* co-first authors; + mentored undergraduate

In Review

Mishra, Sarthak, Megan L. Smith, and Matthew W. Hahn. 2023. reconcILS: A gene tree-species tree reconciliation algorithm that allows for incomplete lineage sorting. In Review. Preprint available on bioRxiv. DOI: 10.1101/2023.11.03.565544. Web.

Smith, Megan L. and Matthew W. Hahn. 2023. Selection leads to false inferences of introgression using popular methods. In Review. Preprint available on bioRxiv. DOI: 10.1101/2023.10.27.564394. Web.

Mu, Yu K., Matthew W. Hahn, and Megan L. Smith. 2023. Application of machine learning in phylogenetics. In Review. Preprint available on EcoEvoRxiv. DOI: 10.32942/X2XG7G. Web.

2023

Smith, Megan L. and Matthew W. Hahn. 2023. Phylogenetic inference using Generative Adversarial Networks. Bioinformatics 39(9): btad543. Web.

Smith, Megan L., Connor Lang+, David Sneddon+, Jessica Wallace+, Anahí Espíndola, Jack Sullivan, and Bryan C. Carstens. Comparative phylogeography of microsnails from the Pacific Northwest. Northwest Science 96(1-2): 117-132.

Arantes, Ísis C., Mariana M. Vasoncellos, Megan L. Smith, Ryan C. Garrick, Guarino R. Colli, and Brice P. Noonan. 2023. Species limits and diversification of the Dendropsophus rubicundulus subgroup (Anura, Hylidae) in Neotropical savannas. Molecular Phylogenetics and Evolution 186: 107843.

Glon, Heather, Vreni Häussermann, Paul E. Brewin, Paul Brickle, Sunsik Kong, Megan L. Smith, and Marymegan Daly. 2023. There and back again: The unexpected journeys of Metridium de Blainville, 1824 between the Old Oceans and throughout the Modern World. The Biological Bulletin 244(1): 9-24.

2022

Smith, Megan L., Jessica Wallace, David C. Tank, Jack Sullivan, and Bryan C. Carstens. The role of multiple Pleistocene refugia in promoting diversification in the Pacific Northwest.. Molecular Ecology 31(16): 4402-4416. Web. PDF.

Fonseca, Emanuel M., Drew J. Duckett, Filipe G. Almeida, Megan L. Smith, Maria Tereza C. Thomé, and Bryan C. Carstens. Assessing model adequacy or Bayesian Skyline Plots using posterior predictive simulations. PLoS ONE 17(7): e0269438. Web. PDF.

Smith, Megan L., Dan Vanderpool, and Matthew W. Hahn. 2022. Using all gene families vastly expands data available for phylogenomic inference. Molecular Biology and Evolution 39(6): msac112. Web. PDF.

Ruffley, Megan, Megan L. Smith, Anahí Espindola, Daniel Turck, Niels Mithcell, Bryan Carstens, Jack Sullivan, and David C. Tank. Genomic evidence of an ancient inland temperate rainforest. Molecular Ecology. 31(10): 2985-3001 Web. PDF.

Smith, Megan L. and Matthew W. Hahn. 2022. The frequency and topology of pseudoorthologs. Systematic Biology. 71(3): 649-659. Web. PDF.

Carstens, Bryan C., Megan L. Smith, Emanuel M. Fonseca, and Maria Tereza C. Thomé. 2022. Assessing model adequacy leads to more robust phylogeographic inference. Trends in Ecology and Evolution. 37(5): 402-410. Web. PDF.

Yan, Zhi*, Megan L. Smith*, Peng Du, Matthew W. Hahn and Luay Nakhleh. 2022. Species tree inference on data with paralogs is accurate using methods intended to deal with incomplete lineage sorting. Systematic Biology. 71(2): 367- 381. Web. PDF.

2021

Fountain-Jones, Nicholas M., Megan L. Smith, and Frédéric Austerlitz. 2021. Machine learning in molecular ecology. Molecular Ecology Resources, 21(8): 2589-2597. Web. PDF.

Smith, Megan L. and Bryan C. Carstens. In Press. Species delimitation using molecular data. In Species and Beyond. Edited by John S. Wilkins, Frank E. Zachos, and Igor Ya Pavlinov. Taylor & Francis Group: Boca Raton, FL. PDF.

