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Faske TM, Agneray AC, Jahner JP, Osuna-Mascaró C, Sheta LM, Richardson BA, Leger EA, Parchman TL. Environment predicts the maintenance of reproductive isolation in a mosaic hybrid zone of rubber rabbitbrush. Evolution 2024; 78:300-314. [PMID: 37962379 DOI: 10.1093/evolut/qpad207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 10/23/2023] [Accepted: 11/09/2023] [Indexed: 11/15/2023]
Abstract
Widely distributed plants of western North America experience divergent selection across environmental gradients, have complex histories shaped by biogeographic barriers and distributional shifts and often illustrate continuums of reproductive isolation. Rubber rabbitbrush (Ericameria nauseosa) is a foundational shrub species that occurs across diverse environments of western North America. Its remarkable phenotypic diversity is currently ascribed to two subspecies-Ericameria nauseosa nauseosa and Ericameria nauseosa consimilis-and 22 named varieties. To understand how genetic variation is partitioned across subspecies, varieties, and environments, we used high throughput sequencing of reduced representation libraries. We found clear evidence for divergence between the two subspecies, despite largely sympatric distributions. Numerous locations exhibiting admixed ancestry were not geographically localized but were widely distributed across a mosaic hybrid zone. The occurrence of hybrid and subspecific ancestries was strongly predicted by environmental variables as well as the proximity to major ecotones between ecoregions. Although this repeatability illustrates the importance of environmental factors in shaping reproductive isolation, variability in the prevalence of hybridization also indicates these factors likely differ across ecological contexts. There was mixed evidence for the evolutionary cohesiveness of varieties, but several genetically distinct and narrow endemic varieties exhibited admixed subspecific ancestries, hinting at the possibility for transgressive hybridization to contribute to phenotypic novelty and the colonization of new environments in E. nauseosa.
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Affiliation(s)
- Trevor M Faske
- Department of Biology, University of Nevada, Reno, Reno, NV 89557, United States
- Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, NV 89557, United States
| | - Alison C Agneray
- Department of Biology, University of Nevada, Reno, Reno, NV 89557, United States
- Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, NV 89557, United States
- Bureau of Land Management, Nevada State Office, Reno, NV 89502, United States
| | - Joshua P Jahner
- Department of Botany, University of Wyoming, Laramie, WY, 82071, United States
| | | | - Lana M Sheta
- Department of Biology, University of Nevada, Reno, Reno, NV 89557, United States
| | - Bryce A Richardson
- Rocky Mountain Research Station, USDA Forest Service, Moscow, ID 83843, United States
| | - Elizabeth A Leger
- Department of Biology, University of Nevada, Reno, Reno, NV 89557, United States
- Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, NV 89557, United States
| | - Thomas L Parchman
- Department of Biology, University of Nevada, Reno, Reno, NV 89557, United States
- Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, NV 89557, United States
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Melton AE, Moran K, Martinez P, Ellestad P, Milliken E, Morales W, Child AW, Richardson BA, Serpe M, Novak SJ, Buerki S. A genotype × environment experiment reveals contrasting response strategies to drought between populations of a keystone species ( Artemisia tridentata; Asteraceae). Plant Environ Interact 2023; 4:201-214. [PMID: 37583876 PMCID: PMC10423975 DOI: 10.1002/pei3.10119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 06/18/2023] [Accepted: 07/11/2023] [Indexed: 08/17/2023]
Abstract
Western North America has been experiencing persistent drought exacerbated by climate change for over two decades. This extreme climate event is a clear threat to native plant communities. Artemisia tridentata is a keystone shrub species in western North America and is threatened by climate change, urbanization, and wildfire. A drought Genotype × Environment (G × E) experiment was conducted to assess phenotypic plasticity and differential gene expression in A. tridentata. The G × E experiment was performed on diploid A. tridentata seedlings from two populations (one from Idaho, USA and one from Utah, USA), which experience differing levels of drought stress during the summer months. Photosynthetic data, leaf temperature, and gene expression levels were compared between treatments and populations. The Utah population maintained higher photosynthetic rates and photosynthetic efficiency than the Idaho population under drought stress. The Utah population also exhibited far greater transcriptional plasticity than the Idaho population and expressed genes of response pathways distinct from those of the Idaho population. Populations of A. tridentata differ greatly in their drought response pathways, likely due to differences in response pathways that have evolved under distinct climatic regimes. Epigenetic processes likely contribute to the observed differences between the populations.
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Affiliation(s)
- Anthony E. Melton
- Department of Biological SciencesBoise State UniversityBoiseIdahoUSA
| | - Kara Moran
- Department of Biological SciencesBoise State UniversityBoiseIdahoUSA
| | - Peggy Martinez
- Department of Biological SciencesBoise State UniversityBoiseIdahoUSA
| | - Paige Ellestad
- Department of Biological SciencesBoise State UniversityBoiseIdahoUSA
| | - Erin Milliken
- Department of Biological SciencesBoise State UniversityBoiseIdahoUSA
| | - Walker Morales
- Department of Biological SciencesBoise State UniversityBoiseIdahoUSA
| | - Andrew W. Child
- Research Computing and Data ServicesUniversity of IdahoMoscowIdahoUSA
| | | | - Marcelo Serpe
- Department of Biological SciencesBoise State UniversityBoiseIdahoUSA
| | - Stephen J. Novak
- Department of Biological SciencesBoise State UniversityBoiseIdahoUSA
| | - Sven Buerki
- Department of Biological SciencesBoise State UniversityBoiseIdahoUSA
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3
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Grossfurthner LP, Milano ER, Hohenlohe PA, Waits LP, Richardson BA. Population structure and hybridization under contemporary and future climates in a heteroploid foundational shrub species ( Artemisia tridentata). Front Plant Sci 2023; 14:1155868. [PMID: 37284723 PMCID: PMC10239881 DOI: 10.3389/fpls.2023.1155868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 04/20/2023] [Indexed: 06/08/2023]
Abstract
Current and past climatic changes can shift plant climatic niches, which may cause spatial overlap or separation between related taxa. The former often leads to hybridization and introgression, which may generate novel variation and influence the adaptive capacity of plants. An additional mechanism facilitating adaptations to novel environments and an important evolutionary driver in plants is polyploidy as the result of whole genome duplication. Artemisia tridentata (big sagebrush) is a landscape-dominating foundational shrub in the western United States which occupies distinct ecological niches, exhibiting diploid and tetraploid cytotypes. Tetraploids have a large impact on the species' landscape dominance as they occupy a preponderance of the arid spectrum of A. tridentata range. Three distinct subspecies are recognized, which co-occur in ecotones - the transition zone between two or more distinct ecological niches - allowing for hybridization and introgression. Here we assess the genomic distinctiveness and extent of hybridization among subspecies at different ploidies under both contemporary and predicted future climates. We sampled five transects throughout the western United States where a subspecies overlap was predicted using subspecies-specific climate niche models. Along each transect, we sampled multiple plots representing the parental and the potential hybrid habitats. We performed reduced representation sequencing and processed the data using a ploidy-informed genotyping approach. Population genomic analyses revealed distinct diploid subspecies and at least two distinct tetraploid gene pools, indicating independent origins of the tetraploid populations. We detected low levels of hybridization (2.5%) between the diploid subspecies, while we found evidence for increased admixture between ploidy levels (18%), indicating hybridization has an important role in the formation of tetraploids. Our analyses highlight the importance of subspecies co-occurrence within these ecotones to maintain gene exchange and potential formation of tetraploid populations. Genomic confirmations of subspecies in the ecotones support the subspecies overlap predicted by the contemporary climate niche models. However, future mid-century projections of subspecies niches predict a substantial loss in range and subspecies overlap. Thus, reductions in hybridization potential could affect new recruitment of genetically variable tetraploids that are vital to this species' ecological role. Our results underscore the importance of ecotone conservation and restoration.
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Affiliation(s)
- Lukas P. Grossfurthner
- Bioinformatics and Computational Biology Graduate Program, University of Idaho, Moscow, ID, United States
- Department of Biological Sciences, University of Idaho, Moscow, ID, United States
| | - Elizabeth R. Milano
- Rocky Mountain Research Station, United States Department of Agriculture (USDA) Forest Service, Moscow, ID, United States
| | - Paul A. Hohenlohe
- Department of Biological Sciences, University of Idaho, Moscow, ID, United States
| | - Lisette P. Waits
- Department of Fish and Wildlife Sciences, University of Idaho, Moscow, ID, United States
| | - Bryce A. Richardson
- Rocky Mountain Research Station, United States Department of Agriculture (USDA) Forest Service, Moscow, ID, United States
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Zaiats A, Requena‐Mullor JM, Germino MJ, Forbey JS, Richardson BA, Caughlin TT. Spatial models can improve the experimental design of field‐based transplant gardens by preventing bias due to neighborhood crowding. Ecol Evol 2022; 12:e9630. [PMCID: PMC9750843 DOI: 10.1002/ece3.9630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 11/23/2022] [Accepted: 11/27/2022] [Indexed: 12/16/2022] Open
Affiliation(s)
| | | | - Matthew J. Germino
- U.S. Geological Survey Forest and Rangeland Ecosystem Science Center Boise Idaho USA
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Richardson BA, Massatti R, Islam‐Faridi N, Johnson S, Kilkenny FF. Assessing population genomic structure and polyploidy: a crucial step for native plant restoration. Restor Ecol 2022. [DOI: 10.1111/rec.13740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Rob Massatti
- Southwest Biological Center, US Geological Survey Flagstaff Arizona
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St.Clair JB, Richardson BA, Stevenson‐Molnar N, Howe GT, Bower AD, Erickson VJ, Ward B, Bachelet D, Kilkenny FF, Wang T. Seedlot Selection Tool and Climate‐Smart Restoration Tool: Web‐based tools for sourcing seed adapted to future climates. Ecosphere 2022. [DOI: 10.1002/ecs2.4089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
| | | | | | - Glenn T. Howe
- Department of Forest Ecosystems and Society Oregon State University Corvallis Oregon USA
| | - Andrew D. Bower
- Olympic National Forest USDA‐Forest Service Olympia Washington USA
| | | | - Brendan Ward
- Conservation Biology Institute Corvallis Oregon USA
| | | | | | - Tongli Wang
- Centre for Forest Conservation Genetics, Department of Forest and Conservation Science University of British Columbia Vancouver British Columbia Canada
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Melton AE, Child AW, Beard RS, Dumaguit CDC, Forbey JS, Germino M, de Graaff MA, Kliskey A, Leitch IJ, Martinez P, Novak SJ, Pellicer J, Richardson BA, Self D, Serpe M, Buerki S. A haploid pseudo-chromosome genome assembly for a keystone sagebrush species of western North American rangelands. G3 (Bethesda) 2022; 12:6585877. [PMID: 35567476 PMCID: PMC9258541 DOI: 10.1093/g3journal/jkac122] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 05/03/2022] [Indexed: 11/14/2022]
Abstract
Increased ecological disturbances, species invasions, and climate change are creating severe conservation problems for several plant species that are widespread and foundational. Understanding the genetic diversity of these species and how it relates to adaptation to these stressors are necessary for guiding conservation and restoration efforts. This need is particularly acute for big sagebrush (Artemisia tridentata; Asteraceae), which was once the dominant shrub over 1,000,000 km2 in western North America but has since retracted by half and thus has become the target of one of the largest restoration seeding efforts globally. Here, we present the first reference-quality genome assembly for an ecologically important subspecies of big sagebrush (A. tridentata subsp. tridentata) based on short and long reads, as well as chromatin proximity ligation data analyzed using the HiRise pipeline. The final 4.2-Gb assembly consists of 5,492 scaffolds, with nine pseudo-chromosomal scaffolds (nine scaffolds comprising at least 90% of the assembled genome; n = 9). The assembly contains an estimated 43,377 genes based on ab initio gene discovery and transcriptional data analyzed using the MAKER pipeline, with 91.37% of BUSCOs being completely assembled. The final assembly was highly repetitive, with repeat elements comprising 77.99% of the genome, making the Artemisia tridentata subsp. tridentata genome one of the most highly repetitive plant genomes to be sequenced and assembled. This genome assembly advances studies on plant adaptation to drought and heat stress and provides a valuable tool for future genomic research.
