Publications

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For an up-to-date version of this rapidly expanding publication list, please see Anne’s Google Scholar!

Year Title Format Project
2024 Integrative taxonomy clarifies the evolution of a cryptic primate clade. van Elst T., et al. Nature Ecology & Evolution. PDF Speciation Dynamics in Mouse Lemurs
2024 Metagenome-assembled microvirus and cressdnavirus genomes from fecal samples of house mice (Mus musculus). Paietta E.N., Kraberger S., Custer J.M., Vargas K.L., Ehmke E., Yoder A.D., and A. Varsani. Microbiology Resource Announcements. PDF One Health
2024 Ancient Introgression in Mouse Lemurs (Microcebus: Cheirogaleidae) Explains 20 Years of Phylogenetic Uncertainty. Fauskee B.D., Crowl A.A., Piatkowski B., Yoder A.D., and G.P. Tiley. Bulletin of the Society of Systematic Biologists. PDF Speciation Dynamics in Mouse Lemurs
2024 Diverse Circular DNA Viral Communities in Blood, Oral, and Fecal Samples of Captive Lemurs. Paietta E.N., Kraberger S., Lund M.C., Vargas K.L., Custer J.M., Ehmke E., Yoder A.D., and A. Varsani. Viruses. PDF One Health
2024 Benefits and Limits of Phasing Alleles for Network Inference of Allopolyploid Complexes. Tiley G.P., Crowl A.A., Manos P.S., Sessa E.B., Solís-Lemus C., Yoder A.D., and J.G. Burleigh. Systematic Biology. PDF Next Generation ‘Omics
2024 Why Do Some Lineages Radiate While Others Do Not? Perspectives for Future Research on Adaptive Radiations. De-Kayne R., et al. Cold Spring Harbor Perspectives in Biology. PDF Phylogenetics and Molecular Evolution
2024 Telomere dynamics during hibernation in a tropical primate. Blanco M.B., Smith D.L., Greene L.K., Yoder A.D., Ehmke E.E., Lin J., and P.H. Klopfer. Journal of Comparative Physiology B. PDF Hibernation in Dwarf Lemurs
2024 Genetic variation in Loudetia simplex supports the presence of ancient grasslands in Madagascar. Tiley G.P., Crowl A.A., Almary T.O., Luke W.Q., Solofondranohatra C.L., Besnard G., Lehmann C.E., Yoder A.D., and M.S. Vorontsova. Plants, People, Planet. PDF Historical Biogeography and Phylogeography
2024 Primate hibernation: The past, present, and promise of captive dwarf lemurs. Blanco M.B., Greene L.K., Welser K.H., Ehmke E.E., Yoder A.D., and P.H. Klopfer. Annals of the New York Academy of Sciences. PDF Hibernation in Dwarf Lemurs
2023 Interspecies Papillomavirus Type Infection and a Novel Papillomavirus Type in Red Ruffed Lemurs (Varecia rubra). Paietta E.N., Kraberger S., Regney M., Custer J.M., Ehmke E., Yoder A.D., and A. Varsani. Viruses. PDF One Health
2023 Characterization of Diverse Anelloviruses, Cressdnaviruses, and Bacteriophages in the Human Oral DNA Virome from North Carolina (USA). Paietta E.N., Kraberger S., Custer J.M., Vargas K.L., Espy C., Ehmke E., Yoder A.D., and A. Varsani. Viruses. PDF One Health
2023 Diversification processes in Gerp’s mouse lemur demonstrate the importance of rivers and altitude as biogeographic barriers in Madagascar’s humid rainforests. van Elst T., Schüßler D., Rakotondravony R., Rovanirina V.S., Veillet A., Hohenlohe P.A., Ratsimbazafy J.H., Rasoloarison R.M., Rasoloharijaona S., Randrianambinina B., Ramilison M.L., Yoder A.D., Louis Jr E.E., and U. Radespiel. Ecology and Evolution. PDF Speciation Dynamics in Mouse Lemurs
2023 Estimation of species divergence times in presence of cross-species gene flow. Tiley G.P., Flouri T., Jiao X., Poelstra J.W., Xu B., Zhu T., Rannala B., Yoder A.D., and Z. Yang. Systematic Biology. PDF Divergence Time Estimation
2023 Phylogenomic analyses provide insights into primate evolution. Shao Y., et al. Science. PDF Phylogenetics and Molecular Evolution
2023 Not one, but multiple radiations underlie the biodiversity of Madagascar’s endangered lemurs. Everson K.M., Pozzi L., Barrett M.A., Blair M.E., Donohue M.E., Kappeler P.M., Kitchener A.C., Lemmon A.R., Lemmon E.M., Pavón-Vázquez C.J., Radespiel U., Randrianambinina B., Rasoloarison R.M., Rasoloharijaona S., Roos C., Salmona J., Yoder A.D., Zenil-Ferguson R., Zinner D., and D.W. Weisrock. BioRxiv. PDF Divergence Time Estimation
2023 New genetic evidence from the Ambatotsirongorongo/Petriky complex in southeast Madagascar calls for an immediate re-evaluation of conservation strategies focusing on the Bemanasy mouse lemur (Microcebus manitatra). Roberts S.H., Segami J., Harinala V.J., Greene L.K., Blanco M.B., and A.D. Yoder. Lemur News. PDF Speciation Dynamics in Mouse Lemurs
2023 Identification of diverse papillomaviruses in captive black-and-white ruffed lemurs (Varecia variegata). Paietta E.N., Kraberger S., Custer J.M., Vargas K.L., Van Doorslaer K., Yoder A.D., and A. Varsani. Archives of virology. PDF One Health
