The species tree paradigm that dominates current molecular systematic practice infers species trees from collections of sequences under assumptions of the multispecies coalescent (MSC), that is, that there is free recombination between the sequences and no (or very low) recombination within them. These coalescent genes (c-genes) are thus defined in an historical rather than molecular sense and can in theory be as large as an entire genome or as small as a single nucleotide. A debate about how to define c-genes centers on the contention that nuclear gene sequences used in many coalescent analyses undergo too much recombination, such that their introns comprise multiple c-genes, violating a key assumption of the MSC. Recently a similar argument has been made for the genes of plastid (e.g., chloroplast) and mitochondrial genomes, which for the last 30 or more years have been considered to represent a single c-gene for the purposes of phylogeny reconstruction because they are nonrecombining in an historical sense. Consequently, it has been suggested that these genomes should be analyzed using coalescent methods that treat their genes—over 70 protein-coding genes in the case of most plastid genomes (plastomes)—as independent estimates of species phylogeny, in contrast to the usual practice of concatenation, which is appropriate for generating gene trees. However, although recombination certainly occurs in the plastome, as has been recognized since the 1970’s, it is unlikely to be phylogenetically relevant. This is because such historically effective recombination can only occur when plastomes with incongruent histories are brought together in the same plastid. However, plastids sort rapidly into different cell lineages and rarely fuse. Thus, because of plastid biology, the plastome is a more canonical c-gene than is the average multi-intron mammalian nuclear gene. The plastome should thus continue to be treated as a single estimate of the underlying species phylogeny, as should the mitochondrial genome. The implications of this long-held insight of molecular systematics for studies in the phylogenomic era are explored. [c-gene; coalescent gene; concatalescence; organelle genome; plastome; recombination; species tree.]

中文翻译：

---

定义结合基因：细胞器系统基因组学的理论与实践

主导当前分子系统实践的物种树范式在多物种合并 (MSC) 的假设下从序列集合中推断出物种树，即序列之间存在自由重组，而序列内没有（或非常低）重组。因此，这些聚结基因（c-基因）是在历史而非分子意义上定义的，理论上可以与整个基因组一样大或小到单个核苷酸。关于如何定义 c 基因的争论集中在许多聚结分析中使用的核基因序列经历了过多的重组，以至于它们的内含子包含多个 c 基因，这违反了 MSC 的一个关键假设。最近对质体（例如叶绿体）和线粒体基因组的基因也提出了类似的论点，在过去的 30 年或更长时间中，出于系统发育重建的目的，它们被认为代表单个 c 基因，因为它们在历史意义上是非重组的。因此，有人建议应该使用合并方法分析这些基因组，将它们的基因——在大多数质体基因组（质体）的情况下，超过 70 个蛋白质编码基因——作为物种系统发育的独立估计，与通常的做法相反级联，这适用于生成基因树。然而，尽管重组肯定发生在质体中，正如自 1970 年代以来所认识到的那样，它不太可能与系统发育相关。这是因为这种历史上有效的重组只有在具有不一致历史的质体聚集在同一个质体中时才会发生。然而，质体迅速分类成不同的细胞谱系，很少融合。因此，由于质体生物学，质体是比平均多内含子哺乳动物核基因更规范的c基因。因此，应继续将质体组视为对潜在物种系统发育的单一估计，线粒体基因组也应如此。探索了这种长期以来对分子系统学的见解对系统基因组时代研究的影响。[c基因；聚结基因；聚合; 细胞器基因组；塑性体；重组；种树。] 线粒体基因组也应该如此。探索了这种长期以来对分子系统学的见解对系统基因组时代研究的影响。[c基因；聚结基因；聚合; 细胞器基因组；塑性体；重组；种树。] 线粒体基因组也应该如此。探索了这种长期以来对分子系统学的见解对系统基因组时代研究的影响。[c基因；聚结基因；聚合; 细胞器基因组；塑性体；重组；种树。]