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 O. mykiss 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 O. mykiss. 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/4ks0b0sm03227nas a2200205 4500008004100000245008600041210006900127260007700196300000800273520254000281653002502821653001202846653001302858653001802871653002002889653001702909653002202926100002802948856004502976 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 a

Perhaps 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 O. mykiss 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 O. mykiss. 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 trout10aMicrosatellites10aOncorhynchus10aTruchas Mexicanas1 aAbadía-Cardoso, Alicia uhttp://escholarship.org/uc/item/4ks0b0sm02085nas a2200337 4500008004100000245011300041210006900154260001200223300001200235490000700247520102100254653001401275653001201289653001701301653001501318653000901333653001801342653001701360653002401377653001801401653001501419653002201434100003101456700002601487700002301513700002401536700002601560700002901586700003601615856009601651 2008 eng d00aMitochondrial haplotype variation in wild trout populations (Teleostei: Salmonidae) from northwestern Mexico0 aMitochondrial haplotype variation in wild trout populations Tele c2008/// a33 - 450 v183 a

The variation and composition of Mexican wild trout mitochondrial DNA haplotypes throughout northwestern Mexico was determined by means of polymerase chain reaction-restriction fragment polymorphism analysis (PCR-RFLP), of one region of mitochondrial DNA between cytochrome b and the D-loop. This analysis was based on 261 specimens taken in 12 basins and four hatcheries from northwestern Mexico. From 23 haplotypes, 15 wild trout haplotypes were identified and classified in four groups: (1) one restricted to Nelson's trout (Oncorhynchus mykiss nelsoni), (2) four restricted to R¡o Mayo and R¡oYaqui trout (O. mykiss sspp.), (3) six to Mexican golden trout (O. chrysogaster) with two subgroups, and (4) one exclusive to R¡o Piaxtla trout. Distributions of native haplotypes broadly overlap the distribution of non-native hatchery rainbow trout reflecting the historical management of introductions of exotic rainbow trout and the artificial transference of these trout among basins.

10aChihuahua10aConchos10aCytochrome b10aendangered10aMayo10aMexican trout10aOncorhynchus10aOncorhynchus mykiss10arainbow trout10aSalmonidae10aTruchas Mexicanas1 aCamarena-Rosales, Faustino1 aRuiz-Campos, Gorgonio1 aRosa-Vélez, Jorge1 aMayden, Richard, L.1 aHendrickson, Dean, A.1 aVarela-Romero, Alejandro1 ade León, Francisco, J. García u⬚d:\users\dean_h\reprints in pdf or other\Camarena_2008_Mt_haplotype_Mexican_trout.pdf⬚07129nas a2200625 4500008004100000020001800041245017900059210006900238260014600307300001400453520510100467653001305568653001405581653001705595653001105612653001205623653001405635653001105649653001805660653001105678653001705689653001305706653001605719653001205735653001105747653002205758100002605780700002105806700002405827700001705851700002205868700003105890700002205921700001705943700003105960700002205991700002906013700002306042700003606065700001706101700001606118700002606134700002106160700002606181700002606207700002406233700002206257700002606279700001706305700002606322700002906348700003506377700003606412856005506448 2007 eng d a970-694-336-600aConservation of Mexican native trout and the discovery, status, protection and recovery of the Conchos trout, the first native Oncorhynchus of the Atlantic drainage in Mexico0 aConservation of Mexican native trout and the discovery status pr aMonterrey, Nuevo León, MéxicobDirección de Publicaciones, Universidad Autónoma de Nuevo León, Facultad de Ciencias Biológicasc2007/// a162 - 2013 a

