(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!
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 (ColeopteraÂ :Â SilphidaeÂ :Â
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.