Professor of Biology
Principal Investigator, Genome Sequencing Laboratory
Curator-in-Charge The Vertebrate Museum
Ph.D. Anatomy, Howard University College of Medicine
NSF Postdoctoral Fellow, Princeton University
Smithsonian Institution Predoctoral Fellow and Research Associate
B.A. Biology, State University of New York at Stony Brook
Pre-Professional Human Anatomy
EvolutionAdvances in Avian Biology
Genomics of Humanity
Research Focus - Ornithology, Molecular Systematics, Anatomy, Vertebrate Palaeontology
"To tentatively entertain these proposals with anything approaching genuine interest, one would have to believe that ornithological systematists know nothing about phylogenetic relationships." -Anonymous Reviewer of Fain and Houde 2004 Parallel Radiations in the Primary Clades of Birds
My interests lie in the very broad areas of the evolutionary biology of birds, and of mammals to a lesser degree. My research covers several areas. 1) Phylogeny reconstruction - the genealogical relationships of organisms to one another. I am most interested in 'higher-level' interfamilial and interordinal relationships. My lab discovered molecular genetic evidence that at least five traditionally recognized orders of birds are polyphyletic, and mistaken to be related on the basis of convergent morphologies. 2) Biogeography - the correlation of patterns of phyletic divergence and the origins of new taxa to the geographic distribution of species and the formation of geophysical barriers through time. Some researchers conjecture that groups of birds with modern endemism to southern continents must have originated there during the Cretaceous when those continents were united. However, among the orders of fossil birds I have described are the sister group to modern ratites, Lithornithiformes, and a primitive ostrich, Palaeotis, whose Northern Hemisphere distributions are quite inconsistent with those of their modern southern relatives. Similarly, our molecular genetic data show that various "gruiform" birds with southern disjunct endemism (e.g., kagu-sunbittern, or the pantropical finfoot family) are too closely related to have diverged in the Cretaceous. Indeed, fossils suggest that these dispersed through the Northern Hemisphere during the Cenozoic, instead. 3) Macroevolution - the plasticity and polarity of morphological evolution within lineages. This is best understood by exploring pattern in the distribution of morphological characters that are superimposed onto a phylogenetic "tree" inferred independently from molecular genetic analysis. I address these diverse problems through the combined study of fossil vertebrates, comparative anatomy (particularly osteology) and DNA sequencing.
I have separate laboratory facilities devoted to molecular and paleontological studies. In 2009 my lab acquired a "NextGen" DNA sequencer, the 454 - FLX+ along with supporting apparati and staff, as the cornerstone of a new Genome Sequencing Facility at NMSU. Among our department's natural history museums are comparative vertebrate collections for use in research and education.
I welcome inquiries from prospective graduate students who are interested in integrating diverse classical and modern disciplines to address the systematics and macroevolution of any taxonomic group of organisms.
Did someone say phylogenomics?
The Hoatzin Genome Project
The Vertebrate Museum
The whale is now on permanent public display
Excavating a fossil mastodont
Cracraft, J., P. Houde, S.Y.W. Ho, D.P. Mindell, J. Fjeldså, B. Lindow, S.V. Edwards, C. Rahbeck, S. Mirarab, T. Warnow, M.T.P. Gilbert, G. Zhang, E.L. Braun, and E.D. Jarvis. 2015. Response to Comment on "Whole-genome analyses resolve early branches in the tree of life of modern birds." Science 2015 Sept 25; 349 (6255): 10.1126/science.aab1578 pdf