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Affiliation(s)
- Anthony E Melton
- Corresponding author: Department of Biological Sciences, Boise State University, Boise, ID 83725, USA.
| | | | - Richard S Beard
- Department of Biological Sciences, Boise State University, Boise, ID 83725, USA
| | | | - Jennifer S Forbey
- Department of Biological Sciences, Boise State University, Boise, ID 83725, USA
| | - Matthew Germino
- Forest and Rangeland Ecosystem Science Center, United States Geological Survey, Boise, ID 83706, USA
| | | | | | | | - Peggy Martinez
- Department of Biological Sciences, Boise State University, Boise, ID 83725, USA
| | - Stephen J Novak
- Department of Biological Sciences, Boise State University, Boise, ID 83725, USA
| | - Jaume Pellicer
- Royal Botanic Gardens, Richmond TW9 3AE, UK,Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Barcelona 08038, Spain
| | - Bryce A Richardson
- Rocky Mountain Research Station, United States Forest Service, Moscow, ID 83843, USA
| | - Desiree Self
- Department of Biological Sciences, Boise State University, Boise, ID 83725, USA
| | - Marcelo Serpe
- Department of Biological Sciences, Boise State University, Boise, ID 83725, USA
| | - Sven Buerki
- Corresponding author: Department of Biological Sciences, Boise State University, Boise, ID 83725, USA.
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Chen Z, Grossfurthner L, Loxterman JL, Masingale J, Richardson BA, Seaborn T, Smith B, Waits LP, Narum SR. Applying genomics in assisted migration under climate change: Framework, empirical applications, and case studies. Evol Appl 2022; 15:3-21. [PMID: 35126645 PMCID: PMC8792483 DOI: 10.1111/eva.13335] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 11/18/2021] [Accepted: 12/01/2021] [Indexed: 12/01/2022] Open
Abstract
The rate of global climate change is projected to outpace the ability of many natural populations and species to adapt. Assisted migration (AM), which is defined as the managed movement of climate-adapted individuals within or outside the species ranges, is a conservation option to improve species' adaptive capacity and facilitate persistence. Although conservation biologists have long been using genetic tools to increase or maintain diversity of natural populations, genomic techniques could add extra benefit in AM that include selectively neutral and adaptive regions of the genome. In this review, we first propose a framework along with detailed procedures to aid collaboration among scientists, agencies, and local and regional managers during the decision-making process of genomics-guided AM. We then summarize the genomic approaches for applying AM, followed by a literature search of existing incorporation of genomics in AM across taxa. Our literature search initially identified 729 publications, but after filtering returned only 50 empirical studies that were either directly applied or considered genomics in AM related to climate change across taxa of plants, terrestrial animals, and aquatic animals; 42 studies were in plants. This demonstrated limited application of genomic methods in AM in organisms other than plants, so we provide further case studies as two examples to demonstrate the negative impact of climate change on non-model species and how genomics could be applied in AM. With the rapidly developing sequencing technology and accumulating genomic data, we expect to see more successful applications of genomics in AM, and more broadly, in the conservation of biodiversity.
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Affiliation(s)
- Zhongqi Chen
- Aquaculture Research InstituteUniversity of IdahoHagermanIdahoUSA
| | - Lukas Grossfurthner
- Bioinformatics and Computational Biology Graduate ProgramUniversity of IdahoHagermanIdahoUSA
| | - Janet L. Loxterman
- Department of Biological SciencesIdaho State UniversityPocatelloIdahoUSA
| | | | | | - Travis Seaborn
- Department of Fish and Wildlife ResourcesUniversity of IdahoMoscowIdahoUSA
| | - Brandy Smith
- Department of Biological SciencesIdaho State UniversityPocatelloIdahoUSA
| | - Lisette P. Waits
- Department of Fish and Wildlife ResourcesUniversity of IdahoMoscowIdahoUSA
| | - Shawn R. Narum
- Columbia River Inter‐Tribal Fish CommissionHagermanIdahoUSA
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Melton AE, Beck J, Galla SJ, Jenkins J, Handley L, Kim M, Grimwood J, Schmutz J, Richardson BA, Serpe M, Novak S, Buerki S. A draft genome provides hypotheses on drought tolerance in a keystone plant species in Western North America threatened by climate change. Ecol Evol 2021; 11:15417-15429. [PMID: 34765187 PMCID: PMC8571618 DOI: 10.1002/ece3.8245] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 08/12/2021] [Accepted: 10/01/2021] [Indexed: 11/17/2022] Open
Abstract
Climate change presents distinct ecological and physiological challenges to plants as extreme climate events become more common. Understanding how species have adapted to drought, especially ecologically important nonmodel organisms, will be crucial to elucidate potential biological pathways for drought adaptation and inform conservation strategies. To aid in genome-to-phenome research, a draft genome was assembled for a diploid individual of Artemisia tridentata subsp. tridentata, a threatened keystone shrub in western North America. While this taxon has few genetic resources available and genetic/genomics work has proven difficult due to genetic heterozygosity in the past, a draft genome was successfully assembled. Aquaporin (AQP) genes and their promoter sequences were mined from the draft genome to predict mechanisms regulating gene expression and generate hypotheses on key genes underpinning drought response. Fifty-one AQP genes were fully assembled within the draft genome. Promoter and phylogenetic analyses revealed putative duplicates of A. tridentata subsp. tridentata AQPs which have experienced differentiation in promoter elements, potentially supporting novel biological pathways. Comparison with nondrought-tolerant congener supports enrichments of AQP genes in this taxon during adaptation to drought stress. Differentiation of promoter elements revealed that paralogues of some genes have evolved to function in different pathways, highlighting these genes as potential candidates for future research and providing critical hypotheses for future genome-to-phenome work.
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Affiliation(s)
- Anthony E. Melton
- Department of Biological SciencesBoise State UniversityBoiseIdahoUSA
| | - James Beck
- Department of ComputingBoise State UniversityBoiseIdahoUSA
| | | | - Jerry Jenkins
- HudsonAlpha Institute for BiotechnologyHuntsvilleAlabamaUSA
| | - Lori Handley
- HudsonAlpha Institute for BiotechnologyHuntsvilleAlabamaUSA
| | - Min Kim
- HudsonAlpha Institute for BiotechnologyHuntsvilleAlabamaUSA
| | - Jane Grimwood
- HudsonAlpha Institute for BiotechnologyHuntsvilleAlabamaUSA
| | - Jeremy Schmutz
- HudsonAlpha Institute for BiotechnologyHuntsvilleAlabamaUSA
| | | | - Marcelo Serpe
- Department of Biological SciencesBoise State UniversityBoiseIdahoUSA
| | - Stephen Novak
- Department of Biological SciencesBoise State UniversityBoiseIdahoUSA
| | - Sven Buerki
- Department of Biological SciencesBoise State UniversityBoiseIdahoUSA
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10
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Richardson BA, Germino MJ, Warwell MV, Buerki S. The role of genome duplication in big sagebrush growth and fecundity. Am J Bot 2021; 108:1405-1416. [PMID: 34460105 DOI: 10.1002/ajb2.1714] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 03/05/2021] [Indexed: 06/13/2023]
Abstract
PREMISE Adaptive traits can be dramatically altered by genome duplication. The study of interactions among traits, ploidy, and the environment are necessary to develop an understanding of how polyploidy affects niche differentiation and to develop restoration strategies for resilient native ecosystems. METHODS Growth and fecundity were measured in common gardens for 39 populations of big sagebrush (Artemisia tridentata) containing two subspecies and two ploidy levels. General linear mixed-effect models assessed how much of the trait variation could be attributed to genetics (i.e., ploidy and climatic adaptation), environment, and gene-environment interactions. RESULTS Growth and fecundity variation were explained well by the mixed models (80% and 91%, respectively). Much of the trait variation was attributed to environment, and 15% of variation in growth and 34% of variation in seed yield were attributed to genetics. Genetic trait variation was mostly attributable to ploidy, with much higher growth and seed production in diploids, even in a warm-dry environment typically dominated by tetraploids. Population-level genetic variation was also evident and was related to the climate of each population's origin. CONCLUSIONS Ploidy is a strong predictor growth and seed yield, regardless of common-garden environment. The superior growth and fecundity of diploids across environments raises the question as to how tetraploids can be more prevalent than diploids, especially in warm-dry environments. Two hypotheses that may explain the abundance of tetraploids on the landscape include selection for drought resistance at the seedling stage, and greater competitive ability in water uptake in the upper soil horizon.
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Affiliation(s)
| | - Matthew J Germino
- U.S. Geological Survey, Forest and Rangeland Ecosystem Service Center, Boise, ID, USA
| | | | - Sven Buerki
- Department of Biological Sciences, Boise State University, Boise, ID, USA
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11
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Zaiats A, Germino MJ, Serpe MD, Richardson BA, Caughlin TT. Intraspecific variation mediates density dependence in a genetically diverse plant species. Ecology 2021; 102:e03502. [PMID: 34314039 DOI: 10.1002/ecy.3502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 05/06/2021] [Indexed: 11/06/2022]
Abstract
Interactions between neighboring plants are critical for biodiversity maintenance in plant populations and communities. Intraspecific trait variation and genome duplication are common in plant species and can drive eco-evolutionary dynamics through genotype-mediated plant-plant interactions. However, few studies have examined how species-wide intraspecific variation may alter interactions between neighboring plants. We investigate how subspecies and ploidy variation in a genetically diverse species, big sagebrush (Artemisia tridentata), can alter the demographic outcomes of plant interactions. Using a replicated, long-term common garden experiment that represents range-wide diversity of A. tridentata, we ask how intraspecific variation, environment, and stand age mediate neighbor effects on plant growth and survival. Spatially explicit models revealed that ploidy variation and subspecies identity can mediate plant-plant interactions but that the effect size varied in time and across experimental sites. We found that demographic impacts of neighbor effects were strongest during early stages of stand development and in sites with greater growth rates. Within subspecies, tetraploid populations showed greater tolerance to neighbor crowding compared to their diploid variants. Our findings provide evidence that intraspecific variation related to genome size and subspecies identity impacts spatial demography in a genetically diverse plant species. Accounting for intraspecific variation in studies of conspecific density dependence will improve our understanding of how local populations will respond to novel genotypes and biotic interaction regimes. As introduction of novel genotypes into local populations becomes more common, quantifying demographic processes in genetically diverse populations will help predict long-term consequences of plant-plant interactions.
