Gene Loss

GlossID	Species	Gene Loss Mechanism	Loss Type	Lineage Specific	Evidence	Accession Nr.
GL_BBPOBI	Monodon monoceros	LOF (frameshift, premature stop, ss)	Full	Yes	Genomic	PVJF01000037.1

Type	Excerpt	DOI
Functional	"Some insights into the possible roles of Lyg1 and Lyg2 come from expression data. The former gene does not appear to show strong tissue-specific expression patterns, with expression reported across several organs and a peak in the kidney (Liu et al. 2017). In contrast, Lyg2 is highly expressed in specific tissues, notably the skin (Irwin 2014), eyes, and testes (Huang et al. 2011). Given that the encoded gene product of Lyg2 is predicted to retain antibacterial activity (Irwin 2014)—and thus might play a role in immunity (Huang et al. 2011)—it is plausible that expression in the skin might serve as the first line of defense. If so, then the fact that whale skin has been reported to regenerate much faster than human skin might lead to a reduced necessity for antimicrobial activity in these species (Hicks et al. 1985)."	10.1093/gbe/evab201
Methodology & Validation	"Putative pseudogene sequences were confirmed by searching the raw sequence data in the SRA database. SRA database."	10.1093/gbe/evab201
Timing of Loss	"In the case of the cetaceans, a 1-bp frame-shifting deletion in exon 5 was shared by all 26 species examined, implying that this mutation occurred early in the evolution of modern whales and likely was the pseudogene generating mutation."	10.1093/gbe/evab201

Although the authors mention SRA validation of the identified mutations, this is not shown in the manuscript and supplemental data.