Department of Zoology, University of Otago, PO Box 56, Dunedin 9054, New Zealand.
Syst Biol. 2010 Oct;59(5):504-17. doi: 10.1093/sysbio/syq031. Epub 2010 Jul 5.
Mechanisms of speciation are best understood in the context of phylogenetic relationships and as such have often been inferred from single gene trees, typically those derived from mitochondrial DNA (mtDNA) markers. Recent studies, however, have noted the potential for phylogenetic discordance between gene trees and underlying species trees (e.g., due to stochastic lineage sorting, introgression, or selection). Here, we employ a variety of nuclear DNA loci to reassess evolutionary relationships within a recent freshwater fish radiation to reappraise modes of speciation. New Zealand's freshwater-limited Galaxias vulgaris complex is thought to have evolved from G. brevipinnis, a widespread migratory species that retains a plesiomorphic marine juvenile phase. A well-resolved tree, based on four mtDNA regions, previously suggested that marine migratory ability has been lost on 3 independent occasions in the evolution of this species flock (assuming that loss of diadromy is irreversible). Here, we use pseudogene (galaxiid Numt: 1801 bp), intron (S: 903 bp), and exon (RAG-1: 1427 bp) markers, together with mtDNA, to reevaluate this hypothesis of parallel evolution. Interestingly, partitioned Bayesian analysis of concatenated nuclear sequences (3141 bp) and concatenated nuclear and mtDNA (4770 bp) both recover phylogenies implying a single loss of diadromy, not three parallel losses as previously inferred from mtDNA alone. This phylogenetic result is reinforced by a multilocus analysis performed using Bayesian estimation of species trees (BEST) software that estimates the posterior distribution of species trees under a coalescent model. We discuss factors that might explain the apparently misleading phylogenetic inferences generated by mtDNA.
物种形成的机制最好在系统发育关系的背景下理解，因此通常是从单个基因树推断出来的，这些基因树通常来自线粒体 DNA (mtDNA) 标记。然而，最近的研究注意到基因树和潜在的物种树之间可能存在系统发育上的不一致（例如，由于随机谱系排序、基因渗入或选择）。在这里，我们使用各种核 DNA 座重新评估了一个最近的淡水鱼类辐射内的进化关系，以重新评估物种形成的模式。新西兰的淡水有限 Galaxias vulgaris 复合体被认为是从广泛迁徙的物种 G. brevipinnis 进化而来的，该物种保留了原始的海洋幼体阶段。一个基于四个 mtDNA 区域的分辨率很高的树之前表明，在这个物种群的进化过程中，海洋迁徙能力已经独立丢失了 3 次（假设双态性的丧失是不可逆转的）。在这里，我们使用假基因（galaxiid Numt：1801bp）、内含子（S：903bp）和外显子（RAG-1：1427bp）标记，以及 mtDNA，重新评估了这个平行进化的假设。有趣的是，串联核序列（3141bp）和串联核和 mtDNA（4770bp）的分区贝叶斯分析都恢复了暗示只有一次双态性丧失的系统发育，而不是以前仅从 mtDNA 推断的三次平行丧失。这个系统发育结果得到了使用贝叶斯估计物种树（BEST）软件进行的多点分析的加强，该软件根据合并模型估计物种树的后验分布。我们讨论了可能解释 mtDNA 产生的误导性系统发育推断的因素。