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Affiliation(s)
- Andrii Zaiats
- Department of Biological Sciences, Boise State University, Boise, Idaho, 83725, USA
| | - Matthew J Germino
- U.S. Geological Survey, Forest and Rangeland Ecosystem Science Center, Boise, Idaho, 83706, USA
| | - Marcelo D Serpe
- Department of Biological Sciences, Boise State University, Boise, Idaho, 83725, USA
| | - Bryce A Richardson
- USDA Forest Service, Rocky Mountain Research Station, Moscow, Idaho, 83843, USA
| | - T Trevor Caughlin
- Department of Biological Sciences, Boise State University, Boise, Idaho, 83725, USA
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12
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Larsen A, Wilson KS, Kinuthia J, John-Stewart G, Richardson BA, Pintye J, Abuna F, Lagat H, Owens T, Kohler P. Standardised patient encounters to improve quality of counselling for pre-exposure prophylaxis (PrEP) in adolescent girls and young women (AGYW) in Kenya: study protocol of a cluster randomised controlled trial. BMJ Open 2020; 10:e035689. [PMID: 32565464 PMCID: PMC7311012 DOI: 10.1136/bmjopen-2019-035689] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 02/03/2020] [Accepted: 05/26/2020] [Indexed: 12/31/2022] Open
Abstract
INTRODUCTION Adolescent girls and young women (AGYW) in sub-Saharan Africa are at high risk of HIV acquisition. Pre-exposure prophylaxis (PrEP) demonstration projects observe that AGYW uptake and adherence to PrEP during risk periods is suboptimal. Judgemental interactions with healthcare workers (HCW) and inadequate counselling can be barriers to PrEP use among AGYW. Improving HCW competency and communication to support PrEP delivery to AGYW requires new strategies. METHODS AND ANALYSIS PrEP Implementation for Young Women and Adolescents Program-standardised patient (PrIYA-SP) is a cluster randomised trial of a standardised patient actor (SP) training intervention designed to improve HCW adherence to PrEP guidelines and communication skills. We purposively selected 24 clinics offering PrEP services under fully programmatic conditions in Kisumu County, Kenya. At baseline, unannounced SP 'mystery shoppers' present to clinics portraying AGYW in common PrEP scenarios for a cross-sectional assessment of PrEP delivery. Twelve facilities will be randomised to receive a 2-day training intervention, consisting of lectures, role-playing with SPs and group debriefing. Unannounced SPs will repeat the assessment in all 24 sites following the intervention. The primary outcome is quality of PrEP counselling, including adherence to national guidelines and communication skills, scored on a checklist by SPs blinded to intervention assignment. An intention-to-treat (ITT) analysis will evaluate whether the intervention resulted in higher scores within intervention compared with control facilities, adjusted for baseline SP scores and accounting for clustering by facility. We hypothesise that the intervention will improve quality of PrEP counselling compared with standard of care. Results from this study will inform guidelines for PrEP delivery to AGYW in low-resource settings and offer a potentially scalable strategy to improve service delivery for this high-risk group. ETHICS AND DISSEMINATION The protocol was approved by institutional review boards at Kenyatta National Hospital and University of Washington. An external advisory committee monitors social harms. Results will be disseminated through peer-reviewed journals and presentations. TRIAL REGISTRATION NUMBER NCT03875950.
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Affiliation(s)
- Anna Larsen
- Department of Global Health, University of Washington, Seattle, Washington, USA
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
| | - Kate S Wilson
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | - John Kinuthia
- Department of Global Health, University of Washington, Seattle, Washington, USA
- Research and Programs, Kenyatta National Hospital/University of Nairobi, Nairobi, Kenya
| | - G John-Stewart
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Department of Pediatrics, University of Washington, Seattle, WA, United States
| | - B A Richardson
- Department of Biostatistics, University of Washington, Seattle, WA, United States
| | - Jillian Pintye
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | - Felix Abuna
- Research and Programs, Kenyatta National Hospital/University of Nairobi, Nairobi, Kenya
| | - Harison Lagat
- Research and Programs, Kenyatta National Hospital/University of Nairobi, Nairobi, Kenya
| | - Tamara Owens
- Health Sciences Simulation & Clinical Skills Center, Howard University, Seattle, Washington, DC, USA
| | - Pamela Kohler
- Department of Child, Family, and Population Health Nursing, University of Washington, Seattle, Washington, USA
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Massatti R, Shriver RK, Winkler DE, Richardson BA, Bradford JB. Assessment of population genetics and climatic variability can refine climate‐informed seed transfer guidelines. Restor Ecol 2020. [DOI: 10.1111/rec.13142] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Rob Massatti
- U.S. Geological SurveySouthwest Biological Science Center Flagstaff Arizona 86001 U.S.A
| | - Robert K. Shriver
- U.S. Geological SurveySouthwest Biological Science Center Flagstaff Arizona 86001 U.S.A
| | - Daniel E. Winkler
- U.S. Geological SurveySouthwest Biological Science Center Moab Utah 84532 U.S.A
| | | | - John B. Bradford
- U.S. Geological SurveySouthwest Biological Science Center Flagstaff Arizona 86001 U.S.A
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14
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Zaiats A, Lazarus BE, Germino MJ, Serpe MD, Richardson BA, Buerki S, Caughlin TT. Intraspecific variation in surface water uptake in a perennial desert shrub. Funct Ecol 2020. [DOI: 10.1111/1365-2435.13546] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Andrii Zaiats
- Department of Biological Sciences Boise State University Boise ID USA
| | - Brynne E. Lazarus
- U.S. Geological Survey, Forest and Rangeland Ecosystem Science Center Boise ID USA
| | - Matthew J. Germino
- U.S. Geological Survey, Forest and Rangeland Ecosystem Science Center Boise ID USA
| | - Marcelo D. Serpe
- Department of Biological Sciences Boise State University Boise ID USA
| | | | - Sven Buerki
- Department of Biological Sciences Boise State University Boise ID USA
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15
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Lazarus BE, Germino MJ, Richardson BA. Freezing resistance, safety margins, and survival vary among big sagebrush populations across the western United States. Am J Bot 2019; 106:922-934. [PMID: 31294835 DOI: 10.1002/ajb2.1320] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 05/01/2019] [Indexed: 06/09/2023]
Abstract
PREMISE Physiological responses to temperature extremes are considered strong drivers of species' demographic responses to climate variability. Plants are typically classified as either avoiders or tolerators in their freezing-resistance mechanism, but a gradient of physiological-threshold freezing responses may exist among individuals of a species. Moreover, adaptive significance of physiological freezing responses is poorly characterized, particularly under warming conditions that relax selection on cold hardiness. METHODS Freezing responses were measured in winter and again for new foliage in spring for 14 populations of Artemisia tridentata collected throughout its range and planted in a warm common garden. The relationships of the freezing responses to survival were evaluated in the warm garden and in two colder gardens. RESULTS Winter and spring freezing resistance were not correlated and appeared to be under differing selection regimes, as evident in correlations with different population climate of origin variables. All populations resisted considerably lower temperatures in winter than in spring, with populations from more continental climates showing narrower freezing safety margins (difference in temperatures at which ice-nucleation occurs and 50% reduction in chlorophyll fluorescence occurs) in spring. Populations with greater winter freezing resistance had lower survivorship in the warmest garden, while populations with greater spring freezing resistance had lower survivorship in a colder garden. CONCLUSIONS These survivorship patterns relative to physiological thresholds suggest excess freezing resistance may incur a survival cost that likely relates to a trade-off between carbon gain and freezing resistance during critical periods of moisture availability. This cost has implications for seed moved from cooler to warmer environments and for plants growing in warming environments.
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Affiliation(s)
- Brynne E Lazarus
- U. S. Geological Survey, Forest and Rangeland Ecosystem Science Center, 970 S. Lusk Street, Boise, ID, 83706, USA
| | - Matthew J Germino
- U. S. Geological Survey, Forest and Rangeland Ecosystem Science Center, 970 S. Lusk Street, Boise, ID, 83706, USA
| | - Bryce A Richardson
- USDA Forest Service, Rocky Mountain Research Station, 1221 S. Main St., Moscow, ID, 83843, USA
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16
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Massatti R, Prendeville HR, Larson S, Richardson BA, Waldron B, Kilkenny FF. Population history provides foundational knowledge for utilizing and developing native plant restoration materials. Evol Appl 2018; 11:2025-2039. [PMID: 30459846 PMCID: PMC6231468 DOI: 10.1111/eva.12704] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 08/21/2018] [Accepted: 08/26/2018] [Indexed: 01/14/2023] Open
Abstract
A species' population structure and history are critical pieces of information that can help guide the use of available native plant materials in restoration treatments and decide what new native plant materials should be developed to meet future restoration needs. In the western United States, Pseudoroegneria spicata (bluebunch wheatgrass; Poaceae) is an important component of grassland and shrubland plant communities and commonly used for restoration due to its drought resistance and competitiveness with exotic weeds. We used next-generation sequencing data to investigate the processes that shaped P. spicata's geographic pattern of genetic variation across the Intermountain West. Pseudoroegneria spicata's genetic diversity is partitioned into populations that likely differentiated since the Last Glacial Maximum. Adjacent populations display varying magnitudes of historical gene flow, with migration rates ranging from multiple migrants per generation to multiple generations per migrant. When considering the commercial germplasm sources available for restoration, genetic identities remain representative of the wildland localities from which germplasm sources were originally developed, and they maintain high levels of heterozygosity and nucleotide diversity. However, the commercial germplasm sources represent a small fraction of the overall genetic diversity of P. spicata in the Intermountain West. Given the low migration rates and long divergence times between some pairs of P. spicata populations, using commercial germplasm sources could facilitate undesirable restoration outcomes when used in certain geographic areas, even if the environment in which the commercial materials thrive is similar to that of the restoration site. As such, population structure and history can be used to provide guidance on what geographic areas may need additional native plant materials so that restoration efforts support species and community resilience and improve outcomes.
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Affiliation(s)
- Rob Massatti
- Southwest Biological Science CenterU.S. Geological SurveyFlagstaffArizona
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17
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Richardson BA, Chaney L. Climate-based seed transfer of a widespread shrub: population shifts, restoration strategies, and the trailing edge. Ecol Appl 2018; 28:2165-2174. [PMID: 30198207 DOI: 10.1002/eap.1804] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 07/24/2018] [Accepted: 08/20/2018] [Indexed: 05/26/2023]
Abstract
Genetic resources have to be managed appropriately to mitigate the impact of climate change. For many wildland plants, conservation will require knowledge of the climatic factors affecting intraspecific genetic variation to minimize maladaptation. Knowledge of the interaction between traits and climate can focus management resources on vulnerable populations, provide guidance for seed transfer, and enhance fitness and resilience under changing climates. In this study, traits of big sagebrush (Artemisia tridentata) were examined among common gardens located in different climates. We focus on two subspecies, wyomingensis and tridentata, that occupy the most imperiled warm-dry spectrum of the sagebrush biome. Populations collected across the sagebrush biome were recorded for flower phenology and survival. Mixed-effects models examined each trait to evaluate genetic variation, environmental effects, and adaptive breadth of populations. Climate variables derived from population-source locations were significantly associated with these traits (P < 0.0001), explaining 31% and 11% of the flower phenology and survival variation, respectively. To illustrate our model and assess variability in prediction, we examine fixed and focal point seed transfer approaches to map contemporary and climate model ensemble projections in two different regions of the sagebrush biome. A comparison of seed transfer areas predicts that populations from warmer climates become more prevalent, replacing colder-adapted populations by mid-century. However, these warm-adapted populations are often located along the trailing edge, margins of the species range predicted to be lost due to a contraction of the climatic niche. Management efforts should focus on the collection and conservation of vulnerable populations and prudent seed transfer to colder regions where these populations are projected to occur by mid-century. Our models provide the foundation to develop an empirical, climate-based seed transfer system for current and future restoration of big sagebrush.
