Benavides, E., R. Baum, H.M. Snell, H.L. Snell, and J.W. Sites, Jr.  "Island biogeography of Galapagos lave lizards (Tropiduridae: Microlophus): species diversity and colonization of the archipelago."  Evolution.  63 (2009): 1606-1626. 

Avila, L.J., M. Morando, and J.W. Sites, Jr.  "New species of the Iguanian lizard genus Liolaemus (Squamata, Iguania, Liolaemini) from central Patagonia, Argentina."  Journal of Herpetology.  42: (2008): 186-196. 

Wiens, J.J., C.A. Kuczynski, S.A. Smith, D. Mulcahy, J.W. Sites, Jr., T.M. Townsend, and T.W. Reeder.  ""Branch length, clade support, and gene-tree congruence: testing the phylogenomic approach with 20 nuclear loci in snakes."  Systematic Biology.  57: (2008): 420-431. 

Victoriano, P.F., J.C. Ortiz, E. Benavides, B.J. Adams, and J.W. Sites, Jr.  "Comparative phylogeography of co-distributed species of Chilean Liolaemus (Squamata: Tropiduridae) from the central southern Andean range."  Molecular Ecology.  17: (2008): 2397-2416. 

Morando, M., L.J. Avila, C. Turner, & J.W. Sites, Jr.  "Phylogeography between valleys and mountains: the history of populations of Liolaemus koslowskyi (Squamata: Liolaemini)."  Zoologica Scripta.  37: (2008): 603-618. 

Avila, L.J., M. Morando, C.H.F. Perez, and J.W. Sites, Jr.  "A new species of Liolaemus (Reptilia: Squamata: Liolaeminii) from southern Mendoza province, Argentina."  Zootaxa.  1452: (2007): 43-54. 

Rodrigues, M.T., K.C.M. Pellegrino, M. Dixo, V.K. Verdade, D. Pavan, A.J.S. Argolo, and J.W. Sites, Jr.  "A new genus of microteiid lizard from the Atlantic Forests of the state of Bahia, Brazil, with a new generic name for Colobosaura mentalis, and a discussion of relationships among the heterodactyline (Squamata, Gymnophthalmidae)."  American Museum Novitates.  Apr. 2007: 1-27. 

Morando, M., L.J. Avila, C.R. Turner, and J.W. Sites, Jr.  "Molecular evidence for a species complex in the Patagonian lizard Liolaemus bibronii and phylogeography of the closely related Liolaemus gracilis (Squamata: Liolaemini)."  Molecular Phylogenetics and Evolution.  42: (2007): 952-973. 

Pramuk, J.B., T. Robertson, J.W. Sites, Jr., and B.P. Noonan.  "Around the world in 10 million years: biogeography of the nearly cosmopolitan true toads (Anura: Bufonidae)."  Global Ecology and Biogeography.  16: (2007): 72-83. 

Benavides, E., R. Baum, D. McClellan, and J.W. Sites, Jr.  "Molecular phylogenetics of the lizard genus Microlophus (Squamata: Tropiduridae): aligning and retrieving signal from nuclear introns."  Systematic Biology.  56: (2007): 776-797. 

Leavitt, D.H., R.L. Bezy, K.A. Crandall, and J.W. Sites, Jr.  "Multi-locus DNA sequence data reveal a history of deep cryptic vicariance and habitat-driven convergence in the Desert Night Lizard Xantusia vigilis (Squamata: Xantusiidae)."  Molecular Ecology.  16: (2007): 4455-4481. 

Fautin, C., C.F. Carvalho, T. Hrbek, J.W. Sites, Jr., L.A. Monjelo, S. Astolfi-Filho, and I.P. Farias.  "Microsatellite DNA markers for Podocnemis unifilis, the endangered Yellow-spotted Amazon River turtle."  Molecular Ecology Notes.  7: (2007): 1235-1238. 

