10.5061/DRYAD.NR654
Berv, Jacob S.
Cornell University
Field, Daniel J.
University of Bath
Yale University
Data from: Genomic Signature of an Avian Lilliput Effect across the K-PG
Extinction
Dryad
dataset
2017
divergence time
Paleogene
molecular clocks
divergence times
mass extinction
K-Pg
National Science Foundation
https://ror.org/021nxhr62
NSF DEB-1700786
2017-07-07T14:57:01Z
2017-07-07T14:57:01Z
en
https://doi.org/10.1093/sysbio/syx064
302065463 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
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.
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
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