Gene Loss

GlossID	Species	Gene Loss Mechanism	Loss Type	Lineage Specific	Evidence	Accession Nr.
GL_YYMOP2	Physeter catodon	Other	Full	No	Genomic

Type	Excerpt	DOI
Methodology & Validation	"For a gene to be classified as lost, we require that a lineage, which descends from an ancestor with an intact gene, exhibits several gene-inactivating mutations that most likely result in a non-functional protein. As gene-inactivating mutations, we consider frameshifting insertions and deletions, inframe stop codon mutations, and splice site-disrupting mutations. In addition, we consider the loss of exons or even entire genes, which could occur due to either large deletions in the genome or the accumulation of numerous mutations that destroy any sequence similarity. For all previously unknown gene losses presented here, we further confirmed the loss by validating the gene-inactivating mutations with unassembled sequencing reads from the respective species."	10.1038/s41467-018-03667-1
Phenotypic	"Searching for gene losses shared between the fully aquatic cetacean and manatee lineages revealed KLK8, a gene loss that correlates with skin and neuroanatomical differences of aquatic mammals."	10.1038/s41467-018-03667-1

Supplementary Table 8 and Supplementary Note 8. Authors do not provide details regarding gene loss mechanism.

GL_ID	Symbol	Species	Order	Gene Loss Mechanism	Loss Type	Lineage Specific	Citation
GL_0YBEXU	KLK8	Physeter catodon	Artiodactyla	LOF (frameshift, premature stop, ss)	Full	No	10.1093/gbe/evx187
GL_HCRWZZ	KLK8	Physeter catodon	Artiodactyla	LOF (frameshift, premature stop, ss)	Full		10.1093/gbe/evx239