Papers
This page summarizes papers and associated research projects coming out of our group. Every entry has a link to the paper as a pdf, while many entries also have links to video recordings of talks, blog posts, analysis code, tutorials, and/or sites.
2024
SW McHugh, MJ Donoghue, MJ Landis. 2024. A phylogenetic model of established and enabled biome shifts. bioRxiv 2024.08.30.610561.
[paper]
MJ Landis, A Thompson. 2024. phyddle: software for phylogenetic model exploration with deep learning.
[paper] [code] [site]
FHK Mendes, MJ Landis. 2024. PhyloJunction: a computational framework for simulating, developing, and teaching evolutionary models. Accepted in Systematic Biology.
[paper] [code] [site]
AC Soewongsono, MJ Landis. 2024. A diffusion-based approach for simulating forward-in-time state-dependent speciation and extinction dynamics. Bulletin of Mathematical Biology 86:101.
[paper]
A Thompson, B Liebeskind, EJ Scully, MJ Landis. 2024. Deep learning and likelihood approaches for viral phylogeography converge on the same answers whether the inference model is right or wrong. Systematic Biology 73:183-206.
[paper] [video]
2023
SK Swiston, MJ Landis. 2023. Testing relationships between multiple regional features and biogeographic processes of speciation, extinction, and dispersal. bioRxiv 2023.06.19.545613.
[paper] [tutorial]
AY Kawahara, C Storer, APS Carvalho, DM Plotkin, F Condamine, MP Braga, et al. [MJ Landis among 89 co-authors] 2023. Evolution and diversification dynamics of butterflies. Nature Ecology and Evolution doi:10.1038/s41559-023-02041-9.
[paper]
I Quintero, MJ Landis, W Jetz, H Morlon. 2023. The build-up of the present-day tropical diversity of tetrapods. Proceedings of the National Academy of Sciences 120: e2220672120.
[paper]
NS Upham, MJ Landis. 2023. Genomics expands the mammalverse. Science 380:358-359.
[paper]
SV Nielsen, AH Vaughn, K Leppala, MJ Landis, T Mailund, R Nielsen. 2023. Bayesian inference of admixture graphs on Native American and Arctic populations. PLOS Genetics 19:e1010410.
[paper]
2022
W Dismukes, MP Braga, DH Hembry, TA Heath, MJ Landis. Cophylogenetic methods to untangle the evolutionary history of ecological interactions. Annual Reviews of Ecology and Evolution 53:275-298.
[paper]
MJ Donoghue, DAR Eaton, CA Maya-Lastra, MJ Landis, PW Sweeney, ME Olson, NI Cacho, MK Moeglin, JR Gardner, NM Heaphy, M Castorena, A Segovia Rivas, WL Clement, EJ Edwards. 2022. Replicated radiation of a plant clade along a cloud forest archipelago. Nature Ecology and Evolution doi:10.1038/s41559-022-01823-x.
[paper]
J Barido-Sottani, JA Justison, R Borges, JM Brown, W Dismukes, B do Rosario Petrucci, L Guimarães, Fabreti, S Höhna, MJ Landis, PO Lewis, MR May, FK Mendes, W Pett, BD Redelings, CM Tribble, AM Wright, R Zenil-Ferguson, TA Heath. 2022. Lessons learned from organizing and teaching virtual phylogenetics workshops. Bulletin of the Society of Systematic Biologists 10.18061/bssb.v1i2.
[paper]
EW Wendt, LR Malabarba, MP Braga, WA Boeger, MJ Landis, TP Carvalho. 2022. Phylogeny, species delimitation, and ecological and morphological diversity of Characithecium (Monogenoidea: Dactylogyridae). Parasitology 149:700-716.
[paper]
MJ Landis, I Quintero, MM Muñoz, F Zapata, MJ Donoghue. 2022. Phylogenetic inference of where species spread or split
across barriers. Proceedings of the National Academy of Sciences 119: e2116948119.
[paper] [video] [blog] [code] [tutorial]
CM Tribble, WA Freyman, JY Lim, MJ Landis, J Barido-Sottani, BJ Kopperud, S Höhna, MR May. 2022. RevGadgets: an R Package for visualizing Bayesian phylogenetic analyses from RevBayes. Methods in Ecology and Evolution 13:314-323.
[paper] [code]
2021
S Höhna, MJ Landis, JP Huelsenbeck. 2021. Parallel power posterior analyses for fast computation of marginal likelihoods in phylogenetics. PeerJ 9:e12438.
[paper]
MP Braga, N Janz, S Nylin, F Ronquist, MJ Landis. 2021. Phylogenetic reconstruction of ancestral ecological networks through time for pierid butterflies and their host plants. Ecology Letters 24: 2134-2145.