2022 Population genomic structure in Goodman’s mouse lemur reveals long-standing separation of Madagascar’s Central Highlands and eastern rainforests. Tiley G.P., van Elst T., Teixeira H., Schüßler D., Salmona J., Blanco M.B., Ralison J.M., Randrianambinina B., Rasoloarison R.M., Stahlke A.R., Hohenlohe P.A., Chikhi L., Louis E.E., Radespiel U., and A.D. Yoder. Molecular ecology. PDF Speciation Dynamics in Mouse Lemurs
2022 RADseq data reveal a lack of admixture in a mouse lemur contact zone contrary to previous microsatellite results. Poelstra J.W., Montero B.K., Lüdemann J., Yang Z., Rakotondranary S.J., Hohenlohe P., Stetter N., Ganzhorn J.U., and A.D. Yoder. Proceedings of the Royal Society B. PDF Next Generation ‘Omics
2022 Variation in gut microbiome structure across the annual hibernation cycle in a wild primate. Greene L.K., Andriambeloson J.B., Rasoanaivo H.A., Yoder A.D., and M.B. Blanco. FEMS microbiology ecology. PDF Hibernation in Dwarf Lemurs
2022 Initiation of the primate genome project. Wu D.D., et al. Zoological Research. PDF Next Generation ‘Omics
2022 Body mass and tail girth predict hibernation expression in captive dwarf lemurs. Blanco M.B., Greene L.K., Klopfer P.H., Lynch D., Browning J., Ehmke E.E., and A.D. Yoder. Physiological and Biochemical Zoology. PDF Hibernation in Dwarf Lemurs
2022 The Earth BioGenome Project 2020: Starting the clock. Lewin H.A., et al. PNAS. PDF Next Generation ‘Omics
2022 The Mutationathon highlights the importance of reaching standardization in estimates of pedigree-based germline mutation rates. Bergeron L.A., Besenbacher S., Turner T., Versoza C.J., Wang R.J., Price A.L., Armstrong E., Riera M., Carlson J., Chen H.Y., Hahn M.W., Harris K., Kleppe A.S., López-Nandam E.H., Moorjani P., Pfeifer S.P., Tiley G.P., Yoder A.D., Zhang G., and M.H. Schierup. Elife. PDF Phylogenetics and Molecular Evolution
2021 Gut Microbial Diversity and Ecological Specialization in Four Sympatric Lemur Species Under Lean Conditions. Greene L.K., Rambeloson E., Rasoanaivo H.A., Foss E.D., Yoder A.D., Drea C.M., and M.B. Blanco. International Journal of Primatology. PDF The Gut Microbiome in Lemurs
2021 Comparative analyses of two primate species diverged by more than 60 million years show different rates but similar distribution of genome-wide UV repair events. Akkose U., Kaya V.O., Lindsey-Boltz L., Karagoz Z., Brown A.D., Larsen P.A., Yoder A.D., Sancar A., and O. Adebali. BMC genomics. PDF Divergence Time Estimation
2021 Living in tiny fragments: a glimpse at the ecology of Goodman’s mouse lemurs (Microcebus lehilahytsara) in the relic forest of Ankafobe, Central Highlands, Madagascar. Andriambeloson J.B., Blanco M.B., Andriantsalohimisantatra A., Rivoharison T.V., Walker N., Birkinshaw C., and A.D. Yoder. Primates. PDF The Impacts of Climate Change and Human Disturbance on Malagasy Biota
2021 Molecular adaptation to folivory and the conservation implications for Madagascar’s lemurs. Guevara E.E., Greene L.K., Blanco M.B., Farmer C., Ranaivonasy J., Ratsirarson J., Mahefarisoa K.L., Rajaonarivelo T., Rakotondrainibe H.H., Junge R.E., Williams C.V., Rambeloson E., Rasoanaivo H.A., Rahalinarivo V., Andrianandrianina L.H., Clayton J.B., Rothman R.S., Lawler R.R., Bradley B.J., and A.D. Yoder. Frontiers in Ecology and Evolution. PDF Phylogenetics and Molecular Evolution
2021 Pedigree-based and phylogenetic methods support surprising patterns of mutation rate and spectrum in the gray mouse lemur. Campbell C.R., Tiley G.P., Poelstra J.W., Hunnicutt K.E., Larsen P.A., Lee H.J., Thorne J.L., Dos Reis M., and A.D. Yoder. Heredity. PDF Phylogenetics and Molecular Evolution
2021 Evolutionary and phylogenetic insights from a nuclear genome sequence of the extinct, giant, “subfossil” koala lemur Megaladapis edwardsi. Marciniak S., Mughal M.R., Godfrey L.R., Bankoff R.J., Randrianatoandro H., Crowley B.E., Bergey C.M., Muldoon K.M., Randrianasy J., Raharivololona B.M., and S.C. Schuster. PNAS. PDF Phylogenetics and Molecular Evolution
2021 Comparative genomic analysis of sifakas (Propithecus) reveals selection for folivory and high heterozygosity despite endangered status. Guevara E.E., Webster T.H., Lawler R.R., Bradley B.J., Greene L.K., Ranaivonasy J., Ratsirarson J., Harris R.A., Liu Y., Murali S., Raveendran M., Hughes D.S., Muzny D.M., Yoder A.D., Worley K.C., and J. Rogers. Science Advances. PDF Next Generation ‘Omics
2021 Cryptic Patterns of Speciation in Cryptic Primates: Microendemic Mouse Lemurs and the Multispecies Coalescent. Poelstra J.W., Salmona J., Tiley G.P., Schüßler D., Blanco M.B., Andriambeloson J.B., Bouchez O., Campbell C.R., Etter P.D., Hohenlohe P.A., Hunnicutt K.E., Iribar A., Johnson E.A., Kappeler P.M., Larsen P.A., Manzi S., Ralison J.M., Randrianambinina B., Rasoloarison R.M., Rasolofoson D.W., Stahlke A.R., Weisrock D.W., Williams R.C., Chikhi L., Louis E.E., Jr., Radespiel U., and A.D. Yoder. Systematic Biology. PDF Speciation Dynamics in Mouse Lemurs
