先看看paralogue（旁系同源的基因）。
同一生物体有两组基因组，有着共同的来源，但却有差异。像是人体中 alpha-hemoglobin和beta-hemoglobin，这两种蛋白质执行相同的功能（血红蛋白，生物体内负责运载氧的一种蛋白质），但却属于不同的基因组，称为paralogue。
再来看orthologue（直系同源的基因）。
不同生物体不同种间的两组基因组，但是却有相同功能，像是人和老鼠有部分的酵素（酶）是相同的，我们称这两种蛋白质的基因组为orthologue。othologue is the British spelling。
Homologous genes have shared a common evolutionary ancestor. Note that homology and similarity are not the same thing - genes which are homologous may have high or low similarity, but the presence of similarity doesn't necessarily make two sequences homologues (could be convergent evolution).
Paralogous and orthologous genes are subdivisions of homologous genes. All homologs are either orthologs or paralogs. Orthologs arise because of speciation events.
Thus if a rat and a human sequence have simply diverged since the last common ancestor of rats and humans, then they are orthologs.
Paralogs arise because of gene duplication events. Thus there may be an alpha and beta form of a human protein which have arisen through gene duplication, and then diverged. These two genes are paralogs.
Also note that if this duplication occurred before the last common human-rat ancestor then alpha-human is a paralog to beta-rat, but an ortholog to alpha-rat.
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