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• 1. [Article] Incompatibility and Speciation Within and Between Species

  60 pages. A thesis presented to the Department of Biology and the Clark Honors College of the University of Oregon in partial fulfillment of the requirements for degree of Bachelor of Science, Spring 2...

  Citation × Citation Citation Abstract Copy Title: Incompatibility and Speciation Within and Between Species Author: Moore, Hanna Year: 2015 60 pages. A thesis presented to the Department of Biology and the Clark Honors College of the University of Oregon in partial fulfillment of the requirements for degree of Bachelor of Science, Spring 2015. Title: Incompatibility and Speciation Within and Between Species Author: Moore, Hanna Year: 2015 60 pages. A thesis presented to the Department of Biology and the Clark Honors College of the University of Oregon in partial fulfillment of the requirements for degree of Bachelor of Science, Spring 2015. Close

• 2. [Article] A Coxiella-Like Endosymbiont Is a PotentialVitamin Source for the Lone Star Tick

  Amblyomma americanum (Lone star tick) is an important disease vector in the United States. It transmits several human pathogens, including the agents of human monocytic ehrlichiosis, tularemia, and southern ...

  Citation × Citation Citation Abstract Copy Title: A Coxiella-Like Endosymbiont Is a PotentialVitamin Source for the Lone Star Tick Author: Smith, Todd A., Driscoll, Timothy, Gillespie, Joseph J., Raghavan, Rahul Year: 2015 Amblyomma americanum (Lone star tick) is an important disease vector in the United States. It transmits several human pathogens, including the agents of human monocytic ehrlichiosis, tularemia, and southern tick-associated rash illness. Blood-feeding insects (Class Insecta) depend on bacterial endosymbionts to provide vitamins and cofactors that are scarce in blood. It is unclear how this deficiency is compensated in ticks (Class Arachnida) that feed exclusively on mammalian blood. A bacterium related to Coxiella burnetii, the agent of humanQfever,has been observedpreviously within cells of A. americanum. Eliminating this bacterium (CLEAA, Coxiella-like endosymbiont of A. americanum) with antibiotics reduced tick fecundity, indicating that it is an essential endosymbiont. In an effort to determine its role within this symbiosis, we sequenced the CLEAA genome. While highly reduced (656,901 bp) compared with C. burnetii (1,995,281 bp), the CLEAA genome encodes most major vitamin and cofactor biosynthesis pathways, implicatingCLEAAas a vitamin provisioningendosymbiont. In contrast,CLEAAlacks any recognizable virulencegenes, indicating that it is not a pathogen despite its presence in tick salivary glands. As both C. burnetii and numerous “Coxiella-like bacteria” have been reported from several species of ticks,we determined the evolutionary relationship between the two bacteria. Phylogeny estimation revealed that CLEAA is a close relative of C. burnetii,but was not derived from it. Our results are important for strategies geared toward controlling A. americanum and the pathogens it vectors, and also contribute novel information regarding the metabolic interdependencies of ticks and their nutrient-provisioning endosymbionts. Title: A Coxiella-Like Endosymbiont Is a PotentialVitamin Source for the Lone Star Tick Author: Smith, Todd A., Driscoll, Timothy, Gillespie, Joseph J., Raghavan, Rahul Year: 2015 Amblyomma americanum (Lone star tick) is an important disease vector in the United States. It transmits several human pathogens, including the agents of human monocytic ehrlichiosis, tularemia, and southern tick-associated rash illness. Blood-feeding insects (Class Insecta) depend on bacterial endosymbionts to provide vitamins and cofactors that are scarce in blood. It is unclear how this deficiency is compensated in ticks (Class Arachnida) that feed exclusively on mammalian blood. A bacterium related to Coxiella burnetii, the agent of humanQfever,has been observedpreviously within cells of A. americanum. Eliminating this bacterium (CLEAA, Coxiella-like endosymbiont of A. americanum) with antibiotics reduced tick fecundity, indicating that it is an essential endosymbiont. In an effort to determine its role within this symbiosis, we sequenced the CLEAA genome. While highly reduced (656,901 bp) compared with C. burnetii (1,995,281 bp), the CLEAA genome encodes most major vitamin and cofactor biosynthesis pathways, implicatingCLEAAas a vitamin provisioningendosymbiont. In contrast,CLEAAlacks any recognizable virulencegenes, indicating that it is not a pathogen despite its presence in tick salivary glands. As both C. burnetii and numerous “Coxiella-like bacteria” have been reported from several species of ticks,we determined the evolutionary relationship between the two bacteria. Phylogeny estimation revealed that CLEAA is a close relative of C. burnetii,but was not derived from it. Our results are important for strategies geared toward controlling A. americanum and the pathogens it vectors, and also contribute novel information regarding the metabolic interdependencies of ticks and their nutrient-provisioning endosymbionts. Close

• 3. [Article] Walking Behavior of Zoo Elephants: Associations between GPS-Measured Daily Walking Distances and Environmental Factors, Social Factors, and Welfare Indicators

  Research with humans and other animals suggests that walking benefits physical health. Perhaps because these links have been demonstrated in other species, it has been suggested that walking is important ...

