Figure 4.
(a) The ratios of number of successful radiations over number of ‘failed’ radiations mapped on a mitochondrial gene tree (ND2) for the African cichlid fish (tree from Klett & Meyer 2002). ‘Node 1’ corresponds to a hard polytomy deep in the African cichlid radiation, that has been interpreted as the signature of an adaptive radiation burst 14 Myr (ago) (Terai et al. 2003; figure 4b). ‘Node 2’ is a second major hard polytomy corresponding with the origin of the four deep lineages of Lake Tanganyika cichlids (Takahashi et al. 2001b). ‘Node 3’ is a third major hard polytomy corresponding to the radiation burst of the modern Lake Tanganyika lineage (Takahashi et al. 2001b; figure 4c). Note that several weakly supported nodes in this gene tree collapse to the same polytomy in multilocus trees (figure 4b,c). The different shading indicates sections of the tree that were compared for the ratio of successful to failed radiations. The light grey branch is the ‘East African’ lineage that emerged in the Tanganyika primary radiation, then radiated again in Lake Tanganyika, and much later seeded Lakes Malawi, Victoria, Makgadikgadi and many others (also figure 4c). Genera that were not sampled for this gene tree, but whose phylogenetic position is known from other mtDNA sequence data, are indicated in the ratio column. Note that the exact position of these does not affect the analysis because all of them are unambiguously assigned to one of the shaded branches. The origins of two proposed key evolutionary innovations, decoupled pharyngeal jaws (at the base of the tree) and egg dummies, are indicated. The third one, female mouthbrooding is not indicated because it evolved multiple times and is scattered throughout the tree. Abbreviations stand for lakes: Na=Natron; My=Manyara; Ji=Jipe; Cha=Chala; T=Tanganyika; V=Victoria; R=Rukwa; PM=Paleo–Makgadikgadi; M=Malawi; B=Bangweulu; Mw=Mweru; K=Kivu; E=Edward; A=Albert; C=Chad; Ki=Kinneret; Tu=Turkana; Ta=Tana; S=Stephanie; Ba=Barombi Mbo; Ej=Ejagham; U=Upemba; F=Fwa; Sa=Saka; Ns=Nshere; Lu=Lutoto; Ci=Chilwa; Nb=Nabugabo; Tm=Tumba; G=Guinas sink hole; Be=Bemin; Ko=Barombi ba Kotto; Nd=Mayi Ndombe. (b) A phylogenetic tree based on short interspersed element (SINE) insertion data. Each boxed number is a SINE locus, and arrowheads indicate their origins. The MVhL lineage is resolved in figure 4c. The grey circle at node 1 indicates the period when retention of ancestral polymorphisms (presence or absence of a SINE) was assumed to have occurred at loci 223, 260, 304, 316, 1223 and 1544. Reproduced with permission from Terai et al. 2003. (c) A phylogenetic tree for cichlid species in the 12 tribes of Lake Tanganyika, based on SINE insertion data. Arrowheads indicate internodes deduced from insertion of a SINE unit at each of 24 loci analysed. The three clades were supported by the patterns of insertion of a SINE unit at loci 213, 214, 245, 247, 254, 314, 455, 1569, 1666 and 1715 (the MVhL clade); at loci 328, 330, 343, 1221, 1238, 1262, 1269, 1277 and 1654 (the MVHT clade); and at loci 1233, 1265, 1281, 1291 and 1528 (the MVH clade). The grey portion of the tree indicates the period during which extensive putative incomplete lineage sorting of ancestral polymorphisms occurred (reproduced with permission from Takahashi et al. 2001b).