Seeing the river through the trees: using cottonwood dendrochronology to reconstruct river dynamics in the Upper Missouri River Basin

2017 Spring.Includes bibliographical references.Understanding the past is critical to preparing for the future, especially regarding rivers where extreme events and gradual changes underlie modern forms and processes. Both biological and human communities rely on the abundant resources provided by rivers and floodplains, particularly in dry regions of the western U.S. where water limits growth. To expand temporal perspectives on river processes, I reconstructed flow, channel migration, and riparian forest growth patterns in the Upper Missouri River Basin. Flow reconstructions typically use tree rings from montane conifers. However, I used riparian plains cottonwoods (Populus deltoides ssp. monilifera) directly connected to the alluvial water table to reconstruct flow on the Yellowstone (n = 389 tree cores), Powder (n = 408), and Little Missouri Rivers (n = 643). A two-curve Regional Curve Standardization approach was used to remove age-related growth trends from tree rings at each site. The flow reconstructions explained 57-58% of the variance in historical discharge and extended back to 1742, 1729, and 1643, respectively. Low-frequency flow patterns revealed wet conditions from 1870 to 1980, a period that includes the majority of the historical record. Two 19th century droughts (1816-1823 and 1861-1865) and one pluvial (1826-1829) were more severe than any recorded, revealing that risks are underestimated when using the instrumental period alone. These are the first flow reconstructions for the Lower Yellowstone and Powder Rivers, and they are the farthest downstream among Rocky Mountain rivers east of the Continental Divide. Cottonwood-based flow reconstructions were possible because the trees used river-connected groundwater, and tree ring width strongly correlated with March-June flow magnitude at the Yellowstone River (r = 0.69). Beyond the site-level growth patterns typically used to reconstruct flow, I found that biological and spatial characteristics affected how individual trees responded to flow and climate. Older trees contained stronger signals of non-growing season flow, precipitation, and temperature, which challenges the common dendrochronological assumption of stable tree ring-climate relationships through time. Although trees both near and far from the channel were better correlated to spring flow than precipitation, more distant trees had a stronger relative connection to precipitation, suggesting that greater distance decreases the ability of river water to fulfill transpirative demands. Like annual growth, cottonwood establishment is related to river flows, and tree age indicated fluvial processes including channel migration. I quantified nearly two centuries of channel migration on the Powder River by integrating measured channel cross-sections (1975-2014), air photos (1939-2013), and transects of aged cottonwoods (1830-2014). The combined data revealed that channel migration rates were lower (0.81 m/yr) in the recent and intensively studied cross-section period compared to the longer air photo (1.52 m/yr) and cottonwood (1.62 m/yr) periods. On the Powder River, extreme floods such as those in 1923 and 1978 increase subsequent channel migration rates and initiate decades of channel morphological adjustments. Across the study rivers, data indicate that fundamental fluvial processes have responded to climatic and watershed pressures. By identifying and quantifying past events, diverse research approaches improve understanding of the river, floodplain, and riparian forest processes that are essential to the persistence of these valuable ecosystems

Bypass transition experiments in subsonic boundary layers

+131hlm.;24c

Climatic and hydrologic processes leading to recent wetland losses in Yellowstone National Park, USA

2012 Spring.Includes bibliographical references.Wetlands provide vital habitat within functioning environments and act as landscape indicators by integrating catchment-scale hydrologic processes. Wetland drying during the past few decades in Yellowstone National Park's Northern Range has caused concern among National Park managers and the public at large. My research was initiated to develop an understanding of the processes controlling wetland water levels and contributing to wetland decline in the Northern Range. To do this I integrated analyses of hydrology, climate, soils, and vegetation. In 2009 I selected 24 study wetlands and instrumented each with an average of five shallow groundwater monitoring well-and-piezometer nests. To quantify historic wetland area I mapped hydric soils, analyzed aerial photographs, and identified geomorphic indicators of higher water. Vegetation was sampled to characterize wetlands and plant-water relationships, and I also conducted a soil seed bank study. The Trumpeter Lake focal site revealed groundwater changes through time and was used to identify the timescale on which an important wetland varies. Climate data indicated that warming and drying occurred during the 20th century, but that this pattern was within the natural range of variation for the study region during the past 800 years. Hydrologic data revealed that study sites included locations of groundwater discharge, recharge, and flow-through as well as water perched above the regional water table. Hydrologic regimes were classified using a shape-magnitude framework and seven wetland classes were characterized. Wetland classes exhibited variable hydrologic permanence within and between the two study summers. Aerial photographs and hydric soil delineation both confirmed formerly greater wetland abundance. These changes were linked to the wetland classes and the presence or absence of surface water outlets. Wetland plant species inhabited areas of distinct water table depth and variation, and can be used to infer subsurface hydrologic regime in the absence of extensive monitoring well networks. Continued monitoring of these wetland basins and their watersheds is critical to expanding our understanding of the processes supporting Northern Range wetlands and allowing us to better manage these valuable habitats