  Citation × Citation Citation Abstract Copy Title: Walking Behavior of Zoo Elephants: Associations between GPS-Measured Daily Walking Distances and Environmental Factors, Social Factors, and Welfare Indicators Author: Holdgate, Matthew Robert, Meehan, Cheryl L., Hogan, Jennifer N., Miller, Lance J., Soltis, Josesph, Andrews, Jeff, Shepherdson, David J. Year: 2016 Research with humans and other animals suggests that walking benefits physical health. Perhaps because these links have been demonstrated in other species, it has been suggested that walking is important to elephant welfare, and that zoo elephant exhibits should be designed to allow for more walking. Our study is the first to address this suggestion empirically by measuring the mean daily walking distance of elephants in North American zoos, determining the factors that are associated with variations in walking distance, and testing for associations between walking and welfare indicators. We used anklets equipped with GPS data loggers to measure outdoor daily walking distance in 56 adult female African (n = 33) and Asian (n = 23) elephants housed in 30 North American zoos. We collected 259 days of data and determined associations between distance walked and social, housing, management, and demographic factors. Elephants walked an average of 5.3 km/day with no significant difference between species. In our multivariable model, more diverse feeding regimens were correlated with increased walking, and elephants who were fed on a temporally unpredictable feeding schedule walked 1.29 km/day more than elephants fed on a predictable schedule. Distance walked was also positively correlated with an increase in the number of social groupings and negatively correlated with age. We found a small but significant negative correlation between distance walked and nighttime Space Experience, but no other associations between walking distances and exhibit size were found. Finally, distance walked was not related to health or behavioral outcomes including foot health, joint health, body condition, and the performance of stereotypic behavior, suggesting that more research is necessary to determine explicitly how differences in walking may impact elephant welfare. Title: Walking Behavior of Zoo Elephants: Associations between GPS-Measured Daily Walking Distances and Environmental Factors, Social Factors, and Welfare Indicators Author: Holdgate, Matthew Robert, Meehan, Cheryl L., Hogan, Jennifer N., Miller, Lance J., Soltis, Josesph, Andrews, Jeff, Shepherdson, David J. Year: 2016 Research with humans and other animals suggests that walking benefits physical health. Perhaps because these links have been demonstrated in other species, it has been suggested that walking is important to elephant welfare, and that zoo elephant exhibits should be designed to allow for more walking. Our study is the first to address this suggestion empirically by measuring the mean daily walking distance of elephants in North American zoos, determining the factors that are associated with variations in walking distance, and testing for associations between walking and welfare indicators. We used anklets equipped with GPS data loggers to measure outdoor daily walking distance in 56 adult female African (n = 33) and Asian (n = 23) elephants housed in 30 North American zoos. We collected 259 days of data and determined associations between distance walked and social, housing, management, and demographic factors. Elephants walked an average of 5.3 km/day with no significant difference between species. In our multivariable model, more diverse feeding regimens were correlated with increased walking, and elephants who were fed on a temporally unpredictable feeding schedule walked 1.29 km/day more than elephants fed on a predictable schedule. Distance walked was also positively correlated with an increase in the number of social groupings and negatively correlated with age. We found a small but significant negative correlation between distance walked and nighttime Space Experience, but no other associations between walking distances and exhibit size were found. Finally, distance walked was not related to health or behavioral outcomes including foot health, joint health, body condition, and the performance of stereotypic behavior, suggesting that more research is necessary to determine explicitly how differences in walking may impact elephant welfare. Close

• 4. [Article] Predicting Parturition in a Long-Gestating Species: Behavioral and Hormonal Indicators in the Asian Elephant (Elephas maximus)

  Captive populations of Asian elephants (Elephas maximus) in North America are not self-sustaining, and increasing reproductive success within captive populations is a high priority. The ability to accurately ...

