A 100% resolved whole-genome phylogeny of placental mammals

[Rumraket (Mikkel R.)]

@Faizal_Ali

I’m not sure why I never asked this before: What does “bootstrap” mean?

As applied to phylogenetic inference it’s this:

"I'm treating the mutation rate as a substitution rate" - Dr. Nathaniel Jeanson

What @John_Harshman said. But I figure it actually takes a bit of explaining. The bootstrap is basically a test of tree consistency. You have to understand something about how the phylogeny is made in the first place, and then how it’s tested for consistency. As it says in the paper it’s inferred on the basis of 54 nuclear genes from each of those 191 species. It’s important to note that those 54 nuclear genes come from different chromosomes, have wildly different functions, some come from coding regions and some from non-coding regions. Introns, exons, genes that regulate other genes and control development, genes that function as enzymes, genes that take part in DNA replication, etc. Some from X and some from Y chromosomes. So whatever functional constraint you might imagine operates on some gene, it’s rather difficult to see how the same constraint can be operating on another, particularly in a sense where that constraint should force trees inferred from each of those 54 loci to g…