Daniel Mulcahy

Daniel Mulcahy joined the Global Genome Initiative as the Molecular Laboratory Technician in January 2015.  He performs analytical laboratory procedures, such as DNA extraction, PCR, DNA sequencing, and quality assessment of genomic collections for GGI projects.  His research interests include both amphibian and reptile phylogenetics.  Dr. Mulcahy received his Ph.D. in Biology from Utah State University.

Journal Article

• Gottscho, Andrew D., Mulcahy, Daniel G., Leaché, Adam D., de Queiroz, Kevin, and Lovich, Robert E. 2024. "Population genomics of flat-tailed horned lizards (Phrynosoma mcallii) informs conservation and management across a fragmented Colorado Desert landscape." Molecular ecology, https://doi.org/10.1111/mec.17308.
• Ray, Julie M., Sanchez-Martinez, Paola, Batista, Abel, Mulcahy, Daniel G., Sheehy, Coleman M., III, Smith, Eric N., Pyron, R. Alexander, and Arteaga, Alejandro. 2023. "A new species of Dipsas (Serpentes, Dipsadidae) from central Panama." Zookeys, (1145) 131–167. https://doi.org/10.3897/zookeys.1145.96616.
• Mulcahy, Daniel G., Ibáñez, Roberto D., Jaramillo, Cesar A., Crawford, Andrew J., Ray, Julie M., Gotte, Steve W., Jacobs, Jeremy F., Wynn, Addison H., Gonzalez-Porter, Gracia, McDiarmid, Roy W., Crombie, Ronald I., Zug, George R., and de Queiroz, Kevin. 2022. "DNA barcoding of the National Museum of Natural History reptile tissue holdings raises concerns about the use of natural history collections and the responsibilities of scientists in the molecular age." PLOS ONE, 17, (3). https://doi.org/10.1371/journal.pone.0264930.
• Myers, Edward A., Mulcahy, Daniel G., Falk, Bryan, Johnson, Kiyomi, Carbi, Marina, and de Queiroz, Kevin. 2021. "Interspecific Gene Flow and Mitochondrial Genome Capture During the Radiation of Jamaican Anolis Lizards (Squamata; Iguanidae)." Systematic Biology, https://doi.org/10.1093/sysbio/syab089.
• Macey, J. Robert, Pabinger, Stephan, Barbieri, Charles G., Buring, Ella S., González, Vanessa L., Mulcahy, Daniel G., DeMeo, Dustin P., Urban, Lara, Hime, Paul M., Prost, Stefan, Elliott, Aaron N., and Gemmell, Neil J. 2021. "Evidence of two deeply divergent co-existing mitochondrial genomes in the Tuatara reveals an extremely complex genomic organization." Communications Biology, 4, (1) Article 116. https://doi.org/10.1038/s42003-020-01639-0.
• Cota, Michael, Makchai, Sunchai, Mulcahy, Daniel G., and Stuart, Bryan L. 2021. "Molecular and morphological evidence for a significant range extension of Bronchocela burmana Blanford, 1878 to eastern Thailand." Herpetology Notes, 14 485–491.
• Miller, Aryeh H., Zug, George R., Wogan, Guinevere O. U., Lee, Justin L., and Mulcahy, Daniel G. 2021. "Phylogeny, Diversity, and Distribution of Micryletta (Anura: Microhylidae) in Myanmar." Ichthyology & Herpetology, 109, (1) 245–257. https://doi.org/10.1643/h2020100.
• Bakkegard, Kristin, Johnson, David A., and Mulcahy, Daniel. 2020. "A New Locality, Naval Station Guantanamo Bay, for the Rare Lizard Leiocephalus onaneyi (Guantánamo Striped Curlytail) and Notes on its Natural History." Caribbean Naturalist, 79 1–22.
• Bell, Rayna C., Mulcahy, Daniel G., Gotte, Steve W., Maley, Abigail J., Mendoza, Cerrie, Steffensen, Gregory, Barron, Joseph C., Hyman, Oliver, Flint, William, Wynn, Addison, McDiarmid, Roy W., and Mcleod, David S. 2020. "The Type Locality Project: collecting genomic-quality, topotypic vouchers and training the next generation of specimen-based researchers." Systematics and Biodiversity, 18, (6) 557–572. https://doi.org/10.1080/14772000.2020.1769224.
