African cichlids (subfamily: Pseudocrenilabrinae) are among the most diverse vertebrates, and their propensity for repeated rapid radiation has made them a celebrated model system in evolutionary research. Nonetheless, despite numerous studies, phylogenetic uncertainty persists, and riverine lineages remain comparatively underrepresented in higher-level phylogenetic studies. Heterogeneous gene histories resulting from incomplete lineage sorting (ILS) and hybridization are likely sources of uncertainty, especially during episodes of rapid speciation. We investigate the relationships of Pseudocrenilabrinae and its close relatives while accounting for multiple sources of genetic discordance using species tree and hybrid network analyses with hundreds of single-copy exons. We improve sequence recovery for distant relatives, thereby extending the taxonomic reach of our probes, with a hybrid reference guided/de novo assembly approach. Our analyses provide robust hypotheses for most higher-level relationships and reveal widespread gene heterogeneity, including in riverine taxa. ILS and past hybridization are identified as the sources of genetic discordance in different lineages. Sampling of various Blenniiformes (formerly Ovalentaria) adds strong phylogenomic support for convict blennies (Pholidichthyidae) as sister to Cichlidae and points to other potentially useful protein-coding markers across the order. A reliable phylogeny with representatives from diverse environments will support ongoing taxonomic and comparative evolutionary research in the cichlid model system. [African cichlids; Blenniiformes; Gene tree heterogeneity; Hybrid assembly; Phylogenetic network; Pseudocrenilabrinae; Species tree.].

Department of Ecology and Evolutionary Biology and Museum of Zoology University of Michigan Biological Science Building 1105 N University Ave Ann Arbor MI 48109 USA

Department of Ecology and Evolutionary Biology University of Toronto 25 Willcocks St Toronto ON M5S 3B2 Canada

Department of Environmental Sciences Zoological Institute University of Basel Vesalgasse 1 CH 4051 Basel Basel Stadt Switzerland

Department of Ichthyology American Museum of Natural History 200 Central Park West New York NY 10024 5102 USA

Department of Natural History Royal Ontario Museum 100 Queens Park Toronto ON M5S 2C6 Canada

Department of Zoology Canadian Museum of Nature 240 McLeod St Ottawa ON K2P 2R1 Canada

Department of Zoology Charles University Prague Vinicna 7 Prague Central Bohemia CZ 128 44 Czech Republic

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Abadi S., Azouri D., Pupko T., Mayrose I.. 2019. Model selection may not be a mandatory step for phylogeny reconstruction. Nat. Commun. 10:934. PubMed PMC

Alter S., Munshi-South J., Stiassny M.L.J.. 2017. Genomewide SNP data reveal cryptic phylogeographic structure and microallopatric divergence in a rapids-adapted clade of cichlids from the Congo River. Mol. Ecol. 26:1401–1419. PubMed

Altschul S.F., Gish W., Miller W., Myers E.W., Lipman D.J.. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403–410. PubMed

Arbour J.H., López-Fernández H.. 2016. Continental cichlid radiations: functional diversity reveals the role of changing ecological opportunity in the Neotropics. Proc. Biol. Sci. 283:20160556. PubMed PMC

Astudillo-Clavijo V., Arbour J.H., López-Fernández H.. 2015. Selection towards different adaptive optima drove the early diversification of locomotor phenotypes in the radiation of Neotropical geophagine cichlids. BMC Evol. Biol. 15:77. PubMed PMC

Betancur-R R., Broughton R.E., Wiley E.O., Carpenter K., López J.A., Li C., Holcroft N.I., Arcila D., Sanciangco M., Cureton li J.C., Zhang F., Buser T., Campbell M.A., Ballesteros J.A., Roa-Varon A., Willis S., Borden W.C., Rowley T., Reneau P.C., Hough D.J., Lu G., Grande T., Arratia G., Ortí G.. 2013. The tree of life and a new classification of bony fishes. PLoS Curr. 18:ecurrents.tol.53ba26640df0ccaee75bb165c8c26288. PubMed PMC

Betancur-R R., Wiley E.O., Arratia G., Acero A., Bailly N., Miya M., Lecointre G., Orti G.. 2017. Phylogenetic classification of bony fishes. BMC Evol. Biol. 17:162. PubMed PMC

Bezanson J., Edelman A., Karpinski S., Shah V.B.. 2017. Julia: a fresh approach to numerical computing. SIAM Review 59:65–98.

Brawand D., Wagner C.E., Li Y.I., Malinsky M., Keller I., Fan S., Simakov O., Ng A.Y., Lim Z.W., Bezault E., Turner-Maier J., Johnson J., Alcazar R., Noh H.J., Russell P., Aken B., Alföldi J., Amemiya C., Azzouzi N., Baroiller J.F., Barloy-Hubler R., Berlin A., Bloomquist R., Carleton K.L., Conte M.A., D’Cotta H., Eshel O., Gaffney L., Galibert F., Gante H.F., Gnerre S., Greuter L., Guyon R., Haddad N.S., Haerty W., Harris R.M., Hofmann H.A., Hourlier R., Hulata G., Jaffe D.B., Lara M., Lee A.P., MacCallum I., Mwaiko S., Nikaido M., Nishihara H., Ozouf-Costaz C., Penman D.J., Przybylski D., Rakotomanga M., Renn S.C.P., Ribeiro F.J., Ron M., Salzburger W., Sanchez-Pulido L., Santos M.E., Searle S., Sharpe T., Swofford R., Tan F.J., Williams L., Young S., Yin S., Okada N., Kocher T.D., Miska E.A., Lander E.S., Venkatesh B., Fernald R.D., Meyer A., Ponting C.P., Streelman J.T., Lindblad-Toh K,Seehausen O., Di Palma F.. 2014. The genomic substrate for adaptive radiation in African cichlid fish. Nature 513:375–381. PubMed PMC

