@article {1531308,
	title = {Many, but not all, lineage-specific genes can be explained by homology detection failure},
	journal = {PLOS Biology},
	year = {2020},
	abstract = {
	Genes for which homologs can be detected only in a limited group of evolutionarily



	related species, called {\textquotedblleft}lineage-specific genes,{\textquotedblright} are pervasive: essentially every



	lineage has them, and they often comprise a sizable fraction of the group{\textquoteright}s total genes.



	Lineage-specific genes are often interpreted as {\textquotedblleft}novel{\textquotedblright} genes, representing genetic



	novelty born anew within that lineage. Here, we develop a simple method to test an



	alternative null hypothesis: that lineage-specific genes do have homologs outside of



	the lineage that, even while evolving at a constant rate in a novelty-free manner, have



	merely become undetectable by search algorithms used to infer homology. We show



	that this null hypothesis is sufficient to explain the lack of detected homologs of a large



	number of lineage-specific genes in fungi and insects. However, we also find that a



	minority of lineage-specific genes in both clades are not well-explained by this noveltyfree



	model. The method provides a simple way of identifying which lineage-specific



	genes call for special explanations beyond homology detection failure, highlighting



	them as interesting candidates for further study.

},
	url = {https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3000862},
	author = {Caroline M. Weisman and Andrew W. Murray and Eddy, Sean R.}
}
