DOI: 10.5061/dryad.nr654
title: Data from: Genomic Signature of an Avian Lilliput Effect across the K-PG Extinction

description: Survivorship following major mass extinctions may be associated with a
 decrease in body size—a phenomenon called the Lilliput Effect. Body size
 is a strong predictor of many life history traits (LHTs), and is known to
 influence demography and intrinsic biological processes. Pronounced
 changes in organismal size throughout Earth history are therefore likely
 to be associated with concomitant genome-wide changes in evolutionary
 rates. Here, we report pronounced heterogeneity in rates of molecular
 evolution (varying up to ~20-fold) across a large-scale avian phylogenomic
 dataset, and show that nucleotide substitution rates are strongly
 correlated with body size and metabolic rate. We also identify potential
 body size reductions associated with the Cretaceous-Paleogene (K-Pg)
 transition, consistent with a Lilliput Effect in the wake of that mass
 extinction event. We posit that selection for reduced body size across the
 K-Pg extinction horizon may have resulted in transient increases in
 substitution rate along the deepest branches of the extant avian tree of
 life. This ‘hidden’ rate acceleration may result in both strict and
 relaxed molecular clocks over-estimating the age of the avian crown group
 through the relationship between life history and demographic parameters
 that scale with molecular substitution rate. If reductions in body size
 (and/or selection for related demographic parameters like short generation
 times) are a common property of lineages surviving mass extinctions, this
 phenomenon may help resolve persistent divergence time debates across the
 tree of life. Furthermore, our results suggest that selection for certain
 life history traits may be associated with deterministic molecular
 evolutionary outcomes.
description: Supplementary Table
 1Life
 history data table formatted for input into the Coevol analytical
 software. Life history data were obtained from the AnAge senescence
 database Build 13 (De Magalhães, J.P. and Costa, J. 2009, Tacutu, R.,
 Craig, T., et al. 2013). We collated the following data: (1) age at sexual
 maturity (days), (2) incubation time (days), (3) number of eggs laid per
 year, (4) mass at hatching (grams), (5) growth rate (1/days), (6), maximum
 recorded longevity (years), and (7) total metabolic rate (watts). Relative
 to the set of 198 avian taxa in (Prum, R.O., Berv, J.S., et al. 2015),
 when matching genera occurred in the AnAge database, we used averages at
 the genus level; otherwise, we used family-level averages. Body mass
 (grams, species average) data were collected from Dunning Jr, J.B. (1992).
 This yielded a data matrix with ~49% missing data overall (with no missing
 data for body mass).SuppTable1.txtSupplementary Table 2Correlation coefficients and posterior probabilities from substitution rate analysis with Coevol 1.4b (partial coefficients summarized in Figure 2 colors). Raw posterior probabilities are reported as ranging from from 0.0 (100% support for a negative correlation) to 1.0 (100% support for a positive correlation). Negative correlations are reported as 1-raw in the main text.SuppTable2.xlsxSupplementary Table 3Data table of estimated crown fossil masses used as body size priors to calibrate ASRs. Mean body mass estimates and associated 95% prediction intervals are derived from published predictive equations (Field, D.J., Lynner, C., et al. 2013). Unless otherwise noted, measurements for these taxa are taken from holotype specimens, and unless otherwise noted, published measurements were used from references noted in the table.SuppTable3.xlsxData File S4We provide as a zip archive the data and script files necessary to reproduce the major analyses in the present work. A detailed readme txt file is included in this zip archive which outlines the analytical procedures needed to replicate the major analyses in the present work.SuppData4.zipSupplementary AppendixSupplementary discussion and analyses, Figures S1-S8, and associated captions.Berv_Field_2017_SupplementaryAppendix.pdf