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Affiliation(s)
- Bryce A Richardson
- USDA Forest Service, Rocky Mountain Research Station, Moscow, Idaho, 83843, USA
| | - Lindsay Chaney
- Division of Natural Science and Mathematics, Snow College, Ephraim, Utah, 84627, USA
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Winkler DE, Backer DM, Belnap J, Bradford JB, Butterfield BJ, Copeland SM, Duniway MC, Faist AM, Fick SE, Jensen SL, Kramer AT, Mann R, Massatti RT, McCormick ML, Munson SM, Olwell P, Parr SD, Pfennigwerth AA, Pilmanis AM, Richardson BA, Samuel E, See K, Young KE, Reed SC. Beyond traditional ecological restoration on the Colorado Plateau. Restor Ecol 2018. [DOI: 10.1111/rec.12876] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Daniel E. Winkler
- Canyonlands Research Station; Southwest Biological Science Center, U.S. Geological Survey; 2290 South West Resource Boulevard, Moab UT 84532 U.S.A
| | - Dana M. Backer
- Grand Staircase Escalante National Monument, Bureau of Land Management; Kanab UT 84741 U.S.A
| | - Jayne Belnap
- Canyonlands Research Station; Southwest Biological Science Center, U.S. Geological Survey; 2290 South West Resource Boulevard, Moab UT 84532 U.S.A
| | - John B. Bradford
- Southwest Biological Science Center, U.S. Geological Survey; 2255 North Gemini Drive, Flagstaff AZ 86001 U.S.A
| | - Bradley J. Butterfield
- Merriam-Powell Center for Environmental Research and Department of Biological Sciences; Northern Arizona University; 805 South Beaver Street, Flagstaff AZ 86011-6077 U.S.A
| | - Stella M. Copeland
- Southwest Biological Science Center, U.S. Geological Survey; 2255 North Gemini Drive, Flagstaff AZ 86001 U.S.A
- Merriam-Powell Center for Environmental Research and Department of Biological Sciences; Northern Arizona University; 805 South Beaver Street, Flagstaff AZ 86011-6077 U.S.A
| | - Michael C. Duniway
- Canyonlands Research Station; Southwest Biological Science Center, U.S. Geological Survey; 2290 South West Resource Boulevard, Moab UT 84532 U.S.A
| | - Akasha M. Faist
- Department of Animal and Range Sciences; New Mexico State University; Las Cruces NM 88003 U.S.A
| | - Stephen E. Fick
- Canyonlands Research Station; Southwest Biological Science Center, U.S. Geological Survey; 2290 South West Resource Boulevard, Moab UT 84532 U.S.A
| | - Scott L. Jensen
- Rocky Mountain Research Station; U.S. Forest Service; 735 North 500 East, Provo UT 84606 U.S.A
| | - Andrea T. Kramer
- Chicago Botanic Garden; 1000 Lake Cook Road, Glencoe IL 60022 U.S.A
| | - Rebecca Mann
- Canyonlands Research Station; Southwest Biological Science Center, U.S. Geological Survey; 2290 South West Resource Boulevard, Moab UT 84532 U.S.A
| | - Robert T. Massatti
- Southwest Biological Science Center, U.S. Geological Survey; 2255 North Gemini Drive, Flagstaff AZ 86001 U.S.A
| | - Molly L. McCormick
- Southwest Biological Science Center, U.S. Geological Survey; 2255 North Gemini Drive, Flagstaff AZ 86001 U.S.A
| | - Seth M. Munson
- Southwest Biological Science Center, U.S. Geological Survey; 2255 North Gemini Drive, Flagstaff AZ 86001 U.S.A
| | - Peggy Olwell
- Bureau of Land Management; 1849 C Street NW, LSB-204, Washington DC 20240 U.S.A
| | - Steve D. Parr
- Upper Colorado Environmental Plant Center; 5538 County Road 4, Meeker CO 81641 U.S.A
| | - Alix A. Pfennigwerth
- Canyonlands Research Station; Southwest Biological Science Center, U.S. Geological Survey; 2290 South West Resource Boulevard, Moab UT 84532 U.S.A
| | - Adrienne M. Pilmanis
- Colorado Plateau Native Plant Program; Bureau of Land Management; 440 West 200 South, Salt Lake City UT 84101 U.S.A
| | - Bryce A. Richardson
- Rocky Mountain Research Station; U.S. Forest Service; 735 North 500 East, Provo UT 84606 U.S.A
| | - Ella Samuel
- New Mexico State Office; Bureau of Land Management; 301 Dinosaur Trail, Santa Fe NM 87508 U.S.A
| | - Kathy See
- Western Colorado Landscape Collaborative; Montrose CO 81402 U.S.A
| | - Kristina E. Young
- Canyonlands Research Station; Southwest Biological Science Center, U.S. Geological Survey; 2290 South West Resource Boulevard, Moab UT 84532 U.S.A
| | - Sasha C. Reed
- Canyonlands Research Station; Southwest Biological Science Center, U.S. Geological Survey; 2290 South West Resource Boulevard, Moab UT 84532 U.S.A
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19
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Pavlinac PB, Lokken EM, Walson JL, Richardson BA, Crump JA, John-Stewart GC. Mycobacterium tuberculosis bacteremia in adults and children: a systematic review and meta-analysis. Int J Tuberc Lung Dis 2018; 20:895-902. [PMID: 27287641 DOI: 10.5588/ijtld.15.0773] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
UNLABELLED SETTINGp: Among human immunodeficiency virus (HIV) infected adults living in tuberculosis (TB) endemic settings, Mycobacterium tuberculosis is a common cause of bloodstream infections. Although young children have an increased propensity for M. tuberculosis dissemination, M. tuberculosis bacteremia is infrequently described in children. OBJECTIVE To determine the prevalence of M. tuberculosis bacteremia in adult and pediatric patients and to examine sources of heterogeneity between estimates. DESIGN Systematic review and meta-analysis. RESULTS Of 1077 reviewed abstracts, 27 publications met the inclusion criteria, yielding 29 independent M. tuberculosis bacteremia prevalence estimates: 22 in adults, 6 in children, and 1 not stratified by age group. The random effects pooled M. tuberculosis bacteremia prevalence in adults was 13.5% (95%CI 10.8-16.2) and 0.4% (95%CI 0-0.9) in children (P for difference = 0.004). Restricting analyses to HIV-infected participants, pooled M. tuberculosis bacteremia prevalence from 21 adult studies was 15.5% (95%CI 12.5-18.5) and 0.8% (95%CI 0-1.8) in three pediatric studies (P = 0.001). Inclusion of pre-determined study-level confounders did not account for observed differences in M. tuberculosis bacteremia prevalence between age groups. CONCLUSION While M. tuberculosis bacteremia appears relatively common in adults, particularly those with HIV infection, bloodstream M. tuberculosis appears to be rare in children.
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Affiliation(s)
- P B Pavlinac
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | - E M Lokken
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
| | - J L Walson
- Department of Global Health, University of Washington, Seattle, Washington, USA; Department of Epidemiology, University of Washington, Seattle, Washington, USA; Department of Pediatrics, University of Washington, Seattle, Washington, USA; Department of Medicine, University of Washington, Seattle, Washington, USA
| | - B A Richardson
- Department of Global Health, University of Washington, Seattle, Washington, USA; Department of Biostatistics, University of Washington, Seattle, Washington, USA
| | - J A Crump
- Centre for International Health, University of Otago, Dunedin, New Zealand
| | - G C John-Stewart
- Department of Global Health, University of Washington, Seattle, Washington, USA; Department ofEpidemiology, University of Washington, Seattle, Washington, USA; Department of Pediatrics, University of Washington, Seattle, Washington, USA; Department ofMedicine, University of Washington, Seattle, Washington, USA
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20
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Forbey JS, Patricelli GL, Delparte DM, Krakauer AH, Olsoy PJ, Fremgen MR, Nobler JD, Spaete LP, Shipley LA, Rachlow JL, Dirksen AK, Perry A, Richardson BA, Glenn NF. Emerging technology to measure habitat quality and behavior of grouse: examples from studies of greater sage-grouse. Wildlife Biology 2017. [DOI: 10.2981/wlb.00238] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
| | - Gail L. Patricelli
- G. L. Patricelli, A. H. Krakauer, A. K. Dirksen and A. Perry, Dept of Evolution and Ecology, Univ. o
| | - Donna M. Delparte
- D. M. Delparte and N. F. Glenn, Dept of Geosciences, Idaho State Univ., Pocatello, Idaho, USA
| | - Alan H. Krakauer
- G. L. Patricelli, A. H. Krakauer, A. K. Dirksen and A. Perry, Dept of Evolution and Ecology, Univ. o
| | - Peter J. Olsoy
- P. J. Olsoy and L. A. Shipley, School of the Environment, Washington State Univ., Pullman, Washingto
| | | | - Jordan D. Nobler
- J. Sorensen Forbey , M. R. Fremgen and J. D. Nobler, Dept of Biologic
| | - Lucas P. Spaete
- L. P. Spaete, Dept of Geosciences, Boise State Univ., Boise, Idaho, USA
| | - Lisa A. Shipley
- P. J. Olsoy and L. A. Shipley, School of the Environment, Washington State Univ., Pullman, Washingto
| | - Janet L. Rachlow
- J. L. Rachlow, Dept of Fish and Wildlife Sciences, Univ. of Idaho, Moscow, Idaho, USA
| | - Amy K. Dirksen
- G. L. Patricelli, A. H. Krakauer, A. K. Dirksen and A. Perry, Dept of Evolution and Ecology, Univ. o
| | - Anna Perry
- G. L. Patricelli, A. H. Krakauer, A. K. Dirksen and A. Perry, Dept of Evolution and Ecology, Univ. o
| | - Bryce A. Richardson
- B. A. Richardson, USDA Forest Service Rocky Mountain Research Station, Provo, Utah, USA
| | - Nancy F. Glenn
- D. M. Delparte and N. F. Glenn, Dept of Geosciences, Idaho State Univ., Pocatello, Idaho, USA
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Richardson BA, Chaney L, Shaw NL, Still SM. Will phenotypic plasticity affecting flowering phenology keep pace with climate change? Glob Chang Biol 2017; 23:2499-2508. [PMID: 27739159 DOI: 10.1111/gcb.13532] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 09/28/2016] [Accepted: 10/01/2016] [Indexed: 06/06/2023]
Abstract
Rising temperatures have begun to shift flowering time, but it is unclear whether phenotypic plasticity can accommodate projected temperature change for this century. Evaluating clines in phenological traits and the extent and variation in plasticity can provide key information on assessing risk of maladaptation and developing strategies to mitigate climate change. In this study, flower phenology was examined in 52 populations of big sagebrush (Artemisia tridentata) growing in three common gardens. Flowering date (anthesis) varied 91 days from late July to late November among gardens. Mixed-effects modeling explained 79% of variation in flowering date, of which 46% could be assigned to plasticity and genetic variation in plasticity and 33% to genetics (conditional R2 = 0.79, marginal R2 = 0.33). Two environmental variables that explained the genetic variation were photoperiod and the onset of spring, the Julian date of accumulating degree-days >5 °C reaching 100. The genetic variation was mapped for contemporary and future climates (decades 2060 and 2090), showing flower date change varies considerably across the landscape. Plasticity was estimated to accommodate, on average, a ±13-day change in flowering date. However, the examination of genetic variation in plasticity suggests that the magnitude of plasticity could be affected by variation in the sensitivity to photoperiod and temperature. In a warmer common garden, lower-latitude populations have greater plasticity (+16 days) compared to higher-latitude populations (+10 days). Mapped climatypes of flowering date for contemporary and future climates illustrate the wide breadth of plasticity and large geographic overlap. Our research highlights the importance of integrating information on genetic variation, phenotypic plasticity and climatic niche modeling to evaluate plant responses and elucidate vulnerabilities to climate change.