2021 The challenge and promise of estimating the de novo mutation rate from whole‐genome comparisons among closely related individuals. Yoder A.D. and G.P. Tiley. Molecular Ecology. PDF Phylogenetics and Molecular Evolution
2021 Genetic confirmation of the Anjiamangirana sportive lemur in the Anjajavy Forest. Rambeloson E., Rasoanaivo H.A., Guevara E.E., Schopler R., Greene L.K., Blanco M.B., and A.D. Yoder. Lemur News. PDF Phylogenetics and Molecular Evolution
2020 Molecular clocks without rocks: new solutions for old problems. Tiley G.P., Poelstra J.W., Dos Reis M., Yang Z., and A.D. Yoder. Trends in Genetics. PDF Divergence Time Estimation
2020 Ecology and morphology of mouse lemurs (Microcebus spp.) in a hotspot of microendemism in northeastern Madagascar, with the description of a new species. Schüßler D., Blanco M.B., Salmona J., Poelstra J., Andriambeloson J.B., Miller A., Randrianambinina B., Rasolofoson D.W., Mantilla‐Contreras J., Chikhi L. and E.E. Louis Jr. American Journal of Primatology. PDF Speciation Dynamics in Mouse Lemurs
2020 Conservation genomic analysis reveals ancient introgression and declining levels of genetic diversity in Madagascar’s hibernating dwarf lemurs. Williams R.C., Blanco M.B., Poelstra J.W., Hunnicutt K.E., Comeault A.A., and A.D. Yoder. Heredity. PDF Hibernation in Dwarf Lemurs
2020 Next-generation technologies applied to age-old challenges in Madagascar. Blanco M.B., Greene L.K., Rasambainarivo F., Toomey E., Williams R.C., Andrianandrasana L., Larsen P.A., and A.D. Yoder. Conservation Genetics. PDF Teaching
2020 Comparative Genomic Analysis of the Pheromone Receptor Class 1 Family (V1R) Reveals Extreme Complexity in Mouse Lemurs (Genus, Microcebus) and a Chromosomal Hotspot across Mammals. Hunnicutt K.E., Tiley G.P., Williams R.C., Larsen P.A., Blanco M.B., Rasoloarison R.M., Campbell C.R., Zhu K., Weisrock D.W., Matsunami H., and A.D. Yoder. Genome Biology and Evolution. PDF Molecular Evolution of Sensory Communication
2019 The importance of scale in comparative microbiome research: new insights from the gut and glands of captive and wild lemurs. Greene L.K., Bornbusch S.L., McKenney E.A., Harris R.L., Gorvetzian S.R., Yoder A.D., and C.M. Drea. American Journal of Primatology. PDF The Gut Microbiome in Lemurs
2019 Pedigree-based measurement of the de novo mutation rate in the gray mouse lemur reveals a high mutation rate, few mutations in CpG sites, and a weak sex bias. Campbell C.R., Tiley G.P., Poelstra J.W., Hunnicutt K.E., Larsen P.A., Lee H., Thorne J.L., dos Reis M., and A.D. Yoder. bioRxiv. PDF Next Generation ‘Omics
2019 Applications of 3D printing in small animal magnetic resonance imaging. Nouls J.C., Virgincar R.S., Culbert A.G., Morand N., Bobbert D.W., Yoder A.D., Schopler R.S., Bashir M.R., Badea A., Hochgeschwender U., and B. Driehuys. Journal of Medical Imaging. PDF Evolutionary Medicine
2018 Tropical heterothermy is “cool”: The expression of daily torpor and hibernation in primates. Blanco M.B, Dausmann K.H, Faherty S.L., and A.D. Yoder. Evolutionary Anthropology. PDF Hibernation in Dwarf Lemurs
2018 What is Speciation Genomics? The roles of ecology, gene flow, and genomic architecture in the formation of species. Campbell C.R., Poelstra J.W., and A.D. Yoder.Biological Journal of the Linnean Society. PDF Next Generation ‘Omics
2018 Neutral Theory Is the Foundation of Conservation Genetics. Yoder A.D., Poelstra J.W., Tiley G.P., and R.C. Williams. Molecular Biology and Evolution. PDF Phylogenetics and Molecular Evolution
2018 Using Phylogenomic Data to Explore the Effects of Relaxed Clocks and Calibration Strategies on Divergence Time Estimation: Primates as a Test Case. dos Reis M., Gunnell G.F., Barba-Montoya J., et al. Systematic Biology. PDF Divergence Time Estimation
2018 The ecosystem services of animal microbiomes. McKenney E.A., Koelle K., Dunn R.R., and A.D. Yoder. Molecular Ecology. PDF The Gut Microbiome in Lemurs
2018 Warning SINEs: Alu elements, evolution of the human brain, and the spectrum of neurological disease. Larsen P.L., Hunnicutt K.E., Larsen R.J., Yoder A.D., and A.M. Saunders. Chromsome Research. PDF  Evolutionary Medicine
2018 Transcriptomics in the wild: hibernation physiology in free-ranging dwarf lemurs. Faherty S.L., Villanueva-Cañas J.L., Blanco M.B., Albà M.M. and A.D. Yoder. Molecular Ecology. PDF  Hibernation in Dwarf Lemurs
2017 Bamboo specialists from two mammalian orders (Primates, Carnivora) share a high number of low-abundance gut microbes. McKenney E.A., Maslanka M., Rodrigo A., and A.D. Yoder. Microbial Ecology. PDF The Gut Microbiome in Lemurs
2017 Feeding strategy shapes gut metagenomic enrichment and functional specialization in captive lemurs. McKenney, E.A., O’Connell, T.M., Rodrigo, A., and A.D. Yoder. Gut Microbes. The Gut Microbiome in Lemurs
