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. 2017 Feb 24;12(2):e0172349.
doi: 10.1371/journal.pone.0172349. eCollection 2017.

One Species or Four? Yes!...and, No. Or, Arbitrary Assignment of Lineages to Species Obscures the Diversification Processes of Neotropical Fishes

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One Species or Four? Yes!...and, No. Or, Arbitrary Assignment of Lineages to Species Obscures the Diversification Processes of Neotropical Fishes

Stuart C Willis. PLoS One. .
Free PMC article


Species are fundamental units in many biological disciplines, but there is continuing disagreement as to what species are, how to define them, and even whether the concept is useful. While some of this debate can be attributed to inadequate data and insufficient statistical frameworks in alpha taxonomy, an equal part results from the ambiguity over what species are expected to represent by the many who use them. Here, mtDNA data, microsatellite data, and sequence data from 17 nuclear loci are used in an integrated and quantitative manner to resolve the presence of evolutionary lineages, their contemporary and historical structure, and their correspondence to species, in a species complex of Amazonian peacock "bass" cichlids (Cichla pinima sensu lato). Results suggest that the historical narrative for these populations is more complex than can be portrayed by recognizing them as one, two, or four species: their history and contemporary dynamics cannot be unambiguously rendered as discrete units (taxa) at any level without both choosing the supremacy of one delimitation criterion and obscuring the very information that provides insight into the diversification process. This calls into question the utility of species as a rank, term, or concept, and suggests that while biologists may have a reasonable grasp of the structure of evolution, our methods of conveying these insights need updating. The lack of correspondence between evolutionary phenomena and discrete species should serve as a null hypothesis, and researchers should focus on quantifying the diversity in nature at whatever hierarchical level it occurs.

Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.


Fig 1
Fig 1. Map of sampling sites and the distribution of mitochondrial DNA clades (from Fig 2) and microsatellite clusters (K* = 2; Fig 4) for Cichla pinima sensu lato.
The pie chart for each locality shows the proportion of individuals bearing The inset shows distributions of all of the species of Cichla clade A.
Fig 2
Fig 2. Mitochondrial DNA genealogy of Cichla clade A.
Node values are posterior clade probability. For Cichla pinima sensu lato (indicated in bold), the localities where those clades were observed, as well which described species (C. pinima sensu stricto, C. jariina, C. vazzoleri, C. thyrorus) were observed in each clade, are denoted. Locality codes follow Table 1 and Fig 1, and the values associated with some localities are (the number of individuals bearing haplotypes from that clade / total individuals collected at that locality). For the endemic western lineages (yellow), each is labeled to match the mtDNA reference in Fig 4 (A,B,C). A fully annotated version of this genealogy is presented as S1 Fig.
Fig 3
Fig 3. Heat map for genetic distances between sampling localities of Cichla pinima sensu lato.
Below diagonal, FST (11 loci); above diagonal, RST (9 loci), after S3 Table. The “core” regions are indicated: “WC”, western core; “SC”, southern core.
Fig 4
Fig 4. Structure results for 11 microsatellite loci from Cichla pinima sensu lato.
Pop = 0, no sample pre-assignment; Pop = 1, some samples pre-assigned to K clusters, indicated by the bars above the Structure plots. The distribution of mtDNA clades (after Fig 1) is provided for reference. Locality codes follow Table 1 and Fig 1.
Fig 5
Fig 5. Species trees for each dataset arrangement under the optimal, four-species model from Bayes Factor Delimitation (BFD) of Cichla pinima sensu lato.
Note: the no mtDNA-upstream only dataset was utilized with the same model but not subjected to path sampling analysis (see Table 2).
Fig 6
Fig 6. Conceptual model for the historical narrative of Cichla.
Solid lines represent natural hybridization (red, recent; green, ancient), while blue dashed lines represent hybridization in anthropogenically altered conditions. Branch lengths are not proportional. See text for details.

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Grant support

The author received no specific funding for this work.