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Affiliation(s)
- Bryce A Richardson
- USDA Forest Service, Rocky Mountain Research Station, Provo, UT, 84606, USA
| | - Lindsay Chaney
- Plant and Wildlife Sciences, Brigham Young University, Provo, UT, 84602, USA
| | - Nancy L Shaw
- USDA Forest Service, Rocky Mountain Research Station, Boise, ID, 83702, USA
| | - Shannon M Still
- UC Davis Arboretum, University of California, Davis, 1 Shields Ave., Davis, CA, 95616, USA
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22
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Su Z, Richardson BA, Zhuo L, Jiang X, Li W, Kang X. Genetic diversity and structure of an endangered desert shrub and the implications for conservation. AoB Plants 2017; 9:plx016. [PMID: 28533899 PMCID: PMC5434794 DOI: 10.1093/aobpla/plx016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 03/21/2017] [Accepted: 04/17/2017] [Indexed: 06/07/2023]
Abstract
Population genetic information can provide valuable insight for the conservation and management of threatened and endangered plant species. Tamarix taklamakanensis is an endangered shrub endemic to arid basins of northwestern China. This species serves to stabilize soils in this region, but has seen substantial loss in its abundance due to depletion of ground water. The populations of this species have become small and fragmented, warranting conservation. Seven microsatellite loci were used to assess the genetic diversity and structure of 15 populations in the Tarim Basin, China. Among populations, the expected heterozygosity and total gene diversity were both moderate (HE = 0.392, hT = 0.432), however the allelic diversity was low (A = 2.4). Eleven populations were detected to have experienced recent bottlenecks using Wilcoxon's test and a model-shift test. Most populations of T. taklamakanensis in the centre of Tarim Basin showed low levels of genetic differentiation, but higher levels in geographically outlying populations. Genetic structure based on Bayesian assignment, the neighbour-joining network and principal coordinates analyses produced similar results, supporting five groups in the Tarim Basin. Gene flow was high among Bayesian groups based on historical gene flow estimated by private alleles. The genetic structure of T. taklamakanensis supports a pattern where gene flow principally occurs along river corridors through hydrochory of seeds and insect-mediated pollination. Populations upstream have contributed to a more diverse mixture of populations near the confluence of several rivers near the centre of Tarim Basin. This pattern of genetic structure could be influenced by the flow of water from different river systems. Conservation efforts should focus on fostering the regeneration of this species, maintaining genetic diversity and preserving the extant genetic structure. Conservation efforts are contingent upon maintaining ground water and streamflows in this arid basin.
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Affiliation(s)
- Zhihao Su
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, no. 818 South Beijing Road, Xinjiang, Urumqi 830011, China
| | - Bryce A. Richardson
- USDA Forest Service, Rocky Mountain Research Station, 735 North 500 East, Provo, UT 84606, USA
| | - Li Zhuo
- Library, Xinjiang Normal University, Urumqi 830054, China
| | - Xiaolong Jiang
- Shanghai Chenshan Plant Science Research Center, Shanghai Chenshan Botanical Garden, Chinese Academy of Sciences, Shanghai 201602, China
| | - Wenjun Li
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, no. 818 South Beijing Road, Xinjiang, Urumqi 830011, China
| | - Xiaoshan Kang
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, no. 818 South Beijing Road, Xinjiang, Urumqi 830011, China
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Chaney L, Richardson BA, Germino MJ. Climate drives adaptive genetic responses associated with survival in big sagebrush ( Artemisia tridentata). Evol Appl 2017; 10:313-322. [PMID: 28352292 PMCID: PMC5367076 DOI: 10.1111/eva.12440] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 09/09/2016] [Indexed: 01/06/2023] Open
Abstract
A genecological approach was used to explore genetic variation for survival in Artemisia tridentata (big sagebrush). Artemisia tridentata is a widespread and foundational shrub species in western North America. This species has become extremely fragmented, to the detriment of dependent wildlife, and efforts to restore it are now a land management priority. Common-garden experiments were established at three sites with seedlings from 55 source-populations. Populations included each of the three predominant subspecies, and cytotype variations. Survival was monitored for 5 years to assess differences in survival between gardens and populations. We found evidence of adaptive genetic variation for survival. Survival within gardens differed by source-population and a substantial proportion of this variation was explained by seed climate of origin. Plants from areas with the coldest winters had the highest levels of survival, while populations from warmer and drier sites had the lowest levels of survival. Survival was lowest, 36%, in the garden that was prone to the lowest minimum temperatures. These results suggest the importance of climatic driven genetic differences and their effect on survival. Understanding how genetic variation is arrayed across the landscape, and its association with climate can greatly enhance the success of restoration and conservation.
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Affiliation(s)
- Lindsay Chaney
- Plant and Wildlife SciencesBrigham Young UniversityProvoUTUSA
- Present address: Department of BiologySnow CollegeEphraimUTUSA
| | | | - Matthew J. Germino
- U.S. Geological SurveyForest and Rangeland Ecosystem Science CenterBoiseIDUSA
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Klopfenstein NB, Stewart JE, Ota Y, Hanna JW, Richardson BA, Ross-Davis AL, Elías-Román RD, Korhonen K, Keča N, Iturritxa E, Alvarado-Rosales D, Solheim H, Brazee NJ, Łakomy P, Cleary MR, Hasegawa E, Kikuchi T, Garza-Ocañas F, Tsopelas P, Rigling D, Prospero S, Tsykun T, Bérubé JA, Stefani FOP, Jafarpour S, Antonín V, Tomšovský M, McDonald GI, Woodward S, Kim MS. Insights into the phylogeny of Northern Hemisphere Armillaria: Neighbor-net and Bayesian analyses of translation elongation factor 1-α gene sequences. Mycologia 2017; 109:75-91. [PMID: 28402796 DOI: 10.1080/00275514.2017.1286572] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Armillaria possesses several intriguing characteristics that have inspired wide interest in understanding phylogenetic relationships within and among species of this genus. Nuclear ribosomal DNA sequence-based analyses of Armillaria provide only limited information for phylogenetic studies among widely divergent taxa. More recent studies have shown that translation elongation factor 1-α (tef1) sequences are highly informative for phylogenetic analysis of Armillaria species within diverse global regions. This study used Neighbor-net and coalescence-based Bayesian analyses to examine phylogenetic relationships of newly determined and existing tef1 sequences derived from diverse Armillaria species from across the Northern Hemisphere, with Southern Hemisphere Armillaria species included for reference. Based on the Bayesian analysis of tef1 sequences, Armillaria species from the Northern Hemisphere are generally contained within the following four superclades, which are named according to the specific epithet of the most frequently cited species within the superclade: (i) Socialis/Tabescens (exannulate) superclade including Eurasian A. ectypa, North American A. socialis (A. tabescens), and Eurasian A. socialis (A. tabescens) clades; (ii) Mellea superclade including undescribed annulate North American Armillaria sp. (Mexico) and four separate clades of A. mellea (Europe and Iran, eastern Asia, and two groups from North America); (iii) Gallica superclade including Armillaria Nag E (Japan), multiple clades of A. gallica (Asia and Europe), A. calvescens (eastern North America), A. cepistipes (North America), A. altimontana (western USA), A. nabsnona (North America and Japan), and at least two A. gallica clades (North America); and (iv) Solidipes/Ostoyae superclade including two A. solidipes/ostoyae clades (North America), A. gemina (eastern USA), A. solidipes/ostoyae (Eurasia), A. cepistipes (Europe and Japan), A. sinapina (North America and Japan), and A. borealis (Eurasia) clade 2. Of note is that A. borealis (Eurasia) clade 1 appears basal to the Solidipes/Ostoyae and Gallica superclades. The Neighbor-net analysis showed similar phylogenetic relationships. This study further demonstrates the utility of tef1 for global phylogenetic studies of Armillaria species and provides critical insights into multiple taxonomic issues that warrant further study.
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Affiliation(s)
- Ned B Klopfenstein
- a United States Department of Agriculture Forest Service , Rocky Mountain Research Station , 1221 South Main Street, Moscow , Idaho 83843
| | - Jane E Stewart
- b Department of Bioagricultural Sciences and Pest Management , Colorado State University , 307 University Avenue, Ft. Collins , Colorado 80523
| | - Yuko Ota
- c College of Bioresource Sciences , Nihon University , 1866 Kameino, Fujisawa, Kanagawa 252-0880 , Japan
| | - John W Hanna
- a United States Department of Agriculture Forest Service , Rocky Mountain Research Station , 1221 South Main Street, Moscow , Idaho 83843
| | - Bryce A Richardson
- d United States Department of Agriculture Forest Service , Rocky Mountain Research Station , 735 North 500 East, Provo , Utah 84606
| | - Amy L Ross-Davis
- a United States Department of Agriculture Forest Service , Rocky Mountain Research Station , 1221 South Main Street, Moscow , Idaho 83843
| | - Rubén D Elías-Román
- e Departamento de Agronomía, División de Ciencias de la Vida , Campus Irapuato-Salamanca, Universidad de Guanajuato , C.P. 36824 , Apdo. Postal 311, Irapuato , Guanajuato , México
| | | | - Nenad Keča
- g Faculty of Forestry , University of Belgrade , Kneza Viseslava 1, 11030 Belgrade , Serbia
| | - Eugenia Iturritxa
- h Neiker Tecnalia, Production and Plant Protection , Granja Modelo de Arkaute , 46 Post, Vitoria-Gasteiz , 01080 , Spain
| | - Dionicio Alvarado-Rosales
- i Colegio de Postgraduados, Campus Montecillo , Instituto de Fitosanidad-Fitopatología , Texcoco 56230 , México
| | - Halvor Solheim
- j Norwegian Institute of Bioeconomy Research , Pb 115, NO-1431 Ås, Norway
| | - Nicholas J Brazee
- k UMass Extension, Center for Agriculture, Food and the Environment , University of Massachusetts , Amherst , Massachusetts 01002
| | - Piotr Łakomy
- l Department of Forest Pathology , Poznan University of Life Sciences , Wojska Polskiego 71c, 60-625 Poznań , Poland
| | - Michelle R Cleary
- m Sveriges Lantbruksuniversitet , Swedish University of Agricultural Sciences, Southern Swedish Forest Research Centre , 230 53 Alnarp , Sweden
| | - Eri Hasegawa
- n Kansai Research Center , Forestry and Forest Products Research Institute , 68 Nagai-Kyutaro, Momoyama, Fushimi , Kyoto 612-0855 , Japan
| | - Taisei Kikuchi
- o Department of Infectious Diseases, Faculty of Medicine , University of Miyazaki, Miyazaki 889-1692, Japan and Forestry and Forest Products Research Institute , Matsunosato 1, Tsukuba , Ibaraki 305-8687 , Japan
| | - Fortunato Garza-Ocañas
- p Facultad de Ciencias Forestales , Universidad Autónoma de Nuevo León , Linares , Nuevo León , Mexico
| | - Panaghiotis Tsopelas
- q NAGREF-Institute of Mediterranean Forest Ecosystems , Terma Alkmanos , 11528 Athens, B.O. 14180 , Greece
| | - Daniel Rigling
- r Swiss Federal Research Institute WSL , Zuercherstrasse 111 , CH-8903 Birmensdorf , Switzerland
| | - Simone Prospero
- r Swiss Federal Research Institute WSL , Zuercherstrasse 111 , CH-8903 Birmensdorf , Switzerland
| | - Tetyana Tsykun
- r Swiss Federal Research Institute WSL , Zuercherstrasse 111 , CH-8903 Birmensdorf , Switzerland
| | - Jean A Bérubé
- s Canadian Forest Service , Natural Resources Canada , PO Box 10380 Stn Sainte-Foy, Quebec City , Quebec G1V 4C7 , Canada
| | - Franck O P Stefani
- t Agriculture and Agri-Food Canada , KW Neatby Bldg , Ottawa , Ontario K1A 0C6 Canada
| | - Saeideh Jafarpour
- u Department of Plant Protection, Faculty of Agricultural Science and Engineering, College of Agriculture and Natural Resources , University of Tehran , Karaj , 31587-77871 , Iran
| | - Vladimír Antonín
- v Moravian Museum , Department of Botany , Zelny trh 6, 659 37 Brno , Czech Republic
| | - Michal Tomšovský
- w Faculty of Forestry and Wood Technology , Mendel University in Brno , Zemědělská 3, CZ-613 00 Brno , Czech Republic
| | - Geral I McDonald
- a United States Department of Agriculture Forest Service , Rocky Mountain Research Station , 1221 South Main Street, Moscow , Idaho 83843
| | - Stephen Woodward
- x Department of Plant and Soil Sciences, Institute of Biological and Environmental Sciences , University of Aberdeen , Aberdeen AB24 2TZ , Scotland , UK
| | - Mee-Sook Kim
- y Department of Forestry, Environment and Systems , Kookmin University , Seoul 02707 , Republic of Korea
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Jaeger DM, Runyon JB, Richardson BA. Signals of speciation: volatile organic compounds resolve closely related sagebrush taxa, suggesting their importance in evolution. New Phytol 2016; 211:1393-1401. [PMID: 27112551 DOI: 10.1111/nph.13982] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 03/22/2016] [Indexed: 06/05/2023]
Abstract
Volatile organic compounds (VOCs) play important roles in the environmental adaptation and fitness of plants. Comparison of the qualitative and quantitative differences in VOCs among closely related taxa and assessing the effects of environment on their emissions are important steps to deducing VOC function and evolutionary importance. Headspace VOCs from five taxa of sagebrush (Artemisia, subgenus Tridentatae) growing in two common gardens were collected and analyzed using GC-MS. Of the 74 total VOCs emitted, only 15 were needed to segregate sagebrush taxa using Random Forest analysis with a low error of 4%. All but one of these 15 VOCs showed qualitative differences among taxa. Ordination of results showed strong clustering that reflects taxonomic classification. Random Forest identified five VOCs that classify based on environment (2% error), which do not overlap with the 15 VOCs that segregated taxa. We show that VOCs can discriminate closely related species and subspecies of Artemisia, which are difficult to define using molecular markers or morphology. Thus, it appears that changes in VOCs either lead the way or follow closely behind speciation in this group. Future research should explore the functions of VOCs, which could provide further insights into the evolution of sagebrushes.