• Derycke, Elizabeth G., Gottscho, Andrew D., Mulcahy, Daniel G., and de Queiroz, Kevin. 2020. "A new cryptic species of fringe-toed lizards from southwestern Arizona with a revised taxonomy of the Uma notata species complex (Squamata: Phrynosomatidae)." Zootaxa, 4778, (1) 67–100. https://doi.org/10.11646/zootaxa.4778.1.3.
• Gemmell, Neil J., Rutherford, Kim, Prost, Stefan, Tollis, Marc, Winter, David, Macey, J. R., Adelson, David L., Suh, Alexander, Bertozzi, Terry, Grau, José H., Organ, Chris, Gardner, Paul P., Muffato, Matthieu, Patricio, Mateus, Billis, Konstantinos, Martin, Fergal J., Flicek, Paul, Petersen, Bent, Kang, Lin, Michalak, Pawel, Buckley, Thomas R., Wilson, Melissa, Cheng, Yuanyuan, Miller, Hilary, Schott, Ryan K. et al. 2020. "Publisher Correction: The tuatara genome reveals ancient features of amniote evolution." Nature, 585 e3. https://doi.org/10.1038/s41586-020-2661-6.
• Gemmell, Neil J., Rutherford, Kim, Prost, Stefan, Tollis, Marc, Winter, David, Macey, J. R., Adelson, David L., Suh, Alexander, Bertozzi, Terry, Grau, José H., Organ, Chris, Gardner, Paul P., Muffato, Matthieu, Patricio, Mateus, Billis, Konstantinos, Martin, Fergal J., Flicek, Paul, Petersen, Bent, Kang, Lin, Michalak, Pawel, Buckley, Thomas R., Wilson, Melissa, Cheng, Yuanyuan, Miller, Hilary, Schott, Ryan K. et al. 2020. "The tuatara genome reveals ancient features of amniote evolution." Nature, 584 403–409. https://doi.org/10.1038/s41586-020-2561-9.
• Kabat, Kristin L., Young, Daniel V., Xiong, Peter X., Van Ee, Noah, Bradke, Danielle R., Hileman, Eric T., Gotte, Steve W., Mulcahy, Daniel G., and Nafus, Melia G. 2020. "Hemidactylus cf. platyurus (Asian Flat- tailed House Gecko) Geographic Distribution Note." Herpetological Review, 51, (3) 540.
• Myers, Edward A. and Mulcahy, Daniel G. 2020. "Six additional mitochondrial genomes for North American nightsnakes (Dipsadidae:Hypsiglena) and a novel gene feature for advanced snakes." Mitochondrial DNA Part B. Resources, 5, (3) 3074–3076. https://doi.org/10.1080/23802359.2020.1797573.
• Van Ee, Noah, Xiong, Peter X., Young, Daniel V., Kabat, Kristin L., Bradke, Danielle R., Hileman, Eric T., Gotte, Steve W., Mulcahy, Daniel G., and Nafus, Melia G. 2020. "Hemidactylus tenkatei (Spotted House Gecko) Geographic Distribution Note." Herpetological Review, 51, (3) 540–541.
• Angeli, Nicole F., Coles, William, McKinley, Shane, and Mulcahy, Daniel G. 2019. "Introduction of an Exotic Constricting Snake (Boa Constrictor) and its Establishment on St. Croix, Us Virgin Islands." Herpetological Conservation and Biology, 14, (1) 288–296.
• Grismer, L. Lee, Wood, Perry L., Jr., Grismer, Jesse L., Quah, Evan S. H., Thy, Neang, Phimmachak, Somphouthone, Sivongxay, Niane, Seateun, Sengvilay, Stuart, Bryan L., Siler, Cameron B., Mulcahy, Daniel G., Anamza, Tashitso, and Brown, Rafe M. 2019. "Geographic structure of genetic variation in the Parachute Gecko Ptychozoon lionotum Annandale, 1905 across Indochina and Sundaland with descripions of three new species." Zootaxa, 4638, (2) 151–198. https://doi.org/10.11646/zootaxa.4638.2.1.
