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| Allohistium anas Near & MacGuigan, in MacGuigan, Taylor, Ghezelayagh, Wood, Simmons, Mollish et Near, 2025. Cinder Darter || DOI: doi.org/10.1093/sysbio/syaf083 |
Abstract
Biologists have relied on morphological characteristics to identify, define, and formally describe species for the past 250 years. The advent of phylogenetic species concepts and the introduction of molecular data have spawned new species delimitation methods applicable to a wide range of eukaryotic lineages. However, these approaches heavily emphasize genomic data, often overlooking phenotypic traits. We present and implement a species delimitation approach that utilizes genome-wide markers from ddRAD-seq and meristic morphological traits, which have long been used to identify and delineate fish species. Our methodology employs unsupervised machine learning to analyze morphological data without a priori species assignments, allowing phenotypic patterns to emerge independently from genomic-based species delimitation. We apply our combined genomic and phenotypic methodology to the freshwater systems of Southeastern North America, a biodiversity hotspot where conservation efforts are hampered by an incomplete knowledge of species diversity. Our investigation focuses on the darter clade Allohistium, a threatened lineage comprising two described species. Through phylogenomic, population genetic, and phenotypic model comparisons, we provide evidence supporting the delimitation of a third species of Allohistium, which we formally describe. Our approach shows how unsupervised machine learning can reveal cryptic morphological diversity that might otherwise be obscured by taxonomic preconceptions. This study demonstrates that model testing using diverse lines of evidence yields a more comprehensive, data-driven hypothesis of species diversity.
Darters, ddRAD-seq, methodology, North America, phenotype, species delimitation
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| Live photographs of Allohistium specimens. Photo credit to Jon M. Mollish. YPM = Yale Peabody Museum, YFTC = Yale Fish Tissue Collection. |
Allohistium anas Near and MacGuigan new species
Cinder Darter
Diagnosis. Allohistium anas differs from Allohistium cinereum and Allohistium maydeni by a higher number of lateral line scales (Supplementary Table S4), modally 43 versus 42 vertebrae (Shepard and Burr 1984), a larger proportion of individuals with greater than 80% of the cheek covered with scales, and more than 50% of the individuals with 10–40% of the nape covered with scales. In addition, Allohistium anas is never resolved as the sister lineage of Allohistium cinereum sensu stricto in mtDNA gene trees (Powers et al. 2004, 2012) or phylogenomic analyses of ddRAD-seq loci (see below). Allohistium maydeni differs from Allohistium anas and Allohistium cinereum in having modally 11 versus 12 dorsal fin spines (Supplementary Table S5; Powers et al. 2012), 12 versus 13 dorsal fin rays (Supplementary Table S6; Powers et al. 2012), and the presence of conspicuous red coloration on the skin covering the upper and lower oral jaws (Fig. 2).
Etymology. The species name anas is from the Latin word for duck, in reference to the distribution of the species in the Duck River system. The common name Cinder Darter is in reference to the common name of A. cinerum, the Ashy Darter.
Daniel J MacGuigan , Adam Taylor , Ava Ghezelayagh , Julia E Wood , Jeffrey W Simmons , Jon M Mollish and Thomas J Near. 2025. Genomic and Phenotypic Delimitation of Species in a Temperate Aquatic Biodiversity Hotspot. Systematic Biology. syaf083. DOI: doi.org/10.1093/sysbio/syaf083 [27 November 2025]