2017 Hybrid de novo genome assembly and centromere characterization of the gray mouse lemur (Microcebus murinus). Larsen, P.A., Harris, R.A., Liu, Y., et al. BMC Biology. PDF Next Generation ‘Omics
2017 Down for the count: Cryptosporidium infection depletes the gut microbiome in Coquerel’s sifakas. McKenney, E.A., Greene, L.K., Drea, C.M., and A.D. Yoder. Microbial Ecology in Health and Disease. PDF The Gut Microbiome in Lemurs
2017 The challenges faced by living stock collections in the USA. McCluskey, K., Boundy-Mills, K., Dye, G., et al. eLife. PDF
2017 The Alu neurodegeneration hypothesis: A primate-specific mechanism for neuronal transcription noise, mitochondrial dysfunction, and manifestation of neurodegenerative disease. Larsen, P.A., Lutz, M.W., Hunnicutt, K.E., et al. Alzheimer’s and Dementia. PDF  Evolutionary Medicine
2016 The effect of body mass and diet composition on torpor patterns in a Malagasy primate (Microcebus murinus). Faherty, S. L., Campbell, C. R., Hilbig, S. A., Yoder, A. D. Journal of Comparative Physiology B. PDF  Hibernation in Dwarf Lemurs
2016 Hibernation in a primate: does sleep occur? Blanco, M. B., Dausmann, K. H., Faherty, S. L., et al. Royal Society Open Science. PDF  Hibernation in Dwarf Lemurs
2016 Geogenetic patterns in mouse lemurs (genus Microcebus) reveal the ghosts of Madagascar’s forests past. Yoder, A.D., Campbell, C.R., Blanco, M.B., et al. Proceedings of the National Academy of Sciences. PDF Next Generation ‘Omics

The Impacts of Climate Change and Human Disturbance on Malagasy Biota
2016 Gene expression profiling in the hibernating primate, Cheirogaleus medius. Faherty, S.L., Villanueva-Canas, J.L., Klopfer, P.H., Alba, M.M., Yoder, A.D. Genome Biology and Evolution. PDF  Hibernation in Dwarf Lemurs
2016 Implications of lemuriform extinctions for the Malagasy flora. Federmana, S., Dornburg A., Dalyc D.C., et al. Proceedings of the National Academy of Sciences, 113(18):5041-5046. PDF  The Impacts of Climate Change and Human Disturbance on Malagasy Biota
2016 Cheirogaleid diversity and evolution: big questions about small primates. Yoder, A.D., D.W. Weisrock, R.M. Rasoloarison, P.M. Kappeler. The Dwarf and Mouse Lemurs of Madagascar: Biology, Behavior and Conservation Biogeography of the Cheirogaleidae. Cambridge University Press. PDF Speciation Dynamics in Mouse Lemurs
2016 Blood transcriptomes reveal novel parasitic zoonoses circulating in Madagascar’s lemurs. Larsen, P.A., Hayes, C.E., Williams, C.V., Junge, R.E., Razafindramanana, J., Mass, V., Rakotondrainibe, H., A.D. Yoder. Biology Letters, 12(1). PDF Next Generation ‘Omics
2015 Evaluating whole transcriptome amplification for gene profiling experiments using RNA-Seq. Faherty, S.L., C.R. Campbell, P.A. Larsen, and A.D. Yoder. BMC Biotechnology, doi:10.1186/s12896-015-0155-7. PDF Next Generation ‘Omics 
2015 Comparative and population mitogenomic analyses of Madagascar’s extinct, giant ‘subfossil’ lemurs. Kistler, L., A. Ratan, L.R. Crowley, et al. Journal of Human Evolution, 79:45-54. PDF Origins of Lemurs and other Malagasy Biota 
2015 Phylogeography of the arid-adapted Malagasy bullfrog, Laliostoma labrosum, influenced by past connectivity and habitat stability. Pabijan, M., J.L. Brown, L.M. Chan, et al. Molecular Phylogenetics and Evolution, 92:11-24. Link to
ScienceDirect
Version		 Comparative Phylogeography of Madagascar
2015 Alteration of the rat cecal microbiota during colonization with the helminth Hymenolepis dimunita. McKenney, E.A., L. Williamson, A.D. Yoder, et al. Gut Microbes, 6(3):182-193. PDF The Gut Microbiome in Lemurs
2015 Patterns of gut bacterial colonization in three primate species. McKenney, E.A., A. Rodrigo, A.D. Yoder. PLoS ONE, 10(5): e0124618. PDF The Gut Microbiome in Lemurs
2015 Assessing the utility of whole genome amplified DNA for next-generation molecular ecology. Blair, C., C.R. Campbell, and A.D. Yoder. Molecular Ecology Resources, doi: 10.111/1755-0998.12376. PDF Next Generation ‘Omics 
2015 Shifting ranges and conservation challenges for lemurs in the face of climate change. Brown, J.L., and A.D. Yoder. Ecology and Evolution, 5:1131–1142. PDF Science Coverage The Impacts of Climate Change and Human Disturbance on Malagasy Biota
2015 Multilocus phylogenetic and geospatial analyses illuminate diversification patterns and the biogeographic history of Malagasy endemic plated lizards (Gerrhosauridae: Zonosaurinae). Blair, C., B.P. Noonan, J.L. Brown, A.P. Raselimanana, M. Vences, and A.D. Yoder. Journal of Evolutionary Biology, 28:481–492. PDF Comparative Phylogeography of Madagascar
2014 The molecular evolutionary dynamics of the vomeronasal receptor (Class 1) genes in primates: a gene family on the verge of a functional breakdown. Yoder, A.D. and P.A. Larsen. Frontiers in Neuroanatomy, 8:153. PDF Molecular Evolution of Sensory Communication