Hawkins, M., B.P. Noonan, and J.W. Sites, Jr.  "Dendrosophus minutus (Anura: Hylidae) of the Guiana Shield: using DNA barcodes to assess identity and diversity."  Zootaxa.  1540: (2007): 61-67. 

McGaugh, S.E., E.A. Alacs, S.V. Edwards, C.R. Feldman, A. Georges, J.W. Sites, Jr., and N. Valenzuela.  "From Molecules to Organisms: Research Applications of Modern Genetic Tools for Turtle Biology and Conservation."  Chelonian Research Monographs.  4: (2007): 47-72. 

Avila, L.J., C.H.F. Perez, M. Morando, & J.W. Sites, Jr.  "New distributional records for the lizard Liolaemus fitzinteri in Argentina."  Herpetological Review.  38: (2007): 352. 

Sinclair, E.A., R. Scholl, R.L. Bezy, K.A. Crandall, & J.W. SITES, JR.  "Isolation and characterization of di- and tetranucleotide microsatellite loci in the Yello-Spotted Night Lizard Lepidophyma flavimaculatum (Squamata: Xantusiidae)."  Molecular Ecology Notes.  6: (2006): 233-236. 

Pearse, D.E., R.B. Dastrup, O. Hernandez, and J.W. SITES, JR.  "Paternity in the Medio Orinoco population of the endangered Arrau river turtles Podocnemis expansa (Pleurodira; Podocnemididae) from Venezuela."  Chelonian Conservation and Biology.  5: (2006): 232-238. 

Pearse, D.E., A. Arndt, N. Valenzuela, B. Miller, V.H. Cantarelli, & J.W. SITES, JR.  "Estimating population structure under non-equilibrium conditions in a conservation context: continent-wide population genetics of the giant Amazon river turtle Podocnemis expansa (Chelonia: Podocnemidae)."  Molecular Ecology.  15: (2006): 985-1006. 

Marshall, J.C., E. Arevalo, E. Benavides, J.L. Sites, & J.W. SITES, JR.  "Delimiting species: comparing methods for Mendelian loci using lizards of the Sceloporus grammicus complex (Phrynosomatidae)."  Evolution.  60: (2006): 1050-1065. 

Avila, L.J., M. Morando, & J.W. SITES, JR.  "Congeneric phylogeography: hypothesizing species boundaries and evolutionary processes in lizards of the Liolaemus boulengeri complex (Squamata: Liolaemini)."  Biological Journal of the Linnean Society.  89: (2006): 241-275. 

Yoke, M.M., M. Morando, L.J. Avila, and J.W. SITES, JR.  "Phylogeography and genetic structure in the Patagonian race-runner, Cnemidophorus longicaudus (Squamata, Teiidae)."  Herpetologica.  62: (2006): 424-438. 

Whiting, A.S., J.W. Sites, Jr., K.C.M. Pellegrino, and M.T. Rodrigues.  "Comparing alignment methods for inferring the history of New World lizards genus Mabuya (Squamata: Scincidae)."  Molecular Phylogenetics and Evolution.  38: (2006): 719-730. 

Pellegrino, K.C.M., M.T. Rodrigues, A.N. Waite, M. Morando, Y. Yonenaga-Yassuda, & J.W. Sites, Jr.  "Phylogeography and species limits in the Gymnodactylus darwinii complex (Gekkonidae, Squamata): genetic structure coincides with river systems in the Brazilian Atlantic Forest."  Biological Journal of the Linnean Society.  85: (2005): 13-26. 

Rodrigues, M.T., E.M. Xavier-F., K.C.M. Pellegrino, & J.W. Sites, Jr.  "Description and phylogenetic relationships of a new genus and species of microteiid lizard from the Atlantic Forest of northeastern Brazil (Squamata, Gymnophthalmidae)."  Zoological Journal of the Linnean Society.  144: (2005): 543-557. 