Burress E.D., Piálek, L., Casciotta J.R., Almirón A., Tan M., Armbruster J.W., Říçan O.. 2017. Island- and lake-like parallel adaptive radiations replicated in rivers. Proc. R. Soc. B 285:20171762. PubMed PMC

Cai L., Xi Z., Lemmon E.M., Lemmon A.R., Mast A., Buddenhagen C.E.. 2021. The perfect storm: gene tree estimation error, incomplete lineage sorting, and ancient gene flow explain the most recalcitrant ancient angiosperm clade, Malpighiales. Syst. Biol. 70:491–507. PubMed

Chau J.H., Rahfeldt W.A., Olmstead R.G.. 2018. Comparison of taxon-specific versus general locus sets for targeted sequence capture in plant phylogenomics. Appl. Plant Sci. 6:e1032. PubMed PMC

Clabaut C., Salzburger W., Meyer A.. 2005. Comparative phylogenetic analyses of the adaptive radiation of Lake Tanganyika cichlid fish: nuclear sequences are less homoplasious but also less informative than mitochondrial DNA. J. Mol. Evol. 61:666–681. PubMed

Clark K., Karsch-Mizrachi I., Lipman D.J., Ostell J., Sayers E.W.. 2016. GenBank. Nucleic Acids Res. 44:D67–D72. PubMed PMC

Cock P.A., Antao T., Chang J.T., Chapman B.A., Cox C.J., Dalke A., Friedberg I., Hamelryck T., Kauff F., Wilczynski B., de Hoon M.J.L.. 2009. Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 25:1422–1423. PubMed PMC

Crawford J. 2010. AssemblyAssembler1.3. GitHub repository: https://github.com/dzerbino/velvet/tree/master/contrib/AssemblyAssembler1.3.

Danley P.D., Husemann M., Ding B., DiPietro L.M., Beverly E.J., Peppe D.J.. 2012. The impact of the geologic history and paleoclimate on the diversification of East African Cichlids. Int. J. Evol. Biol. 2012:574851–20. PubMed PMC

Davidson R., Vachaspati P., Mirarab S., Warnow T.. 2015. Phylogenomic species tree estimation in the presence of incomplete lineage sorting and horizontal gene transfer. BMC Genomics 16:S1. PubMed PMC

Day J.J., Cotton J.A., Barraclough T.G.. 2008. Tempo and mode of diversification of Lake Tanganyika cichlids. PLoS One 3: doi: 10.1371/journal.pone.0001730. PubMed PMC

Degnan J.H., Rosenberg N.A.. 2009. Gene tree discordance, phylogenetic inference and the multispecies coalescent. Trends Ecol. Evol. 24:332–340. PubMed

Deutsch J.C. 1997. Colour diversification in Malawi cichlids: evidence for adaptation, reinforcement or sexual selection? Biol. J. Linn. Soc. 62:1–14.

Dunz A.R., Schliewen U.K.. 2013. Molecular phylogeny and revised classification of the haplotilapiine cichlid fishes. Mol. Phylogenet. Evol. 68:64–80. PubMed

Edgar R.C. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32:1792–1797. PubMed PMC

Edwards S.V. 2009. Is a new and general theory of molecular systematics emerging? Evolution 63:1–19. PubMed

Eytan R.I., Evans B.R., Dornburg A., Lemmon A.R., Lemmon E.M., Wainwright P.C., Near T.J.. 2015. Are 100 enough? Inferring acanthomorph teleost phylogeny using Anchored Hybrid Enrichment. BMC Evol. Biol. 15:113. PubMed PMC

Farias I.P., Ortí G., Meyer A.. 2000. Total evidence: molecules, morphology, and the phylogenetics of cichlid fishes. J. Exp. Zool. B 288:76–92. PubMed

Farias I.P., Ortí G., Sampaio I., Schneider H., Meyer A.. 1999. Mitochondrial DNA phylogeny of the family Cichlidae: monophyly and fast molecular evolution of the Neotropical assemblage. J. Mol. Evol. 48:703–711. PubMed

Faircloth B.C., McCormack J.E., Crawford N.G., Harvey M.G., Brumfield R.T., Glenn T.C.. 2012. Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales. Syst. Biol. 61:717–726. PubMed

Felsenstein J. 1978. Cases in which parsimony or compatibility methods will be positively misleading. Syst. Zool. 27:401–410.

