Effect of different types of sequence data on palaeognath phylogeny

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 es..., 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) (> 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) ..., \"tar command\" was used to make archive files of sequence data used.
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