  Citation × Citation Citation Abstract Copy Title: Predicting Parturition in a Long-Gestating Species: Behavioral and Hormonal Indicators in the Asian Elephant (Elephas maximus) Author: Velonis, Heather Kelly Year: 2017 Captive populations of Asian elephants (Elephas maximus) in North America are not self-sustaining, and increasing reproductive success within captive populations is a high priority. The ability to accurately predict parturition can have a direct impact on elephant welfare. Elephants in captivity often require significant preparation and management throughout the birthing process, and complications during labor and delivery can necessitate immediate intervention, including stillbirth, protracted labor, maternal aggression towards a newborn calf, and dystocia. Being able to predict when parturition will commence can ensure appropriate staff is available and adequate monitoring is performed. Routine endocrine sampling can be used to predict parturition in Asian elephants, with a drop in progesterone (P4) to baseline levels signaling parturition in 2-5 days. However, we determined this method is not without limitations, and it is not used in all institutions that house elephants. As changes in hormones regulate and alter behaviors, we investigated behavioral indicators as an additional management tool for predicting parturition, a time of drastic hormone changes. We conducted a study of five pregnancies in Asian elephants at the Oregon Zoo, U.S.A, and Taronga Zoo, Australia, between 2008 and 2012. In Chapter 2, I evaluated progesterone (P4) and cortisol levels across three time periods: Baseline; Pre, (the week preceding the drop in P4); and Post, (the period after the P4 drop). Levels of P4 were significantly lower, and levels of cortisol were significantly higher in the days just prior to parturition. I found considerable intra- and inter-individual variation in both endocrine profiles, which can make endocrine assessments difficult to interpret in real time. In Chapter 3, I investigated whether behaviors in the preparturition period could be predictive of impending parturition in the Asian elephant. ANOVA results indicated a significant difference in the amount of time that elephants spent walking backwards across three time periods (F(2) = 3.723, p = 0.033), with the behavior increasing as parturition approached. These results were supported by a non-parametric Kruskal- Wallis. Using a generalized linear mixed model (GLMM), I found that as P4 levels decrease, walking backwards behavior significantly increases. In Chapter 4, I evaluated investigative trunk behaviors, or “trunk checks”, directed towards the temporal gland near the ear, mammary glands, vulva and anus of the pregnant dam. Investigative behaviors included both self-directed behaviors and those sent from herd mates towards the pregnant dam. Self-directed behaviors are most likely associated with physical changes in the pregnant dam, such as using the trunk to pull on swollen teats. Other-directed behaviors may stem from chemo-sensory signaling or other types of communication between herd mates, such as detecting changes in progesterone or cortisol. I ran GLMM and found that four trunk-check behaviors varied significantly with P4 and/or cortisol profiles. These were: self-checks of mammary glands increased with decreasing P4 levels; herd-mate-checks of mammary glands increased with decreasing P4 levels; self-checks of vulva increased with decreasing P4 levels and increasing cortisol levels; herd-mate-checks of anus increased with increasing cortisol levels. In Chapter 5, I evaluated activity budget behaviors in the pregnant elephants. Generalized comparisons were made to published activity budgets of typical captive Asian elephants. I report that activity budgets are within the range of normal activity, though I note a high level of inter-individual variation. In addition, I compared two sampling techniques, including one-zero and instantaneous sampling, that were used for activity budget data collection. I discuss the different results obtained by each sampling technique. These results are a very promising indication that behaviors, including walking backwards and multiple trunk-check behaviors, are changing over time or with parturition-related hormone profiles. We recommend that keepers, veterinary staff, and other observers that are familiar with the regular behavioral repertoire of a pregnant female should pay close attention to these highlighted behaviors. Keeping track of these behaviors, especially in conjunction with P4 and cortisol tracking, can help staff refine existing windows of expected parturition. Title: Predicting Parturition in a Long-Gestating Species: Behavioral and Hormonal Indicators in the Asian Elephant (Elephas maximus) Author: Velonis, Heather Kelly Year: 2017 Captive populations of Asian elephants (Elephas maximus) in North America are not self-sustaining, and increasing reproductive success within captive populations is a high priority. The ability to accurately predict parturition can have a direct impact on elephant welfare. Elephants in captivity often require significant preparation and management throughout the birthing process, and complications during labor and delivery can necessitate immediate intervention, including stillbirth, protracted labor, maternal aggression towards a newborn calf, and dystocia. Being able to predict when parturition will commence can ensure appropriate staff is available and adequate monitoring is performed. Routine endocrine sampling can be used to predict parturition in Asian elephants, with a drop in progesterone (P4) to baseline levels signaling parturition in 2-5 days. However, we determined this method is not without limitations, and it is not used in all institutions that house elephants. As changes in hormones regulate and alter behaviors, we investigated behavioral indicators as an additional management tool for predicting parturition, a time of drastic hormone changes. We conducted a study of five pregnancies in Asian elephants at the Oregon Zoo, U.S.A, and Taronga Zoo, Australia, between 2008 and 2012. In Chapter 2, I evaluated progesterone (P4) and cortisol levels across three time periods: Baseline; Pre, (the week preceding the drop in P4); and Post, (the period after the P4 drop). Levels of P4 were significantly lower, and levels of cortisol were significantly higher in the days just prior to parturition. I found considerable intra- and inter-individual variation in both endocrine profiles, which can make endocrine assessments difficult to interpret in real time. In Chapter 3, I investigated whether behaviors in the preparturition period could be predictive of impending parturition in the Asian elephant. ANOVA results indicated a significant difference in the amount of time that elephants spent walking backwards across three time periods (F(2) = 3.723, p = 0.033), with the behavior increasing as parturition approached. These results were supported by a non-parametric Kruskal- Wallis. Using a generalized linear mixed model (GLMM), I found that as P4 levels decrease, walking backwards behavior significantly increases. In Chapter 4, I evaluated investigative trunk behaviors, or “trunk checks”, directed towards the temporal gland near the ear, mammary glands, vulva and anus of the pregnant dam. Investigative behaviors included both self-directed behaviors and those sent from herd mates towards the pregnant dam. Self-directed behaviors are most likely associated with physical changes in the pregnant dam, such as using the trunk to pull on swollen teats. Other-directed behaviors may stem from chemo-sensory signaling or other types of communication between herd mates, such as detecting changes in progesterone or cortisol. I ran GLMM and found that four trunk-check behaviors varied significantly with P4 and/or cortisol profiles. These were: self-checks of mammary glands increased with decreasing P4 levels; herd-mate-checks of mammary glands increased with decreasing P4 levels; self-checks of vulva increased with decreasing P4 levels and increasing cortisol levels; herd-mate-checks of anus increased with increasing cortisol levels. In Chapter 5, I evaluated activity budget behaviors in the pregnant elephants. Generalized comparisons were made to published activity budgets of typical captive Asian elephants. I report that activity budgets are within the range of normal activity, though I note a high level of inter-individual variation. In addition, I compared two sampling techniques, including one-zero and instantaneous sampling, that were used for activity budget data collection. I discuss the different results obtained by each sampling technique. These results are a very promising indication that behaviors, including walking backwards and multiple trunk-check behaviors, are changing over time or with parturition-related hormone profiles. We recommend that keepers, veterinary staff, and other observers that are familiar with the regular behavioral repertoire of a pregnant female should pay close attention to these highlighted behaviors. Keeping track of these behaviors, especially in conjunction with P4 and cortisol tracking, can help staff refine existing windows of expected parturition. Close

• 5. [Article] Endogenous ROS Levels in C. Elegans Under Exogenous Stress Support Revision of Oxidative Stress Theory of Life-History Tradeoffs

  Background: The oxidative stress theory of life-history tradeoffs states that oxidative stress caused by damaging free radicals directly underpins tradeoffs between reproduction and longevity by altering ...