Flicek P., Ahmed I., Amode M.R., Barrell D., Beal K., Brent S., Carvalho-Silva D., Clapham P., Coates G., Fairley S., Fitzgerald S., Gil L., García-Girón C., Gordon L., Hourlier T., Hunt S., Juettemann T., Kähäri A.K., Keenan S., Komorowska M., Kulesha E., Longden I., Maurel T., McLaren W.M., Muffato M., Nag R., Overduin B., Pignatelli M., Pritchard B., Pritchard E., Riat H.S., Ritchie G.R., Ruffier M., Schuster M., Sheppard D., Sobral D., Taylor K., Thormann A., Trevanion S., White S., Wilder S.P., Aken B.L., Birney E., Cunningham F., Dunham I., Harrow J., Herrero J., Hubbard T.J., Johnson N., Kinsella R., Parker A., Spudich G., Yates A., Zadissa A., Searle S.M.. 2013. Ensembl 2013. Nucleic Acids Res. 41:D48–D55. PubMed PMC

Foster P.G. 2004. Modeling compositional heterogeneity. Syst. Biol. 53:485–495. PubMed

Ford A.G.P., Bullen T.R., Pang L., Genner M.J., Bills R., Flouri T., Ngatunga B.P., Rüber L., Schliewen U.K., Seehausen O., Shechonge A., Stiassny M.L.J., Turner G.F., Day J.J.. 2019. Molecular phylogeny of Oreochromis (Cichlidae: Oreochromini) reveals mito-nuclear discordance and multiple colonisation of adverse aquatic environments. Mol. Phylogenet. Evol. 136:215–226. PubMed

Ford A.G.P., Dasmahapatra K.K., Rüber L., Gharbi K., Cezard T., Day J.J.. 2015. High levels of interspecific gene flow in an endemic cichlid fish adaptive radiation from an extreme lake environment. Mol. Ecol. 24:3421–3440. PubMed PMC

Ford A.G.P., Rüber L., Newton J., Dasmahapatra K.K., Balarin J.D., Brunn K., Day J.J.. 2016. Niche divergence facilitated by fine-scale ecological partitioning in a recent cichlid fish adaptive radiation. Evolution 70:2718–2735. PubMed PMC

Friedman M., Keck B.P., Dornburg A., Eytan R.I., Martin C.H., Hulsey C.D., Wainwright P.C., Near T.J.. 2013. Molecular and fossil evidence place the origin of cichlid fishes long after Gondwanan rifting. Proc. R. Soc. B. 280:20131733. PubMed PMC

Froese R., Pauly D.. 2021. Fishbase. www.fishbase.org

Gatesy J., Springer M.S.. 2014. Phylogenetic analysis at deep timescales: unreliable gene trees, bypassed hidden support, and the coalescence/concatalescence conundrum. Mol. Phylogenet. Evol. 80:231–266. PubMed

Genner M.J., Seehausen O., Lunt D.H., Joyce D.A., Shaw P.W., Carvalho R., Turner G.F.. 2007. Age of cichlids: new dates for ancient lake fish radiations. Mol. Biol. Evol. 24:1269–1282. PubMed

Ghezelayagh A., Harrington R.C., Burress E.D., Campbell M.A., Buckner J.C., Chakrabarty P., Glass J.R., McCraney W.T., Unmack P.J., Thacker C.E., Alfaro M.E., Friedman S.T., Ludt W.B., Cowman P.F., Friedman M., Price S.A., Dornburg A., Faircloth B.C., Wainwright P.C., Near T.J.. 2021. Prolonged morphological expansion of spiny-rayed fishes following the end-Cretaceous. bioRxiv 2021.07.12.452083. doi: 10.1101/2021.07.12.452083. PubMed

Grant P.P.R., Grant R.. 2019. Hybridization increases population variation during adapting radiation. Proc. Natl. Acad. Sci. USA 116:23216–23224. PubMed PMC

Hughes L.C., Ortí G., Huang Y., Sun Y., Baldwin C.C., Thompson A.W., Arcila D., Betancur-R R., Li C., Becker L., Bellora N., Zhao X., Li X., Wang M., Fang C., Xie B., Zhou Z., Huang H., Chen S., Venkatesh B., Shi Q.. 2018. Comprehensive phylogeny of ray-finned fishes (Actinopterygii) based on transcriptomic and genomic data. Proc. Natl. Acad. Sci. USA 115:6249–6254. PubMed PMC

Hulsey C.D., García de León F.. 2005. Cichlid jaw mechanics: linking morphology to feeding specialization. Funct. Ecol. 19:487–494.

Ilves K.L., López-Fernández H.. 2014. A targeted next-generation sequencing toolkit for exon-based cichlid phylogenomics. Mol. Ecol. Resour. 14:802–811. PubMed

Ilves K.L., Torti D., López-Fernández H.. 2018. Exon-based phylogenomics strengthens the phylogeny of Neotropical cichlids and identifies remaining conflicting clades (Cichliformes: Cichlidae: Cichlinae). Mol. Phylogenet. Evol. 118:232–243. PubMed

Irisarri I., Singh P., Koblmüller S., Torres-Dowdall J., Henning F., Franchini P., Fischer C., Lemmon A.R., Lemmon E.M., Thallinger G.G., Sturmbauer C., Meyer A.. 2018. Phylogenomics uncovers early hybridization and adaptive loci shaping the radiation of Lake Tanganyika cichlid fishes. Nat. Commun. 9:3159–12. PubMed PMC

Ivory S.J., Blome M.W., King J.W., McGlue M.M., Cole J.E., Cohen A.S.. 2016. Environmental change explains cichlid adaptive radiation at Lake Malawi over the past 1.2 million year. Proc. Natl. Acad. Sci. USA 113:11895–11900. PubMed PMC