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Affiliation(s)
- Deidre M Jaeger
- USDA Forest Service, Rocky Mountain Research Station, 735 N. 500 East, Provo, UT, 84606, USA
| | - Justin B Runyon
- USDA Forest Service, Rocky Mountain Research Station, 1648 S. 7th Avenue, Bozeman, MT, 59717, USA
| | - Bryce A Richardson
- USDA Forest Service, Rocky Mountain Research Station, 735 N. 500 East, Provo, UT, 84606, USA
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Brabec MM, Germino MJ, Richardson BA. Climate adaption and post-fire restoration of a foundational perennial in cold desert: insights from intraspecific variation in response to weather. J Appl Ecol 2016. [DOI: 10.1111/1365-2664.12679] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Martha M. Brabec
- US Geological Survey, Forest and Rangeland Ecosystem Science Center; 970 Lusk Street Boise ID 83706 USA
| | - Matthew J. Germino
- US Geological Survey, Forest and Rangeland Ecosystem Science Center; 970 Lusk Street Boise ID 83706 USA
| | - Bryce A. Richardson
- US Forest Service, Rocky Mountain Research Station; 735 North 500 East Provo UT 84606 USA
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Su Z, Richardson BA, Zhuo L, Jiang X. Divergent Population Genetic Structure of the Endangered Helianthemum (Cistaceae) and Its Implication to Conservation in Northwestern China. Front Plant Sci 2016; 7:2010. [PMID: 28105040 PMCID: PMC5214710 DOI: 10.3389/fpls.2016.02010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 12/19/2016] [Indexed: 05/13/2023]
Abstract
Population genetic studies provide a foundation for conservation planning, especially for endangered species. Three chloroplast SSRs (mtrnSf-trnGr, mtrnL2-trnF, and mtrnL5-trnL3) and the internal transcribed spacer were used to examine the population structure of Helianthemum in northwestern China. A total of 15 populations of the genus were collected. Nine chloroplast haplotypes and two nuclear genotypes were detected. Both the nuclear and chloroplast data showed two lineages in Helianthemum songaricum, respectively, distributed in Yili Valley and western Ordos Plateau. A total of 66.81% (p < 0.001) of the genetic variation was supported by this lineage split. A Mantel test showed a significant correlation between genetic distance and geographical distance (r = 0.937, p < 0.001). Based on genetic analyses, cpSSRs data support strong genetic divergence between regions. We speculate that the climate change during the late Tertiary and early Quaternary isolated H. songaricum into their current distribution, resulting in interruption of gene flow, leading to isolation and genetic divergence between the two regions. Meanwhile, possible selfing would increase genetic drift in small fragmented populations, that might account for the observed genetic divergence in both regions. Given the loss of genetic diversity and genetic divergence in small populations of Helianthemum in northwestern China immediate conservation management steps should be taken on the species.
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Affiliation(s)
- Zhihao Su
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of SciencesUrumqi, China
- *Correspondence: Zhihao Su
| | | | - Li Zhuo
- Library, Xinjiang Normal UniversityUrumqi, China
| | - Xiaolong Jiang
- Shanghai Chenshan Plant Science Research Center, Shanghai Chenshan Botanical Garden, Chinese Academy of SciencesShanghai, China
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Richardson BA, Ortiz HG, Carlson SL, Jaeger DM, Shaw NL. Genetic and environmental effects on seed weight in subspecies of big sagebrush: applications for restoration. Ecosphere 2015. [DOI: 10.1890/es15-00249.1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Masese L, Wanje G, Avuvika E, Kabare E, Budambula V, Mutuku F, Omoni G, Baghazal A, Richardson BA, McClelland RS. P03.19 Screening for sexually transmitted infections in adolescent girls and young women in mombasa, kenya. Br J Vener Dis 2015. [DOI: 10.1136/sextrans-2015-052270.247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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30
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Noguchi LM, Hillier SL, Richardson BA, Chirenje ZM, Balkus JE, Piper JM, Marrazzo JM. O18.2 Injectable progestin contraception and acquisition of hsv-2 infection among south african women participating in the voice trial. Br J Vener Dis 2015. [DOI: 10.1136/sextrans-2015-052270.177] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Abstract
We report the sequencing and assembly of three transcriptomes from Big (Artemisia tridentata ssp. wyomingensis and A. tridentata ssp. tridentata) and Low (A. arbuscula ssp. arbuscula) sagebrush. The sequence reads are available in the Sequence Read Archive of NCBI. We demonstrate the utilities of these transcriptomes for gene discovery and phylogenomic analysis. An assembly of 61,883 transcripts followed by transcript identification by the program TRAPID revealed 16 transcripts directly related to terpene synthases, proteins critical to the production of multiple secondary metabolites in sagebrush. A putative terpene synthase was identified in two of our sagebrush samples. Using paralogs with synonymous mutations we reconstructed an evolutionary time line of ancient genome duplications. By applying a constant mutation rate to the data we estimate that these three ancient duplications occurred about 18, 34 and 60 million years ago. These transcriptomes offer a foundation for future studies of sagebrush, including inferences in chemical defense and the identification of species and subspecies of sagebrush for restoration and preservation of the threatened sage-grouse.
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Affiliation(s)
- Mark D. Huynh
- Plant and Wildlife Science Department, Brigham Young University, Provo, UT, 84602, United States of America
| | - Justin T. Page
- Plant and Wildlife Science Department, Brigham Young University, Provo, UT, 84602, United States of America
| | - Bryce A. Richardson
- Rocky Mountain Research Station, USDA Forest Service, Provo, UT, 84606, United States of America
| | - Joshua A. Udall
- Plant and Wildlife Science Department, Brigham Young University, Provo, UT, 84602, United States of America
- * E-mail:
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Schilling MP, Wolf PG, Duffy AM, Rai HS, Rowe CA, Richardson BA, Mock KE. Genotyping-by-sequencing for Populus population genomics: an assessment of genome sampling patterns and filtering approaches. PLoS One 2014; 9:e95292. [PMID: 24748384 PMCID: PMC3991623 DOI: 10.1371/journal.pone.0095292] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Accepted: 03/25/2014] [Indexed: 12/19/2022] Open
Abstract
Continuing advances in nucleotide sequencing technology are inspiring a suite of genomic approaches in studies of natural populations. Researchers are faced with data management and analytical scales that are increasing by orders of magnitude. With such dramatic advances comes a need to understand biases and error rates, which can be propagated and magnified in large-scale data acquisition and processing. Here we assess genomic sampling biases and the effects of various population-level data filtering strategies in a genotyping-by-sequencing (GBS) protocol. We focus on data from two species of Populus, because this genus has a relatively small genome and is emerging as a target for population genomic studies. We estimate the proportions and patterns of genomic sampling by examining the Populus trichocarpa genome (Nisqually-1), and demonstrate a pronounced bias towards coding regions when using the methylation-sensitive ApeKI restriction enzyme in this species. Using population-level data from a closely related species (P. tremuloides), we also investigate various approaches for filtering GBS data to retain high-depth, informative SNPs that can be used for population genetic analyses. We find a data filter that includes the designation of ambiguous alleles resulted in metrics of population structure and Hardy-Weinberg equilibrium that were most consistent with previous studies of the same populations based on other genetic markers. Analyses of the filtered data (27,910 SNPs) also resulted in patterns of heterozygosity and population structure similar to a previous study using microsatellites. Our application demonstrates that technically and analytically simple approaches can readily be developed for population genomics of natural populations.
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Affiliation(s)
- Martin P. Schilling
- Department of Biology, Utah State University, Logan, Utah, United States of America
- Ecology Center, Utah State University, Logan, Utah, United States of America
| | - Paul G. Wolf
- Department of Biology, Utah State University, Logan, Utah, United States of America
- Ecology Center, Utah State University, Logan, Utah, United States of America
| | - Aaron M. Duffy
- Department of Biology, Utah State University, Logan, Utah, United States of America
| | - Hardeep S. Rai
- Department of Wildland Resources, Utah State University, Logan, Utah, United States of America
| | - Carol A. Rowe
- Department of Wildland Resources, Utah State University, Logan, Utah, United States of America
| | - Bryce A. Richardson
- Rocky Mountain Research Station, USDA Forest Service, Provo, Utah, United States of America
| | - Karen E. Mock
- Department of Wildland Resources, Utah State University, Logan, Utah, United States of America
- Ecology Center, Utah State University, Logan, Utah, United States of America
- * E-mail:
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Richardson BA, Kitchen SG, Pendleton RL, Pendleton BK, Germino MJ, Rehfeldt GE, Meyer SE. Adaptive responses reveal contemporary and future ecotypes in a desert shrub. Ecol Appl 2014; 24:413-427. [PMID: 24689151 DOI: 10.1890/13-0587.1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Interacting threats to ecosystem function, including climate change, wildfire, and invasive species necessitate native plant restoration in desert ecosystems. However, native plant restoration efforts often remain unguided by ecological genetic information. Given that many ecosystems are in flux from climate change, restoration plans need to account for both contemporary and future climates when choosing seed sources. In this study we analyze vegetative responses, including mortality, growth, and carbon isotope ratios in two blackbrush (Coleogyne ramosissima) common gardens that included 26 populations from a range-wide collection. This shrub occupies ecotones between the warm and cold deserts of Mojave and Colorado Plateau ecoregions in western North America. The variation observed in the vegetative responses of blackbrush populations was principally explained by grouping populations by ecoregions and by regression with site-specific climate variables. Aridity weighted by winter minimum temperatures best explained vegetative responses; Colorado Plateau sites were usually colder and drier than Mojave sites. The relationship between climate and vegetative response was mapped within the boundaries of the species-climate space projected for the contemporary climate and for the decade surrounding 2060. The mapped ecological genetic pattern showed that genetic variation could be classified into cool-adapted and warm-adapted ecotypes, with populations often separated by steep dines. These transitions are predicted to occur in both the Mojave Desert and Colorado Plateau ecoregions. While under contemporary conditions the warm-adapted ecotype occupies the majority of climate space, climate projections predict that the cool-adapted ecotype could prevail as the dominant ecotype as the climate space of blackbrush expands into higher elevations and latitudes. This study provides the framework for delineating climate change-responsive seed transfer guidelines, which are needed to inform restoration and management planning. We propose four transfer zones in blackbrush that correspond to areas currently dominated by cool-adapted and warm-adapted ecotypes in each of the two ecoregions.