• Lee, Justin L., Miller, Aryeh H., Zug, George R., and Mulcahy, Daniel G. 2019. "The discovery of Rock Geckos Cnemaspis Strauch, 1887 (Squamata: Gekkonidae) in the Tanintharyi Region, Myanmar with the description of two new species." Zootaxa, 4661, (1) 40–64. https://doi.org/10.11646/zootaxa.4661.1.2.
• Barron, Joseph C., II, Gotte, Steve W., Collette, Bruce B., McDiarmid, Roy W., Mulcahy, Daniel G., and Davis, Drew R. 2018. "Scaphiopus holbrookii (Eastern Spadefoot)." Herpetological Review, 49, (4) 710.
• González, Vanessa L., Devine, Amanda M., Trizna, Mike, Mulcahy, Daniel G., Barker, Katherine, and Coddington, Jonathan A. 2018. "Open access genomic resources for terrestrial arthropods." Current Opinion in Insect Science, 25 91–98. https://doi.org/10.1016/j.cois.2017.12.003.
• Lee, Justin L., Miller, Aryeh H., Connette, Grant M., Oo, Khin Swe, Zug, George R., and Mulcahy, Daniel G. 2018. "First record of the Malaysian Bridle Snake, Dryocalamus subannulatus (Duméril, Bibron & Duméril, 1854), in Myanmar (Reptilia, Serpentes, Colubridae)." Check List, 14, (2) 341–345. https://doi.org/10.15560/14.2.341.
• Mulcahy, Daniel G., Lee, Justin L., Miller, Aryeh H., Chand, Mia, Thura, Myint Kyaw, and Zug, George R. 2018. "Filling the BINs of life: Report of an amphibian and reptile survey of the Tanintharyi (Tenasserim) Region of Myanmar, with DNA barcode data." ZooKeys, 757 85–152. https://doi.org/10.3897/zookeys.757.24453.
• Zug, George R., Mulcahy, Daniel G., Vindum, Jens V., and Wilkinson, Jeffery A. 2018. "Anurans of the Tanintharyi Region, Myanmar: a preview of increasing species diversity." Alytes, 36, (1–4) 266–275.
• Connette, Grant M., Oswald, Patrick, Thura, Myint Kyaw, LaJeunesse Connette, Katherine J., Grindley, Mark E., Songer, Melissa A., Zug, George R., and Mulcahy, Daniel G. 2017. "Rapid forest clearing in a Myanmar proposed national park threatens two newly discovered species of geckos (Gekkonidae: Cyrtodactylus)." PLOS ONE, 12, (4) 1–18. https://doi.org/10.1371/journal.pone.0174432.
• Deichmann, Jessica L., Mulcahy, Daniel G., Vanthomme, Hadrien, Tobi, Elie, Wynn, Addison H., Zimkus, Breda M., and McDiarmid, Roy W. 2017. "How many species and under what names? Using DNA barcoding and GenBank data for west Central African amphibian conservation." PLOS ONE, 12, (11). https://doi.org/10.1371/journal.pone.0187283.
• Mulcahy, Daniel G., Lee, Justin L., Miller, Aryeh H., and Zug, George R. 2017. "Troublesome Trimes: Potential cryptic speciation of the Trimeresurus (Popeia) popeiorum complex (Serpentes: Crotalidae) around the Isthmus of Kra (Myanmar and Thailand)." Zootaxa, 4347, (2) 301–315. https://doi.org/10.11646/zootaxa.4347.2.6.
• Myers, Edward A., Burgoon, Jamie L., Ray, Julie M., Martínez-Gómez, Juan E., Matías-Ferrer, Noemí, Mulcahy, Daniel G., and Burbrink, Frank T. 2017. "Coalescent Species Tree Inference of Coluber and Masticophis." Copeia, 105, (4) 642–650. https://doi.org/10.1643/CH-16-552.
• Zug, George R., Mulcahy, Daniel G., and Vindum, Jens V. 2017. "Resurrection of Bronchocela burmana Blanford, 1878 for the Green Crested Lizard (Squamata, Agamidae) of southern Myanmar." ZooKeys, 657 141–156. https://doi.org/10.3897/zookeys.657.11600.