Jarvis E.D., Mirarab S., Aberer A.J., Li B., Houde P., Li C., Ho S.Y.W., Faircloth B.C., Nabholz B., Howard J.T., Suh A., Weber C.C., da Fonseca R.R., Li J., Zhang F., Li H., Zhou L., Narula N., Liu L., Ganapathy G., Boussau B., Bayzid M.S., Zavidovych V., Subramanian S., Gabaldón T., Capella-Gutiérrez S., Huerta-Cepas J., Rekepalli B., Munch K., Schierup M., Lindow B., Warren W.C., Ray D., Green R.E., Bruford M.W, Zhan X., Dixon A., Li S., Li N., Huang Y., Derryberry E.P, Bertelsen M.F., Sheldon F.H., Brumfield R.T., Mello C.V., Lovell P.V., Wirthlin M., Schneider M.P.C., Prosdocimi F., Samaniego J.A., Velazquez A.M.V., Alfaro-Núñez A., Campos P.F., Petersen B., Sicheritz-Ponten T., Pas A., Bailey T., Scofield P., Bunce M., Lambert D.M., Zhou Q., Perelman P., Driskell A.C., Shapiro B., Xiong Z., Zeng Y., Liu S., Li Z., Liu B., Wu K., Xiao J., Yinq X., Zheng Q., Zhang Y., Yang H., Wang J., Smeds L., Rheindt F.E., Braun M., Fjeldsa J., Orlando L., Barker F.K., Jønsson K., Johnson W., Koepfli K.P., O’Brien S., Haussler D., Ryder O.A., Rahbek C., Willerslev E., Graves G.R., Glenn T.C., McCormack J., Burt D., Ellegren H., Alström P., Edwards S.V., Stamatakis A., Mindell D.P., Cracraft J., Braun E.L., Warnow T., Jun W., Gilbert M.T.P., Zhang G.. 2014. Whole-genome analyses resolve early branches in the tree of life of modern birds. Science 346:1320–1331. PubMed PMC

Jiang W., Chen S.Y., Wang H., Li D.Z., Wiens J.J.. 2014. Should genes with missing data be excluded from phylogenetic analyses? Mol. Phylogenet. Evol. 80:308–318. PubMed

Jiang J., Yuan H., Zheng X., Wang Q., Kuang T., Li J., Liu J., Song S., Wang S., Cheng F., Li H., Huang J., Li C.. 2019. Gene markers for exon capture and phylogenomics in ray-finned fishes. Ecol. Evol. 9:3973–3983. PubMed PMC

Jombart T., Kendall M., Almagro-Garcia J., Colijn C.. 2017. treespace: statistical exploration of landscapes of phylogenetic trees. Mol. Ecol. Resour. 17:1385–1392. PubMed PMC

Joyce D.A., Lunt D.H., Bills R., Turner G.F., Katongo C., Duftner N., Sturmbauer C., Seehausen O.. 2005. An extant cichlid fish radiation emerged in an extinct Pleistocene Lake. Nature 435:90–95. PubMed

Kearse M., Moir R., Wilson A., Stones-Havas S., Cheung M., Sturrock S., Buxton S., Cooper A., Markowitz S., Duran C., Thierer T., Ashton B., Meintjes P., Drummond A.. 2012. Geneious basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28:1647–1649. PubMed PMC

Keck B.P., Hulsey C.D.. 2014. Continental monophyly of cichlid fishes and the phylogenetic position of Heterochromis multidens. Mol. Phylogenet. Evol. 73:53–59. PubMed

Kendall M., Colijn C.. 2016. Mapping phylogenetic trees to reveal distinct patterns of evolution. Mol. Biol. Evol. 33:2735–2743. PubMed PMC

Koblmüller S., Duftner N., Sefc K.M., Aibara M., Stipacek M., Blanc M., Egger B., Sturmbauer C.. 2007. Reticulate phylogeny of gastropod-shell-breeding cichlids from Lake Tanganyika – the result of repeated introgressive hybridization. BMC Evol. Biol. 7:7. PubMed PMC

Koblmüller S., Egger B., Sturmbauer C., Sefc K.M.. 2010. Rapid radiation, ancient incomplete lineage sorting and ancient hybridization in the endemic Lake Tanganyika cichlid tribe Tropheini. Mol. Phylogenet. Evol. 55:318–334. PubMed

Kocher T., Conroy J.A., McKaye K.R., Stauffer J.R., Lockwood S.F.. 1995. Evolution of NADH Dehydrogenase Subunit 2 in East African cichlid fish. Mol. Phylogenet. Evol. 4:420–432. PubMed

Kocher T. 2004. Adaptive evolution and explosive speciation: the cichlid fish model. Nat. Rev. Genet. 5:288–298. PubMed

Kubatko L.S. 2009. Identifying hybridization events in the presence of coalescence via model selection. Syst. Biol. 58:478–488. PubMed

Kubatko L.S., Degnan J.H.. 2007. Inconsistency of phylogenetic estimates from concatenated data under coalescence. Syst. Biol. 56:17–24. PubMed

Kubatko L.S., Carstens B.C., Knowles L.L.. 2009. STEM: species tree estimation using maximum likelihood for gene trees under coalescence. Bioinformatics 25:971–973. PubMed

