03319nas a2200253   4500008004100000245008600041210006900127260007700196300000800273520249100281653002502772653001202797653001302809653001802822653002002840653001702860653001402877653001802891653002402909653003702933653002202970100002802992856004503020       2014                        eng d00aGenetic Investigation Of The Pacific Trout Complex: From Pedigrees To Phylogenies0 aGenetic Investigation Of The Pacific Trout Complex From Pedigree  aSanta Cruz, CaliforniabUniversity of California Santa Cruzc2014/01/01/  a1643 aPerhaps one of the world's most important groups of fish are the species within the Pacific trout complex, due to their harvest in fisheries and use in aquaculture. This dissertation consists of an in-depth evaluation of this group at different scales, from the assessment of biological traits throughout the reconstruction of pedigrees in two populations to a phylogeographic examination of multiple largely undescribed species. Here, a combination of novel molecular techniques allowed me to address critical ecological questions for the management and conservation of this group.In chapter one, I describe the discovery, characterization and development of single nucleotide polymorphisms for <italic>O. mykiss<italic> for the study of ecological interactions, phylogeography, and conservation status. These tools have great power for population genetic analysis, and for individual identification and pedigree reconstruction. The last allows the tracking of families, and an unprecedented level of evaluation of natural and hatchery populations.Chapter two expands the scope of these molecular tools to provide a powerful means of understanding of biological traits for steelhead hatchery programs in the Russian River, California. Reconstruction of cohort age distributions revealed a strong component of fish that spawn at age two, in contrast to program goals and distinct from naturally spawning steelhead. Correlations between family members in the day of spawning revealed a strongly heritable component to this life history trait and demonstrated the potential for selection to alter life history traits. These results demonstrate the promise of SNP-based pedigree reconstruction for providing biological inference in high-fecundity organisms.Chapter three describes how the molecular tools developed were applied to population genetics of trout inhabiting northwestern Mexico, to elucidate biodiversity, and evolutionary history, and measure introgression from hatchery rainbow trout. Here, I confirmed the vast genetic diversity present in northwestern Mexican trout and provided evidence that trout inhabiting the Sierra Madre Occidental correspond to independent lineages separated from <italic>O. mykiss<italic>. Introgression from non-native trout was detected, but the genetic integrity of native trout is still maintained. All the information presented in this document will help to guide effective conservation strategies for this globally important group of fishes.10aConservation biology10aEcology10aGenetics10aMexican trout10aMicrosatellites10aOncorhynchus10aPedigrees10aPhylogenetics10aPopulation genetics10aSingle nucleotride polymorphisms10aTruchas Mexicanas1 aAbadía-Cardoso, Alicia  uhttp://escholarship.org/uc/item/4ks0b0sm02005nas a2200325   4500008004100000020001400041245008800055210006900143260001600212300001600228490000700244520098600251653002601237653002601263653001801289653002401307653001801331653002801349653002201377100002301399700003401422700002101456700003601477700001701513700003501530700002201565700002201587700002201609856004801631       2014                        eng d  a1566-062100aGenetic introgression of cultured rainbow trout in the Mexican native trout complex0 aGenetic introgression of cultured rainbow trout in the Mexican n  c2014/10/01/  a1063 - 10710 v153 a<p>The Mexican native trout complex is the group of salmonids that naturally has the southernmost distribution in the world. Despite its unique status and evidence of more than 13 distinct lineages, there are only two described species (Oncorhynchus mykiss nelsoni and O. chrysogaster). These fishes are threatened by environmental and anthropogenic factors, most notably the introduction of the exotic species O. mykiss (rainbow trout) for aquaculture. Here we applied population genetics analysis in 1,017 wild and cultured trout to understand the extent of genetic introgression of rainbow trout in Mexican native trout. Present results indicate a high degree of introgression and genetic admixture among introduced rainbow trout and some populations of Mexican native trout, exposing them to loss of genetic diversity. Thus, introduction of exotic trout for aquaculture purposes must be strictly regulated or avoided and we advise the use of native trout for aquaculture.</p>
10aGenetic hybridization10agenetic introgression10aMexican trout10aNorthwestern Mexico10arainbow trout10aSierra Madre Occidental10aTruchas Mexicanas1 aEscalante, MarcoA.1 aGarcía-De-León, FranciscoJ.1 aDillman, CaseyB.1 aCamarillo, Anabelia, de los San1 aGeorge, Anna1 aBarriga-Sosa, Irene, de los A.1 aRuiz-Luna, Arturo1 aMayden, RichardL.1 aManel, Stéphanie  uhttp://dx.doi.org/10.1007/s10592-014-0599-7