Fig 1.
Map of sampling sites and the distribution of mitochondrial DNA clades (from Fig 2) and microsatellite clusters (K* = 2; Fig 4) for Cichla pinima sensu lato.
The pie chart for each locality shows the proportion of individuals bearing The inset shows distributions of all of the species of Cichla clade A.
Table 1.
Sample sizes per locality of Cichla pinima sensu lato for mitochondrial DNA, 11 microsatellite loci, and sequences from 2 more variable and 15 remaining nuclear loci.
Fig 2.
Mitochondrial DNA genealogy of Cichla clade A.
Node values are posterior clade probability. For Cichla pinima sensu lato (indicated in bold), the localities where those clades were observed, as well which described species (C. pinima sensu stricto, C. jariina, C. vazzoleri, C. thyrorus) were observed in each clade, are denoted. Locality codes follow Table 1 and Fig 1, and the values associated with some localities are (the number of individuals bearing haplotypes from that clade / total individuals collected at that locality). For the endemic western lineages (yellow), each is labeled to match the mtDNA reference in Fig 4 (A,B,C). A fully annotated version of this genealogy is presented as S1 Fig.
Fig 3.
Heat map for genetic distances between sampling localities of Cichla pinima sensu lato.
Below diagonal, FST (11 loci); above diagonal, RST (9 loci), after S3 Table. The “core” regions are indicated: “WC”, western core; “SC”, southern core.
Fig 4.
Structure results for 11 microsatellite loci from Cichla pinima sensu lato.
Pop = 0, no sample pre-assignment; Pop = 1, some samples pre-assigned to K clusters, indicated by the bars above the Structure plots. The distribution of mtDNA clades (after Fig 1) is provided for reference. Locality codes follow Table 1 and Fig 1.
Table 2.
Results from *Beast runs with different species and dataset arrangements for Bayes Factor Delimitation of Cichla pinima sensu lato.
Fig 5.
Species trees for each dataset arrangement under the optimal, four-species model from Bayes Factor Delimitation (BFD) of Cichla pinima sensu lato.
Note: the no mtDNA-upstream only dataset was utilized with the same model but not subjected to path sampling analysis (see Table 2).
Table 3.
Results from runs of STACEY with different data arrangements and different collapseHeight summary values including the Machado locality.
Table 4.
Results from Analysis of Molecular Variance (AMOVA) of Cichla pinima sensu lato with 11 or 9 microsatellite loci.
Fig 6.
Conceptual model for the historical narrative of Cichla.
Solid lines represent natural hybridization (red, recent; green, ancient), while blue dashed lines represent hybridization in anthropogenically altered conditions. Branch lengths are not proportional. See text for details.