Ancestral niche reconstruction using bins
Our new package, nichevol, contains tools for performing ancestral state reconstructions on binned datasets using two methods: maximum parsimony (as implemented in castor v.1.4.3; Louca and Doebeli 2018) and maximum likelihood (as implemented in apev.5.3; Paradis and Schliep 2018). For each algorithm, ancestral state reconstructions are first performed for each bin separately, treating bin scores as discrete characters under an equal transition rate model. The results are then smoothed such that the reconstructed ancestral niche at each node is uninterrupted by “unsuitable” scores, again following the assumption of a unimodal response to environmental conditions (Maguire, 1973). This smoothing algorithm also adjusts reconstructions to account for the evolutionary non-independence of single bins. As a simple illustration of how this analysis works, we simulated data for a scenario in which there was a shift from the ancestral warm niche to the cool niche took place, to demonstrate the ability of our new methods to identify instances of niche evolution. To this end, we generated a single, 6-taxon stochastic birth-death tree (birth rate = 1, death rate = 0), and assigned simulated niche characterizations from the warm niche group to tips in the tree (“t1”, “t2”, “t3”, and “t6”). The remaining monophyletic clade of tips in the tree (“t4” and “t5”) were assigned simulated niche characterizations from the cool niche simulation group. We then performed parsimony and likelihood ancestral state reconstructions on binned niche characterizations as described above.
We note that we have kept these initial explorations simple for the purpose of illustration—many improvements could be made to this methodology, such as implementing different evolutionary models (e.g. Ornstein-Uhlenbeck), Bayesian approaches in inferring ancestral character states, and consideration of joint effects of environmental dimensions (e.g. temperature, precipitation) that are here considered independently. Furthermore, phylogenetic comparative methods are notoriously “data-hungry”, and our proposed ancestral character inference strategy will benefit from further detailed simulation-based examinations in the future. Our purpose overall was to illustrate the crucial importance of explicit incorporation of uncertainty in these analyses of climate niche evolution. Code for analyses can be found in Supplement 5; further explanation and illustration can be found in annotated code with tables and figures provided as an HTML document in Supplement 6.