Lanfear R., Calcott B., Ho S.Y.W., Guindon S.. 2012. PartitionFinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses. Mol. Biol. Evol. 29:1695–1701. PubMed

Langmead B., Salzberg S.. 2012. Fast gapped-read alignment with Bowtie2. Nat. Methods 9:357–359. PubMed PMC

Lemmon A.R., Emme S.A., Lemmon E.M.. 2012. Anchored hybrid enrichment for massively high-throughput phylogenomics. Syst. Biol. 61:727–744. PubMed

Li C., Hofreiter M., Straube N., Corrigan S., Naylor G.J.P.. 2013. Capturing protein-coding genes across highly divergent species. Biotechniques 54:321–326. PubMed

Li H. 2013. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv 1303.3997v2 doi: 10.48550/arXiv.1303.3997.

Li H., Durbin R.. 2009. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25:1754–1760. PubMed PMC

Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R., 1000 Genome Project Data Processing Subgroup. 2009. The sequence alignment/map (SAM) format and SAMtools. Bioinformatics 25:2078–2079. PubMed PMC

Litsios G., Salamin N.. 2014. Hybridisation and diversification in the adaptive radiation of clownfishes. BMC Evol. Biol. 14:245. PubMed PMC

Liu L., Wu S., Yu L.. 2015. Coalescent methods for estimating species trees from phylogenomic data. J. Syst. Evol. 53:380–390.

Loh Y.-H.E., Bezault E., Muenzel F.M., Roberts R.B., Swofford R., Barluenga M., Kidd C.E., Howe A.E., Di Palma F., Linbald-Toh K., Hey J., Seehausen O., Salzburger W., Kocher T.D., Streelman J.T.. 2013. Origins of shared genetic variation in African cichlids. Mol. Biol. Evol. 30:906–917. PubMed PMC

López-Fernández H., Arbour J.H., Winemiller K.O., Honeycutt R.L.. 2013. Testing for ancient adaptive radiations in Neotropical cichlid fishes. Evolution 67:1321–1337. PubMed

Maddison W.P. 1997. Gene trees in species trees. Syst. Biol. 46:523–536.

Maglott D., Ostell J., Pruitt K.D., Tatusova T.. 2005. Entrez Gene: gene-centered information at NCBI. Nucleic Acids Res. 33:D52–D57. PubMed PMC

Malinsky M., Svardal H., Tyers A.M., Miska E.A., Genner M.J., Turner G.F., Durbin R.. 2018. Whole-genome sequences of Malawi cichlids reveal multiple radiations interconnected by gene flow. Nat. Ecol. Evol. 2:1940–1955. PubMed PMC

Markert J.A., Schelly R.C., Stiassny M.L.J.. 2010. Genetic isolation and morphological divergence mediated by high-energy rapids in two cichlid genera from the lower Congo rapids. BMC Evol. Biol. 10:149. PubMed PMC

Martin C.H., Cutler J.S., Friel J.P., Dening Touokong C., Coop G., Wainwright P.C.. 2015. Complex histories of repeated gene flow in Cameroon crater lake cichlids cast doubt on one of the clearest examples of sympatric speciation. Evolution 69:1406–1422. PubMed

Matschiner M. 2019. Gondwanan vicariance or trans-Atlantic dispersal of cichlid fishes. A review of the molecular evidence. Hydrobiologia 832:9–37.

Matschiner M., Böhne A., Ronco F., Salzburger W.. 2020. The genomic timeline of cichlid fish diversification across continents. Nat. Commun. 11:5895. PubMed PMC

Matschiner M., Musilová Z., Barth J.M.I., Starostová Z., Salzburger W., Steel M., Bouckaert R.. 2017. Bayesian phylogenetic estimation of clade ages supports Trans-Atlantic dispersal of cichlid fishes. Syst. Biol. 66:3–22. PubMed

Mayer W.E., Tichy H., Klein J.. 1998. Phylogeny of African cichlid fishes as revealed by molecular markers. Heredity 80:702–714. PubMed

McGee M.D., Borstein S.R., Meier J.I., Marques D.A., Mwaiko S., Taabu A., Kishe M.A., O’Meara B., Bruggmann R., Excoffier L., Seehausen O.. 2020. The ecological and genomic basis of explosive adaptive radiation. Nature 586:75–59. PubMed

McMahan C.D., Chakrabarty P., Sparks J.S., Smith W.L., Davis M.P.. 2013. Temporal patterns of diversification across global cichlid biodiversity (Acanthomorpha: Cichlidae). PLoS One 8:e71162. PubMed PMC

Minh B.Q., Hahn M.W., Lanfear R.. 2020a. New methods to calculate concordance factors for phylogenomic datasets. Mol. Biol. Evol. 37:2727–2733. PubMed PMC

Minh B.Q., Schmidt H.A., Chernomor O., Schrempf D., Woodhams M.D., von Haeseler A., Lanfear R.. 2020b. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol. Biol. Evol. 37:1530–1534. PubMed PMC

Meier J.I., Marques D.A., Mwaiko S., Wagner C.E., Excoffier L., Seehausen O.. 2017. Ancient hybridization fuels rapid cichlid fish adaptive radiations. Nat. Commun. 8:14363. PubMed PMC

