Genes for which homologs can be detected only in a limited group of evolutionarily related species, called “lineage-specific genes,” are pervasive: Essentially every lineage has them, and they often comprise a sizable fraction of the group’s total genes. Lineage-specific genes are often interpreted as “novel” 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 novelty-free 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.

只能在有限的进化相关物种中检测到同源基因的基因，称为“谱系特异性基因”，是普遍存在的：基本上每个谱系都有它们，而且它们通常占该组总基因的相当大一部分。谱系特异性基因通常被解释为“新”基因，代表在该谱系中重新诞生的遗传新奇。在这里，我们开发了一种简单的方法来测试替代的零假设：谱系特异性基因确实具有谱系之外的同源物，即使以无新奇的方式以恒定速率进化，也只是变得无法被使用的搜索算法检测到推断同源性。我们表明该无效假设足以解释在真菌和昆虫中缺乏检测到的大量谱系特异性基因的同源物。然而，我们还发现，这种无新颖性模型不能很好地解释两个进化枝中的少数谱系特异性基因。该方法提供了一种简单的方法来识别哪些谱系特异性基因需要在同源性检测失败之外进行特殊解释，将它们突出显示为进一步研究的有趣候选者。