  Citation × Citation Citation Abstract Copy Title: Endogenous ROS Levels in C. Elegans Under Exogenous Stress Support Revision of Oxidative Stress Theory of Life-History Tradeoffs Author: Smith, Samson W., Latta, Leigh C., IV, Denver, Dee R., Estes, Suzanne Year: 2014 Background: The oxidative stress theory of life-history tradeoffs states that oxidative stress caused by damaging free radicals directly underpins tradeoffs between reproduction and longevity by altering the allocation of energetic resources between these tasks. We test this theory by characterizing the effects of exogenous oxidative insult and its interaction with thermal stress and diet quality on a suite of life-history traits and correlations in Caenorhabditis elegans nematodes. We also quantify demographic aging rates and endogenous reactive oxygen species (ROS) levels in live animals. Results: Our findings indicate a tradeoff between investment in reproduction and antioxidant defense (somatic maintenance) consistent with theoretical predictions, but correlations between standard life-history traits yield little evidence that oxidative stress generates strict tradeoffs. Increasing oxidative insult, however, shows a strong tendency to uncouple positive phenotypic correlations and, in particular, to reduce the correlation between reproduction and lifespan. We also found that mild oxidative insult results in lower levels of endogenous ROS accompanied by hormetic changes in lifespan, demographic aging, and reproduction that disappear in combined-stress treatments–consistent with the oxidative stress theory of aging. Conclusions: Our findings demonstrate that oxidative stress is a direct contributor to life-history trait variation and that traditional tradeoffs are not necessary to invoke oxidative stress as a mediator of relationships between life-history traits, supporting previous calls for revisions to theory. Title: Endogenous ROS Levels in C. Elegans Under Exogenous Stress Support Revision of Oxidative Stress Theory of Life-History Tradeoffs Author: Smith, Samson W., Latta, Leigh C., IV, Denver, Dee R., Estes, Suzanne Year: 2014 Background: The oxidative stress theory of life-history tradeoffs states that oxidative stress caused by damaging free radicals directly underpins tradeoffs between reproduction and longevity by altering the allocation of energetic resources between these tasks. We test this theory by characterizing the effects of exogenous oxidative insult and its interaction with thermal stress and diet quality on a suite of life-history traits and correlations in Caenorhabditis elegans nematodes. We also quantify demographic aging rates and endogenous reactive oxygen species (ROS) levels in live animals. Results: Our findings indicate a tradeoff between investment in reproduction and antioxidant defense (somatic maintenance) consistent with theoretical predictions, but correlations between standard life-history traits yield little evidence that oxidative stress generates strict tradeoffs. Increasing oxidative insult, however, shows a strong tendency to uncouple positive phenotypic correlations and, in particular, to reduce the correlation between reproduction and lifespan. We also found that mild oxidative insult results in lower levels of endogenous ROS accompanied by hormetic changes in lifespan, demographic aging, and reproduction that disappear in combined-stress treatments–consistent with the oxidative stress theory of aging. Conclusions: Our findings demonstrate that oxidative stress is a direct contributor to life-history trait variation and that traditional tradeoffs are not necessary to invoke oxidative stress as a mediator of relationships between life-history traits, supporting previous calls for revisions to theory. Close

• 6. [Article] Assessing the Utility of Transcriptome Data for Inferring Phylogenetic Relationships Among Coleoid Cephalopods

  Historically, deep-level relationships within the molluscan class Cephalopoda (squids, cuttlefishes, octopods and their relatives) have remained elusive due in part to the considerable morphological diversity ...

