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Reproductive phenology of fishes of the Rio Grande, New Mexico : a genes-to-community approach


Please use this identifier to cite or link to this item: http://hdl.handle.net/1928/21050

Reproductive phenology of fishes of the Rio Grande, New Mexico : a genes-to-community approach

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dc.contributor.author Krabbenhoft, Trevor James
dc.date.accessioned 2012-08-28T16:31:20Z
dc.date.available 2012-08-28T16:31:20Z
dc.date.issued 2012-08-28
dc.date.submitted July 2012
dc.identifier.uri http://hdl.handle.net/1928/21050
dc.description.abstract Reproductive phenology is a key life history attribute of long lived organisms that can strongly affect reproductive success and, ultimately, drive community composition. Understanding the ecological causes and consequences and genetic mechanisms shaping reproductive timing is key to predicting the outcome of environmental change (e.g., climate change). The three chapters that comprised this dissertation were focused on elucidating the ecological and genetic underpinnings of reproductive timing in the fish community of an arid-land river, the Rio Grande, New Mexico. In Chapter 1, we assessed reproductive phenology in the Rio Grande fish community with four years of young-of-year sampling data and spanning 16 years, from 1995 to 2010. Spawning data suggested that, in addition to known spatial habitat partitioning of resources, species also partition resources temporally by differential spawning periodicity. Inter-annual variation in environmental conditions (e.g., river discharge) appears to drive community-level shifts in reproductive phenology. However, the magnitude of phenological shifts differed among species. We discuss these data in light of biotic-interactions among species and scenarios for future climate change. In Chapter 2, we examined within- and among-species DNA sequence variation in a candidate gene, Clock, which is a key circadian rhythm gene that may shape reproductive phenology of fishes of the Rio Grande. Previous research has demonstrated a role for Clock in migratory and reproductive timing in disparate organisms, from songbirds to salmon. In this study, we tested whether patterns of allele length variation in Clock are consistent with: (1) among-species differences in reproductive timing, (2) phylogenetic inertia, or (3) functional-constraint in this key circadian gene. We present evidence that all three of these evolutionary processes may shape patterns of variation in Clock observed in Rio Grande fishes. Finally, in Chapter 3 we broadened our search for genetic underpinnings of reproductive timing beyond Clock, to assess amino acid sequence variation in dozens of candidate genes among three species of Rio Grande cyprinid fishes: fathead minnow (Pimephales promelas), red shiner (Cyprinella lutrensis), and Rio Grande silvery minnow (Hybognathus amarus). We used next-generation 454 DNA sequencing to characterize the transcriptomes and explore sequence level variation among these three species. Using gene ontology analysis, we identified 86 candidate genes with functions potentially associated with reproductive timing and circadian rhythms. The 86 candidate genes had a total of 342 inferred amino acid substitutions among the three species, which could have functional implications and underlie some of the species-specificity in reproductive biology of these three species. Additionally, fifteen of the candidate genes had simple sequence repeats in their inferred amino acid sequences, which might be targets of natural selection for shaping circadian rhythms and reproduction. The variation described in this study affords candidate loci for future comparative studies of reproductive timing.   en_US
dc.language.iso en_US en_US
dc.subject reproductive phenology en_US
dc.subject spawning periodicity en_US
dc.subject clock genes en_US
dc.subject comparative biology en_US
dc.subject transcriptomics en_US
dc.subject next-generation sequencing en_US
dc.subject functional genomics en_US
dc.subject ecology en_US
dc.subject fish en_US
dc.subject.lcsh Fishes--Reproduction--Environmental aspects--Rio Grande (Colo.-Mexico and Tex.)
dc.subject.lcsh Phenology--Rio Grande (Colo.-Mexico and Tex.)
dc.title Reproductive phenology of fishes of the Rio Grande, New Mexico : a genes-to-community approach en_US
dc.type Dissertation en_US
dc.description.degree Biology en_US
dc.description.level Doctoral en_US
dc.description.department University of New Mexico. Biology Dept. en_US
dc.description.advisor Turner, Thomas
dc.description.committee-member Collins, Scott
dc.description.committee-member Cunningham, Charles
dc.description.committee-member O'Malley, Kathleen

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