Meng C., Kubatko L.S.. 2009. Detecting hybrid speciation in the presence of incomplete lineage sorting using gene tree incongruence: a model. Theor. Popul. Biol. 75:35–45. PubMed

Meyer B.S., Matschiner M., Salzburger W.. 2015. A tribal level phylogeny of Lake Tanganyika fishes based on a genomic multi-marker approach. Mol. Phylogenet. Evol. 83:56–71. PubMed PMC

Meyer B.S., Matschiner M., Salzburger W.. 2017. Disentangling incomplete lineage sorting and introgression to refine species-tree estimates for Lake Tanganyika cichlid fishes. Syst. Biol. 66:531–550. PubMed

Miller M.R., Dunham J.P., Amores A., Cresko W.A., Johnson E.A.. 2007. Rapid and cost-effective polymorphism identification and genotyping using restriction site associated NDA (RAD) markers. Genome Res. 17:240–248. PubMed PMC

Miller M.A., Pferiffer W., Schwartz T.. 2010. Creating the CIPRES Science Gateway for inference of large phylogenetic trees. Proceedings of the Gateway Computing Environments Workshop (GCE), New Orleans, LA. p. 1–8.

Mirarab S., Warnow T.. 2015. ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes. Bioinformatics 31:i44–i52. PubMed PMC

Mirarab S., Bayzid M.S., Warnow T.. 2016. Evaluating summary methods for multilocus species tree estimation in the presence of incomplete lineage sorting. Syst. Biol. 65:366–380. PubMed

Morales-Briones D.F., Kadereit G., Tefarikis D.T., Moore M.J., Smith S.A., Brockington S.F., Timoneda A., Yim W.C., Cushman J.C., Yang Y.. 2021. Disentangling sources of gene tree discordance in phylogenomic data sets: testing ancient hybridizations in Amaranthaceae s.l. Syst. Biol. 70:219–235. PubMed PMC

Murphy W.J., Pringle T.H., Crider T.A., Springer M.S., Miller W.. 2007. Using genomic data to unravel the root of the placental mammal phylogeny. Genome Res. 17:413–421. PubMed PMC

Murray A.M. 2001a. The fossil record and biogeography of the Cichlidae (Actinopterygii: Labroidei). Biol. J. Linn. Soc. 74:517–532.

Murray A.M. 2001b. Eocene cichlid fishes from Tanzania, East Africa. J. Vertebr. Paleontol. 20:651–664.

Muschick M., Indermaur A., Salzburger W.. 2012. Convergent evolution within an adaptive radiation of cichlid fishes. Curr. Biol. 22:2362–2368. PubMed

Musilova Z., Indermaur A., Bitja-Nyom A.R., Omelchenko D., Kłodawska M., Albergati L., Remišová K., Salzburger W.. 2019. Evolution of the visual sensory system in cichlid fishes from crater lake Barombi Mbo in Cameroon. Mol. Ecol. 28:5010–5031. PubMed

Near T.J., Dornburg A., Eytana R.I., Keck B.P., Smith W.L., Kuhn K.L., Moore J.A., Price S.A., Burbrink F.T., Friedman M., Wainwright P.C.. 2013. Phylogeny and tempo of diversification in the superradiation of spiny-rayed fishes. Proc. Natl. Acad. Sci. USA 110:12738–12743. PubMed PMC

Nishida M. 1991. Lake Tanganyika as an evolutionary reservoir of old lineages of East African cichfid fishes: inferences from allozyme data. Experiencia 47:974–979.

Nguyen L.-T., Schmidt H.A., von Haeseler A., Minh B.Q.. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol. Biol. Evol. 32:268–274. PubMed PMC

Nute M., Chou J., Molloy E.K., Warnow T.. 2018. The performance of coalescent-based species tree estimation methods under models of missing data. BMC Genomics 19:133. PubMed PMC

Paradis E., Schliep K.. 2019. ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R. Bioinformatics 35:526–528. PubMed

Piálek L., Burress E., Dragová K., Almirón A., Casciotta J., Říçan O.. 2019. Phylogenomics of pike cichlids. (Cichlidae: Crenicichla) of the C. manderlburgeri species complex: rapid ecological speciation in the Iguazú River basin. Hydrobiologia 832:355–375.

Piálek L., Říçan O., Casciotta J., Almirón A., Zrzavý.. 2012. Multilocus phylogeny of Crenicichla (Teleostei: Cichlidae), with biogeography of the C. lacustris group: species flocks as a model for sympatric speciation in rivers. Mol. Phylogenet. Evol. 62:46–61. PubMed

Poll M. 1986. Classification des Cichlidae du lac Tanganika. Tribus, genres et espéces. Acad. R. Belgium Mem. Classe Sci. 45:1–163.

R Core Team. 2015. R: a language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing. http://www.R-project.org/.

Richards E.J., Poelstra J.W., Martin C.H.. 2018. Don’t throw out the sympatric speciation with the crater lake water: fine-scale investigation of introgression provides equivocal support for causal role of secondary gene flow in one of the clearest examples of sympatric speciation. Evol. Lett. 2:524–540. PubMed PMC

Ring U. 2014. The East African Rift System. Aust. J. Earth. Sci. 107:132–146.

Roberts T., Kullander S.O.. 1994. Endemic cichlid fishes of the Fwa River, Zaire: Systematics and ecology. Ichthyol. Explor. Fres. 2:97–154.