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Madan RP, Dezzutti CS, Rabe L, Hillier SL, Marrazzo J, McGowan I, Richardson BA, Herold BC. P3.363 Inflammatory Soluble Immune Mediators and Pathogenic Vaginal Bacteria Impact E. Coli Bactericidal Activity in Female Genital Tract Secretions. Br J Vener Dis 2013. [DOI: 10.1136/sextrans-2013-051184.0816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Balkus JE, Richardson BA, Rabe LK, Taha T, Mgodi N, Kasaro MP, Maslankowski LA, Ramjee G, Hoffman IF, Karim SSA. P3.090 Bacterial Vaginosis and the Risk of Trichomonas Vaginalis Acquisition Among HIV-1 Negative Women. Br J Vener Dis 2013. [DOI: 10.1136/sextrans-2013-051184.0549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Bajgain P, Richardson BA, Price JC, Cronn RC, Udall JA. Transcriptome characterization and polymorphism detection between subspecies of big sagebrush (Artemisia tridentata). BMC Genomics 2011; 12:370. [PMID: 21767398 PMCID: PMC3150299 DOI: 10.1186/1471-2164-12-370] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Accepted: 07/18/2011] [Indexed: 12/14/2022] Open
Abstract
Background Big sagebrush (Artemisia tridentata) is one of the most widely distributed and ecologically important shrub species in western North America. This species serves as a critical habitat and food resource for many animals and invertebrates. Habitat loss due to a combination of disturbances followed by establishment of invasive plant species is a serious threat to big sagebrush ecosystem sustainability. Lack of genomic data has limited our understanding of the evolutionary history and ecological adaptation in this species. Here, we report on the sequencing of expressed sequence tags (ESTs) and detection of single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) markers in subspecies of big sagebrush. Results cDNA of A. tridentata sspp. tridentata and vaseyana were normalized and sequenced using the 454 GS FLX Titanium pyrosequencing technology. Assembly of the reads resulted in 20,357 contig consensus sequences in ssp. tridentata and 20,250 contigs in ssp. vaseyana. A BLASTx search against the non-redundant (NR) protein database using 29,541 consensus sequences obtained from a combined assembly resulted in 21,436 sequences with significant blast alignments (≤ 1e-15). A total of 20,952 SNPs and 119 polymorphic SSRs were detected between the two subspecies. SNPs were validated through various methods including sequence capture. Validation of SNPs in different individuals uncovered a high level of nucleotide variation in EST sequences. EST sequences of a third, tetraploid subspecies (ssp. wyomingensis) obtained by Illumina sequencing were mapped to the consensus sequences of the combined 454 EST assembly. Approximately one-third of the SNPs between sspp. tridentata and vaseyana identified in the combined assembly were also polymorphic within the two geographically distant ssp. wyomingensis samples. Conclusion We have produced a large EST dataset for Artemisia tridentata, which contains a large sample of the big sagebrush leaf transcriptome. SNP mapping among the three subspecies suggest the origin of ssp. wyomingensis via mixed ancestry. A large number of SNP and SSR markers provide the foundation for future research to address questions in big sagebrush evolution, ecological genetics, and conservation using genomic approaches.
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Affiliation(s)
- Prabin Bajgain
- Plant and Wildlife Science Department, Brigham Young University, Provo, UT 84602, USA
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Katz DA, John-Stewart GC, Richardson BA, Majiwa M, Mabuka JM, Lohman-Payne B, Farquhar C. CCR5, RANTES and SDF-1 polymorphisms and mother-to-child HIV-1 transmission. Int J Immunogenet 2010; 37:301-5. [PMID: 20518834 DOI: 10.1111/j.1744-313x.2010.00924.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Summary Among 288 HIV-1-infected, breastfeeding women who received zidovudine prophylaxis and were followed with their infants in Nairobi, we found no associations between maternal genetic polymorphisms in CCR5 (59029G/A, 59353T/C, 59356T/C, 59402G/A), RANTES (-403G/A) and SDF-1 (3'801G/A) and mother-to-child HIV-1 transmission; plasma, cervical and breastmilk viral loads; or breastmilk chemokine concentrations.
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Affiliation(s)
- D A Katz
- Department of Epidemiology, University of Washington, Seattle, WA 98104, USA.
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Katz DA, Kiarie JN, John-Stewart GC, Richardson BA, John FN, Farquhar C. HIV testing men in the antenatal setting: understanding male non-disclosure. Int J STD AIDS 2009; 20:765-7. [PMID: 19833691 DOI: 10.1258/ijsa.2009.009139] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Prevention of infant HIV is a powerful incentive for maternal HIV diagnosis and an opportunity to increase male HIV testing and disclosure of HIV status within couples. We examined male HIV disclosure in couples who attended a Nairobi antenatal clinic (ANC), had individual HIV testing, and were counselled to disclose to their partner. At two-week follow-up, men and women independently reported HIV disclosure. Of 2104 women, 1993 requested partner attendance; 313 male partners came, of whom 183 chose individual HIV testing. Of 106 couples who followed up, 93% of both partners reported disclosure by women versus 71% by men (P < 0.0001); 27% of men reported disclosure while their female partner reported not knowing partner HIV status. In these couples, male ANC HIV testing did not result in shared knowledge of HIV status. Couple counselling models that incorporate disclosure may yield greater HIV prevention benefits than offering individual partner HIV testing services at ANC.
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Affiliation(s)
- D A Katz
- Department of Epidemiology, University of Washington, Seattle, WA 98104, USA.
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Lohman-Payne B, Slyker JA, Richardson BA, Farquhar C, Majiwa M, Maleche-Obimbo E, Mbori-Ngacha D, Overbaugh J, Rowland-Jones S, John-Stewart G. Infants with late breast milk acquisition of HIV-1 generate interferon-gamma responses more rapidly than infants with early peripartum acquisition. Clin Exp Immunol 2009; 156:511-7. [PMID: 19438605 PMCID: PMC2691981 DOI: 10.1111/j.1365-2249.2009.03937.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/18/2009] [Indexed: 02/04/2023] Open
Abstract
Infants infected with HIV-1 after the first month of life have a lower viral set-point and slower disease progression than infants infected before 1 month. We investigated the kinetics of HIV-1-specific CD8(+) T lymphocyte secretion of interferon (IFN)-gamma in infants infected before 1 month of life compared with those infected between months 1 and 12 (late infection). HIV-1 infection was assessed at birth and at months 1, 3, 6, 9 and 12 and timing of infection was determined by HIV-1 gag DNA from dried blood spots and verified by plasma HIV-1 RNA levels. HIV-1 peptide-specific IFN-gamma responses were measured by enzyme-linked immunospot at months 1, 3, 6, 9 and 12. Timing of development of IFN-gamma responses was compared using the log-rank test and Kaplan-Meier survival curves. Infants infected late developed HIV-1-specific CD8(+) T cell responses 2.8 months sooner than infants infected peripartum: 2.3 versus 5.1 months after HIV-1 infection (n = 52, P = 0.04). Late-infected infants had more focused epitope recognition than early-infected infants (median 1 versus 2 peptides, P = 0.03); however, there were no differences in the strength of IFN-gamma responses. In infants infected with HIV-1 after the first month of life, emergence of HIV-1-specific CD8(+) IFN-gamma responses is coincident with the decline in viral load, nearly identical to what is observed in adults and more rapid than in early-infected infants.
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Affiliation(s)
- B Lohman-Payne
- Department of Paediatrics, University of Nairobi, Nairobi, Kenya.
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Baeten JM, Hassan WM, Chohan V, Richardson BA, Mandaliya K, Ndinya-Achola JO, Jaoko W, McClelland RS. Prospective study of correlates of vaginal Lactobacillus colonisation among high-risk HIV-1 seronegative women. Sex Transm Infect 2009; 85:348-53. [PMID: 19329442 DOI: 10.1136/sti.2008.035451] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
OBJECTIVE Vaginal colonisation with Lactobacillus species is characteristic of normal vaginal ecology. The absence of vaginal lactobacilli, particularly hydrogen peroxide (H(2)O(2))-producing isolates, has been associated with symptomatic bacterial vaginosis (BV) and increased risk for HIV-1 acquisition. Identification of factors associated with vaginal Lactobacillus colonisation may suggest interventions to improve vaginal health. METHODS We conducted a prospective cohort study of correlates of vaginal Lactobacillus colonisation among Kenyan HIV-1 seronegative female sex workers. At monthly follow-up visits, vaginal Lactobacillus cultures were obtained. Generalised estimating equations were used to examine demographic, behavioural and medical correlates of Lactobacillus isolation, including isolation of H(2)O(2)-producing strains. RESULTS Lactobacillus cultures were obtained from 1020 women who completed a total of 8896 follow-up visits. Vaginal washing, typically with water alone or with soap and water, was associated with an approximately 40% decreased likelihood of Lactobacillus isolation, including isolation of H(2)O(2)-producing strains. Recent antibiotic use, excluding metronidazole and treatments for vaginal candidiasis, reduced Lactobacillus isolation by approximately 30%. H(2)O(2)-producing lactobacilli were significantly less common among women with Trichomonas vaginalis infection and those who were seropositive for herpes simplex virus type 2. In contrast, H(2)O(2)-producing lactobacilli were significantly more common among women with concurrent vaginal candidiasis. CONCLUSIONS Modifiable biological and behavioural factors are associated with Lactobacillus colonisation in African women. Our results suggest intervention strategies to improve vaginal health in women at high risk for HIV-1.
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Affiliation(s)
- J M Baeten
- Department of Global Health, University of Washington, Seattle, Washington 98104, USA.
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Richardson BA, Klopfenstein NB, Zambino PJ, McDonald GI, Geils BW, Carris LM. Influence of host resistance on the genetic structure of the white pine blister rust fungus in the western United States. Phytopathology 2008; 98:413-420. [PMID: 18944189 DOI: 10.1094/phyto-98-4-0413] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Cronartium ribicola, the causal agent of white pine blister rust, has been devastating to five-needled white pines in North America since its introduction nearly a century ago. However, dynamic and complex interactions occur among C. ribicola, five-needled white pines, and the environment. To examine potential evolutionary influences on genetic structure and diversity of C. ribicola in western United States, population genetic analyses of C. ribicola were conducted using amplified fragment length polymorphism (AFLP) molecular markers. The fungus was sampled at six sites. Collections for two of the six sites were from separate plantings of resistant-selected western white pine and sugar pine. Heterozygosity based on polymorphic loci among populations ranged from 0.28 to 0.40, with resistant-selected plantations at the extremes. Genetic differentiation was also highest between these two populations. Principal coordinates analysis and Bayesian assignment placed most isolates that are putative carriers of virulence to major-gene resistance into a discernable cluster, while other isolates showed no clustering by site or host species. These results indicate that C. ribicola in western North America is not genetically uniform, despite its presumed single site of introduction and relatively brief residence. Moreover, major-gene resistance appears to have imposed strong selection on the rust, resulting in reduced genetic diversity. In contrast, no evidence of selection was observed in C. ribicola from hosts that exhibit only multigenic resistance.
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Affiliation(s)
- B A Richardson
- USDA Forest Service, Rocky Mountain Research Station, Moscow, ID 83843, USA.
