Fast likelihood calculation for multivariate Gaussian phylogenetic models with shifts

Venelin Mitov, Krzysztof Bartoszek, Georgios Asimomitis and Tanja Stadler

Theoretical Population Biology, 2020, vol. 131, issue C, 66-78

Abstract: Phylogenetic comparative methods (PCMs) have been used to study the evolution of quantitative traits in various groups of organisms, ranging from micro-organisms to animal and plant species. A common approach has been to assume a Gaussian phylogenetic model for the trait evolution along the tree, such as a branching Brownian motion (BM) or an Ornstein–Uhlenbeck (OU) process. Then, the parameters of the process have been inferred based on a given tree and trait data for the sampled species. At the heart of this inference lie multiple calculations of the model likelihood, that is, the probability density of the observed trait data, conditional on the model parameters and the tree. With the increasing availability of big phylogenetic trees, spanning hundreds to several thousand sampled species, this approach is facing a two-fold challenge. First, the assumption of a single Gaussian process governing the entire tree is not adequate in the presence of heterogeneous evolutionary forces acting in different parts of the tree. Second, big trees present a computational challenge, due to the time and memory complexity of the model likelihood calculation.

Keywords: Pruning; Drift; Selection; Punctuated equilibrium; Lévy process; Jumps (search for similar items in EconPapers)
Date: 2020
References: View complete reference list from CitEc
Citations:

Downloads: (external link)
http://www.sciencedirect.com/science/article/pii/S0040580919301947
Full text for ScienceDirect subscribers only

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:eee:thpobi:v:131:y:2020:i:c:p:66-78

DOI: 10.1016/j.tpb.2019.11.005

Access Statistics for this article

Theoretical Population Biology is currently edited by Jeremy Van Cleve

More articles in Theoretical Population Biology from Elsevier
Bibliographic data for series maintained by Catherine Liu ().