Salazar, K.A., N.R. Joffe, N. Dinguirard, P. Houde, and M.G. Castillo. 2015. Transcriptome Analysis of the White Body of the Squid Euprymna tasmanica with Emphasis on Immune and Hematopoietic Gene Discovery. PloS One, 2015 Mar 16;10(3):e0119949. doi: 10.1371/journal.pone.0119949 pdf
Jarvis, E.D., S. Mirarab, A.J. Aberer, B. Li, P. Houde, C. Li, S.Y.W. Ho, B.C. Faircloth, B. Nabholz, J.T. Howard, A. Suh, C.C. Weber, R.R. da Fonseca, A. Alfaro-Núñez, N. Narula, L. Liu1, D. Burt, H. Ellegren, S.V. Edwards, A. Stamatakis, D. P. Mindell, J. Cracraft, E.L. Braun, T. Warnow, W. Jun, M.T.P. Gilbert, G. Zhang, and The Avian Phylogenomics Consortium. 2015. Phylogenomic analyses data of the avian phylogenomics project. Gigascience 4: 4. pdf
Jarvis ED, Mirarab S, Aberer AJ, Li B, Houde P, Li C, Ho SY, Faircloth BC, Nabholz B, Howard JT, Suh A, Weber CC, da Fonseca RR, Li J, Zhang F, Li H, Zhou L, Narula N, Liu L, Ganapathy G, Boussau B, Bayzid MS, Zavidovych V, Subramanian S, Gabaldón T, Capella-Gutiérrez S, Huerta-Cepas J, Rekepalli B, Munch K, Schierup M, Lindow B, Warren WC, Ray D, Green RE, Bruford MW, Zhan X, Dixon A, Li S, Li N, Huang Y, Derryberry EP, Bertelsen MF, Sheldon FH, Brumfield RT, Mello CV, Lovell PV, Wirthlin M, Schneider MP, Prosdocimi F, Samaniego JA, Vargas Velazquez AM, Alfaro-Núñez A, Campos PF, Petersen B, Sicheritz-Ponten T, Pas A, Bailey T, Scofield P, Bunce M, Lambert DM, Zhou Q, Perelman P, Driskell AC, Shapiro B, Xiong Z, Zeng Y, Liu S, Li Z, Liu B, Wu K, Xiao J, Yinqi X, Zheng Q, Zhang Y, Yang H, Wang J, Smeds L, Rheindt FE, Braun M, Fjeldsa J, Orlando L, Barker FK, Jønsson KA, Johnson W, Koepfli KP, O'Brien S, Haussler D, Ryder OA, Rahbek C, Willerslev E, Graves GR, Glenn TC, McCormack J, Burt D, Ellegren H, Alström P, Edwards SV, Stamatakis A, Mindell DP, Cracraft J, Braun EL, Warnow T, Jun W, Gilbert MT, Zhang G. 2014. Whole-genome analyses resolve early branches in the tree of life of modern birds.Science. 2014 Dec 12;346(6215):1320-31. doi: 10.1126/science.1253451. pdf supp
Zhang G, Li C, Li Q, Li B, Larkin DM, Lee C, Storz JF, Antunes A, Greenwold MJ, Meredith RW, Ödeen A, Cui J, Zhou Q, Xu L, Pan H, Wang Z, Jin L, Zhang P, Hu H, Yang W, Hu J, Xiao J, Yang Z, Liu Y, Xie Q, Yu H, Lian J, Wen P, Zhang F, Li H, Zeng Y, Xiong Z, Liu S, Zhou L, Huang Z, An N, Wang J, Zheng Q, Xiong Y, Wang G, Wang B, Wang J, Fan Y, da Fonseca RR, Alfaro-Núñez A, Schubert M, Orlando L, Mourier T, Howard JT, Ganapathy G, Pfenning A, Whitney O, Rivas MV, Hara E, Smith J, Farré M, Narayan J, Slavov G, Romanov MN, Borges R, Machado JP, Khan I, Springer MS, Gatesy J, Hoffmann FG, Opazo JC, Håstad O, Sawyer RH, Kim H, Kim KW, Kim HJ, Cho S, Li N, Huang Y, Bruford MW, Zhan X, Dixon A, Bertelsen MF, Derryberry E, Warren W, Wilson RK, Li S, Ray DA, Green RE, O'Brien SJ, Griffin D, Johnson WE, Haussler D, Ryder OA, Willerslev E, Graves GR, Alström P, Fjeldså J, Mindell DP, Edwards SV, Braun EL, Rahbek C, Burt DW, Houde P, Zhang Y, Yang H, Wang J; Avian Genome Consortium, Jarvis ED, Gilbert MT, Wang J. 2014. Comparative genomics reveals insights into avian genome evolution and adaptation. Science. 2014 Dec 12;346(6215):1311-20. doi: 10.1126/science.1251385. Epub 2014 Dec 11. pdf supp
Romanov MN, Farré M, Lithgow PE, Fowler KE, Skinner BM, O'Connor R, Fonseka G, Backström N, Matsuda Y, Nishida C, Houde P, Jarvis ED, Ellegren H, Burt DW, Larkin DM, Griffin DK. 2014. Reconstruction of gross avian genome structure, organization and evolution suggests that the chicken lineage most closely resembles the dinosaur avian ancestor.BMC Genomics. 2014 Dec 11;15:1060. doi: 10.1186/1471-2164-15-1060. pdf
