. For large trees this can get tedious: you could also write out part of the tree and then modify it, by adding taxa, removing taxa and collapsing clades in a GUI, such as Mesquite. R has some of these tools but it doesn't make wholesale tree editing easy. If you're eventual goal is to put the tree in R, I've found it is sometimes necessary to save Mesquite files as PHYLIP format and then open them and resave them in TreeFig before using read.tree. If you're curious how long this will take, I've often found I can copy over a large tree in half a day or so.

Now, let's continue on the path of assuming you found a cladogram. (Yes, reader who cannot find a cladogram, I'll get to you in a moment.) If your question just needs the nesting relationships shown by the cladogram, you're done. You got what you wanted. But maybe you want to go further. Maybe you want to make time-scaled phylogenies, which is what paleotree is for, and probably why you're reading this blog to begin with. These time-scaled phylogenies are what we want for making most evolutionary inferences.

If you want a time-scaled phylogeny, you'll need to find stratigraphic data to use, in addition to the cladogram. These stratigraphic data should record at least which intervals or dates the taxa you want to analyze first and last appear at. These might be in the same publication as the cladogram you found, but they may not. You will probably need to go look at published range charts for this group and spend some time figuring out where obscure regional stages correlated to the global time-scale (this is where Gradstein and Ogg volumes become very useful). You should also check the PBDB, although for some groups the data can be very coarse and will requite some cleaning. Again, there is a right way to do this, but again I'm imagining you have a class project you want to complete with some rapidly approaching deadline. To do anything with paleotree, you just need to get the tree to the point you can read it into R as a 'phylo' object and read the ranges in as a matrix. The functions in paleotree can be applied once you have that. Note, by the way, about these stratigraphic ranges, I'm assuming you have almost all the known species in your dataset. If you are doing something like sampling one species per family, the first appearance times of taxa in your dataset will be poor indicators of when clades branched from each other, at least using the sort of methods I offer in paleotree.

Okay, so what if you couldn't find a cladogram for the group you wanted to work on? Or what if you found a cladogram, but its at the genus-level and your data is species? Or what if the cladogram has half the species you want to analyze, but not the other half, and its non-random with respect to your question (like, let's say body size affects taphonomy in your group, so the cladogram has all the big individuals, but you're interested in body size evolution...). Well, you have several possibilities. You may just be out of luck and maybe you will need to start over or consider making a tree yourself.

If it's just the problem that your taxa are on a bunch of trees and you don't know how to make any sense of all the conflicting relationships, don't worry, supertree methods were invented for a reason and you might want to look into those. However, more likely the issue is the taxa you want on the tree have never been on the tree. So, what you might want to do is look for data on relationships that isn't the product of an explicit phylogenetic analysis. For example, some invert groups have a number of stratophenetic diagrams, which are built based on expert opinion relating to morphological and stratigraphic data. There is also an increasing number of analyses being conducted with informal trees built from a combination of cladistic hypotheses and traditional taxonomic data (like the widely-used Phylomatic for plants; Webb and Donoghue, 2006), or just from taxonomic data alone (e.g. Green et al., 2011 or 'Common Tree', see http://schamberlain.github.com/2013/02/common-tree/). These non-cladistic options, or options which are only partly based on cladistic evidence, *might* be okay to use. 

 Whether such shortcuts are acceptable approaches or not are you and your question. You should carefully consider how sensitive your analyses are to uncertain relationships. It's not really an easy question to ask, but maybe for a first-pass rough cut (such as for a class project), a summary hypothesis based on taxonomic information in replace of a tree may be okay. Some people will feel very strongly about this one way or another, and you'll ultimately be the one who will have to defend what you did and how you did it. The function expandTaxonTree in paleotree can be useful if you do decide to go this route, as it can do helpful things like turning a rough genus-level tree into a species-level tree by treating each genus as a soft polytomy. (Also, as I stated above, if you want a time-scaled tree of fossil taxa, you still need stratigraphic ranges, unless you are using a stratophenetic tree, in which case it should already be time-scaled.) 

Now, for those of you who read this and maybe think this post could inadvertently serve to inspire risky behavior, I agree you might have a point. Phylogenetics can be slow, because good phylogenetics requires patience, care and due consideration. All I can say is that students will always end up in situations where they need datasets as part of coursework (or whatever) and this questions will thus always come up, because making a new morphology-based tree from scratch isn't a feasible solution for most classes (or most students). Overall, I hope people go and do simple analyses with back-of-the-envelope trees, see how awesome phylogeny-based analyses are and get inspired to construct trees for doing those same analyses as part of a larger project where they have more time.

Anyway, I hope all this helps!
-Dave