  Citation × Citation Citation Abstract Copy Title: Assessing the Utility of Transcriptome Data for Inferring Phylogenetic Relationships Among Coleoid Cephalopods Author: Lindgren, Annie R., Anderson, Frank E. Year: 2018 Historically, deep-level relationships within the molluscan class Cephalopoda (squids, cuttlefishes, octopods and their relatives) have remained elusive due in part to the considerable morphological diversity of extant taxa, a limited fossil record for species that lack a calcareous shell and difficulties in sampling open ocean taxa. Many conflicts identified by morphologists in the early 1900s remain unresolved today in spite of advances in morphological, molecular and analytical methods. In this study we assess the utility of transcriptome data for resolving cephalopod phylogeny, with special focus on the orders of Decapodiformes (open-eye squids, bobtail squids, cuttlefishes and relatives). To do so, we took new and previously published transcriptome data and used a unique cephalopod core ortholog set to generate a dataset that was subjected to an array of filtering and analytical methods to assess the impacts of: taxon sampling, ortholog number, compositional and rate heterogeneity and incongruence across loci. Analyses indicated that datasets that maximized taxonomic coverage but included fewer orthologs were less stable than datasets that sacrificed taxon sampling to increase the number of orthologs. Clades recovered irrespective of dataset, filtering or analytical method included Octopodiformes (Vampyroteuthis infernalis + octopods), Decapodiformes (squids, cuttlefishes and their relatives), and orders Oegopsida (open-eyed squids) and Myopsida (e.g., loliginid squids). Ordinal-level relationships within Decapodiformes were the most susceptible to dataset perturbation, further emphasizing the challenges associated with uncovering relationships at deep nodes in the cephalopod tree of life. Title: Assessing the Utility of Transcriptome Data for Inferring Phylogenetic Relationships Among Coleoid Cephalopods Author: Lindgren, Annie R., Anderson, Frank E. Year: 2018 Historically, deep-level relationships within the molluscan class Cephalopoda (squids, cuttlefishes, octopods and their relatives) have remained elusive due in part to the considerable morphological diversity of extant taxa, a limited fossil record for species that lack a calcareous shell and difficulties in sampling open ocean taxa. Many conflicts identified by morphologists in the early 1900s remain unresolved today in spite of advances in morphological, molecular and analytical methods. In this study we assess the utility of transcriptome data for resolving cephalopod phylogeny, with special focus on the orders of Decapodiformes (open-eye squids, bobtail squids, cuttlefishes and relatives). To do so, we took new and previously published transcriptome data and used a unique cephalopod core ortholog set to generate a dataset that was subjected to an array of filtering and analytical methods to assess the impacts of: taxon sampling, ortholog number, compositional and rate heterogeneity and incongruence across loci. Analyses indicated that datasets that maximized taxonomic coverage but included fewer orthologs were less stable than datasets that sacrificed taxon sampling to increase the number of orthologs. Clades recovered irrespective of dataset, filtering or analytical method included Octopodiformes (Vampyroteuthis infernalis + octopods), Decapodiformes (squids, cuttlefishes and their relatives), and orders Oegopsida (open-eyed squids) and Myopsida (e.g., loliginid squids). Ordinal-level relationships within Decapodiformes were the most susceptible to dataset perturbation, further emphasizing the challenges associated with uncovering relationships at deep nodes in the cephalopod tree of life. Close

• 7. [Article] Data From: <i>Pseudo-De Novo</i> Assembly and Analysis of Unmapped Genome Sequence Reads in Wild Zebrafish Reveals Novel Gene Content

  Zebrafish represents the third vertebrate with an officially completed genome, yet it remains incomplete with additions and corrections continuing with the current release, GRCz10, having 13% of zebrafish ...

  Citation × Citation Citation Abstract Copy Title: Data From: <i>Pseudo-De Novo</i> Assembly and Analysis of Unmapped Genome Sequence Reads in Wild Zebrafish Reveals Novel Gene Content Author: Faber-Hammond, Joshua J., Brown, Kim H. Year: 2015 Zebrafish represents the third vertebrate with an officially completed genome, yet it remains incomplete with additions and corrections continuing with the current release, GRCz10, having 13% of zebrafish cDNA sequences unmapped. This disparity may result from population differences given the reference was generated from clonal individuals with limited genetic diversity. This is supported by the recent analysis of a single wild zebrafish which identified over 5.2 million SNPs and 1.6 million in/dels in the previous genome build, zv9. Re-examination of this sequence dataset indicated that 13.8% of quality sequence reads failed to align to GRCz10. Using a novel bioinformatics de novo assembly pipeline on these unmappable reads we identified 1,514,491 novel contigs covering ~224 Mb of genomic sequence. Among these, 1,083 contigs were found to contain potential gene coding sequence. RNA-seq data comparison confirmed 362 contigs contained transcribed DNA sequence, suggesting that a large amount of functional genomic sequence remains unannotated in zebrafish. By utilizing the bioinformatics pipeline developed in this study the zebrafish genome will be bolstered as a model for human disease research. Adaptation of the pipeline described here also offers a cost-efficient and effective method to identify and map novel genetic content across any genome and will ultimately aid in the completion of additional genomes for a broad range of species. Title: Data From: <i>Pseudo-De Novo</i> Assembly and Analysis of Unmapped Genome Sequence Reads in Wild Zebrafish Reveals Novel Gene Content Author: Faber-Hammond, Joshua J., Brown, Kim H. Year: 2015 Zebrafish represents the third vertebrate with an officially completed genome, yet it remains incomplete with additions and corrections continuing with the current release, GRCz10, having 13% of zebrafish cDNA sequences unmapped. This disparity may result from population differences given the reference was generated from clonal individuals with limited genetic diversity. This is supported by the recent analysis of a single wild zebrafish which identified over 5.2 million SNPs and 1.6 million in/dels in the previous genome build, zv9. Re-examination of this sequence dataset indicated that 13.8% of quality sequence reads failed to align to GRCz10. Using a novel bioinformatics de novo assembly pipeline on these unmappable reads we identified 1,514,491 novel contigs covering ~224 Mb of genomic sequence. Among these, 1,083 contigs were found to contain potential gene coding sequence. RNA-seq data comparison confirmed 362 contigs contained transcribed DNA sequence, suggesting that a large amount of functional genomic sequence remains unannotated in zebrafish. By utilizing the bioinformatics pipeline developed in this study the zebrafish genome will be bolstered as a model for human disease research. Adaptation of the pipeline described here also offers a cost-efficient and effective method to identify and map novel genetic content across any genome and will ultimately aid in the completion of additional genomes for a broad range of species. Close

• 8. [Article] Pseudo-De Novo Assembly and Analysis of Unmapped Genome Sequence Reads in Wild Zebrafish Reveal Novel Gene Content

  Zebrafish represents the third vertebrate with an officially completed genome, yet it remains incomplete with additions and corrections continuing with the current release, GRCz10, having 13% of zebrafish ...

