A new preprint in open access:
Clouter A, Sackton TB, Grayson P, Clamp M, Baker AJ, Edwards EV 2018 Whole-genome analyses resolve the phylogeny of flightless birds (Palaeognathae) in the presence of an empirical anomaly zone. bioRxiv doi:10.1101/262949
http://www.biorxiv.org/content/biorxiv/early/2018/02/ 09/262949.1.full.pdf
Palaeognathae represent one of the two basal lineages in modern birds, and comprise theÂvolant (flighted) tinamous and the flightless ratites. Resolving palaeognath phylogeneticÂrelationships has historically proved difficult, and short internal branches separating majorÂpalaeognath lineages in previous molecular phylogenies suggest that extensive incompleteÂlineage sorting (ILS) might have accompanied a rapid ancient divergence. Here, we investigateÂpalaeognath relationships using genome-wide data sets of three types of noncoding nuclearÂmarkers, together totalling 20,850 loci and over 41 million base pairs of aligned sequence data.ÂWe recover a fully resolved topology placing rheas as the sister to kiwi and emu + cassowaryÂthat is congruent across marker types for two species tree methods (MP-EST and ASTRAL-II).ÂThis topology is corroborated by patterns of insertions for 4,274 CR1 retroelements identifiedÂfrom multi-species whole genome screening, and is robustly supported by phylogenomicÂsubsampling analyses, with MP-EST demonstrating particularly consistent performance acrossÂsubsampling replicates as compared to ASTRAL. In contrast, analyses of concatenated dataÂsupermatrices recover rheas as the sister to all other non-ostrich palaeognaths, an alternative thatÂlacks retroelement support and shows inconsistent behavior under subsampling approaches.ÂWhile statistically supporting the species tree topology, conflicting patterns of retroelementÂinsertions also occur and imply high amounts of ILS across short successive internal branches,Âconsistent with observed patterns of gene tree heterogeneity. Coalescent simulations indicateÂthat the majority of observed topological incongruence among gene trees is consistent withÂcoalescent variation rather than arising from gene tree estimation error alone, and estimatedÂbranch lengths for short successive internodes in the inferred species tree fall within theÂtheoretical range encompassing the anomaly zone. Distributions of empirical gene trees confirmÂthat the most common gene tree topology for each marker type differs from the species tree,Âsignifying the existence of an empirical anomaly zone in palaeognaths.Â
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David ÄernÃ