Information from intraspecific studies as well as data on sister taxa and endemicity would be useful - after all, the only difference between cryptic species and species is that one happened to evolve some phenotypic traits too!
1. yellowfin shiner, Notropis lutipinnis:
Two patterns here - the mitochondrial and nuclear partitions tell distinct stories. I think.
The mitochondrial data exhibit a roughly east-to-west pattern of divergence by drainage: the Flint river is monophyletic (but small sample); a diverse clade containing mostly fish from Chattahoochee, Altamaha, Etowah, some Savannah, some Little Tennessee; middle-of-the-tree haplotype diversity associated with the Little Tennessee; and then another clade of mostly Savannah, Santee (but also some Etowah, some Chattahoochee, some Little Tennessee).
The nuclear data (also backed up by some microsatellite work by Christine, unpublished) harbors two clades: one is predominantly ACF/Altamaha, the other is predominantly everything else, but not as mutually exclusive.
2. Genetic calibration of species diversity among North America' freshwater fishes
Standard Reference Library for 752 North American Freshwater Species
138 named species may represent as many as 347 candidate species, this study identifies 151 fish species for which taxonomic revision is required
Freshwater ecosystems are being heavily exploited and degraded by human activities all over the world, including in North America, where fishes and fisheries are strongly affected. Despite centuries of taxonomic inquiry, problems inherent to species identification continue to hamper the conservation of North American freshwa- ter fishes. Indeed, nearly 10% of species diversity is thought to remain undescribed. To provide an independent calibration of tax- onomic uncertainty and to establish a more accessible molecular identification key for its application, we generated a standard reference library of mtDNA sequences (DNA barcodes) derived from expert-identified museum specimens for 752 North American freshwater fish species. This study demonstrates that 90% of known species can be delineated using barcodes. Moreover, it reveals numerous genetic discontinuities indicative of indepen- dently evolving lineages within described species, which points to the presence of morphologically cryptic diversity. From the 752 species analyzed, our survey flagged 138 named species that rep- resent as many as 347 candidate species, which suggests a 28% increase in species diversity. In contrast, several species of parasitic and nonparasitic lampreys lack such discontinuity and may repre- sent alternative life history strategies within single species. Therefore, it appears that the current North American freshwater fish taxonomy at the species level significantly conceals diversity in some groups, although artificially creating diversity in others. In addition to providing an easily accessible digital identification system, this study identifies 151 fish species for which taxonomic revision is required.
3. Supplementary Information for Genetic calibration of species diversity .........
Methods for Genetic Calibration paper. They use COI cocktail with M13 sequencing primers
Note the parsimony network for Nocomis