Skinner BM, Al Mutery A, Smith D, Völker M, Hojjat N, Raja S, Trim S, Houde P, Boecklen WJ, Griffin DK. 2014. Global patterns of apparent copy number variation in birds revealed by cross-species comparative genomic hybridization. Chromosome Res. 2014 Apr;22(1):59-70. doi: 10.1007/s10577-014-9405-0. pdf
Churbanov, A., R. Ryan, N. Hasan, D. Bailey, H. Chen, B. Milligan, and P. Houde. 2012. HighSSR: high-throughput SSR characterization and locus development from next-gen sequencing data. Bioinformatics 28 (21): 2797-2803. pdf
Silcox, M.T., A. Hrenchuk, J.I. Bloch, D.M. Boyer, and P. Houde. 2011. Endocranial morphology of Labidolemur kayi (Apatemyidae, Apatotheria) and its relevance to the study of brain evolution in Euarchontoglires. Journal of Vertebrate Paleontology 31: 1-12. pdf
Price, D.P., V. Nagarajan, A. Churbanov, P. Houde, B. Milligan, L.L. Drake, J.E. Gustafson, I.A. Hansen. 2011. The fat body transcriptomes of the yellow fever mosquito Aedes aegypti, pre- and postblood meal. PloS ONE 6 (7): e22573. pdf
Armstrong, S.D., J.I. Bloch, P. Houde, and M.T. Silcox. 2011. Cochlear labyrinth volume in Euarchontoglirans: implications for the evolution of hearing in Primates. Anatomical Record 294: 263-266. pdf
Silcox, M.T., J.I. Bloch, D.M. Boyer, and P. Houde. 2010. Cranial anatomy of Paleocene and Eocene Labidolemur kayi (Mammalia: Apatotheria), and the relationships of the Apatemyidae to other mammals. Zoological Journal of the Linnean Society 160: 773-825. pdf
Houde, P. 2009. Gruiformes. in Timetree of Life (S.B. Hedges and S. Kumar, eds.) Oxford Univ. Press, NY. pdf.
Heinrich, R.E., S. G. Strait, and P. Houde. 2008. Earliest Eocene Miacidae (Mammalia, Carnivora) from Northwestern Wyoming. Journal of Paleontology 82: 153-161. pdf
Fain, M.G., C. Krajewski, and P. Houde. 2007. Phylogeny of "core Gruiformes" (Aves: Grues) and resolution of the Limpkin-Sungrebe problem. Molecular Phylogenetics and Evolution 43: 515-529. pdf GenBank Accessions
Fain, M.G., and P. Houde. 2007. Multilocus perspectives on the monophyly and phylogeny of the order Charadriiformes (Aves). BMC Evolutionary Biology 2007, 7:35 pdf GenBank Accessions
Polly, P.D., D.G. Wesley-Hunt, R.E. Heinrich, G. Davis, and P. Houde. 2006. Earliest known carnivoran auditory bulla and support for a recent origin of crown-group Carnivora (Eutheria: Mammalia). Paleontology 49: 1019-1027. pdf
Heinrich, R.E., and P. Houde. 2006. Postcranial anatomy of Viverravus (Mammalia, Carnivora) and implications for substrate use in basal Carnivora. Journal of Vertebrate Paleontology 26: 422-435 pdf
Bailey, C.D. M.G. Fain, and P. Houde. 2006. Problems with conditioned reconstruction as means of recovering fusion genomes. Molecular Phylogenetics and Evolution 39: 263-270. pdf
Fain, M.G., and P. Houde. 2004. Parallel radiations in the primary clades of birds. Evolution 58: 2558-2573. pdf GenBank Accessions
Houde, P., A. Cooper, E. Leslie, A.E. Strand, and G. A. Montano. 1997. Phylogeny and evolution of 12S rDNA in Gruiformes (Aves). pp. 117-154 in Avian Molecular Evolution and Systematics (D. P. Mindell, ed.) Academic Press. pdf GenBank Accessions
Houde, P., F.H. Sheldon, and M. Kreitman. 1995. A comparison of solution and membrane-bound DNA X DNA hybridization, as used to infer phylogeny. Journal of Molecular Evolution 40: 678-688. pdf
Houde, P. 1994. Evolution of the Heliornithidae: reciprocal illumination by morphology, biogeography, and DNA hybridization. Cladistics 10: 1-19. pdf
Rose, K.D., K.C. Beard, and P. Houde. 1993. Exceptional new dentitions of the diminutive plesiadapiforms Tinimomys and Niptomomys (Mammalia), with comments on the upper incisors of Plesiadapiformes. Annals of the Carnegie Museum 62 (4): 351-361.
