The rapid rise of phenotypic and ecological diversity in independent lake-dwelling groups of cichlids is emblematic of the East African Great Lakes. In this study, we show that similar ecologically-based diversification has occurred in pike cichlids (Crenicichla) throughout the Uruguay River drainage of South America. We collected genomic data from nearly 500 ultraconserved element (UCEs) loci and >260,000 base pairs across 33 species, to obtain a phylogenetic hypothesis for the major species-groups and to evaluate the relationships and genetic structure among five closely-related, endemic, co-occurring species (the Uruguay River species flock; URSF). Additionally, we evaluated ecological divergence of the URSF based on body and lower pharyngeal jaw (LPJ) shape and gut contents. Across the genus, we recovered novel relationships among the species groups. We found strong support for the monophyly of the URSF; however, relationships among these species remain problematic, likely because of the rapid and recent evolution of this group. Clustered co-ancestry analysis recovered most species as well delimited genetic groups. The URSF species exhibit species-specific body and LPJ shapes associated with specialized trophic roles. Collectively, our results suggest that the URSF consists of incipient species that arose via ecological speciation associated with the exploration of novel trophic roles.
Supplementary_Materials_tables_and_Figure_legends
Supplementary tables and figure legends. Includes voucher specimen information for the genetic and morphological aspects of the study.
FIG_S1_existing_hypotheses
Hypotheses of the relationships among Crenicichla species groups based on morphology (a) Ploeg (1991) and molecules (b) López-Fernández et al. (2010), (c) Kullander et al. (2010), (d) Piálek et al. (2012). Representatives of the species groups: (e) Crenicichla lugubris (AUM43158), (f) C. saxatilis (AUM65898), (g) C. wallacii (AUM44460), (h) C. reticulata (AUM48266), (i) C. lacustris (UFRGS13073), the type species: (j) C. macrophthalma (ANSP195888), and (k) Teleocichla monogramma (ANSP194664). Photos: T. monogramma courtesy of Mark Sabaj; all others by EDB.
FIG_S2_Landmark_schemes
Landmark schemes used to quantify (left) body and (right) lower pharyngeal jaw shape: homologous (red) and sliding (purple) landmarks.
FIG_S2_LM.png
FIG_S3_Maximum_Likelihood
Concatenated Maximum likelihood Crenicichla phylogenies based on data sets with different proportions of missing data (A-D). Nodal support was assessed by 500 non-parametric bootstrap replicates.
FIG_S3_ML.pdf
FIG_S4_Bayesian_Inference
Bayesian inference Crenicichla phylogenies based on data sets with different proportions of missing data (A-D). Nodal support was assessed by 500 non-parametric bootstrap replicates.
FIG_S4_BI.pdf
FIG_S5_SVDquartets
Species trees (SVDquartets) Crenicichla phylogenies based on data sets with different proportions of missing data (A-D). Nodal support was assessed by 500 non-parametric bootstrap replicates.
FIG_S5_SVD.pdf
crenicichla_min100_concatenated
Complete matrix (loci common to all taxa) of concatenated UCE data from pike cichlids of the genus Crenicichla. Data were generated using the UCE Ray-finned Fish (Actinopterygians) 0.5K probe kit from MYcroarray.
crenicichla_min100_loci
Individual UCE loci alignments that are common to all taxa of pike cichlids of the genus Crenicichla. Data were generated using the UCE Ray-finned Fish (Actinopterygians) 0.5K probe kit from MYcroarray.
crenicichla_min95_concatenated
Incomplete 95% matrix (loci common to at least 95% of taxa) of concatenated UCE data from pike cichlids of the genus Crenicichla. Data were generated using the UCE Ray-finned Fish (Actinopterygians) 0.5K probe kit from MYcroarray.
crenicichla_min95_loci
Individual UCE loci alignments that are common to at least 95% of taxa of pike cichlids of the genus Crenicichla. Data were generated using the UCE Ray-finned Fish (Actinopterygians) 0.5K probe kit from MYcroarray.
crenicichla_min80_concatenated
Incomplete 80% matrix (loci common to at least 80% of taxa) of concatenated UCE data from pike cichlids of the genus Crenicichla. Data were generated using the UCE Ray-finned Fish (Actinopterygians) 0.5K probe kit from MYcroarray.
crenicichla_min80_loci
Individual UCE loci alignments that are common to at least 80% of taxa of pike cichlids of the genus Crenicichla. Data were generated using the UCE Ray-finned Fish (Actinopterygians) 0.5K probe kit from MYcroarray.
crenicichla_min50_concatenated
Incomplete 50% matrix (loci common to at least 50% of taxa) of concatenated UCE data from pike cichlids of the genus Crenicichla. Data were generated using the UCE Ray-finned Fish (Actinopterygians) 0.5K probe kit from MYcroarray.
crenicichla_min50_loci
Individual UCE loci alignments that are common to at least 50% of taxa of pike cichlids of the genus Crenicichla. Data were generated using the UCE Ray-finned Fish (Actinopterygians) 0.5K probe kit from MYcroarray.