[paper] [video] [code]
MJ Landis, EJ Edwards, MJ Donoghue. 2021. Modeling phylogenetic biome shifts on a planet with a past. Systematic Biology 70: 86-107.
[paper] [video] [code]
MJ Landis, DAR Eaton, WL Clement, B Park, EL Spriggs, PW Sweeney, EJ Edwards, MJ Donoghue. 2021. Joint phylogenetic estimation of geographic movements and biome shifts during the global diversification of Viburnum. Systematic Biology 70: 67-85.
[paper] [video] [code]
2020
MJ Landis. 2020. “Biogeographic dating of phylogenetic divergence times using priors and processes” (pp 135-155) in The Molecular Evolutionary Clock: Theory and Practice (SYW Ho, ed.). Springer.
[paper]
AS Kim, O Zimmerman, JM Fox, CA Nelson, K Basore, R Zhang, L Durnell, C Desai, C Bullock, SL Deem, J Oppenheimer, B Shapiro, T Wang, S Cherry, CB Coyne, SA Handley, MJ Landis (+), DH Fremont (+), MS Diamond (+). 2020. An evolutionary insertion in the Mxra8 receptor binding site confers resistance to alphavirus infection and pathogenesis. Cell Host & Microbe 27:428-440.
[paper]
MP Braga, MJ Landis, S Nylin, N Janz, F Ronquist. 2020. Bayesian inference of ancestral host-parasite interactions under a phylogenetic model of host repertoire evolution. Systematic Biology 69: 1149-1162.
[paper] [video] [tutorial]
I Quintero, MJ Landis 2020. Interdependent phenotypic and biogeographic evolution driven by biotic interactions. Systematic Biology 69: 739-755.
[paper] [video] [code]
before 2020
DJ Field, JS Berv, AY Hsiang, R Lanfear, MJ Landis, A Dornburg. 2019. Timing the extant avian radiation: The rise of modern birds, and the importance of modeling molecular rate variation. Bulletin of the American Natural History Museum 440: 159-181
[paper]
MJ Landis, WA Freyman, BG Baldwin. 2018. Retracing the silversword radiation despite phylogenetic, biogeographic, and paleogeographic uncertainty. Evolution, 72: 2343-2359.
[paper] [video]
[code] [tutorial]
B Park, M Sinnott-Armstrong, C Schlutius, JC Zuluaga, EL Spriggs, RG Simpson, E Benavides, MJ Landis, PW Sweeney, DAR Eaton, MJ Donoghue. 2018. Sterile marginal flowers increase visitation and fruit set in the hobblebush (Viburnum lantanoides, Adoxaceae) at multiple spatial scales. Annals of Botany, 123: 381-390.
MJ Landis, JG Schraiber. 2017. Pulsed evolution shaped modern vertebrate body sizes. Proceedings of the National Academy of Sciences, 114: 13224-13229.
[paper] [video] [news] [code]
MJ Landis. 2017. Biogeographic dating of speciation times using paleogeographically informed processes. Systematic Biology, 66: 128-144.
[paper] [video] [code]
S Höhna, MJ Landis, TA Heath. 2017. Phylogenetic Inference Using RevBayes. Current Protocols in Bioinformatics, 57: 6.16-6.16.34.
[paper]
S Höhna, MJ Landis, TA Heath, B Boussau, N Lartillot, BR Moore, JP Huelsenbeck, F Ronquist. 2016. RevBayes: Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language. Systematic Biology, 65: 726-736.
[paper] [code]
JG Schraiber, MJ Landis. 2015. Sensitivity of quantitative traits to mutational effects and number of loci. Theoretical Population Biology, 102:85-93.
[paper] [code]
S Höhna, TA Heath, B Boussau, MJ Landis, F Ronquist, JP Huelsenbeck. 2014. Probabilistic graphical model representation in phylogenetics. Systematic Biology, 63: 753-771.
[paper]
MJ Landis, T Bedford. 2014. Phylowood: interactive web-based animations of biogeographic and phylogeographic histories. Bioinformatics, 30: 123-124.
[paper] [code]
MJ Landis, NJ Matzke, BR Moore, JP Huelsenbeck. 2013. Bayesian Analysis of Biogeography when the Number of Areas is Large. Systematic Biology, 62: 789-804.
[paper] [code]
MJ Landis(*), JG Schraiber (*), M Liang. 2013. Phylogenetic Analysis Using Lévy Processes: Finding Jumps in the Evolution of Continuous Traits. Systematic Biology, 62: 193-204.
[paper] [code]
work from lab in bold; (*) shared first authorship; (+) shared corresponding authorship