2014 Extinction risks and the conservation of Madagascar’s reptiles. Jenkins, R.K.B., M.F. Tognelli, P. Bowles, et al. PLoS ONE, 9:e100173. PDF Comparative Phylogeography of Madagascar
2014 A deep divergence time between sister species of Eidolon (Pteropodidae) with evidence for widespread panmixia. Shi, J.J., L.M. Chan, A.J. Peel, R. Lai, A.D. Yoder, and S.M. Goodman. Acta Chiropterologica, 16:279–292. PDF Comparative Phylogeography of Madagascar
2014 Populations genetics of the Mauritian Flying Fox, Pteropus niger. Larsen, P.A., C.E. Hayes, M.A. Wilkins, Y. Gomard, R. Sookhareea, A.D. Yoder, and S.M. Goodman. Acta Chiropterologica, 16:293–300. PDF Comparative Phylogeography of Madagascar
2014 Discovery of prosimian and afrotherian foamy viruses and potential cross species transmissions amidst stable and ancient mammalian co-evolution. Katzourakis, A., P. Aiewsakan, H. Jia, N.D. Wolfe, M. LeBreton, A.D. Yoder, and W.M. Switzer. Retrovirology, 11:61. PDF Evolutionary Medicine
2014 A necessarily complex model to explain the biogeography of the amphibians and reptiles of Madagascar. Brown, J.L., A. Cameron, A.D. Yoder, and Miguel Vences. Nature Communications, 5:5056. PDF Historical Biogeography and Phylogeography

Comparative Phylogeography of Madagascar
2014 Multilocus coalescent analyses reveal the demographic history and speciation patterns of mouse lemur sister species. Blair, C., K.L. Heckman, A.L. Russell, and A.D. Yoder. BMC Evolutionary Biology, 14:57. PDF Speciation Dynamics in Mouse Lemurs
2014 Next-generation approaches to advancing eco-immunogenomic research in critically endangered primates. Larsen, P.A., C.R. Campbell, and A.D. Yoder. Molecular Ecology Resources, 14:1198–1209. PDF National Geographic Interview Next Generation ‘Omics
2014 The utility of PacBio circular consensus sequencing
for characterizing complex gene families in
non-model organisms. Larsen, P.A., A.M. Heilman, and A.D. Yoder. BMC Genomics, 15:720.		 PDF Next Generation ‘Omics
2014 The founding of Mauritian endemic coffee trees by a synchronous long-distance dispersal event. Nowak, M. D., Haller, B.C. and A.D. Yoder. Journal of Evolutionary Biology, 27(6):1229-39. PDF Origins of Lemurs and other Malagasy Biota 
2014 Theme and variations: heterothermy in mammals. Martin, S.L., and A.D. Yoder. Integrative & Comparative Biology, 54:439–442. PDF Hibernation in Dwarf Lemurs
2014 Comparative genomics of mammalian hibernators using gene networks. Villanueva-Cañas, J.L, S.L. Faherty, A.D. Yoder, and M.M. Alba. Integrative & Comparative Biology, 54:452–462. PDF Hibernation in Dwarf Lemurs
2014 Life history profiles for 27 strepsirrhine primate taxa generated using captive data from the Duke Lemur Center. Zehr, S.M., R.G. Roach, D. Haring, J. Taylor, F.H. Cameron, and A.D. Yoder. Scientific Data, 1:140019. PDF
2014 Gene flow happens. Yoder, A.D.Evolutionary Anthropology, 23:15-17. PDF Speciation Dynamics in Mouse Lemurs
2014 Molecular evolutionary characterization of a V1R subfamily unique to strepsirrhine primates. Yoder, A.D., L.M. Chan, M. dos Reis, P.A. Larsen, C.R. Campbell, R. Rasoloarison, M. Barrett, C. Roos, P. Kappler, J. Bielawski, and Z. Yang. Genome Biology and Evolution, 6:213-227. PDF Molecular Evolution of Sensory Communication
2013 Latitude drives diversification in Madagascar’s endemic dry forest rodent Eliurus myoxinus (subfamily Nesomyinae). Shi, J.J., L.M. Chan, Z. Rakotomalala, A.M. Heilman, S.M. Goodman, and A.D. Yoder. Biological Journal of the Linnean Society, 110: 500-517 PDF Comparative Phylogeography of Madagascar
2013 The relationship of sleep with temperature and metabolic rate in a hibernating primate. Krystal, A.D., B. Schopler, S. Kobbe, C. Williams, H. Rakatondrainibe, A.D. Yoder, and P. Klopfer. PLoS ONE, 8: e69913. PDF Hibernation in Dwarf Lemurs
2013 Protection for trade of precious rosewood. Barrett, M.A., J.L. Brown, and A.D. Yoder. Nature, 499: 29. PDF The Impacts of Climate Change and Human Disturbance on Malagasy Biota
2013 Review of the systematic status of Sceloporus arenicolus Degenhardt and Jones, 1972 with an estimate of divergence time. Chan, L.M., J.W. Archie, A.D. Yoder, and L.A. Fitzgerald. Zootaxa, 3664: 312-320. PDF
2013 Two new species of mouse lemurs (Cheirogaleidae: Microcebus) from eastern Madagascar. Rasoloarison, R.M., D.W. Weisrock, A.D. Yoder, D. Rakotondravony, and P.M. Kappeler. International Journal of Primatology, 34:455-469 PDF Speciation Dynamics in Mouse Lemurs
2013 Underground hibernation in a primate. Blanco, M.B., K.H. Dausmann, J.F. Ranaivoarisoa, and A.D. Yoder. Scientific Reports, 3: 1768. PDF Hibernation in Dwarf Lemurs
2013 Fossils Versus Clocks. Yoder, A.D. Science, 339:656-658. PDF Divergence Time Estimation
2013 The lemur revolution starts now: The genomic coming of age for a non-model organism.

Yoder, A.D. Molecular Phylogenetics and Evolution, 66:442-452.

