DOI: 10.5061/dryad.7qs13
title: Data from: Phylogenomics of pike cichlids (Cichlidae: Crenicichla): the rapid evolution and trophic diversification of an incipient species flock

description: 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 &gt;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.
description: Supplementary_Materials_tables_and_Figure_legendsSupplementary tables and figure legends. Includes voucher specimen information for the genetic and morphological aspects of the study.FIG_S1_existing_hypothesesHypotheses 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_schemesLandmark schemes used to quantify (left) body and (right) lower pharyngeal jaw shape: homologous (red) and sliding (purple) landmarks.FIG_S2_LM.pngFIG_S3_Maximum_LikelihoodConcatenated 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.pdfFIG_S4_Bayesian_InferenceBayesian 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.pdfFIG_S5_SVDquartetsSpecies 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.pdfcrenicichla_min100_concatenatedComplete 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_lociIndividual 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_concatenatedIncomplete 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_lociIndividual 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_concatenatedIncomplete 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_lociIndividual 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_concatenatedIncomplete 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_lociIndividual 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.