  Citation × Citation Citation Abstract Copy Title: Pseudo-De Novo Assembly and Analysis of Unmapped Genome Sequence Reads in Wild Zebrafish Reveal Novel Gene Content Author: Faber-Hammond, Joshua, Brown, Kim Year: 2016 Zebrafish represents the third vertebrate with an officially completed genome, yet it remains incomplete with additions and corrections continuing with the current release, GRCz10, having 13% of zebrafish cDNA sequences unmapped. This disparity may result from population differences, given that the genome reference was generated from clonal individuals with limited genetic diversity. This is supported by the recent analysis of a single wild zebrafish, which identified over 5.2 million SNPs and 1.6 million in/dels in the previous genome build, zv9. Re-examination of this sequence data set indicated that 13.8% of quality sequence reads failed to align to GRCz10. Using a novel bioinformatics de novo assembly pipeline on these unmappable reads, we identified 1,514,491 novel contigs covering ∼224 Mb of genomic sequence. Among these, 1083 contigs were found to contain a potential gene coding sequence. RNA-seq data comparison confirmed that 362 contigs contained a transcribed DNA sequence, suggesting that a large amount of functional genomic sequence remains unannotated in the zebrafish reference genome. By utilizing the bioinformatics pipeline developed in this study, the zebrafish genome will be bolstered as a model for human disease research. Adaptation of the pipeline described here also offers a cost-efficient and effective method to identify and map novel genetic content across any genome and will ultimately aid in the completion of additional genomes for a broad range of species. Title: Pseudo-De Novo Assembly and Analysis of Unmapped Genome Sequence Reads in Wild Zebrafish Reveal Novel Gene Content Author: Faber-Hammond, Joshua, Brown, Kim Year: 2016 Zebrafish represents the third vertebrate with an officially completed genome, yet it remains incomplete with additions and corrections continuing with the current release, GRCz10, having 13% of zebrafish cDNA sequences unmapped. This disparity may result from population differences, given that the genome reference was generated from clonal individuals with limited genetic diversity. This is supported by the recent analysis of a single wild zebrafish, which identified over 5.2 million SNPs and 1.6 million in/dels in the previous genome build, zv9. Re-examination of this sequence data set indicated that 13.8% of quality sequence reads failed to align to GRCz10. Using a novel bioinformatics de novo assembly pipeline on these unmappable reads, we identified 1,514,491 novel contigs covering ∼224 Mb of genomic sequence. Among these, 1083 contigs were found to contain a potential gene coding sequence. RNA-seq data comparison confirmed that 362 contigs contained a transcribed DNA sequence, suggesting that a large amount of functional genomic sequence remains unannotated in the zebrafish reference genome. By utilizing the bioinformatics pipeline developed in this study, the zebrafish genome will be bolstered as a model for human disease research. Adaptation of the pipeline described here also offers a cost-efficient and effective method to identify and map novel genetic content across any genome and will ultimately aid in the completion of additional genomes for a broad range of species. Close

• 9. [Article] Intestinal Microbiota Diversity of Pre-Smolt Steelhead (Oncorhynchus mykiss) Across Six Oregon and Washington Hatcheries

  The Pacific Northwest is known for its once-abundant wild salmonid populations that have been in decline for more than 50 years due to habitat destruction and commercial overexploitation. To compensate, ...