 Link to
ScienceDirect
Version		 Next Generation ‘Omics
2013 Climate change, predictive modeling and lemur health: Assessing impacts of changing climate on health and conservation in Madagascar. Barrett, M.A., J.L. Brown, R.E. Junge, and A.D. Yoder. Biological Conservation, 157:409-422. PDF The Impacts of Climate Change and Human Disturbance on Malagasy Biota
2012 Sequence data from new plastid and nuclear
COSII regions resolves early diverging lineages in Coffea (Rubiaceae) Nowak, M.D., Davis, A.P. and A.D. Yoder. Systematic Botany, 37(4):995-1005.		 PDF Origins of Lemurs and other Malagasy Biota
2012 Defining spatial and temporal patterns of phylogeographic structure in Madagascar’s iguanid lizards (genus Oplurus). Chan, L.M., D. Choi, A.P. Raselimanana, H.A. Rakotondravony, and A.D. Yoder. Molecular Ecology, 21:3839-3851. PDF Comparative Phylogeography of Madagascar
2012 Concatenation and Concordance in the Reconstruction of Mouse Lemur Phylogeny: An Empirical Demonstration of the Effect of Allele Sampling in Phylogenetics. Weisrock, D.W., S.D. Smith, L.M. Chan, K. Biebouw, P.M. Kappler, and A.D. Yoder. Molecular Biology and Evolution, 29(6):1615-1630. PDF Speciation Dynamics in Mouse Lemurs

Phylogenetics and Molecular Evolution
2012 Comparative RNA sequencing reveals substantial genetic variation in endangered primates. 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. Genome Research, 22:602-610. PDF Next Generation ‘Omics
2011 Effects of anthropogenic disturbance on indri (Indri indri) health in Madagascar. Junge, R.E., M. Barrett, and A.D. Yoder. American Journal of Primatology, 73(7):632-642. Featured article. PDF The Impacts of Climate Change and Human Disturbance on Malagasy Biota
2011 Expression and Trans-Specific Polymorphism of Self-Incompatibility RNases in Coffea (Rubiaceae). Nowak, M.D., A. P. Davis, F. Anthony, and A. D. Yoder. PLoS ONE, 6(6):e21019. PDF Next Generation ‘Omics
2011 Increased population sampling confirms low genetic divergence among Pteropus (Chiroptera: Pteropodidae) fruit bats of Madagascar and other western Indian Ocean islands. Chan, L. M., S. M. Goodman, M. D. Nowak, D. W. Weisrock, and A. D. Yoder. PLoS Currents: Tree of Life. Online Comparative Phylogeography of Madagascar
2011 Integrating statistical genetic and geospatial methods brings new power to phylogeography.Chan, L. M., J. L. Brown, and A. D. Yoder. Molecular Phylogenetics and Evolution, 59: 523–537. Link to
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Version		 Historical Biogeography and Phylogeography
2010 CITES designation for endangered rosewood in Madagascar. Barrett, M. A., J. L. Brown, M. K. Morikawa, J-N Labat, and A. D. Yoder. Science, 328: 1109-1110. The Impacts of Climate Change and Human Disturbance on Malagasy Biota
2010 Delimiting species without nuclear monophyly in Madagascar’s Mouse Lemurs. Weisrock, D. W., R. M. Rasoloarison, I. Fiorentino, J. M. Ralison, S. M. Goodman, P. M. Kappeler, and A. D. Yoder. PLoS ONE, 5(3): e9883. PDF Speciation Dynamics in Mouse Lemurs
2010 Phylogeography’s past, present, and
future: 10 years after Avise, 2000.
M. J. Hickerson, B. C. Carstens, J. Cavender-Bares, K. A. Crandall, C. H. Graham, J.
Johnson, L. Rissler, P. F. Victoriano, and A.D. Yoder. Molecular Phylogenetics and Evolution 54(1): 291-301.		 Link to
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Version 		 Historical Biogeography and Phylogeography
2010 Phylogeny and biogeography of western Indian Ocean Rousettus (Chiroptera: Pteropodidae). Goodman, S. M., L. M. Chan, M. D. Nowak, and A. D. Yoder. Journal of Mammalogy, 91(3): 593-606 Comparative Phylogeography of Madagascar
2009 Species delimitation in lemurs: multiple genetic loci reveal low levels of species diversity in the genus Cheirogaleus. Groeneveld, L.F., Weisrock, D.W., Rasoloarison, R., Yoder, A.D. and P.M. Kappeler. BMC Evolutionary Biology, 9:30. PDF Speciation Dynamics in Mouse Lemurs
2009 Multiple colonisations of the Western Indian Ocean by Pteropus fruit bats (Megachiroptera: Pteropodidae): the furthest islands were colonised first.

O’Brien, J., Mariani, C., Olson, L.E., Russell, A.L., Say, L., Yoder, A.D. and T.J. Hayden. Mol. Phyl. & Evol., 51: 294-303.

 Link to
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Version		 Comparative Phylogeography of Madagascar
2009 Geographic origins of aDNA samples and prospects for aDNA studies in the tropics. Karanth, K.P. and A.D. Yoder. In: Molecular Markers, PCR, Bioinformatics and Ancient DNA – Technology, Troubleshooting And Applications (G. Dorado, ed.) Science Publishers.