The Northwestern Sierra Madre Occidental of Mexico is a rugged mountain range covering portions of Sonora, Chihuahua, Durango and Sinaloa, and is drained by multiple Pacific Slope Rivers to the west and the Casas Grandes, Conchos, and Nazas to the east. The overall area is topographically, climatically and biotically diverse, ranging from endorheic basins (Casas Grandes) to mountainous areas elevations up to 3348 m, average mean temperatures from 10-20°C and precipitation from 250- 1100 mm/yr. The region is also geological complex that, combined with these other variables, provides a great diversity of both aquatic and terrestrial habitats conducive to both biotic endemicity and diversity. The overall diversity of the region has contribiited to the recent listing of this region by Conservation International as one of six new high-priority biodiversity hotspots. Our understanding of the aquatic and terrestrial biodiversity of this region, however, is poor and in urgent need of rapid investigation by collaborative communities. The combination of an incredibly rugged landscape, drug and bandit activities and indigenous peoples that have not always been welcoming to visitors has resulted in a general paucity of roads in the region, and the lack of access has limited inventory studies. Recently, however, access to the region has changed dramatically and many of the areas are now accessible enough for logging, mining, and agriculture practices, all exerting extreme pressures in some areas on the biodiversity. In addition to human-induced changes to these diverse ecosystems, impacts of invasive aquatic species are becoming more and more apparent, and the potential for severely reducing population sizes of species or their extirpation or extinction is real. While several invasive or exotic species are identified as potentially destructive to these communities, the exotic Rainbow Trout (Oncorhynchus mykiss) that is derived from hatcheries or culture facilities within the region represents one of the most critical threats to the aquatic and semi-aquatic biodiversity. The native trout of mainland Mexico represent the southern- most salmonids, and are at imminent risk of introgression and/or replacement by feral Rainbow Trout, Oncorhynchus mykiss. Our recent survey efforts have expanded the known diversity and ranges of each of several distinct forms, which we feel represent valid species. We discuss our discovery of multiple new species from the Sierra Madre Occidental and focus on a new species of trout restricted to the upper Conchos drainage, the first native species of Oncorhynchus known to occupy the Atlantic Slope in Mexico. Many of these taxa are restricted to small areas of intact habitat in headwater areas of high-elevation streams, and are at risk from a suite of human-associated perturbations, emerging diseases, and introduced species. These fishes occupy unique habitats, and represent a diverse portion of the Mexican montane ichthyofauna. The habitats on which they depend support a wide range of other aquatic organisms, most of which are grossly understudied. The discovery of the Conchos Trout derived primarily by GARP niche modeling of a subset of localities of previously sampled undescribed native Mexican trout, provides only a snapshot of the biodiversity awaiting to be discovered in this region. The rugged landscape of the Sierra Madre Occidental simply precludes routine sampling at easily accesible locations of streams and most sampling locations require time-intensive access. In an effort to rapidly assess the biodiversity of rivers of this region we employed this method to aid in predicting the most suitable and highly probable Mexican trout niches in the region. This method offered highly efficient and powerful results that not only predicted the occurrence of a previously unknown trout in the upper Rio Conchos but also provided excellent predictions of available habitats in drainages where previously unknown trout have been discovered by the Truchas Mexicanas team in the last nine years. Multiple threats exist to the biodiversity of the northern Sierra Madre Occidental, including uncontrolled introductions of exotic and invasive species, emerging diseases such as whirling disease, Myxobolus cerebralis, infectious pancreatic necrosis (IPN), iridioviruses and pathogenic water mold, Saprolegnia ferax, land-use practices leading to habitat degradation via overgrazing, logging, deforestation and road construction, increasing human population growth, over-fishing or overharvesting of aquatic resources and global climate cliange reducing surface and ground water in the area and creating environments more conducive to the spread of invasive species, congregated and dense human populations, and emerging diseases. Immediate actions need to be developed to aid in public education as to the threats to these ecosystems, protection of areas, assessment of diversity, and sustainable development throughout the region that incorporates a likely highly successful ecotourism system for the region.

10aAtlantic10aChihuahua10aconservation10adesert10aDurango10aEcosystem10afishes10aMexican trout10aMEXICO10aOncorhynchus10arecovery10aRio Conchos10aSinaloa10aSonora10aTruchas Mexicanas1 aHendrickson, Dean, A.1 aNeely, David, A.1 aMayden, Richard, L.1 aAnderson, K.1 aBrooks, James, E.1 aCamarena-Rosales, Faustino1 aCutter, Ralph, F.1 aCutter, Lisa1 aCamarillo, Ana, Belia De L1 aErnsting, Guy, W.1 aEspinosa-Pérez, Héctor1 aFindley, Lloyd, T.1 ade León, Francisco, J. García1 aGeorge, A.L.1 aHatch, John1 aKuhajda, Bernanrd, R.1 aMayden, Kyle, E.1 aMcNyset, Kristina, M.1 aNielsen, Jennifer, L.1 aPfeiffer, Frank, W.1 aPropst, David, L.1 aRuiz-Campos, Gorgonio1 aSt.Clair, E.1 aTomelleri, Joseph, R.1 aVarela-Romero, Alejandro1 aLozano-Vilano, Ma., de Lourdes1 aContreras-Balderas, Armando, J. uhttps://truchasmexicanas.myspecies.info/es/node/15