Data from: Phylogeography and species delimitation in convict cichlids (Cichlidae: Amatitlania): implications for taxonomy and Plio–Pleistocene evolutionary history in Central America

We investigate phylogeographic patterns and delimit species boundaries
within Amatitlania, a genus of Central American cichlid fishes.
Phylogenetic analyses of mitochondrial DNA sequences from 318 individuals
spanning the geographical ranges of all three currently recognized
Amatitlania species strongly supported one major clade, with a relatively
diverged subclade corresponding to A. kanna samples from eastern Costa
Rica and Panama. Gene trees and networks revealed marked incongruences
between phylogeographic structure and morpho-species taxonomy as a result
of species-level polyphyly. Bayes factor comparisons of species
delimitation models accounting for incomplete lineage sorting under the
multispecies coalescent decisively supported the recognition of two
distinct species within Amatitlania corresponding to Amatitlania
nigrofasciata and A. kanna lineages. The only clearly genetically and
morphologically diagnosable species was A. kanna. These results strongly
suggest that incomplete lineage sorting provides the best explanation for
the polyphyly of A. kanna, whereas the polyphyly of A. siquia is likely a
result of an imperfect taxonomy. Additional insights from
coalescent-dating, network, and historical demographic analyses suggested
that the two species of Amatitlania diversified only since the early
Pleistocene, and that A. nigrofasciata experienced population expansions
from approximately 200 000 years ago in the mid-late Pleistocene onward.
We discuss implications of our results for the taxonomy and evolutionary
history of Amatitlania and, more broadly, of Central American freshwater
fishes.