• Zúñiga, Jose D., Gostel, Morgan R., Mulcahy, Daniel G., Barker, Katharine, Hill, Asia, Sedaghatpour, Maryam, Vo, Samantha Q., Funk, Vicki Ann, and Coddington, Jonathan A. 2017. "Data Release: DNA barcodes of plant species collected for the Global Genome Initiative for Gardens Program, National Museum of Natural History, Smithsonian Institution." PhytoKeys, 88 119–122. https://doi.org/10.3897/phytokeys.88.14607.
• Jezkova, Tereza, Jaeger, Jef R., Oláh-Hemmings, Viktória, Jones, K. B., Lara-Resendiz, Rafael, Mulcahy, Daniel G., and Riddle, Brett R. 2016. "Range and niche shifts in response to past climate change in the desert horned lizard Phrynosoma platyrhinos." Ecography, 39, (5) 437–448. https://doi.org/10.1111/ecog.01464.
• Lee, Justin L., Thompson, Adrian, and Mulcahy, Daniel G. 2016. "Relationships between Numbers of Vertebrae, Scale Counts, and Body Size, with Implications for Taxonomy in Nightsnakes (Genus: Hypsiglena)." Journal of Herpetology, 50, (4) 616–620. https://doi.org/10.1670/15-066.
• Mulcahy, Daniel G., Macdonald, Kenneth S., Brady, Seán G., Meyer, Christopher, Barker, Katharine B., and Coddington, Jonathan. 2016. "Greater than X kb: a quantitative assessment of preservation conditions on genomic DNA quality, and a proposed standard for genome-quality DNA." PeerJ, 4 e2528. https://doi.org/10.7717/peerj.2528.
• Schachat, Sandra R., Mulcahy, Daniel G., and Mendelson, Joseph R., III. 2016. "Conservation threats and the phylogenetic utility of IUCN Red List rankings in Incilius toads." Conservation Biology, 30, (1) 72–81. https://doi.org/10.1111/cobi.12567.
• Lee, Justin L., Myint, Kyaw Thura, Mulcahy, Daniel G., and Zug, George R. 2015. "Three Colubrid Snakes New To Myanmar." Herpetology Notes, 8 217–220.
• Reeder, Tod W., Townsend, Ted M., Mulcahy, Daniel G., Noonan, Brice P., Wood, Perry L., Sites, Jack W., and Wiens, John J. 2015. "Integrated Analyses Resolve Conflicts over Squamate Reptile Phylogeny and Reveal Unexpected Placements for Fossil Taxa." PloS One, 10, (3). https://doi.org/10.1371/journal.pone.0118199.
• Mulcahy, Daniel G., Martínez-Gómez, Juan E., Aguirre-León, Gustavo, Cervantes-Pasqualli, Juan, and Zug, George R. 2014. "Rediscovery of an Endemic Vertebrate from the Remote Islas Revillagigedo in the Eastern Pacific Ocean: The Clarión Nightsnake Lost and Found." PLoS ONE, 9, (5) 1–8. https://doi.org/10.1371/journal.pone.0097682.
• Weisrock, David W., Macey, J. R., Matsui, Masafumi, and Mulcahy, Daniel G. 2013. "Molecular phylogenetic reconstruction of the endemic Asian salamander family Hynobiidae (Amphibia, Caudata)." Zootaxa, 3626, (1) 77. https://doi.org/10.11646/zootaxa.3626.1.3.
• Avila-Pires, Teresa, Mulcahy, Daniel G., Werneck, Fernanda P., and Sites, Jack W. 2012. "Phylogeography of the Teiid Lizard Kentropyx calcarata and the Sphaerodactylid Gonatodes humeralis (Reptilia: Squamata): Testing A Geological Scenario for the Lower Amazon-Tocantins Basins, Amazonia, Brazil." Herpetologica, 68, (2) 272–287. https://doi.org/10.1655/HERPETOLOGICA-D-11-00021.1.
• Mendelson, Joseph R., III, Mulcahy, Daniel G., Snell, Sara, Acevedo, Manuel E., and Campbell, Jonathan A. 2012. "A New Golden Toad (Bufonidae: Incilius) from Northwestern Guatemala and Chiapas, Mexico." Journal of Herpetology, 46, (4) 473–479. https://doi.org/10.1670/11-140.
