Adaptive radiations such as the Darwin’s   finches on the Galapagos archipelago, the Hawaiian silver swords, the Caribbean   anoles lizards, and the cichlid fish of the East African Great Lakes provide   opportunities for studying the processes underlying rapid speciation   (Schluter, 2000; Brakefield, 2006; Salzburger, 2009). Yet, resolving the   phylogeny of adaptive radiations still remains a challenge. Due to the   extreme rapidity of the radiations, lineage sorting often lags behind   cladogenesis, complicating phylogenetic inference based on single or a few   molecular markers (Pamilo and Nei, 1988; Maddison and Knowles, 2006). Furthermore,   the short basal branches typical for rapid radiations can make the   phylogenetic reconstructions sensitive to the choice of outgroup taxa. In   particular if the phylogenetic distance between outgroup and ingroup taxa is   large, there is a high   likelihood of homoplasy between ingroup and outgroup taxa.   Consequently, the outgroup may attach randomly to the ingroup and bias the   inferred ingroup tree topology (Wheeler, 1990; Huelsenbeck et al., 2002;   Rota-Stabelli and Telford, 2008; Rosenfeld et al., 2012).

适应辐射，如加拉帕戈斯群岛上的达尔文雀、夏威夷银剑菊、加勒比安乐蜥和东非五大湖中的慈鲷鱼，为研究快速物种形成过程提供了机会（Schluter, 2000;   Brakefield, 2006; Salzburger, 2009）。然而，解决适应性辐射的系统发育仍然是一个挑战。由于辐射速度极快，谱系分类往往落后于枝状进化，使得基于单个或几个分子标记的系统发育推断复杂化变得复杂（Pamilo and Nei,   1988; Maddison and Knowles, 2006）。此外，以快速辐射为代表的短基枝可以使系统发育重建对外群的选择敏感。尤其是当外群与内群之间的系统发育距离较大时，内外群分来单元之间很可能存在趋同现象。因此，外群可能被随机附加到内群，并导致内群系统发育树的拓扑结构推断出现偏差（Wheeler, 1990; Huelsenbeck et al., 2002; Rota-Stabelli and   Telford, 2008; Rosenfeld et al., 2012）。