Taxonomic Relationships: The systematics of tui chubs are confusing because there are many populations that are outwardly morphologically similar but genetically divergent. Not only do many isolated drainages in the Great Basin have their own distinctive populations, but many large lake populations have two sympatric morphs a pelagic form with many fine gillrakers and a benthic form with fewer, courser gillrakers. Compounding the taxonomic confusion are incomplete meristic and genetic studies.
Almost all prominent ichthyologists who have worked with the native fishes of the Great Basin have voiced an opinion about S. b. pectinifers taxonomy. Rarely have those opinions agreed. The range of opinions has spanned the entire gamut from no valid standing as a taxonomic unit (La Rivers 196, p. 420) to having been assigned its own genus by J. O. Snyder in 1917. Consequently, La Rivers (1962) considered S. b. pectinifer to have the most complex taxonomic history of any member of the Great Basin fish fauna. It was first described as Leucidius pectinifer by Snyder (1917) who simultaneously described the sympatric stream form as Siphateles obesus notice that the morphological differences between morphs were great enough for Snyder to place obesa and pectinifer in different genera. Hubbs and Miller (1943) considered L. pectinifer to be a subspecies of Siphateles obesus and thus called it Siphateles obesus pectinifer. Shapovalov and Dill (1950) recognized that both forms were part of the Siphateles bicolor complex and renamed them S. b. pectinifer and S. b. obesus, respectively. Bailey and Uyeno (1964) designated Siphateles as a subgenus of Gila and designated the fine gill raker tui chub as Gila bicolor pectinifer. However, biochemical evidence suggests that the tui chubs are more closely related to other Californian minnows than they are to other species of Gila (Simons and Mayden 1998). In light of this evidence, Moyle (2002) resurrected the generic name Siphateles, first used by Cope (1883) and popularized by Snyder (1918).
Presently there are ten Siphateles taxa recognized in California (Moyle 2002), although three lack formal taxonomic descriptions: Lahontan lake tui chub (Siphateles bicolor pectinifer), Eagle Lake tui chub, (S. b. ssp.), Goose Lake tui chub (S. t. thalassinus), Cow Head tui chub (S. thalassinus vaccaceps), High Rock Spring tui chub (S. b. ssp.), Owens tui chub (S. b. snyderi), Mohave tui chub (S. mohavensis), Lahontan creek tui chub (S. b. obesa), Klamath tui chub (S. b. bicolor), and Pit River tui chub (S. b. ssp.). The first four subspecies are included in this report, while the Owens and Mohave tui chubs are already listed as endangered species by both state and federal governments. The Pit River tui chub was listed by Hubbs et al. (1979) as an undescribed subspecies. The tui chub of the upper Pit River are now considered to be part of the Goose Lake population (Chen et al. 2009) but questions remain about the taxonomic affinities of the tui chub of the lower Pit River basin. The High Rock Springs tui chub is extinct.
Recent genetic studies have shown that considerable variation exists among populations of tui chub all of which were formerly classified as subspecies of S. bicolor (Harris 2000, Chen et al. 2007, Chen et al. 2009). Hence, the subspecific status of S. b. pectinifer remains controversial. Not only is the zoogeographic range of S. b. pectinifer contained within that of S. b. obesa but Harris (2000) suggested that S. b. obesa should be elevated to species status and that S. b. pectinifer be submerged within it.
Conversely, studies in both Lake Tahoe and Pyramid Lake, Nevada, indicate that the two forms segregate ecologically (Miller 1951, Galat and Vucinich 1983) and do not interbreed. The existence of sympatric, morphologically distinct tui chub morphs has been repeatedly and consistently observed in large lakes throughout the range of Siphateles, most famously in Pyramid Lake and Lake Tahoe but also in Walker Lake, Goose Lake, Eagle Lake and Honey Lake among others. The main character distinguishing the morphs is number and morphology of gill rakers, although only in Pyramid Lake and Lake Tahoe are the two morphs clearly separated.
It is possible that the distinctive fine gill raker form of tui chub has arisen multiple times in each of these large lake systems, although it may be just a single lineage in the Truckee basin. Similar situations of parallel evolution in California fish taxa may exist, for example, in the run timing of summer steelhead populations and in bony plate development and migratory behavior of threespine stickleback in coastal California streams. A sizeable literature has developed on trophic polymorphism; of particular relevance to the lake tui chub are trophic polymorphisms among other fishes in lacustrine environments. Examples include char in arctic lakes, whitefish in Canadian and Idaho Lakes, cichlids in African Rift Lakes, threespine stickleback in British Columbia lakes and sunfish in the eastern United States. The papers are too numerous to cite here but can be found compiled in reviews on the subject by Smith and Skulason (1996) and more recently by Dayan and Simberloff (2005). Until taxonomic studies are completed, all potential populations of this form should be managed as distinctive taxa.