2013	Blanco, M.B., K.H. Dausmann, J.F. Ranaivoarisoa, and A.D. Yoder. Underground hibernation in a primate. Scientific Reports, 3: 1768 pdf
2013	Yoder, A.D. Fossils Versus Clocks. Science, 339:656-658. pdf
2013	Yoder, A.D. The lemur revolution starts now: The genomic coming of age for a non-model organism. Molecular Phylogenetics and Evolution, 66:442-452. pdf
2013	Barrett, M.A., J.L. Brown, R.E. Junge, and A.D. Yoder. Climate change, predictive modeling and lemur health: Assessing impacts of changing climate on health and conservation in Madagascar. Biological Conservation, 157:409-422. pdf
2012	Chan, L.M., D. Choi, A.P. Raselimanana, H.A. Rakotondravony, and A.D. Yoder. Defining spatial and temporal patterns of phylogeographic structure in Madagascar's iguanid lizards (genus Oplurus). Molecular Ecology, 21:3839-3851. pdf
2012	Weisrock, D.W., S.D. Smith, L.M. Chan, K. Biebouw, P.M. Kappler, and A.D. Yoder. Concatenation and Concordance in the Reconstruction of Mouse Lemur Phylogeny: An Empirical Demonstration of the Effect of Allele Sampling in Phylogenetics. Molecular Biology and Evolution, 29(6):1615-1630. pdf
2012	Perry, G.H., P. Melsted, J. C. Marioni, Y. Wang, R. Bainer, J.K. Pickrell, K. Michelini, S. Zehr, A.D. Yoder, M. Stephens, J.K. Pritchard, and Y. Gilad. Comparative RNA sequencing reveals substantial genetic variation in endangered primates. Genome Research, 22:602-610. pdf
2011	Junge, R.E., M. Barrett, and A.D. Yoder. Effects of anthropogenic disturbance on indri (Indri indri) health in Madagascar. American Journal of Primatology, 73(7):632-642. Featured article. pdf
2011	Nowak, M.D., A. P. Davis, F. Anthony, and A. D. Yoder. Expression and Trans-Specific Polymorphism of Self-Incompatibility RNases in Coffea (Rubiaceae. PLOS One, 6(6):e21019. pdf
2011	Chan, L. M., S. M. Goodman, M. D. Nowak, D. W. Weisrock, and A. D. Yoder. Increased population sampling confirms low genetic divergence among Pteropus (Chiroptera: Pteropodidae) fruit bats of Madagascar and other western Indian Ocean islands. PLoS Currents: Tree of Life. online
2011	Chan, L. M., J. L. Brown, and A. D. Yoder. Integrating statistical genetic and geospatial methods brings new power to phylogeography. Molecular Phylogenetics and Evolution, 59: 523–537. pdf | supplementary material
2010	Barrett, M. A., J. L. Brown, M. K. Morikawa, J-N Labat, and A. D. Yoder. CITES designation for endangered rosewood in Madagascar. Science, 328: 1109-1110.
2010	Weisrock, D. W., R. M. Rasoloarison, I. Fiorentino, J. M. Ralison, S. M. Goodman, P. M. Kappeler, and A. D. Yoder. Delimiting species without nuclear monophyly in Madagascar's Mouse Lemurs. PLoS One, 5(3): e9883. pdf
2010	Goodman, S. M., L. M. Chan, M. D. Nowak, and A. D. Yoder. Phylogeny and biogeography of western Indian Ocean Rousettus (Chiroptera: Pteropodidae). Journal of Mammalogy, 91(3): 593-606 pdf
2009	Groeneveld, L.F., Weisrock, D.W., Rasoloarison, R., Yoder, A.D. and P.M. Kappeler. Species delimitation in lemurs: multiple genetic loci reveal low levels of species diversity in the genus Cheirogaleus. BMC Evolutionary Biology, 9:30. pdf
2009	O’Brien, J., Mariani, C., Olson, L.E., Russell, A.L., Say, L., Yoder, A.D. and T.J. Hayden. Multiple colonisations of the Western Indian Ocean by Pteropus fruit bats (Megachiroptera: Pteropodidae): the furthest islands were colonised first. Mol. Phyl. & Evol., 51: 294-303. pdf
2009	Karanth, K.P. and A.D. Yoder. Geographic origins of aDNA samples and prospects for aDNA studies in the tropics. In: Molecular Markers, PCR, Bioinformatics and Ancient DNA – Technology, Troubleshooting And Applications (G. Dorado, ed.) Science Publishers.
