New paper on bird phenomics vs. genomics

On July 11, 2020, 
just 3 days after first published online, announced this manuscript has had 50 reads. Thank you.

As longtime readers know,
and every paleontologist seems to acknowledge,cladograms based on genes don’t match cladograms based on traits.

So, here’s an unpublished paper
available on that simply lifts the rock off this buried problem by laying out the differences in bird phenomics vs. genomics, based on problems found in the Prum et al. 2015 bird cladogram that relied on genomics.

Bird phylogeny: false positives detected in a gene sequencing study
(click on the blue text above to access the PDF.)

From the 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.”

After a few days
I received a comment on from professor and bird expert, Peter Houde, New Mexico State University. My reply follows.

Figure 1. Comment on bird phenomics paper by Peter Houde, NMSU.

Figure 1. Comment on bird phenomics paper by Peter Houde, NMSU.

If anyone has ever wondered about the law of unintended consequences,
this example of unanticipated neotony in a teacher is but one of many stemming from Darren Naish’s critique of in 2012.

Peters D 2020. Bird phylogeny: false positives detected in a gene sequencing study. (unpublished, seeking and awaiting comments)
Prum et al. (6 co-authors) 2015. A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing. Nature 526:569–573. online

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