2009 Anonymous nuclear markers for Malagasy plated lizards (Zonosaurus). Noonan, B.P. and A.D. Yoder. Molecular Ecology Resources, 9:402-404. PDF Next Generation ‘Omics
2009 Phylogeny and Evolution of Malagasy Plated Lizards. Raselimanana, A., Noonan, B.P., Karanth, P., Gauthier, J., and A.D. Yoder. Mol. Phyl. & Evol. 50: 336-344. Link to
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Version		 Origins of Lemurs and other Malagasy Biota
2008 The role of molecular genetics in sculpting the future of integrative biogeography. Riddle, BR; Dawson, MN; Hadly, EA, Hafner, D.J., Hickerson MJ, Mantooth SJ, and A.D. Yoder. Progress in Physical Geography, 32 (2): 173-202. PDF Historical Biogeography and Phylogeography
2008 The development and application of a phylogenomic toolkit: resolving the evolutionary history of Madagascar’s lemurs. Horvath, J., Weisrock, D., Embry, S.L., Fiorentino, Balhoff, J.P., I., Kappeler, P., Wray, G.A., Willard, H., and A.D. Yoder. Genome Research 18(3): 489-499. PDF Origins of Lemurs and other Malagasy Biota
2008 Population genetic analysis of Myzopoda spp. (Chiroptera: Myzopodidae) in Madagascar. Russell, A.L., Goodman, S.M., Fiorentino, I., and A.D. Yoder. J. Mamm. 89 (1): 209-221. PDF Comparative Phylogeography of Madagascar
2007 Lemurs: a Quick Guide. Yoder, A.D. Current Biology, 17 (20): 866-868. PDF
2007 Multiple nuclear loci reveal patterns of incomplete lineage sorting and complex species history within western mouse lemurs (Microcebus).Heckman, K.L., Hanley, C.L., Rasoloarison, R. and A.D. Yoder. Mol. Phyl. & Evol. 43 (2): 353-367. Link to
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Version		 Speciation Dynamics in Mouse Lemurs
2007 Evolution of a tumorigenic property conferred by Glycophosphatidyl-inositol membrane anchors of CEA gene family members during the primate radiation. Naghibalhossaini, F., Yoder, A.D., Tobi, M., and C.P. Stanners. Molecular Biology of the Cell 18 (4): 1366-1374). PDF Evolutionary Medicine
2007 Working at the interface of phylogenetics and population genetics: a biogeographic analysis of Triaenops spp (Chiroptera: Hipposideridae). Russell, A.L., Ranivo, J., Palkovacs, E.P., Goodman, S.M., and A.D. Yoder. Molecular Ecology, 16:839-851. PDF Comparative Phylogeography of Madagascar
2006 Incongruence between genetic and morphological diversity in Microcebus griseorufus of Beza Mahafaly. Heckman, K. L., Rasoazanabary, E., Machlin, E., Godfrey, L.R., and A. D. Yoder. BMC Evolutionary Biology, 6:98 (16 Nov 2006). PDF Speciation Dynamics in Mouse Lemurs
2006 Has vicariance or dispersal been the predominant biogeographic force in Madagascar?: only time will tell. Yoder, A.D. and M. Nowak. Ann. Rev. Ecol. Evol. Syst., 37:405-431. PDF Origins of Lemurs and other Malagasy Biota
2006 A new species of Emballonura (Emballonuridae: Chiroptera) from the dry regions of Madagascar. Goodman, S.M., Cardiff, S. G., Ranivo, J., Russell, A.L. and A.D. Yoder. American . Museum Novitates, No. 3538: 1-24. PDF Comparative Phylogeography of Madagascar
2006 Mouse lemur phylogeography revises a model of ecogeographic constraint in Madagascar. Yoder, A.D. and K. Heckman. In: Primate Biogeography: Progress and Prospects (J. Fleagle and S.M. Lehman, eds.) Kluwer Press, pp. 255 – 268. PDF Speciation Dynamics in Mouse Lemurs
2005 The biogeography of Madagascar: where to turn when the fossils aren’t there. Yoder, A.D. Paleontological Society Papers, V. 11, 129-139. Origins of Lemurs and other Malagasy Biota
2005 Evidence from opsin genes rejects nocturnality in ancestral primates. Tan, Y., Yoder, A.D., Yamashita, N. and W.-H. Li. Proceedings of the National Academy of Sciences 102: 14712-14716. PDF Molecular Evolution of Sensory Communication
2005 A multidimensional approach for detecting species patterns in Malagasy vertebrates. 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. Proceedings of the National Academy of Sciences 102: 6587-6594, Suppl. 1 (invited Colloquium contribution). PDF Comparative Phylogeography of Madagascar
2005 Ancient DNA from giant extinct lemurs verifies single origin of Malagasy primates. Karanth, P. Rakotosamimanana, B., Parsons, T.J. and A.D. Yoder. Proceedings of the National Academy of Sciences 102: 5090-5095. PDF Origins of Lemurs and other Malagasy Biota
2005 Native Seychelles tortoises or Aldabran imports? The importance of radiocarbon dating for ancient DNA studies. Karanth, K.P., Palkovacs, E., Gerlach, J., Glaberman, S., Caccone, A., and A.D. Yoder. Amphibia-Reptilia 26(1): 116-121. PDF
2004 Illumination of cryptic species boundaries in long-tailed shrew tenrecs (Mammalia: Tenrecidae; Microgale) provides insights into geographic variation and distributional constraints. Olson, L.E., Goodman, S., and A.D. Yoder. Biological Journal of the Linnean Society, 83:1-22. PDF Comparative Phylogeography of Madagascar
2004 Divergence dates for Malagasy lemurs estimated from multiple gene loci: geological and evolutionary context. Yoder, A.D. and Z. Yang. Molecular Ecology, 13:757-773. PDF Divergence Time Estimation
2004 Review of A Primer of Conservation Genetics, by Frankahm, R., Ballou, J.D. and D.A. Briscoe. Yoder, A.D. Journal of Mammalogy (info).