2009	Noonan, B.P. and A.D. Yoder. Anonymous nuclear markers for Malagasy plated lizards (Zonosaurus). Molecular Ecology Resources, 9:402-404. pdf
2009	Raselimanana, A., Noonan, B.P., Karanth, P., Gauthier, J., and A.D. Yoder. Phylogeny and Evolution of Malagasy Plated Lizards. Mol. Phyl. & Evol. 50: 336-344. pdf
2008	Riddle, BR; Dawson, MN; Hadly, EA, Hafner, D.J., Hickerson MJ, Mantooth SJ, and A.D. Yoder. The role of molecular genetics in sculpting the future of integrative biogeography. Progress in Physical Geography, 32 (2): 173-202. pdf
2008	Horvath, J., Weisrock, D., Embry, S.L., Fiorentino, Balhoff, J.P., I., Kappeler, P., Wray, G.A., Willard, H., and A.D. Yoder. The development and application of a phylogenomic toolkit: resolving the evolutionary history of Madagascar’s lemurs. Genome Research 18(3): 489-499. pdf
2008	Russell, A.L., Goodman, S.M., Fiorentino, I., and A.D. Yoder. Population genetic analysis of Myzopoda spp. (Chiroptera: Myzopodidae) in Madagascar. J. Mamm. 89 (1): 209-221. pdf
2007	Yoder, A.D. Lemurs: a Quick Guide. Current Biology, 17 (20): 866-868. pdf
2007	Heckman, K.L., Hanley, C.L., Rasoloarison, R. and A.D. Yoder. Multiple nuclear loci reveal patterns of incomplete lineage sorting and complex species history within western mouse lemurs (Microcebus). Mol. Phyl. & Evol. 43 (2): 353-367. . pdf
2007	Naghibalhossaini, F., Yoder, A.D., Tobi, M., and C.P. Stanners. Evolution of a tumorigenic property conferred by Glycophosphatidyl-inositol membrane anchors of CEA gene family members during the primate radiation. Molecular Biology of the Cell 18 (4): 1366-1374). pdf
2007	Russell, A.L., Ranivo, J., Palkovacs, E.P., Goodman, S.M., and A.D. Yoder. Working at the interface of phylogenetics and population genetics: a biogeographic analysis of Triaenops spp (Chiroptera: Hipposideridae) Molecular Ecology, 16:839-851. pdf
2006	Heckman, K. L., Rasoazanabary, E., Machlin, E., Godfrey, L.R., and A. D. Yoder. Incongruence between genetic and morphological diversity in Microcebus griseorufus of Beza Mahafaly. BMC Evolutionary Biology, 6:98 (16 Nov 2006). pdf
2006	Yoder, A.D. and M. Nowak. Has vicariance or dispersal been the predominant biogeographic force in Madagascar?: only time will tell. Ann. Rev. Ecol. Evol. Syst., 37:405-431. pdf
2006	Goodman, S.M., Cardiff, S. G., Ranivo, J., Russell, A.L. and A.D. Yoder. A new species of Emballonura (Emballonuridae: Chiroptera) from the dry regions of Madagascar. American . Museum Novitates, No. 3538: 1-24. pdf
2006	Yoder, A.D. and K. Heckman. Mouse lemur phylogeography revises a model of ecogeographic constraint in Madagascar. In: Primate Biogeography: Progress and Prospects (J. Fleagle and S.M. Lehman, eds.) Kluwer Press, pp. 255 – 268. pdf
2005	Yoder, A.D. The biogeography of Madagascar: where to turn when the fossils aren’t there. Paleontological Society Papers, V. 11, 129-139.
