mammal_arboreality

R code for reconstructing the evolution of mammal arboreality

Ecological selectivity and the evolution of mammalian substrate preference across the K–Pg boundary

Accepted for publication at Ecology and Evolution, August 2021 DOI NA

Jonathan J. Hughes (1,ƛ,%), Jacob S. Berv (1,2,3,ƛ,@), Stephen G. B. Chester (4,5,6), Eric J. Sargis (7,8,9), Daniel J. Field (9,10,11,%)

1. Department of Ecology & Evolutionary Biology, Cornell University, Ithaca, NY, USA
2. Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
3. University of Michigan Museum of Paleontology, University of Michigan, Ann Arbor, MI, USA
4. Department of Anthropology, Brooklyn College, City University of New York, Brooklyn, NY, USA
5. Department of Anthropology, The Graduate Center, City University of New York, New York, NY, USA
6. New York Consortium in Evolutionary Primatology, New York, NY, USA
7. Department of Anthropology, Yale University, New Haven, CT, USA
8. Divisions of Vertebrate Paleontology and Vertebrate Zoology, Yale Peabody Museum of Natural History, New Haven, CT, USA
9. Yale Institute for Biospheric Studies, New Haven, CT, USA
10. Department of Earth Sciences, University of Cambridge, Cambridge, UK
11. Museum of Zoology, University of Cambridge, UK

ƛAuthors contributed equally

%Authors for correspondence: jjh359@cornell.edu; djf70@cam.ac.uk

@Code author: jsb439@cornell.edu

Summary of contents:

Meredith_2011.R and Upham_2019.R are respectively, R scripts for producing analyses of ancestral ecologies using the Meredith et al 2011 and Upham et al 2019 consensus topologies. In the case of Upham et al 2019, additional analyses are performed on a sample of 1000 posterior trees. These primary scripts rely on and source functions contained within rate_through_time.R, helpers.R, and simmap_parallel.R R documents. These will eventually be implemented in a separate R package.

mammal_data_v2 is the dataset used for reconstructions on the Meredith_2011 topology. mammal_data_v2_upham is the dataset used for reconstructions on the Upham_2019 topology.

Analysis output files are deposited inside analyses_out