2003 Structure and Function of CC-Chemokine Receptor 5 Homologues Derived from Representative Primate Species and Subspecies of the Taxonomic Suborders Prosimii and Anthropoidea. 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. Journal of Virology, 77(22): 12310-12318. PDF Evolutionary Medicine
2003 Origin of Malagasy Carnivora. Yoder, A.D. and J.J. Flynn. In: The Natural History of Madagascar (S. M. Goodman and J. Benstead, eds.) University of Chicago Press, pp. 1253-1256. Origins of Lemurs and other Malagasy Biota 
2003 Phylogeny of the lemurs. Yoder, A.D. In: The Natural History of Madagascar (S. M. Goodman and J. Benstead, eds.) University of Chicago Press, pp. 1242-1247. Origins of Lemurs and other Malagasy Biota 
2003 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. Yang, Z. and A.D. Yoder. Systematic Biology, 52(5):705-716. PDF Divergence Time Estimation
2003 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.) Yoder, A.D. Rutgers University Press, pp. 161-175. Phylogenetics and Molecular Evolution
2003 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. Eriksson, T., Hibbs, M.S., Yoder, A.D., Delwiche, C.F., and M.J. Donoghue. International Journal of Plant Sciences, 164(2):197-211. PDF
2003 Single origin of Malagasy Carnivora from an African ancestor. Yoder, A.D., Burns, M.M., Zehr, S., Delefosse, T., Veron, G., Goodman, S.M., and J.J. Flynn. Nature, 421: 734-737. PDF Origins of Lemurs and other Malagasy Biota 
2002 Molecular evidence of reproductive isolation in sympatric sibling species of mouse lemurs. Yoder, A.D., Burns, M.M., and F. Genin. International Journal of Primatology, 23: 1335-1343. PDF Origins of Lemurs and other Malagasy Biota 
2002 Using secondary structure to identify ribosomal numts: cautionary examples from the human genome. Olson, L.E. and A.D. Yoder. Molecular Biology and Evolution, 19(1): 93-100. PDF Phylogenetics and Molecular Evolution
2002 Ancient DNA Yoder, A.D. and T. Delefosse.. McGraw-Hill, Yearbook of Science and Technology, pp. 9-14. PDF
2001 Failure of the ILD to determine data combinability for slow loris phylogeny. Yoder, A.D., Irwin, J.A., and B. Payseur. Systematic Biology, 50: 408-424. PDF Phylogenetics and Molecular Evolution
2001 Ancient DNA from Megaladapis edwardsi. Yoder, A.D. Folia Primatol (Basel), 72(6):342-344. PDF
2000 Remarkable species diversity in Malagasy mouse lemurs (Primates, Microcebus). Yoder, A.D., Rasoloarison, R., Goodman, S., Irwin, J.A., Atsalis, S. Ravosa, M.J., and J.U. Ganzhorn. Proceedings of the National Academy of Sciences, 97: 11325-11330. PDF Speciation Dynamics in Mouse Lemurs
2000 Genetic tests of the taxonomic status of Lemur catta from the high mountain zone of the Andringtra Massif, Madagascar. Yoder, A.D., Irwin, J.A., Rakotoarisoa, S.V., and S. Goodman. Journal of Zoology, 252:1-9. PDF Comparative Phylogeography of Madagascar
2000 Estimation of primate speciation dates using local molecular clocks. Yoder, A.D. and Z. Yang. Molecular Biology and Evolution, 17(7):1081-1090. PDF Divergence Time Estimation
1999 Phylogeny of the Lemuridae: effects of taxon and character sampling on resolution of species relationships within Eulemur. Yoder, A.D. and J.A. Irwin. Cladistics, 15:351-361. PDF Phylogenetics and Molecular Evolution
1999 Ancient DNA in subfossil lemurs: methodological challenges and their solutions. Yoder, A.D., Rakotosamimanana, B. and T.J. Parsons. In: Rasaminanana, H., B. Rakotosamimanana, S. Goodman and J. Ganzhorn (eds.), New Directions in Lemur Studies. Plenum Press, pp. 1-17. PDF
1999 Estimation of the transition/transversion rate bias and species sampling. Yang, Z. and A.D. Yoder. Journal of Molecular Evolution, 48(3): 274-283. PDF Dataset Phylogenetics and Molecular Evolution
1998 Review of Introduction to the Primates, by Daris R. Swindler. Yoder, A.D. American Zoologist, 39(1):186-187.
1997 Back to the future: a synthesis of strepsirrhine systematics. Yoder, A.D. Evolutionary Anthropology, 6(1):11-22.
1997 An infinitude of connecting links. Yoder, A.D. Trends in Ecology and Evolution, 12(3):86-88. PDF
1996 Molecular evolutionary dynamics of cytochrome b in strepsirrhine primates: the phylogenetic significance of third position transversions. Yoder, A.D., Vilgalys, R., and M. Ruvolo. Molecular Biology and Evolution, 13(10):1339-1350. PDF Phylogenetics and Molecular Evolution
1996 Ancient single origin for Malagasy primates. Yoder, A.D., Cartmill, M., Ruvolo, M., Smith, K., and R. Vilgalys. Proceedings of the National Academy of Sciences, 93:5122-5126. PDF Origins of Lemurs and other Malagasy Biota 
1996 The use of phylogeny for reconstructing lemuriform biogeography. Yoder, A.D. In: Biogeographie de Madagascar. (W.R. Lourenco, ed.) Editions de l’ORSTROM, Paris, pp. 245-258. Historical Biogeography and Phylogeography
1994 The relative position of the Cheirogaleidae in strepsirhine phylogeny: a comparison of morphological and molecular methods and results. Yoder, A.D. American Journal of Physical Anthropology, 94(1):25-46. Phylogenetics and Molecular Evolution
1994 Molecules and Morphology in Primate Systematics: An Introduction. Cartmill, M. and A.D. Yoder. American Journal of Physical Anthropology, 94(1):1. Phylogenetics and Molecular Evolution
1994 Molecules and Morphology in Primate Systematics. G. Conroy, M. Cartmill and A.D. Yoder. Editors. New York: Wiley-Lyss; special volume of American Journal of Physical Anthropology, 94(1). Phylogenetics and Molecular Evolution
1993 Review of Classification, Evolution, and the Nature of Biology, by Alec L. Panchen. Yoder, A.D. American Journal of Physical Anthropology, 91(4):535-537.
1992 Applications and limitations of ontogenetic comparisons for phylogeny reconstruction: the case of the strepsirhine internal carotid artery. Yoder, A.D. Journal of Human Evolution, 23:183-195. Phylogenetics and Molecular Evolution
1992 Cranial anatomy of Ignacius graybullianus and the affinities of the Plesiadapiformes. Kay, R.F., Thewissen, J.G.M. and A.D. Yoder. American Journal of Physical Anthropology 89:477-498.
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