Comprehensive phylogenomic reconstruction of Ameerega (Anura: Dendrobatidae) and introduction of a new method for phylogenetic niche modeling

• Main Author: Guillory, Wilson
• Format: Others
• Published: OpenSIUC 2020
• Subjects: amphibians; ancestral state reconstruction; biogeography; niche modeling; phylogenetics; systematics
• Online Access: https://opensiuc.lib.siu.edu/theses/2654; https://opensiuc.lib.siu.edu/cgi/viewcontent.cgi?article=3668&context=theses

To understand present patterns of biodiversity, knowledge of a lineage’s past – both evolutionary and geographic – is required. Here I present the first comprehensive phylogenomic study of an Amazonian poison frog genus, Ameerega, as well as the introduction of a new method for characterizing ancestral distributions via phylogenetic niche modeling, which I use to investigate Ameerega’s biogeographic past. I sequenced thousands of ultraconserved elements from over 100 tissue samples, representing almost every described Ameerega species, as well as undescribed cryptic diversity. My phylogenetic inference diverged strongly from those of previous studies. I also introduce a new phylogenetic niche modeling method, which accounts for issues of bias in other methods by incorporating knowledge of evolutionary relationships into niche models. Given modern-day and paleoclimatic data, species occurrence data, and a time-calibrated phylogeny, my method constructs niche models for each extant taxon, uses ancestral character estimation to reconstruct ancestral niche models, and projects these models into paleoclimate data to provide a historical estimate of the geographic range of a lineage. I demonstrate my method on the Ameerega bassleri group. I also use simulations to show that my method can reliably reconstruct the niche of a known ancestor in both geographic and environmental space.