Diversity and evolution of the Middle American cichlid fishes (Teleostei: Cichlidae) with revised classification

We present a taxonomically complete and topologically robust molecular phylogeny of the Middle American heroine cichlids based on which we review their diversity and genus-level systematics. In order to ascertain the diversity of the group and its phylogeny we have used three nested taxon sampling analyses of the concatenated nDNA/mtDNA datasets and additionally to these analyses we present a summary of the results of a new Next Generation Sequencing-generated nuclear phylogeny based on a data set of ~ 140,000 informative characters. The NGS ddRAD phylogeny has a species-level sampling covering virtually all species (including the enigmatic Cichlasoma microlepis Dahl, 1960) with multiple sequenced specimens per species. Based on our results the Middle American heroine cichlids are made up of three main clades. The three clades (the herichthyines, the amphilophines, and the astatheroines) are however not each other sister groups since they are interspersed with South American (Australoheros, Caquetaia, Chocoheros, Heroina, Mesoheros) and Antillean (Nandopsis) genera and they represent probably two separate colonization events of Middle America from South America, probably via the Antilles. Our study reveals many cases of cytonuclear discordance and/or introgressive hybridization both at the genus and deeper levels stressing the importance to study the nuclear and mitochondrial phylogenetic signals independently and not solely in concatenated analyses. We have found that a great majority of morphological characters are ecologically correlated and that they form only a limited number of functionally-determined combinations – i.e. ecomorphs. We have found five main cranial ecomorphs but only two postcranial ecomorphs (the lotic and lentic ecomorphs, plus the undifferentiated ancestral character combination). The cranial and postcranial ecomorphs are not combined completely randomly having produced thirteen modular whole-body ecomorphs. Both the cranial and postcranial ecomorphs, and even their combinations, have evolved repeatedly in the Middle American cichlids in the same habitats both in sympatry as well as in allopatry. Our analyses of the diversity of Middle American cichlid clade support the existence of 31 genera in Middle America (plus six in South America and one in the Greater Antilles) as separate evolutionary lineages occupying separate adaptive zones. Nine new genera are described here for species and species groups that have lacked a genus level name to this day or were associated with other unrelated genera. We also review the species level diversity based on the mtDNA cytb gene population-level analysis. Furthermore, we provide a new biogeographical analysis of the group which explains their evolutionary history and demonstrates that biogeography is a much better indicator of evolutionary relationships in this fish group than are most morphological characters due to their ecological correlation.