Abstract
BackgroundIntrogression likely plays a significant role in evolution, but understanding the extent and consequences of this process requires a clear identification of species boundaries in each focal group. The delimitation of species, however, is a contentious endeavor. This is true not only because of the inadequacy of current tools to identify species lineages, but also because of the inherent ambiguity between natural populations and species paradigms. The result has been a debate about the supremacy of various species concepts and criteria. Here, we utilized multiple separate sources of molecular data, mtDNA, nuclear sequences, and microsatellites, to delimit species under a polytypic species concept (PTSC) and estimate the frequency and genomic extent of introgression in a Neotropical genus of cichlid fishes (Cichla). We compared our inferences of species boundaries and introgression under this paradigm to those when species are identified under a diagnostic species concept (DSC).ResultsWe find that, based on extensive molecular data and an inclusive species concept, 8 separate biological entities should be recognized rather than the 15 described species of Cichla. Under the PTSC, fewer individuals are expected to exhibit hybrid ancestry than under the DSC (~2% vs. ~12%), but a similar number of the species exhibit introgression from at least one other species (75% vs. 60%). Under either species concept, the phylogenetic breadth of introgression in this group is notable, with both sister species and species from different major mtDNA clades exhibiting introgression.ConclusionsIntrogression was observed to be a widespread phenomenon for delimited species in this group. While several instances of introgressive hybridization were observed in anthropogenically altered habitats, most were found in undisturbed natural habitats, suggesting that introgression is a natural but ephemeral part of the evolution of many tropical species. Nevertheless, even transient introgression may facilitate an increase in genetic diversity or transfer of adaptive mutations that have important consequences in the evolution of tropical biodiversity.
Highlights
Introgression likely plays a significant role in evolution, but understanding the extent and consequences of this process requires a clear identification of species boundaries in each focal group
Removal of redundant sequences from each of the four sequence sets aligned separately resulted in 11 haplotypes in C. intermedia, 61 haplotypes in C. orinocensis, 154 haplotypes in C. monoculus and the remaining clade B1 species, and 98
As in our previous analyses [32,34], three major lineages (A, B1, and B2) are defined by the mtDNA data set but, with the new data, 16 divergent monophyletic groups of haplotypes are highly supported (Figure 2). These 16 clades are distinguished by the length of their subtending branches and their restricted distribution geographically and/or morphologically
Summary
Introgression likely plays a significant role in evolution, but understanding the extent and consequences of this process requires a clear identification of species boundaries in each focal group. Despite the ambiguous correspondence between species concepts and natural groups, most biologists implicitly or explicitly consider species to be real entities reflecting the discontinuous nature of biological variation [17], and individuals ascribed to a given species are often treated interchangeably in an array of biological investigations [18,19,20,21] This implies an expectation that there should be some natural distinction between introgressive hybridization and intraspecific gene flow, a conjecture that can be investigated in nature by surveying large numbers of individuals and examining them for phenotypic and genetic disjunctions [i.e. multimodality along continuous axes of variation; 10]. It should be directly clear from this kind of data what qualifies as introgression rather than intraspecific gene exchange [22], but it is possible to consider inferences about hybridization and introgression in light of different species concepts and criteria [23]
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