Warwick, Alexa R., Lisa N. Barrow, Megan L. Smith, D. Bruce Means, Alan R. Lemmon, and Emily Moriarty Lemon. 2021. Signatures of north-eastern expansion and multiple refugia: genomic phylogeography of the Pine Barrens tree frog, Hyla andersonii (Anura: Hylidae). Biological Journal of the Linnean Society, 133(1): 120-134. Web. PDF.

Smith, Megan L. and Matthew W. Hahn. 2021. New approaches for inferring phylogenies in the presence of paralogs. Trends in Genetics, 37(2): 174-187. Web. PDF.

Marden, Emily, et al. 2021. Sharing and reporting benefits from biodiversity research. Molecular Ecology, 30(5): 1103-1107. Web. PDF.

2020

Lado, Paula, Megan L. Smith, Bryan Carstens, and Hans Klompen. 2020. Population genetic structure and demographic history of the lone star tick. Molecular Ecology, 29(15): 2810-2823. Web. PDF.

Colston, Timothy J., Brice P. Noonan, Megan L. Smith, R. Alexander Pyron. 2020. On the availability of recently described Ptychadena (Anura: Ptychadenidae) nomina from Ethiopia. Zootaxa, 4786(2): 289-294. Web. PDF.

Watters, George T., Megan L. Smith, and D.J. Sneddon+. 2020. The subfamily Abbottellinae (Annulariidae): origins, associations, and a review of the Hispaniolan taxa. The Nautilus, 134(1): 1-34. PDF.

Weiringa, Jamin G., Matthew R. Boot, Marcos V. Dantas-Queiroz, Drew Duckett, Emanuel M. Fonseca, Heather Glon, Natalie Hamilton, Sungsik Kong, Flavia M. Lanna, Kali Z. Mattingly, Danielle J. Parsons, Megan L. Smith, Benjamin W. Stone, Coleen Thompson, Lei Zuo, and Bryan C. Carstens. 2020. Does habitat stability structure intraspecific genetic diversity? It’s complicated. Frontiers of Biogeography, 12(2): e45377. Web. PDF.

Smith, Megan L. and Bryan C. Carstens. 2020. Process-based species delimitation leads to identification of more biologically relevant species. Evolution, 74(2): 216-229. Web. PDF.

2019

Rankin, Andrew M., Thomas Wilke, Michael Lucid, William Leonard, Anahí Espíndola, Megan L. Smith, Megan Ruffley, Dave Tank, Bryan C. Carstens, and Jack Sullivan. 2019. Complex interplay of ancient vicariance and recent secondary contact in northwestern North American temperate rainforests. Biological Journal of the Linnean Society, 127(4): 876-889. Web. PDF.

Sullivan, J.*, Megan L. Smith*, Anahí Espíndola, Megan Ruffley, Andrew Rankin, David C. Tank, and Bryan C. Carstens. 2019. Integrating life history traits into predictive phylogeography. Molecular Ecology, 28(8): 2062-2073. Web. PDF.

2018

Smith, Megan L., Megan Ruffley, Andrew M. Rankin, Anahí Espíndola, David C. Tank, Jack Sullivan, and Bryan C. Carstens. 2018. Testing for the presence of cryptic diversity in tail-dropper slugs (Prophysaon) using molecular data. Biological Journal of the Linnean Society, 124(3): 518-532. Web. PDF.

Ruffley, Megan R., Megan L. Smith, Anahí Espíndola, Bryan C. Carstens, David C. Tank, and Jack Sullivan. 2018. Combining allele frequency and tree-based approaches improves phylogeographic inference from natural history collections. Molecular Ecology, 27(4): 1012-1024. Web. PDF.

2017

Smith, Megan L., Megan Ruffley, Anahí Espíndola, David C. Tank, Jack Sullivan, and Bryan C. Carstens. 2017. Demographic model selection using Random Forests and the Site Frequency Spectrum. Molecular Ecology, 26(17): 4562-4573. Web. PDF.

Smith, Megan L., Brice P. Noonan, and Timothy J. Colston. 2017. The role of climatic and geological events in generating diversity in Ethiopian grass frogs (Genus Ptychadena). Royal Society Open Science, 4(8): 170021. Web. PDF.

2016

Espíndola, Anahí, Megan Ruffley, Megan L. Smith, Bryan C. Carstens, David C. Tank, and Jack Sullivan. 2016. Identifying cryptic diversity with predictive phylogeography. Proceedings of the Royal Society B, 283(1841): 20161529. Web. PDF.