Houde, P., and S.L. Olson. 1992. A radiation of coly-like birds from the Eocene of North America (Aves: Sandcoleiformes, new order). Natur. Hist. Mus. Los Angeles Co., Science Ser., No. 36: 137-160. pdf
Kay, R. F., R. W. Thorington, Jr., and P. Houde. 1990. Eocene plesiadapiform shows affinities with flying lemurs not primates. Nature 345: 342-344. pdf
Houde, P., and S.L. Olson. 1989. Small arboreal non-passerine birds from the early Tertiary of the Northern Hemisphere. pp. 2030-2036 in Acta XIX Congressus Internationalis Ornithologici, Vol. 2. (H. Ouellet, ed.) University of Ottawa Press.
Beard, K.C., and P. Houde. 1989. An unusual assemblage of diminutive plesiadapiforms (Mammalia, ?Primates) from the early Eocene of the Clark's Fork Basin, Wyoming. Journal of Vertebrate Paleontology 9: 388-399.
Houde, P. 1988. Paleognathous birds from the early Tertiary of the Northern Hemisphere (R. A. Paynter, Jr. ed.) Publications of the Nuttall Ornithological Club, No. 22, Cambridge MA, 148 pp. pdf
Houde, P., and M. J. Braun. 1988. Museum collections as a source of DNA for studies of avian phylogeny. Auk 105: 773-776. pdf
Houde, P., and H. Haubold. 1987. Palaeotis weigelti restudied: a small middle Eocene ostrich. Palaeovertebrata 17 (2): 27-42. pdf
Houde, P. 1987. Critical evaluation of DNA hybridization studies in avian systematics. Auk 104: 17-32.
Houde, P. 1987. Histological evidence for the systematic position of Hesperornis (Odontornithae: Hesperornithiformes). Auk 104: 125-129. pdf
Houde, P. 1987. Reply to A. H. Bledsoe, [Estimation of phylogeny from molecular data: the issue of variable rates] and J. E. Ahlquist, et al. [DNA hybridization and avian systematics: a response to Houde]. Auk 104: 566-568.
Houde, P. 1986. Ancestors of ostriches found in the Northern Hemisphere suggest a new hypothesis for origin of ratites. Nature 324: 563-565. pdf
Gingerich, P.D., P. Houde, and D.W. Krause. 1983. A new earliest Tiffanian (late Paleocene) mammalian fauna from Bangtail Plateau, Western Crazy Mountain Basin, Montana. Journal of Paleontology 57 (5): 957-970.
Houde, P., and S.L. Olson. 1981. Paleognathous carinate birds from the early Tertiary of North America. Science 214: 1236-1237.
Houde, P. 1977. Low productivity of terns on Hicks Island, 1975. Proceedings, Linnaean Society of New York (1977) 73: 49-57.
Houde, P. 1977. Gull-tern interactions on Hicks Island, 1975. Proceedings, Linnaean Society of New York (1977) 73: 58-64.
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