Avila, L.J., M. Morando, C.H.F. Perez, and J.W. Sites, Jr.  "Phylogenetic relationships of lizards of the Liolaemus petrophilus group (Squamata, Liolaemidae), with descriptions of two new species from western Argentina."  Herpetologica.  60: (2004): 187-203. 

Sinclair, E.A., R.L. Bezy, K. Bolles, J.L. Camarillo R., K.A. Crandall, and J.W. Sites, Jr.  "Testing species boundaries in an ancient species complex with deep phylogeographic structure: genus Xantusia (Squamata: Xantusiidae)."  American Naturalist.  163: (2004): 396-414. 

Sites, J.W., Jr., and J.C. Marshall.  "Operational Criteria for Delimiting Species."  Annual Review of Ecology, Evolution, and Systematics.  35: (2004): 199-229. 

Morando, M., L.J. Avila, J. Baker, and J.W. Sites, Jr.  "Phylogeny and phylogeography of the Liolaemus darwinii complex (Squamata: Liolaemidae): evidence for introgression and incomplete lineage sorting."  Evolution.  58 (2004): 842-861. 

Sites, J.W., Jr., M. Morando, R. Highton, F. Huber, and R.E. Jung.  "Phylogenetic relationships in the endangered Shenandoah salamander (Plethodon shenandoah) and other salamanders of the P. cinereus group (Caudata: Plethodontidae)."  Journal of Herpetology.  38: (2004): 96-104. 

Avila, L.J., M. Morando, C.H.F. Perez, and J.W. Sites, Jr.  "New records and natural history notes on lizaards of the genus Liolaemus in northern Patagonia."  Herpetozoa.  17: (2004): 83-86. 

Whiting, A.S., J.W. Sites, Jr., and A.M. Bauer.  "Molecular phylogenetics of Malagasy skinks (Squamata: Scincidae)."  African Journal of Herpetology.  53: (2004): 135-146. 

Morando, M., L.J. Avila, and J.W. Sites, Jr.  "Sampling strategies for delimiting species: genes, individuals, and populations in the Liolaemus elongatus-kriegi complex (Squamata; Liolaemidae) in Andean - Patagonian South America."  Systematic Biology.  52:159-185. (2003). 

Whiting, A.S., A.M. Bauer, and J.W. Sites, Jr.  "Phylogenetic relationships and limb loss in sub-Saharan African scincine lizards (Squamata: Scincidae)."  Molecular Phylogenetics and Evolution.  26: (2003): 582-598. 

Sites, J.W., Jr., and J.C. Marshall.  "Species delimitation: a Renaissance issue in systematic biology."  Trends in Ecology and Evolution.  18:462-470 (2003). 

Crother, B.I., J. Boundy, J.A. Campbell, K. de Quieroz, D. Frost, D.M. Green, R. Highton, J.B. Iverson, R.W. McDiarmid, P.A. Meylan, T.W. Reeder, M.E. Seidel, J.W. Sites, Jr., S.G. Tilley, and D.B. Wake.  "Scientific and standard English names of amphibians and reptiles of North America north of Mexico: update."  Herpetological Review.  34: (2003): 196-203. 

Marshall, J.C., and J.W. Sites, Jr.  "Un resume de los metodos para delimitar limites entre especies."  Boletin de la Sociedad Herpetologica Mexicana.  11: (2003): 1-8. 

Benavides, E., J.C. Ortiz, and J.W. Sites, Jr.  "Species boundaries among the Telmatobius (Anura: Leptodactylidae) of the Lake Titicaca basin: allozyme and morphological evidence."  Herpetologica.  58:31-55 (2002). 

Ramírez-Bautista, A., O. Ramos-Flores, and J.W. Sites, Jr.  "Reproductive cycle of the spiny lizard Sceloporus jarrovii (Sauria: Phrynosomatidae) from north-central México."  J. Herpetol.  36:225-233 (2002).