Robinson D.R., Foulds L.R.. 1981. Comparison of phylogenetic trees. Math. Biosci. 53:131–147.

Roch S., Steel M.. 2015. Likelihood-based tree reconstruction on a concatenation of aligned sequence data sets can be statistically inconsistent. Theor. Popul. Biol. 100C:56–62. PubMed

Roch S., Warnow T.. 2015. On the robustness to gene tree estimation error (or lack thereof) of coalescent-based species tree methods. Syst. Biol. 64:663–676. PubMed

Ronco F., Matschiner M., Böhne A., Boila A., Büscher H.H., El Taher A., Indermaur A., Malinsky M., Ricci V., Kahem A., Jentoft S., Salzburger W.. 2021. Drivers and dynamics of a massive adaptive radiation in cichlid fishes. Nature 589:76–81. PubMed

Salzburger W. 2018. Understanding explosive diversification through cichlid fish genomics. Nat. Rev. Genet. 19:705–717. PubMed

Salzburger W., Mack T., Verheyen E., Meyer A.. 2005. Out of Tanganyika: Genesis, explosive speciation, key-innovations and phylogeography of the haplochromine cichlid fishes. BMC Evol. Biol. 5:17. PubMed PMC

Salzburger W., Meyer A., Maric S., Verheyen E., Sturmbauer C.. 2002. Phylogeny of the Lake Tanganyika cichlid species flock and its relationship to the central and East African haplochromine cichlid fish faunas. Syst. Biol. 5:113–135. PubMed

Schedel F.D.B., Musilova Z., Schliewen U.K.. 2019. East African cichlid lineages (Teleostei: Cichlidae) might be older than their ancient host lakes: new divergence estimates for the east African cichlid radiation. BMC Evol. Biol. 19:94. PubMed PMC

Schliep K. 2011. phangorn: phylogenetic analysis in R. Bioinformatics 27:592–593. PubMed PMC

Schliewen U.K., Klee B.. 2004. Reticulate sympatric speciation in Cameroonian crater lake cichlids. Front. Zool. 41:5. PubMed PMC

Schliewen U.K., Stiassny M.L.J.. 2003. Etia nguti, a new genus and species of cichlid fish from the River Mamfue, Upper Cross River basin, Cameroon, Central Africa. Ichthyol. Explor. Fres. 14:61–72.

Schliewen U.K., Tautz D., Pääbo S.. 1994. Sympatric speciation suggested by monophyly of crater lake cichlids. Nature 368:629–632. PubMed

Schmieder R., Edwards R.. 2011. Quality control and preprocessing of metagenomic datasets. Bioinformatics 27:863–864. PubMed PMC

Schwarzer J., Lamboj A., Langen K., Misof B., Schliewen U.K.. 2015. Phylogeny and age of chromidotilapiini cichlids (Teleostei: Cichlidae). Hydrobiologia 748:185–199.

Schwarzer J., Misof B., Ifuta S.N., Schliewen U.K.. 2011. Time and origin of cichlid colonization of the lower Congo rapids. PLoS One 6:e22380. PubMed PMC

Schwarzer J., Misof B., Schliewen U.K.. 2012a. Speciation within genomic networks: a case study based on Steatocranus cichlids of the lower Congo rapids. J. Evol. Biol. 25:138–148. PubMed

Schwarzer J., Misof B., Tautz D., Schliewen U.K.. 2009. The root of the East African cichlid radiations. BMC Evol. Biol. 9:186. PubMed PMC

Schwarzer J., Swartz E.R., Vreven E., Snoeks S.M., Cotterill F.P.D., Misof B., Schliewen U.K.. 2012b. Repeated trans-watershed hybridization among haplochromine cichlids (Cichlidae) was triggered by Neogene landscape evolution. Proc. R. Soc. 279:4389–4398. PubMed PMC

Seehausen O. 2006. African cichlid fish: a model system in adaptive radiation research. Proc. R. Soc. B 273:1987–1998. PubMed PMC

Seehausen O. 2015. Process and pattern in cichlid radiations – inferences for understanding unusually high rates of evolutionary diversification. New Phytol. 207:304–312. PubMed

Smith W.L., Chakrabarty P., Sparks J.S.. 2008. Phylogeny, taxonomy, and evolution of Neotropical cichlids (Teleostei: Cichlidae: Cichlinae). Cladistics 24:625–641.

Solís-Lemus C., Ané C.. 2016. Inferring phylogenetic networks with maximum pseudolikelihood under incomplete lineage sorting. PLoS Genet. 12:e1005896. PubMed PMC

Solís-Lemus C., Bastide P., Ané C.. 2017. Phylonetworks: a package for phylogenetic networks. Mol. Biol. Evol. 34:3292–3298. PubMed

Solís-Lemus C., Yang M., Ané C.. 2016. Inconsistency of species tree methods under gene flow. Syst. Biol. 65:843–851. PubMed

Sparks J.S., Smith W.L.. 2004. Phylogeny and biogeography of cichlid fishes (Teleostei: Perciformes: Cichlidae). Cladistics 20:501:517. PubMed

Stamatakis A. 2014. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30:1312–1313. PubMed PMC

Stankiewicz J., de Wit M.J.. 2006. A proposed drainage evolution model for Central Africa—did the Congo flow east? J. Afr. Earth Sci. 44:75–84.