  Citation × Citation Citation Abstract Copy Title: Intestinal Microbiota Diversity of Pre-Smolt Steelhead (Oncorhynchus mykiss) Across Six Oregon and Washington Hatcheries Author: Yildirimer, Christina Carrell Year: 2017 The Pacific Northwest is known for its once-abundant wild salmonid populations that have been in decline for more than 50 years due to habitat destruction and commercial overexploitation. To compensate, federal and state agencies annually release hundreds of thousands of hatchery-reared fish into the wild. However, accumulating data indicate that hatchery fish have lower fitness in natural environments, and that hatchery rearing negatively influences return rates of anadromous salmonids. Recently, mounting evidence revealed that the richness and diversity of intestinal microbial species influence host health. We examined the gut microbiota of pre-migratory hatchery-reared steelhead (Oncorhynchus mykiss) to assess microbial community diversity. The Cascade Mountains serve as an allopatric border between two distinct clades of steelhead that show significant differences in genomic and mitochondrial diversity. We identified differences in core microbiota of hatchery-reared fish that correlate with this divergent phylogeographic distribution. Steelhead sampled from hatcheries east of the Cascades had overall greater core gut microbiota diversity. These differences were found despite similarities in diet and rearing conditions. In addition to taxonomic variation across the geographic divide, we identified significant differences in metabolic pathways using PICRUSt gene prediction software. Our analysis revealed significant enrichment of genes associated with lipid metabolism in the gut microbiome of western fish. 8 of 19 individual lipid metabolism pathways were more prominent in western populations. Lipids are a vital nutritional component for teleost species involved in migration and subsequent return for spawning in natal environments. We hypothesize that the observed differences in lipid metabolism across this phylogenetic divide results from an increased ability of eastern Cascade (O. m. gairdneri) fish to utilize lipids taken in via the diet. This increased absorption and utilization would make lipids less available for the intestinal microbiota of the eastern fish, as evidenced by the lower abundance of lipid metabolism genes in the east. Our research utilizes information from the microbiome to understand the phenotypic implications occurring in segregated populations of hatchery-reared steelhead, further confirming elements of coevolution between an organism and its internal environment. Title: Intestinal Microbiota Diversity of Pre-Smolt Steelhead (Oncorhynchus mykiss) Across Six Oregon and Washington Hatcheries Author: Yildirimer, Christina Carrell Year: 2017 The Pacific Northwest is known for its once-abundant wild salmonid populations that have been in decline for more than 50 years due to habitat destruction and commercial overexploitation. To compensate, federal and state agencies annually release hundreds of thousands of hatchery-reared fish into the wild. However, accumulating data indicate that hatchery fish have lower fitness in natural environments, and that hatchery rearing negatively influences return rates of anadromous salmonids. Recently, mounting evidence revealed that the richness and diversity of intestinal microbial species influence host health. We examined the gut microbiota of pre-migratory hatchery-reared steelhead (Oncorhynchus mykiss) to assess microbial community diversity. The Cascade Mountains serve as an allopatric border between two distinct clades of steelhead that show significant differences in genomic and mitochondrial diversity. We identified differences in core microbiota of hatchery-reared fish that correlate with this divergent phylogeographic distribution. Steelhead sampled from hatcheries east of the Cascades had overall greater core gut microbiota diversity. These differences were found despite similarities in diet and rearing conditions. In addition to taxonomic variation across the geographic divide, we identified significant differences in metabolic pathways using PICRUSt gene prediction software. Our analysis revealed significant enrichment of genes associated with lipid metabolism in the gut microbiome of western fish. 8 of 19 individual lipid metabolism pathways were more prominent in western populations. Lipids are a vital nutritional component for teleost species involved in migration and subsequent return for spawning in natal environments. We hypothesize that the observed differences in lipid metabolism across this phylogenetic divide results from an increased ability of eastern Cascade (O. m. gairdneri) fish to utilize lipids taken in via the diet. This increased absorption and utilization would make lipids less available for the intestinal microbiota of the eastern fish, as evidenced by the lower abundance of lipid metabolism genes in the east. Our research utilizes information from the microbiome to understand the phenotypic implications occurring in segregated populations of hatchery-reared steelhead, further confirming elements of coevolution between an organism and its internal environment. Close

• 10. [Article] Investigations of Larval Pacific Lamprey Entosphenus tridentatus Osmotic Stress Tolerance and Occurrence in a Tidally-Influenced Estuarine Stream

  Pacific lamprey is a culturally valuable species to indigenous people, and has significant ecological importance in freshwater and marine ecosystems. Over the past several decades, constrictions in range ...

