Species identification of Klamath Basin suckers (Pisces : Catostomidae) and an assessment of hybridization using anonymous nuclear loci Public Deposited

http://ir.library.oregonstate.edu/concern/graduate_thesis_or_dissertations/1n79h685f

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  • Low copy number anonymous nuclear loci were used to search for species markers in four species of Klamath Basin suckers. We sequenced 28 randomly chosen loci representing 10,421 bp; 21 loci were similar to sequences in GenBank. Eight fixed sequence differences were found among Klamath species. Locus 120 contained rare but diagnostic markers for Deltistes luxatus and for Catostomus rimiculus. Locus 4 also contained three rare but unique sites in Catostomus rimiculus. No sequence differences were found between Chasmistes brevirostris and Catostomus snyderi. Loci 4 and 120 exhibited allele frequency differences between Rogue River C. rimiculus and all Klamath Basin suckers. Genotype BB of locus 4 was a fixed diagnostic marker and genotype BB of locus 120 was a frequency dependent marker for Rogue C. rimiculus. Although Klamath suckers represent three genera, very limited variation was found among 10,431 base pairs. We examined phylogenetic patterns of five loci in eleven catostomid genera and 25 species to determine if the homogeneity in the Upper Klamath Basin was due to massive hybridization and introgression or to retention of ancestral sequences. Two loci with no similarity to GenBank sequences (non-coding loci) and three loci with substantial similarity to GenBank sequences (coding loci) gave similar results, providing support for various subfamilies and tribes, more support for eastern genera and little support for western genera. Each locus was a mosaic of species or population markers, sometimes providing discriminatory power for allopatric populations of a species, such as C. macrocheilus, while not discriminating other species. Upper Klamath Basin species were noteworthy in their lack of autapomorphies, but had similar numbers of derived informative sites as other catostomins. Upper Klamath Basin species consistently shared ancestral or equivocal informative sites either with moxostomatins or a variable group of western species and shared derived sites with other western species, especially C. occidentalis. The data suggest that Upper Klamath Basin species have retained a largely ancestral genome at these loci. Thus, the failure of this technique to uncover significant variation in Upper Klamath Basin species may be a reflection of their plesiomorphic genome at these loci and not necessarily hybridization.
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