Steel M.A., Penny D.. 1993. Distribution of tree comparison metrics – some new results. Syst Biol 42:126–141.

Stiassny M.L.J. 1987. Cichlid familial interrelationships and the placement of the neotropical genus Cichla (Perciformes, Labroidei). J. Nat. Hist. 21:1311–1331.

Stiassny M.L.J., Alter S.E.. 2021. Life in the fast lane: diversity, ecology, and speciation of cichlids in the lower Congo River. In: Abate M.E., Noakes D.L.G., editors. The behavior, ecology and evolution of cichlid fishes. Dordrecht, The Netherlands: Springer Publishing. p. 107–133.

Stiassny M.L.J., Schliewen U.K., Dominey W.J.. 1992. A new species flock of cichlid fishes from Lake Bermin, Cameroon with a description of eight new species of Tilapia (Labroidei: Cichlidae). Ichthyol. Explor. Fres. 3:311–346.

Streelman J.T., Karl S.A.. 1997. Reconstructing labroid evolution using single-copy nuclear DNA. Proc. R Soc. Lond. B 264:1011–1020. PubMed PMC

Streelman J.T., Zardoya R., Meyer A., Karl S.A.. 1998. Multilocus phylogeny of cichlid fishes (Pisces: Perciformes): evolutionary comparison of microsatellite and single-copy nuclear loci. Mol. Biol. Evol. 15:798–808. PubMed

Suh A., Smeds L., Ellegren H.. 2015. The dynamics of incomplete lineage sorting across the ancient adaptive radiations of Neoavian birds. PLoS Biol. 13:e1002224. PubMed PMC

Sültmann H., Mayer W.E., Figueroa F., Tichy H., Klein J.. 1995. Phylogenetic analysis of cichlid fishes using nuclear DNA markers. Mol. Biol. Evol. 12:1033–1047. PubMed

Svardal H., Quah F.X., Malinsky M., Ngatunga B.P., Miska E.A., Salzburger W., Genner M.J., Turner G.F., Durbin R.. 2020. Ancestral hybridization facilitated species diversification in the Lake Malawi cichlid fish adaptive radiation. Mol. Biol. Evol. 37: 1100–1113. PubMed PMC

Takahashi T., Sota T.. 2016. A robust phylogeny among major lineages of the East African cichlids. Mol. Phylogenet. Evol. 100:234–242. PubMed

Takahashi T., Terai Y., Nishida M., Okada N.. 2001. Phylogenetic relationships and incomplete lineage sorting among cichlid fishes in Lake Tanganyika as revealed by analyses of the insertion retroposons. Mol. Biol. Evol. 18:2057–2066. PubMed

Takahashi T. 2003. Systematics of Tanganyika cichlid fishes (Teleostei: Perciformes). Ichthyol. Res. 50:367–382.

Trewavas E. 1983. Tilapiine fishes of the genera Sarotherodon, Oreochromis and Danakilia. British Museum (Natural History): London.

Turner G.F. 2007. Adaptive radiation of cichlid fish. Curr. Biol. 19:R827–R831. PubMed

Wagner C.E., Harmon L.J., Seehausen O.. 2012. Ecological opportunity and sexual selection together predict adaptive radiation. Nature 487:366–370. PubMed

Wainwright P.C., Smith W.L., Price S.A., Tang K.L., Sparks J.S., Ferry L.A., Kuhn K.L., Eytan R.I., Near T.J.. 2012. The evolution of pharyngognathy: a phylogenetic and functional appraisal of the pharyngeal jaw key innovation in labroid fishes and beyond. Syst. Biol. 61:1001–1027. PubMed

Weiss J.D., Cotterill F.P.D., Schliewen U.K.. 2015. Lake Tanganyika- a ‘melting pot’ of ancient and young cichlid lineages (Teleostei: Cichlidae)? PLoS One 10:e0125043. PubMed PMC

Whitefield J.B., Lockhard P.J.. 2007. Deciphering ancient rapid radiations. Trends Ecol. Evol. 22:258–265. PubMed

Xi Z., Liu L., Davis C.C.. 2016. The impact of missing data on species tree estimation. Mol. Biol. Evol. 33:838–860. PubMed

Yu Y., Degnan L., Nakhleh L.. 2012. The probability of a gene tree topology within a phylogenetic network with applications to hybridization detection. PLoS Genet. 8:e1002660. PubMed PMC

Yu Y., Dong J., Liu K.J., Nakhleh L.. 2014. Maximum likelihood inference of reticulate evolutionary histories. Proc. Natl. Acad. Sci. USA 111:16448–16453. PubMed PMC

Zaccara S., Crosa G., Vanetti I., Binelli G., Harper D.M., Mavuti K.M., Balarin J.D., Britton J.R.. 2014. Genetic and morphological analyses indicate high population mixing in the endangered cichlid Alcolapia flock of East Africa. Conserv. Genet. 15:429–440.

Zebrino D.R., Birney E.. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18: 821–829. PubMed PMC

Zebrino D.R. 2009. extractContigReads. GitHub repository: https://github.com/dzerbino/velvet/blob/master/contrib/extractContigReads/extractContigReads.pl.

Zhang C., Rabiee M., Sayyari E., Mirarab S.. 2018. ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees. BMC Bioinformatics 19:153. PubMed PMC

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