Those are fixed gene-duplicates in yeast, not the rate of occurrence of duplication mutations “in vertebrates” that you asked for.
I quote that paper for you again like I did a month ago:
Note that by “gene duplication rate we” mean the rate at which a duplicated gene is created by mutation and becomes fixed in the population. The fixation probability of duplicated genes should be largely affected by natural selection (14).
I could of course just refer to that offshoot of the Lenski experiment in which the total genome size for E coli increased by over 20% from hundreds of duplications in less than 3000 generations to show what happens when a locus prone to duplication suddenly has a positive fitness effect when amplified.
Incidentally the method used in the paper you link is phylogenetic, that is they’re using common ancestry to calculate a rate of fixed duplicates over deep time by counting differences between species thought to share common ancestry. A method you explicitly reject when applied to the Howe et al diagram to infer the rate at which novel genes have evolved there(whether by duplication or other mechanisms), and you also reject when used to show de novo gene evolution in yeast too. Back to the old double standard again eh Bill?
What does this paper on de novo genes in yeast species say? Hmmm…
Fig. 2Identification of de novo transcripts in S. cerevisiae .
a Pipeline for the identification of de novo transcripts and other conservation classes. For each of the S. cerevisiae transcripts which were expressed above our threshold (>15 TPM), we estimated their phylogenetic conservation using genomic synteny and homology searches. b Identification of genomic synteny blocks by using MUMs. Diagram illustrating maximal unique matching subsequences (MUMs) across a chromosome in different species of the Saccharomyces genus. The synteny blocks were defined by clustering contiguous MUMs in close proximity. c Examples of different classes of transcripts depending on their phylogenetic conservation. Diagram of a hypothetical syntenic genomic region shared by all 11 species with different classes of genes indicate. d Number of transcripts depending on their phylogenetic conservation. The genes were divided in three classes: ‘de novo’ (213 transcripts), ‘genus-specific’ (251 transcripts) and ‘conserved’ (4,409 transcripts). We found that 213 transcripts were likely to have arisen de novo over the past ~20 million years i.e. there were no homologues in species more distant than S. mikatae (purple). Only transcripts expressed at more than 15 TPM were considered here. Below are the number of transcripts identified at each internal branch in the tree leading to S. cerevisiae , before and after applying different computational filters. e The majority of de novo transcripts are not present in the annotations and are expressed in different conditions. Number of transcripts in each class that correspond to annotated transcripts (light grey) and unannotated transcripts (dark grey). Fraction of transcript expression above 15 TPM in rich media (yellow), in oxidative stress (red), or both conditions (blue). The vast majority of transcripts are either expressed in both conditions or in normal conditions. Source data are provided as a Source Data file.
Take a good look at Fig2 D, bottom:
I guess that refutes common ancestry of yeasts then, right Bill? Or do phylogenetic methods only count when you mistakenly think you can spin the numbers to support this unsupported axiom against novel gene evolution that you have?