Genome-Wide Footprints of Pig Domestication and Selection Revealed through Massive Parallel Sequencing of Pooled DNA

Background Artificial selection has caused rapid evolution in domesticated species. The identification of selection footprints across domesticated genomes can contribute to uncover the genetic basis of phenotypic diversity. Methodology/Main Findings Genome wide footprints of pig domestication and selection were identified using massive parallel sequencing of pooled reduced representation libraries (RRL) representing ~2% of the genome from wild boar and four domestic pig breeds (Large White, Landrace, Duroc and Pietrain) which have been under strong selection for muscle development, growth, behavior and coat color. Using specifically developed statistical methods that account for DNA pooling, low mean sequencing depth, and sequencing errors, we provide genome-wide estimates of nucleotide diversity and genetic differentiation in pig. Widespread signals suggestive of positive and balancing selection were found and the strongest signals were observed in Pietrain, one of the breeds most intensively selected for muscle development. Most signals were population-specific but affected genomic regions which harbored genes for common biological categories including coat color, brain development, muscle development, growth, metabolism, olfaction and immunity. Genetic differentiation in regions harboring genes related to muscle development and growth was higher between breeds than between a given breed and the wild boar. Conclusions/Significance These results, suggest that although domesticated breeds have experienced similar selective pressures, selection has acted upon different genes. This might reflect the multiple domestication events of European breeds or could be the result of subsequent introgression of Asian alleles. Overall, it was estimated that approximately 7% of the porcine genome has been affected by selection events. This study illustrates that the massive parallel sequencing of genomic pools is a cost-effective approach to identify footprints of selection

Translating Human Cancer Sequences Into Personalized Porcine Cancer Models

The global incidence of cancer is rapidly rising, and despite an improved understanding of cancer molecular biology, immune landscapes, and advancements in cytotoxic, biologic, and immunologic anti-cancer therapeutics, cancer remains a leading cause of death worldwide. Cancer is caused by the accumulation of a series of gene mutations called driver mutations that confer selective growth advantages to tumor cells. As cancer therapies move toward personalized medicine, predictive modeling of the role driver mutations play in tumorigenesis and therapeutic susceptibility will become essential. The development of next-generation sequencing technology has made the evaluation of mutated genes possible in clinical practice, allowing for identification of driver mutations underlying cancer development in individual patients. This, combined with recent advances in gene editing technologies such as CRISPR-Cas9 enables development of personalized tumor models for prediction of treatment responses for mutational profiles observed clinically. Pigs represent an ideal animal model for development of personalized tumor models due to their similar size, anatomy, physiology, metabolism, immunity, and genetics compared to humans. Such models would support new initiatives in precision medicine, provide approaches to create disease site tumor models with designated spatial and temporal clinical outcomes, and create standardized tumor models analogous to human tumors to enable therapeutic studies. In this review, we discuss the process of utilizing genomic sequencing approaches, gene editing technologies, and transgenic porcine cancer models to develop clinically relevant, personalized large animal cancer models for use in co-clinical trials, ultimately improving treatment stratification and translation of novel therapeutic approaches to clinical practice

Genetic Resources, Genome Mapping and Evolutionary Genomics of the Pig (Sus scrofa)

