Bird phylogeny: molecules vs. morphology

A not so recent paper in Nature
by Prum 2015, employed phylogenemics (gene sequencing) to recover a cladogram of bird relationships. Earlier here, here and here we looked at problems with results recovered by that study.

Fig. 1. Cladogram from Cloutier et al. 2018 on palaeognath relations based on whole-genome analyses.

Fig. 1. Cladogram from Cloutier et al. 2018 on palaeognath relations based on whole-genome analyses. Compare to figure 2 based on morphology.

A more recent paper
by Coutier 2018, also employed phylogenemics to recover a cladogram of palaeognath bird relationships. This one (Fig. 1) used a chicken (genus: Gallus) as a DNA outgroup.

Figure 2. Basal bird phylogeny based on the LRT (morphology)

Figure 2. Basal bird phylogeny based on the LRT (morphology). Palaeognaths are gray lines. Note, none of these early birds are great flyers. Those evolved later.

A manuscript to Nature
pointed out the fallacies of the results and the faith that paleontologists have put in their DNA studies based on comparisons to the trait studies that include fossil taxa in the large reptile tree (LRT, 1087 taxa, illustrated subset Fig. 2). I also reported a certain level of faith that attend all DNA studies. They hope they will recover tree topologies that will result in branches that demonstrate a gradual accumulation of traits (GATs). With birds, DNA studies too often do not produce GATs.

Nature declined to publish
the manuscript. It pointed out previously published errors (e.g. nesting flamingos with grebes, nesting the ostrich at the base of all birds and all paleognaths, nesting chickens and ducks together).

Like many academic publications,
novel discoveries are welcome in Nature. Critical reports that test those hypotheses, exposing overlooked flaws, are not so welcome. Why? Not only did the authors overlook their own flaws, but the editors at Nature and their hand-picked referees/reviewers also overlooked those flaws. Every time a publication or a scientist admits such errors they fear loss of prestige and/or confidence.

Remember when everyone thought
Yi qi had a large extra forelimb bone, and forgot to note the extra bones were actually just a displaced radius and ulna? Sometimes ‘the emperor has no clothes‘ is an apt metaphor. The solution may be plain to see, but some people just don’t see it.

At least now
the editors at Nature have seen that DNA studies should be considered acceptable only if they deliver the expected gradual accumulation of derived traits that is the benchmark by which all phylogenetic and phylogenomic studies must be measured.

You can read that manuscript
in MSWord/PDF format here. I will not submit it elsewhere.

The critical manuscript is titled:
Bird phylogeny: false positives detected in a gene sequencing study.”

Abstract:
“Traditionally a matrix of taxa and physical traits provides data for phylogenetic analysis. In recent years gene sequencing has taken on a dominant role. Ideally both methods should recover identical family trees that model evolutionary events. Too often they do not. While DNA analysis has proven its validity within genera (e.g. criminal identification), here a competing morphological analysis (the only method that can include fossils) finds several false positives in the results of a recent gene sequencing study of crown clade birds. Unfortunately gene studies have to rely on the hope that they will recover a series of taxa with a gradual accumulation of physical traits that model evolutionary events—without using those physical traits. Based on this benchmark and the present results, it is inappropriate to circumvent direct observation with gene sequencing in bird studies, at least until gene sequencing study results mirror those based on morphology.”

Figure 2. Which taxa share more traits? Phoenicopterus, the flamingo nests with Cariama, the seriema in the LRT, but with Gavia in the Prum et al. DNA study. Gavia nests with Thalasseus, the tern in the LRT.

Figure 2. Which taxa share more traits? Phoenicopterus, the flamingo nests with Cariama, the seriema in the LRT, but with Gavia in the Prum et al. DNA study. Gavia nests with Thalasseus, the tern in the LRT.

Bottom line: 
False positives plague DNA studies when tested against morphology. DNA studies can never employ ancient fossils. Why ignore great data?

No matter what your results are, at some time or another you’re going to have to validate DNA studies against trait studies… and HOPE they match.

References
Prum et al. (6 co-authors) 2015. A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing. Nature 526:569–573. online
Cloutier A et al. 2018. Whole-genome analyses resolve the phylogeny of flightless birds (Palaeognathae) in the presence of an empirical anomaly zone. bioRxiv doi:10.1101/262949 PDF online

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