2005	Tan, Y., Yoder, A.D., Yamashita, N. and W.-H. Li. Evidence from opsin genes rejects nocturnality in ancestral primates. Proceedings of the National Academy of Sciences 102: 14712-14716. pdf
2005	Yoder, A.D., Olson, L.E., Hanley, C., Heckman, K., Rasoloarison, R., Russell, A.L., Ranivo, J., Soarimalala, V., Karanth, K.P., Raselimanana, A.P. and S.M. Goodman. A multidimensional approach for detecting species patterns in Malagasy vertebrates. Proceedings of the National Academy of Sciences 102: 6587-6594, Suppl. 1 (invited Colloquium contribution). pdf
2005	Karanth, P. Rakotosamimanana, B., Parsons, T.J. and A.D. Yoder. Ancient DNA from giant extinct lemurs verifies single origin of Malagasy primates. Proceedings of the National Academy of Sciences 102: 5090-5095. pdf
2005	Karanth, K.P., Palkovacs, E., Gerlach, J., Glaberman, S., Caccone, A., and A.D. Yoder. Native Seychelles tortoises or Aldabran imports? The importance of radiocarbon dating for ancient DNA studies. Amphibia-Reptilia 26(1): 116-121. pdf
2004	Olson, L.E., Goodman, S., and A.D. Yoder. Illumination of cryptic species boundaries in long-tailed shrew tenrecs (Mammalia: Tenrecidae; Microgale) provides insights into geographic variation and distributional constraints. Biological Journal of the Linnean Society, 83:1-22. pdf
2004	Yoder, A.D. and Z. Yang. Divergence dates for Malagasy lemurs estimated from multiple gene loci: geological and evolutionary context. Molecular Ecology, 13:757-773. pdf
2004	Yoder, A.D. Review of A Primer of Conservation Genetics, by Frankahm, R., Ballou, J.D. and D.A. Briscoe. Journal of Mammalogy (info).
2003	Kunstman, K., Puffer, B., Korber, B., Kuiken, C., Smith, U., Kunstman, J., Stanton, J., Agy, M., Shibata, R., Yoder, A.D., Pillai, S., Doms, R., Marx, P., and S. Wolinsky. Structure and Function of CC-Chemokine Receptor 5 Homologues Derived from Representative Primate Species and Subspecies of the Taxonomic Suborders Prosimii and Anthropoidea. Journal of Virology, 77(22): 12310-12318. pdf
2003	Yoder, A.D. and J.J. Flynn. Origin of Malagasy Carnivora. In: The Natural History of Madagascar (S. M. Goodman and J. Benstead, eds.) University of Chicago Press, pp. 1253-1256.
2003	Yoder, A.D. Phylogeny of the lemurs. In: The Natural History of Madagascar (S. M. Goodman and J. Benstead, eds.) University of Chicago Press, pp. 1242-1247.
2003	Yang, Z. and A.D. Yoder. Comparison of likelihood and Bayesian methods for estimating divergence times using multiple gene loci and calibration points, with application to a radiation of cute-looking mouse lemur species. Systematic Biology, 52(5):705-716. pdf
2003	Yoder, A.D. The phylogenetic position of genus Tarsius: whose side are you on? In: Tarsiers: Past, Present, and Future (P.C. Wright, E.L. Simons and S. Gursky, eds.) Rutgers University Press, pp. 161-175.
