DOI: 10.5061/dryad.1jwstqjzs
title: Effect of different types of sequence data on palaeognath phylogeny

description: Palaeognathae consists of five groups of extant species: flighted tinamous
 (1) and four flightless groups: kiwi (2), cassowaries and emu (3), rheas
 (4), and ostriches (5). Molecular studies supported the groupings of
 extinct moas with tinamous and ele- phant birds with kiwi as well as
 ostriches as the group that diverged first among the five groups. However,
 phylogenetic re- lationships among the five groups are still
 controversial. Previous studies showed extensive heterogeneity in
 estimated gene tree topologies from conserved nonexonic elements, introns,
 and ultraconserved elements. Using the noncoding loci to- gether with
 protein-coding loci, this study investigated the factors that affected
 gene tree estimation error and the relation- ships among the five groups.
 Using closely related ostrich rather than distantly related chicken as the
 outgroup, concatenated and gene tree–based approaches supported rheas as
 the group that diverged first among groups (1)–(4). Whereas gene tree
 estimation error increased using loci with low sequence divergence and
 short length, topological bias in estimated trees oc- curred using loci
 with high sequence divergence and/or nucleotide composition bias and
 heterogeneity, which more occurred in trees estimated from coding loci
 than noncoding loci. Regarding the relationships of (1)–(4), the site
 patterns by parsimony criterion appeared less susceptible to the bias than
 tree construction assuming stationary time-homogeneous model and sug-
 gested the clustering of kiwi and cassowaries and emu the most likely with
 ∼40% support rather than the clustering of kiwi and rheas and that of kiwi
 and tinamous with 30% support each.
description: Sequence data of Cloutier et al. (2019) and Sackton et al. (2019)
 were downloaded from Dryad Digital Repository. From
 Cloutier et al. (2019)'s data locus data in which branch lengths from
 the common ancestral node of palaeognaths except ostrich were 5 times
 longer than those of concatenated sequences were excluded in introns and
 UCE. From Sackton et al.'s (2019) expanded data,
 loci with all the five groups of palaegnaths [(1) kiwi, (2) cassowary and
 emu, (3) rheas, (4) tinamous and moa, (5) ostrich] and chicken were
 extracted. Loci in which there were long branches to species from the
 common ancestral node of palaeognaths excluding the outgroup ostrich (NCA;
 see fig. 1a) (&gt; 1) and the branch length of a species was 5 times
 longer than those of other species in the same group were also excluded.
 To detect positively selected loci, the likelihood ratio test was carried
 out for site models M1a (nearly neutral) vs. M2a (positive selection) and
 M8 (positive selection) vs. M8a (dN/dS = 1) by using codeml of PAML 4.9j
 (Yang 2007). When at least either of the results of the likelihood ratio
 test and the BEB method was significant at 1% level, the locus was
 excluded. For the remaining loci from Cloutier et al.
 (2019) and Sackton et al. (2019) recombination was detected by using 3SEQ
 version 1.7 build 170612 (Lam et al. 2018). Loci in which recombination
 was detected between any pair of the five groups of paleognaths and
 chicken were excluded. Cloutier A, Sackton TB, Grayson
 P, Clamp M, Baker AJ, Edwards SV. 2019. Whole-genome analyses resolve the
 phylogeny of flightless birds (Palaeognathae) in the Presence of an
 empirical anomaly zone. Syst Biol 68:937-955. Sackton
 TB, Grayson P, Cloutier A, Hu Z, Liu JS, Wheeler NE, Gardner PP, Clarke
 AJ, Baker AJ, Clamp M, Edwards SV. 2019. Convergent regulatory evolution
 and loss of flight in paleognathous birds. Science 364: 74-78.
description: "tar command" was used to make archive files of
 sequence data used. All data are in text format. They
 can be opened by text editor.