The genomic signatures of evolutionary stasis

Evolutionary stasis characterizes lineages that seldom speciate and show little phenotypic change over long stretches of geological time. Although lineages that appear to exhibit evolutionary stasis are often called living fossils, no single mechanism is thought responsible for their slow rates of morphological evolution and low species diversity. Some analyses of molecular evolutionary rates in a handful of living fossil lineages have indicated they exhibit slow rates of genomic change. Here, we investigate mechanisms of evolutionary stasis using a dataset of 1,105 exons for 481 vertebrate species. We demonstrate that two ancient clades of ray-finned fishes classically called living fossils, gars, and sturgeons, exhibit the lowest rates of molecular substitution in protein-coding genes among all jawed vertebrates. Comparably low rates of evolution are observed at four-fold degenerate sites in gars and sturgeons, implying a mechanism of stasis decoupled from selection that we speculate ..., Molecular evolutionary rates among major lineages of jawed vertebrates.
To test whether slow rates of morphological evolution are paired with low rates of molecular evolution in living fossils like gars, sturgeons, and paddlefishes, we estimated molecular rate variation across 1,105 exons from a sample of 471 jawed vertebrate species. We identified orthologous exon sequences from the genomes of selected species in the NCBI database for the following major jawed vertebrate lineages: Acipenseriformes, Aves, Crocodylia, Chondrichthyes, Lepidosauria, Lissamphibia, Marsupialia, Placentalia, Polypteridae, and Teleostei (Figure S1a). The HMM protocol available in HMMER 3.1 (Wheeler and Eddy 2013) was used to search each of the downloaded genomes for orthologous exons. These exon sequences were extracted using Python scripts from a phylogenomic analysis of ray-finned fishes using these loci (Hughes et al. 2018). For each group of the exon sequences, we aligned them using MAFFT v.7.3 (Katoh and ..., , # The genomic signatures of evolutionary stasis

Note that blank cell entries in all spreadsheets and datasets are missing data/absent data and should be treated as such. All measurements are in mm unless explicitly noted.

### GAR\_PHYLOGENY.zip

**Vertebrate_Rate_Estimation:**

* plotScripts = Custom scripts for extracting and plotting rate data
* logs = Log files produced from analysis of 1,105 exons in 11 clades of 478 vertebrates including genomic substitution rates
* filteringScripts = Custom scripts for filtering out problematic log files/invariant or non-converging analyses
* 4D_logs = Log files produced from analysis of 4D sites in 9 clades of 472 vertebrates

### RESULTS

This zipped archive includes all direct output from primary analyses and reruns for convergence for all clade-wide rate estimates, as well as the sarcopterygian branch estimation runs:lo

* xml = folder in each directory contains XML files generated using fixed tree topology for each clade (see meth...