Abstract Detail

Phylogenomics

Maya Lastra, Carlos Alonso [1], Hoffberg, Sandra [2], Landis, Henry [3], Eaton, Deren [4], Landis, Michael [5].

SuperBPP: a new method for inferring large-scale time-calibrated species trees.

Estimating the time of divergence between species is central to understanding evolution. However, it is difficult to infer time-calibrated trees for young plant radiations that lack fossil calibrations. Current approaches typically infer trees from concatenated genetic sequence data under a relaxed molecular clock model (e.g., BEAST), or transform branch lengths with a relaxed-clock model after tree inference (e.g., penalized likelihood). However, branch lengths from concatenated sequences are known to harbor consistent biases from incomplete lineage sorting (ILS). Multi-species coalescent (MSC) methods can infer more accurate node age estimates from multi-locus sequence data, but scale poorly to large trees. Here we introduce SuperBPP, a distributed framework for iteratively performing MSC-based node age estimation over large species trees. This new software samples subtrees from larger phylogenies sequentially from the root to tips and infers ancestral node ages using multi-locus sequences, which inform priors on subsequently younger nodes. SuperBPP has the advantage over previous methods that it allows users to estimate dates for every node and can accommodate trees with more taxa. Based on empirical and simulated study cases, SuperBPP is a fast and reliable alternative to concatenated analysis, even without fossil information, to estimate clade ages based on estimated mutation rates and generation times, capable of processing trees with >40 taxa (including multiple individuals per taxon) in a matter of hours.

1 - Columbia University, Ecology, Evolution and Environmental Biology Department, 10th floor Schermerhorn Ext., 1200 Amsterdam Avenue, New York, NY, 10027, USA
2 - Columbia University, E3B, 1200 Amsterdam Ave, Schermerhorn Ext, 10th Floor, New York, NY, 10027, United States
3 - Columbia University, Ecology, Evolution and Environmental Biology, 1200 Amsterdam Avenue, 10th Floor Schermerhorn EXT, New York, NY, 10027, United States
4 - Columbia University, Ecology, Evolution, And Environmental Biology, 1200 Amsterdam Ave. , Schermerhorn Ext. Office 1007, New York, NY, 10027, United States
5 - Washington University, St Louis, MO, USA

Keywords:
multispecies  coalescent model
Divergence time
species tree.

Presentation Type: Oral Paper
Session: PHYLOV, Phylogenomics V
Location: Virtual/Virtual
Date: Friday, July 23rd, 2021
Time: 3:00 PM(EDT)
Number: PHYLOV001
Abstract ID:868
Candidate for Awards:None