• Mulcahy, Daniel G., Noonan, Brice P., Moss, Travis, Townsend, Ted M., Reeder, Tod W., Sites, Jack W., Jr., and Wiens, John J. 2012. "Estimating divergence dates and evaluating dating methods using phylogenomic and mitochondrial data in squamate reptiles." Molecular phylogenetics and evolution, 65, (3) 974–991. https://doi.org/10.1016/j.ympev.2012.08.018.
• Wiens, John J., Hutter, Carl R., Mulcahy, Daniel G., Noonan, Brice P., Townsend, Ted M., Sites, Jack W., Jr., and Reeder, Tod W. 2012. "Resolving the phylogeny of lizards and snakes (Squamata) with extensive sampling of genes and species." Biology Letters, 8, (6) 1043–1046. https://doi.org/10.1098/rsbl.2012.0703.
• Heideman, Neil J. L., Mulcahy, Daniel G., Sites, Jack W., Hendricks, Martin G. J., and Daniels, Savel R. 2011. "Cryptic diversity and morphological convergence in threatened species of fossorial skinks in the genus Scelotes (Squamata: Scincidae) from the Western Cape Coast of South Africa: Implications for species boundaries, digit reduction and conservation." Molecular phylogenetics and evolution, 61, (3) 823–833. https://doi.org/10.1016/j.ympev.2011.08.021.
• Mendelson, Joseph R., III, Mulcahy, Daniel G., Williams, Tyler S., and Sites, Jr,Jack W. 2011. "A Phylogeny and Evolutionary Natural History of Mesoamerican Toads (Anura: Bufonidae: Incilius), based on morphology, life history, and molecular data." Zootaxa, 3138 1–34. https://doi.org/10.11646/zootaxa.3138.1.1.
• Mulcahy, Daniel G., Beckstead, Thomas H., and Sites, Jack W., Jr. 2011. "Molecular Systematics of the Leptodeirini (Colubroidea: Dipsadidae) Revisited: Species-tree Analyses and Multi-locus Data." Copeia, (3) 407–417. https://doi.org/10.1643/CH-10-058.
• Swei, Andrea, Rowley, Jodi J. L., Rödder, Dennis, Diesmos, Mae L. L., Diesmos, Arvin C., Briggs, Cheryl J., Brown, Rafe, Cao, Trung Tien, Cheng, Tina L., Chong, Rebecca A., Han, Ben, Hero, Jean-Marc, Hoang, Huy Duc, Kusrini, Mirza D., Le Duong, Thi Thuy, McGuire, Jimmy A., Meegaskumbura, Madhava, Min, Mi-Sook, Mulcahy, Daniel G., Neang, Thy, Phimmachak, Somphouthone, Rao, Ding-Qi, Reeder, Natalie M., Schoville, Sean D., Sivongxay, Niane et al. 2011. "Is Chytridiomycosis an Emerging Infectious Disease in Asia?" PLoS ONE, 6, (8) 1–9. https://doi.org/10.1371/journal.pone.0023179.
• Townsend, Ted M., Mulcahy, Daniel G., Noonan, Brice P., Sites, Jack W., Kuczynski, Caitlin A., Wiens, John J., and Reeder, Tod W. 2011. "Phylogeny of iguanian lizards inferred from 29 nuclear loci, and a comparison of concatenated and species-tree approaches for an ancient, rapid radiation." Molecular phylogenetics and evolution, 61, (2) 363–380. https://doi.org/10.1016/j.ympev.2011.07.008.
• Mendelson, Joseph R., III and Mulcahy, Daniel G. 2010. "A new species of toad (Bufonidae: Incilius) from central Panama." Zootaxa, (2396) 61–68.
• Reyes-Velasco, Jacobo and Mulcahy, Daniel G. 2010. "Additional Taxonomic Remarks on the Genus Pseudoleptodeira (Serpentes: Colubridae) and the Phylogenetic Placement of "P. Uribei"." Herpetologica, 66, (1) 99–110. https://doi.org/10.1655/09-019.1.
• Wiens, John J., Kuczynski, Caitlin A., Townsend, Ted M., Reeder, Tod W., Mulcahy, Daniel G., and Sites, Jack W., Jr. 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. https://doi.org/10.1093/sysbio/syq048.

Book

• Zug, George R. and Mulcahy, Daniel G. 2020. Identification Guide Amphibians & Reptiles of South Tanintharyi. Yangon: Fauna & Flora International.