The pig, a representative of the artiodactyla clade, is one of the first animals domesticated, and has become an important agriculture animal as one of the major human nutritional sources of animal based protein. The pig is also a valuable biomedical model organism for human health. The pig's importance to human health and nutrition is reflected in the decision to sequence its genome (3X). As an animal species with its wild ancestors present in the world, the pig provides a unique opportunity for tracing mammalian evolutionary history and defining signatures of selection resulting from both domestication and natural selection. Completion of the pig genome sequencing project will have significant impacts on both agriculture and human health. Following the pig whole genome sequence drafts, along with large-scale polymorphism data, it will be possible to conduct genome sweeps using association mapping, and identify signatures of selection. Here, we provide a description of the pig genome sequencing project and perspectives on utilizing genomic technologies to exploit pig genome evolution and the molecular basis for phenotypic traits for improving pig production and health

Porcine Genomic Sequencing Initiative

Rationale and Objectives. Completion of the human genome sequence provides the starting point for understanding the genetic complexity of humans and how genetic variation contributes to diverse phenotypes and disease. It is clear that model organisms have played an invaluable role in the synthesis of this understanding. It is also noted that additional species must be sequenced to resolve the genetic complexity of human evolution and to effectively extrapolate genetic information from comparative (veterinary) medicine to human medicine. Certainly the pig has been a valuable biomedical model organism and its role will expand in the future. The pig also represents an evolutionary clade distinct from primates or rodents, and thus, provides considerable power in the analysis of human genomic sequences. The pig, a domesticated eutherian mammal, has co-evolved with humans and represents a taxa with diverse selected phenotypes [Rothschild and Ruvinsky, 1998]. The pig has a central position in the scientific and veterinary medical communities that supports the utility of securing genome sequence information. Thus, this white paper provides scientific justification for sequencing the porcine genome (6X coverage) to identify new genes and novel regulatory elements in the pig and in humans, mice and rats. The porcine genome will serve as a reference non-primate, non-rodent, eutherian genome. The recent ability to genetically modify the porcine genome, genetically manipulate embryonic fibroblasts, and �clone� genetically modified somatic cells through nuclear transfer attests to how the pig can provide relevant genetic models (of appropriate phenotypes). This further demonstrates the unique role the pig will play in biomedical research, hence warranting the value for genomic sequencing. The porcine genome is uniquely positioned for genomic sequencing because of the advanced stage of the necessary reagents. A porcine BAC map with 20X coverage, constructed via an international consortium, will be fingerprinted and all fingerprinted clones end-sequenced by June, 2003. This resource will permit selection of the minimum tilling path of BAC clones to be sequenced and complement a whole-genome shotgun sequencing approach. This approach was selected since its affords increased efficiency, saving time and money, and yields a better product since the BAC map will be completed prior to initiation of genomic sequencing. Linking the sequence to the BAC clone map allows for subsequent targeted closure of the genomic sequence in regions of particular interest. This strategy is justified through the outcomes associated with the human, mouse, and rat sequencing efforts that were done in parallel with the BAC map development

Cry1 expression during postnatal development is critical for the establishment of normal circadian period

The mammalian circadian system generates an approximate 24-h rhythm through a complex autoregulatory feedback loop. Four genes, Period1 (Per1), Period2 (Per2), Cryptochrome1 (Cry1), and Cryptochrome2 (Cry2), regulate the negative feedback within this loop. Although these proteins have distinct roles within the core circadian mechanism, their individual functions are poorly understood. Here, we used a tetracycline trans-activator system (tTA) to examine the role of transcriptional oscillations in Cry1 and Cry2 in the persistence of circadian activity rhythms. We demonstrate that rhythmic Cry1 expression is an important regulator of circadian period. We then define a critical period from birth to postnatal day 45 (PN45) where the level of Cry1 expression is critical for setting the endogenous free running period in the adult animal. Moreover, we show that, although rhythmic Cry1 expression is important, in animals with disrupted circadian rhythms overexpression of Cry1 is sufficient to restore normal behavioral periodicity. These findings provide new insights into the roles of the Cryptochrome proteins in circadian rhythmicity and further our understanding of the mammalian circadian clock