  Citation × Citation Citation Abstract Copy Title: Investigations of Larval Pacific Lamprey Entosphenus tridentatus Osmotic Stress Tolerance and Occurrence in a Tidally-Influenced Estuarine Stream Author: Silver, Gregory Shell Year: 2015 Pacific lamprey is a culturally valuable species to indigenous people, and has significant ecological importance in freshwater and marine ecosystems. Over the past several decades, constrictions in range and reductions in Pacific lamprey abundance have been observed in Western North America, and may be indicators of range-wide declines. In the face of declining populations, the U.S. Fish and Wildlife Service has partnered with tribal, state, federal, and local entities to implement a regional Pacific lamprey conservation agreement aimed at reducing threats to Pacific lamprey and improving their habitats and population status. Research needs identified in the conservation agreement include assessing larval Pacific lamprey occupancy and distribution, habitat requirements, and the limiting factors of larval distribution in the freshwater ecosystem. As part of the effort to address these knowledge gaps, we investigated the potential for larval lampreys to occur in tidally-influenced estuarine environments. Research of this type may be valuable for future conservation, management or recovery efforts of Pacific lamprey throughout its range. We employed a two-phased approach, consisting of laboratory and field components to address our aims. We first conducted a series of controlled laboratory experiments to evaluate osmotic stress tolerance and osmoregulatory status of larval Pacific lamprey exposed to a range of (1) fixed salinity in various dilutions of saltwater and (2) oscillating salinity treatments designed to simulate tidal activity. Tolerance was assessed by monitoring and comparing survival of larvae in various treatments through 96 h. Osmoregulatory status was assessed by quantifying and comparing total body water content, plasma osmolality, and plasma cation (i.e., sodium) concentrations among larvae surviving various treatments. In fixed salinity experiments, 100% survival was observed in 0‰, 6‰, 8‰ and 10‰ through 96 h, while 0% survival was observed through 48 h in 12‰, 30 h in 15‰, and 12 h in 25‰ and 35‰. In oscillating salinity experiments, on the other hand, a significant increase in survival (100%) was observed through 96 h in treatments that oscillated between 12‰ and 0‰ (freshwater) at about 6 h intervals versus fixed 12‰ salinity experiments. A significant increase in survival also occurred in oscillating 15‰ treatments (60%) versus fixed 15‰ through 96 h. Linear regression analysis indicated higher environmental salinity in laboratory experiments was significantly related to increases in plasma osmolality and plasma sodium (the most abundant osmotically active plasma cation) concentrations, and concurrent decreases in total body water content among larvae that survived various treatments. Tidal oscillations in salinity appeared to temper the desiccating effects of salinity, as changes in body water content and sodium ion concentration were less abrupt than fixed salinity treatments. These results suggest larvae cannot osmoregulate in hyperosmotic environments, but are able to tolerate some fixed and oscillating hyperosmotic salinity exposure. Consequently, larvae may be able to occur in certain areas of estuaries, such as oligohaline habitats that are characterized by low levels of salinity. Experimental results were used, in part, to guide larval sampling in a tidally-influenced habitat. Occurrence of larval Pacific lamprey and Lampetra spp. (western brook and river lampreys) was subsequently investigated across a gradient of salinity in Ellsworth Creek (Pacific County, Washington) by electrofishing. Larval Pacific and Lampetra spp. were detected within an approximately 300 m long tidally-influenced segment of the study area. Salinity monitoring was conducted in six tidally-influenced reaches where larvae were detected for up to 14 d following electrofishing. Maximum tidal cycle salinity exceeded 15 ppt during 52% to 80% of tidal cycles within tidally-influenced reaches where larvae were detected. These results suggest potential for larval lamprey to occur in certain portions of tidal estuaries. However, long-term residence of larvae in tidally-influenced habitats and whether larvae are able to subsequently survive, grow, transform, and out-migrate is not known and requires further study. Given the potential for tidally-influenced habitats to be occupied by larvae, assessments of larval occurrence in other areas, such as the lower Columbia River, may be warranted. Knowledge of larval lamprey distribution in estuarine environments may be valuable for habitat restoration, and mitigating potential impacts from dredging and other human disturbances. Title: Investigations of Larval Pacific Lamprey Entosphenus tridentatus Osmotic Stress Tolerance and Occurrence in a Tidally-Influenced Estuarine Stream Author: Silver, Gregory Shell Year: 2015 Pacific lamprey is a culturally valuable species to indigenous people, and has significant ecological importance in freshwater and marine ecosystems. Over the past several decades, constrictions in range and reductions in Pacific lamprey abundance have been observed in Western North America, and may be indicators of range-wide declines. In the face of declining populations, the U.S. Fish and Wildlife Service has partnered with tribal, state, federal, and local entities to implement a regional Pacific lamprey conservation agreement aimed at reducing threats to Pacific lamprey and improving their habitats and population status. Research needs identified in the conservation agreement include assessing larval Pacific lamprey occupancy and distribution, habitat requirements, and the limiting factors of larval distribution in the freshwater ecosystem. As part of the effort to address these knowledge gaps, we investigated the potential for larval lampreys to occur in tidally-influenced estuarine environments. Research of this type may be valuable for future conservation, management or recovery efforts of Pacific lamprey throughout its range. We employed a two-phased approach, consisting of laboratory and field components to address our aims. We first conducted a series of controlled laboratory experiments to evaluate osmotic stress tolerance and osmoregulatory status of larval Pacific lamprey exposed to a range of (1) fixed salinity in various dilutions of saltwater and (2) oscillating salinity treatments designed to simulate tidal activity. Tolerance was assessed by monitoring and comparing survival of larvae in various treatments through 96 h. Osmoregulatory status was assessed by quantifying and comparing total body water content, plasma osmolality, and plasma cation (i.e., sodium) concentrations among larvae surviving various treatments. In fixed salinity experiments, 100% survival was observed in 0‰, 6‰, 8‰ and 10‰ through 96 h, while 0% survival was observed through 48 h in 12‰, 30 h in 15‰, and 12 h in 25‰ and 35‰. In oscillating salinity experiments, on the other hand, a significant increase in survival (100%) was observed through 96 h in treatments that oscillated between 12‰ and 0‰ (freshwater) at about 6 h intervals versus fixed 12‰ salinity experiments. A significant increase in survival also occurred in oscillating 15‰ treatments (60%) versus fixed 15‰ through 96 h. Linear regression analysis indicated higher environmental salinity in laboratory experiments was significantly related to increases in plasma osmolality and plasma sodium (the most abundant osmotically active plasma cation) concentrations, and concurrent decreases in total body water content among larvae that survived various treatments. Tidal oscillations in salinity appeared to temper the desiccating effects of salinity, as changes in body water content and sodium ion concentration were less abrupt than fixed salinity treatments. These results suggest larvae cannot osmoregulate in hyperosmotic environments, but are able to tolerate some fixed and oscillating hyperosmotic salinity exposure. Consequently, larvae may be able to occur in certain areas of estuaries, such as oligohaline habitats that are characterized by low levels of salinity. Experimental results were used, in part, to guide larval sampling in a tidally-influenced habitat. Occurrence of larval Pacific lamprey and Lampetra spp. (western brook and river lampreys) was subsequently investigated across a gradient of salinity in Ellsworth Creek (Pacific County, Washington) by electrofishing. Larval Pacific and Lampetra spp. were detected within an approximately 300 m long tidally-influenced segment of the study area. Salinity monitoring was conducted in six tidally-influenced reaches where larvae were detected for up to 14 d following electrofishing. Maximum tidal cycle salinity exceeded 15 ppt during 52% to 80% of tidal cycles within tidally-influenced reaches where larvae were detected. These results suggest potential for larval lamprey to occur in certain portions of tidal estuaries. However, long-term residence of larvae in tidally-influenced habitats and whether larvae are able to subsequently survive, grow, transform, and out-migrate is not known and requires further study. Given the potential for tidally-influenced habitats to be occupied by larvae, assessments of larval occurrence in other areas, such as the lower Columbia River, may be warranted. Knowledge of larval lamprey distribution in estuarine environments may be valuable for habitat restoration, and mitigating potential impacts from dredging and other human disturbances. Close