2003	Eriksson, T., Hibbs, M.S., Yoder, A.D., Delwiche, C.F., and M.J. Donoghue. The phylogeny of Rosoideae (Rosaceae) based on sequences of the internal transcribed spacers (ITS) of nuclear ribosomal DNA and the trnL/F region of chloroplast DNA. International Journal of Plant Sciences, 164(2):197-211. pdf
2003	Yoder, A.D., Burns, M.M., Zehr, S., Delefosse, T., Veron, G., Goodman, S.M., and J.J. Flynn. Single origin of Malagasy Carnivora from an African ancestor. Nature, 421: 734-737. pdf
2002	Yoder, A.D., Burns, M.M., and F. Genin. Molecular evidence of reproductive isolation in sympatric sibling species of mouse lemurs. International Journal of Primatology, 23: 1335-1343. pdf
2002	Olson, L.E. and A.D. Yoder. Using secondary structure to identify ribosomal numts: cautionary examples from the human genome. Molecular Biology and Evolution, 19(1): 93-100. pdf
2002	Yoder, A.D. and T. Delefosse. Ancient DNA. McGraw-Hill, Yearbook of Science and Technology, pp. 9-14. pdf
2001	Yoder, A.D., Irwin, J.A., and B. Payseur. Failure of the ILD to determine data combinability for slow loris phylogeny. Systematic Biology, 50: 408-424. pdf
2001	Yoder, A.D. Ancient DNA from Megaladapis edwardsi. Folia Primatol (Basel), 72(6):342-344. pdf
2000	Yoder, A.D., Rasoloarison, R., Goodman, S., Irwin, J.A., Atsalis, S. Ravosa, M.J., and J.U. Ganzhorn. Remarkable species diversity in Malagasy mouse lemurs (Primates, Microcebus) Proceedings of the National Academy of Sciences, 97: 11325-11330. pdf
2000	Yoder, A.D., Irwin, J.A., Rakotoarisoa, S.V., and S. Goodman. Genetic tests of the taxonomic status of Lemur catta from the high mountain zone of the Andringtra Massif, Madagascar. Journal of Zoology, 252:1-9. pdf
2000	Yoder, A.D. and Z. Yang. Estimation of primate speciation dates using local molecular clocks. Molecular Biology and Evolution, 17(7):1081-1090. pdf
1999	Yoder, A.D. and J.A. Irwin. Phylogeny of the Lemuridae: effects of taxon and character sampling on resolution of species relationships within Eulemur. Cladistics, 15:351-361. pdf
1999	Yoder, A.D., Rakotosamimanana, B. and T.J. Parsons. Ancient DNA in subfossil lemurs: methodological challenges and their solutions. In: Rasaminanana, H., B. Rakotosamimanana, S. Goodman and J. Ganzhorn (eds.), New Directions in Lemur Studies. Plenum Press, pp. 1-17. pdf
1999	Yang, Z. and A.D. Yoder. Estimation of the transition/transversion rate bias and species sampling. Journal of Molecular Evolution, 48(3): 274-283. pdf |  dataset
1998	Yoder, A.D. Review of Introduction to the Primates, by Daris R. Swindler. American Zoologist, 39(1):186-187.
1997	Yoder, A.D. Back to the future: a synthesis of strepsirrhine systematics. Evolutionary Anthropology, 6(1):11-22.
1997	Yoder, A.D. An infinitude of connecting links. Trends in Ecology and Evolution, 12(3):86-88. pdf
1996	Yoder, A.D., Vilgalys, R., and M. Ruvolo. Molecular evolutionary dynamics of cytochrome b in strepsirrhine primates: the phylogenetic significance of third position transversions. Molecular Biology and Evolution, 13(10):1339-1350. pdf
1996	Yoder, A.D., Cartmill, M., Ruvolo, M., Smith, K., and R. Vilgalys. Ancient single origin for Malagasy primates. Proceedings of the National Academy of Sciences, 93:5122-5126. pdf
1996	Yoder, A.D. The use of phylogeny for reconstructing lemuriform biogeography. In: Biogeographie de Madagascar. (W.R. Lourenco, ed.) Editions de l’ORSTROM, Paris, pp. 245-258.
1994	Yoder, A.D. The relative position of the Cheirogaleidae in strepsirhine phylogeny: a comparison of morphological and molecular methods and results. American Journal of Physical Anthropology, 94(1):25-46.
1994	Cartmill, M. and A.D. Yoder. Molecules and Morphology in Primate Systematics: An Introduction. American Journal of Physical Anthropology, 94(1):1.
1994	G. Conroy, M. Cartmill and A.D. Yoder. Editors. Molecules and Morphology in Primate Systematics. New York: Wiley-Lyss; special volume of American Journal of Physical Anthropology, 94(1).
1993	Yoder, A.D. Review of Classification, Evolution, and the Nature of Biology, by Alec L. Panchen. American Journal of Physical Anthropology, 91(4):535-537.
1992	Yoder, A.D. Applications and limitations of ontogenetic comparisons for phylogeny reconstruction: the case of the strepsirhine internal carotid artery. Journal of Human Evolution, 23:183-195.
1992	Kay, R.F., Thewissen, J.G.M. and A.D. Yoder. Cranial anatomy of Ignacius graybullianus and the affinities of the Plesiadapiformes. American Journal of Physical Anthropology 89:477-498.