直系同源与旁系同源

Homologous sequences.

Orthologs and Paralogs are two types of homologous sequences. Orthology describes genes in different species that derive from a common ancestor. Orthologous genes may or may not have the same function.Paralogy describes homologous genes within a single species that diverged by gene duplication.

Orthologs 和 Paralogs 是同源序列的两种类型。Orthology描述在不同物种中来自于共同祖先的基因。Orthologous基因可能有相同的功能，也可能没有。Paralogy描述在同一物种内由于基因复制而分离的同源基因。Orthology通常译作直系同源、直向同源、垂直同源。Paralogy通常译作旁系同源、并系同源、横向同源。

NCBI的Glossary中对paralog的定义是： A paralog is one of a set of homologous genes that have diverged from each other as a consequence of gene duplication. For example, the mouse a-globin andb-globin genes are paralogs. The relationship between mouse a-globin and chick b-globin is also considered paralogous (see the figure).

即，祖先基因经过复制后分离产生的基因是paralog，例如鼠的a球蛋白和b球蛋白基因。并且，鼠的a球蛋白和鸡的b球蛋白基因的关系也是paralog。

因此不能说：来自不同物种的就不是paralog。这一点就与前面的定义不一致了，前面说：“Paralogy describes homologous genes within a single species that diverged by gene duplication.”

NCBI的Glossary中对ortholog的定义是： Orthology describes genes in different species that derive from a single ancestral gene in the last common ancestor of the respective species.

即，Orthology 指的是这样一些基因，它们起源于这些基因所在物种的最近的共同祖先的一条基因。

TRENDS in Genetics Vol.18 No.12 December 2002 的一篇文章：《Orthology, paralogy and proposed classification for paralog subtypes》对两者的定义做了进一步的探究。作者指出：

Paralogs are defined as genes that derive from a single gene that was duplicated within a genome.The latter definition does not specify that paralogs can only be found in a single organism, and hence genes in different organisms that arose from gene duplication in an ancestral genome are also paralogs according to the definition。

作者根据复制事件与物种分化事件发生的先后关系，提出了inparalog和outparalog的概念，对于一个给定的世系，在物种分化后发生复制事件产生的基因称为inparalog，而复制事件在分化之前，则称为outparalog。

 As we know ,there are two kinds of homolog, ortholog and paralog. Genes in two  species that have directly evolved from a single gene in the last common ancestor are called orthologs. A set of homologous genes that have diverged from each other as a consequence of genetic duplication are called paralogs. Sometime those paralogs which arose from a duplication after the speciation event are called in-paralogs.

文献下载：http://www.sciencedirect.com/science/article/pii/S0168952502027932