Available via license: CC BY 4.0
Content may be subject to copyright.
Supplementary Material for the paper:
Phylogenomic history of enigmatic pygmy perches:
implications for biogeography, taxonomy and
conservation
Table S1: Divergence estimates and mutation rates for all major nodes of the pygmy perch
phylogeny using r8s and constraining the node NP with the formation of the Nullarbor Plain as a
barrier to dispersal 14-16 Mamya. Nodes are listed and shown within Figure 2 for simplicity, with
E/W divergence events listed here (mixed specifies downstream lineages containing both
geographies). Divergences were estimated using the penalized-likelihood (PL) method under the
truncated Newton [64] algorithm. Rates are estimated in substitutions per site per million years,
with the estimated rate for the entire tree and the local rate done for only the relevant branch point.
Confidence intervals of estimations were estimated using 100 independent RRHS trees, with the
means and standard deviation of nodes reported here. CI = confidence interval.
Node Geography
of resultant
branches
MCC
estimated
age
(Mamya)
Mean
RRHS
estimated
age
RRHS
standard
deviation
of
estimated
ages
Estimated
rate
Local rate Mean divergence
estimate (Mamyr)
from Unmack et al.
(2011) [95% CI]
Root West/Mixed 46.71 - - -- -- 41.8 [27.7-56.3]
BalRoot West/Mixed 20.76 22.97 0.09 9.66E-04 2.80E-03 26.9 [20.8-34.1]
VarRoot East/Mixed 18.81 20.08 0.05 9.67E-04 2.26E-03 21.3 [17.0-26.6]
NP East/West 16.00 16.00 0.00 9.67E-04 1.89E-03 15.9 [14.1-19.1]
VitPair West 9.27 9.07 0.02 9.67E-04 9.80E-04 9.6 [6.3-13.0]
VitB West 3.35 3.22 0.01 9.67E-04 7.96E-04 -
VitAPyg West 4.00 3.87 0.01 9.67E-04 1.15E-03 -
EasRoot East 13.04 12.87 0.01 9.67E-04 1.89E-03 12.3 [9.4-15.6]
NoxRoot East 12.06 11.87 0.01 9.67E-04 1.80E-03 11.2 [8.2-14.6]
AusRoot East 6.07 5.84 0.02 9.67E-04 1.06E-03 4.05 [2.3-5.9]
Figure S1: Phylogenetic tree of pygmy perches based on the strict dataset of 4,381 ddRAD loci, rooted using Bostockia porosa. Branch lengths were estimated using RAxML
under the GTRGAMMA model of evolution for maximum likelihood (ML) and PhyloBayes under the CAT model of evolution for Bayesian analysis. ML bootstrap values are
based on 1,000 replicates (left) and Bayesian posterior probabilities estimated every 10 samples with the first 200 trees discarded as burn-in (right). Node support values are
shown for all major species and population divisions. Lineages in parentheses represent species groups used for further species delimitation analysis in BPP, with their
geographic location specified in the tree. Codes for individuals and localities relate to the abbreviations in Table 1.
Figure S2: Maximum likelihood tree of pygmy perches based on the relaxed dataset of 13, 991 ddRAD loci, rooted using Bostockia porosa. Branch lengths were estimated
using RAxML under the GTRGAMMA model of evolution. Bootstrap values are based on 1, 000 replicates, with values shown for all major species and population divisions.
Lineages in parentheses represent species groups used for further species delimitation analysis in BPP, with their geographic location specified in the tree. Codes for
individuals and localities relate to the abbreviations in Table 1.