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Zambino PJ, Richardson BA, McDonald GI. First Report of the White Pine Blister Rust Fungus, Cronartium ribicola, on Pedicularis bracteosa. Plant Dis 2007; 91:467. [PMID: 30781214 DOI: 10.1094/pdis-91-4-0467a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Until recently, Cronartium ribicola J.C. Fisch. was thought to utilize only Ribes spp. (Grossulariaceae) as telial hosts in North America. During 2004, Pedicularis racemosa Dougl. ex Benth. and Castilleja miniata Dougl. (Orobanchaceae) were proven as natural telial hosts at a subalpine site (48.634109°N, 116.570817°W, elevation 1,800 m) near Roman Nose Lake, ID, where whitebark pine (Pinus albicaulis Engelm.) and western white pine (Pinus monticola Dougl. ex D. Don) are aecial hosts, and Pedicularis, Castilleja, and Ribes spp. are common herbs/shrubs (2). During August 2006, teliospore columns typical of C. ribicola or the morphologically indistinguishable (2) C. coleosporioides J.C. Arthur were found on two Pedicularis bracteosa Benth. plants at this site, within 3 m of a large, sporulating canker on whitebark pine. ITS/5.8S rDNA regions were sequenced using detached teliospore column samples from the two plants, ITS1F and ITS4 primers (3), and standard PCR protocols (2). One sample sequence was identified as C. ribicola and the other as C. coleosporioides (GenBank Accession Nos. EF185857 and EF185858, respectively), by exact matches in comparisons with published sequences (2). Artificial inoculation confirmed P. bracteosa's ability to host C. ribicola. Sections of leaves collected near Freezeout Saddle, ID (47.00885°N, 116.00846°W, elev. 1,600 m) were rinsed in water, placed abaxial side up on moistened filter paper in 150-mm petri plates, inoculated with seven diverse sources of urediniospores/aeciospores, misted with distilled water, and incubated at 18°C with 12 h of light. A single leaf section produced urediniospores 17 days and teliospores 26 days after inoculation with one of two Roman Nose aeciospore sources. Urediniospores from this leaf section caused infections on Ribes nigrum L., and teliospore columns yielded a DNA sequence that matched C. ribicola. Though P. bracteosa is confirmed as yet another natural host of C. ribicola in North America, it may be producing less C. ribicola inoculum for pine infection than do the P. racemosa and Ribes spp. telial hosts at the collection site. Uredinia and telia of C. ribicola on P. bracteosa were much less frequent and smaller than those on P. racemosa and Ribes spp. and those of C. coleosporioides on this same host (2). Pedicularis (but not Castilleja) spp. are significant telial hosts of C. ribicola strains at some high elevation sites in eastern Asia (1). Discovery of multiple North American telial hosts in the Orobanchaceae suggests unrecognized complexity in C. ribicola's ability to exploit ecological niches in recently established pathosystems of North America (2). References: (1) G. I. McDonald et al. Pages 41-57 in: Forest Pathology: From Genes to Landscapes. J. Lundquist and R. Hamelin, eds. The American Phytopathological Society. St. Paul, MN, 2005. (2) G. I. McDonald et al. For. Pathol. 36:73, 2006. (3) T. J. White et al. Pages 315-322 in: PCR Protocols: A Guide to Methods and Applications. M. A. Innis et al. eds. Academic Press, San Diego, CA, 1990.
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Affiliation(s)
- P J Zambino
- USDA Forest Service, Rocky Mountain Research Station, Moscow, ID 83843
| | - B A Richardson
- USDA Forest Service, Rocky Mountain Research Station, Moscow, ID 83843
| | - G I McDonald
- USDA Forest Service, Rocky Mountain Research Station, Moscow, ID 83843
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Richardson BA, Zambino PJ, Klopfenstein NB, McDonald GI, Carris LM. Assessing host specialization among aecial and telial hosts of the white pine blister rust fungus,Cronartium ribicola. ACTA ACUST UNITED AC 2007. [DOI: 10.1139/b07-031] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The white-pine blister rust fungus, Cronartium ribicola Fisch. in Rabenh., continues to spread in North America, utilizing various aecial (primary) and telial (alternate) hosts, some of which have only recently been discovered. This introduced pathogen has been characterized as having low genetic diversity in North America, yet it has demonstrated a capacity to invade diverse environments. The recent discovery of this rust fungus on the telial host Pedicularis racemosa Dougl. ex Benth., raises questions of whether this host association represents a recent acquisition by C. ribicola or a long-standing host association that was overlooked. Here we explore two questions: (i) is host specialization detectable at a local scale and (ii) is the capacity to infect Pedicularis racemosa local or widespread? Genetic analysis of C. ribicola isolates from different aecial and telial hosts provided no evidence for genetic differentiation and showed similar levels of expected heterozygosity within a geographic population. An inoculation test showed that diverse C. ribicola sources from across North America had the capacity to infect Pedicularis racemosa. These results support a hypothesis that ability to infect Pedicularis racemosa is common in C. ribicola from North America. Utilization of Pedicularis racemosa by C. ribicola may be dependent on the co-occurrence of this host, inoculum, and favorable environments.
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Affiliation(s)
- Bryce A. Richardson
- USDA Forest Service, Rocky Mountain Research Station, 1221 S. Main St, Moscow, ID 83843, USA
- Department of Plant Pathology, Washington State University, Pullman, WA 99164, USA
| | - Paul J. Zambino
- USDA Forest Service, Rocky Mountain Research Station, 1221 S. Main St, Moscow, ID 83843, USA
- Department of Plant Pathology, Washington State University, Pullman, WA 99164, USA
| | - Ned B. Klopfenstein
- USDA Forest Service, Rocky Mountain Research Station, 1221 S. Main St, Moscow, ID 83843, USA
- Department of Plant Pathology, Washington State University, Pullman, WA 99164, USA
| | - Geral I. McDonald
- USDA Forest Service, Rocky Mountain Research Station, 1221 S. Main St, Moscow, ID 83843, USA
- Department of Plant Pathology, Washington State University, Pullman, WA 99164, USA
| | - Lori M. Carris
- USDA Forest Service, Rocky Mountain Research Station, 1221 S. Main St, Moscow, ID 83843, USA
- Department of Plant Pathology, Washington State University, Pullman, WA 99164, USA
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Morrison CS, Richardson BA, Celentano DD, Chipato T, Mmiro F, Mugerwa R, Padian NS, Rugpao S, Salata RA. Prospective Clinical Trials Designed to Assess the Use of Hormonal Contraceptives and Risk of HIV Acquisition. J Acquir Immune Defic Syndr 2005; 38 Suppl 1:S17-8. [PMID: 15867602 DOI: 10.1097/01.qai.0000167029.41149.ad] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Richardson BA, Brunsfeld SJ, Klopfenstein NB. DNA from bird-dispersed seed and wind-disseminated pollen provides insights into postglacial colonization and population genetic structure of whitebark pine (Pinus albicaulis). Mol Ecol 2002; 11:215-27. [PMID: 11856423 DOI: 10.1046/j.1365-294x.2002.01435.x] [Citation(s) in RCA: 105] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Uniparentally inherited mitochondrial (mt)DNA and chloroplast (cp)DNA microsatellites (cpSSRs) were used to examine population genetic structure and biogeographic patterns of bird-dispersed seed and wind-disseminated pollen of whitebark pine (Pinus albicaulis Engelm.). Sampling was conducted from 41 populations throughout the range of the species. Analyses provide evidence for an ancestral haplotype and two derived mtDNA haplotypes with distinct regional distributions. An abrupt contact zone between mtDNA haplotypes in the Cascade Range suggests postglacial biogeographic movements. Among three cpSSR loci, 42 haplotypes were detected within 28 cpSSR sample populations that were aggregated into six regions. Analysis of molecular variance (amova) was used to determine the hierarchical genetic structure of cpSSRs. amova and population pairwise comparisons (FST ) of cpSSR, and geographical distribution of mtDNA haplotypes provide insights into historical changes in biogeography. The genetic data suggest that whitebark pine has been intimately tied to climatic change and associated glaciation, which has led to range movements facilitated by seed dispersal by Clark's nutcracker (Nucifraga columbiana Wilson). The two hypotheses proposed to explain the genetic structure are: (i) a northward expansion into Canada and the northern Cascades in the early Holocene; and (ii) historical gene flow between Idaho and the Oregon Cascades when more continuous habitat existed in Central Oregon during the late Pleistocene. Genetic structure and insights gained from historical seed movements provide a basis on which to develop recovery plans for a species that is at risk from multiple threats.
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Affiliation(s)
- B A Richardson
- Department of Forest Resources, University of Idaho, Moscow, ID 83844, USA
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Baeten JM, Nyange PM, Richardson BA, Lavreys L, Chohan B, Martin HL, Mandaliya K, Ndinya-Achola JO, Bwayo JJ, Kreiss JK. Hormonal contraception and risk of sexually transmitted disease acquisition: results from a prospective study. Am J Obstet Gynecol 2001; 185:380-5. [PMID: 11518896 DOI: 10.1067/mob.2001.115862] [Citation(s) in RCA: 189] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
OBJECTIVES To examine the relationship between use of oral contraceptive pills or depot medroxyprogesterone acetate and sexually transmitted disease acquisition. STUDY DESIGN Prospective cohort included 948 Kenyan prostitutes. Multivariate Andersen-Gill proportional hazards models were constructed, adjusting for sexual behavioral and demographic variables. RESULTS When compared with women who were using no contraception, users of oral contraceptive pills were at increased risk for acquisition of chlamydia (hazard ratio, 1.8; 95% confidence interval, 1.1-2.9) and vaginal candidiasis (hazard ratio, 1.5; 95% confidence interval, 1.2-1.9) and at decreased risk for bacterial vaginosis (hazard ratio, 0.8; 95% confidence interval, 0.7-1.0). Women using depot medroxyprogesterone acetate had significantly increased risk of chlamydia infection (hazard ratio, 1.6; 95% confidence interval, 1.1-2.4) and significantly decreased risk of bacterial vaginosis (hazard ratio, 0.7; 95% confidence interval, 0.5-0.8), trichomoniasis (hazard ratio, 0.6; 95% confidence interval, 0.4-1.0), and pelvic inflammatory disease (hazard ratio, 0.4; 95% confidence interval, 0.2-0.7). Consistent condom use was associated with significantly decreased risk of gonorrhea, chlamydia, genital ulcer disease, bacterial vaginosis, and pelvic inflammatory disease. CONCLUSIONS The use of oral or injectable hormonal contraception altered susceptibility to sexually transmitted diseases, which may in turn influence transmission of human immunodeficiency virus type 1. Consistent condom use was protective with regards to sexually transmitted disease and should be encouraged for the prevention of sexually transmitted disease and human immunodeficiency virus type 1 among women who use hormonal contraception.
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Affiliation(s)
- J M Baeten
- Department of Epidemiology, University of Washington, Seattle, WA 98104-2499, USA.
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Richardson BA, Lavreys L, Martin HL, Stevens CE, Ngugi E, Mandaliya K, Bwayo J, Ndinya-Achola J, Kreiss JK. Evaluation of a low-dose nonoxynol-9 gel for the prevention of sexually transmitted diseases: a randomized clinical trial. Sex Transm Dis 2001; 28:394-400. [PMID: 11460023 DOI: 10.1097/00007435-200107000-00006] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND Low-dose nonoxynol-9 products have a potential advantage of reduced toxicity. However, little is known about their efficacy in reducing the incidence of sexually transmitted diseases (STDs). GOAL To determine the effect that an intravaginal gel containing 52.5 mg of nonoxynol-9 has on the acquisition of STDs in a cohort of HIV-1-seronegative female sex workers in Mombasa, Kenya. STUDY DESIGN A randomized double-blind placebo controlled trial was performed. RESULTS In this study, 139 women were randomized to the nonoxynol-9 group and 139 to the placebo group. No significant differences were found between the two study groups in terms of safety outcomes and reported symptoms, except for a lower incidence of vaginal erythema in the nonoxynol-9 group. There was a significantly higher incidence of gonorrhea in the nonoxynol-9 group than in the placebo group. No significant differences were observed between the groups for acquisition of Candida, trichomonas, bacterial vaginosis, C trachomatis, syphilis, or HIV-1, although the statistical power to detect differences for some of these STDs was limited. CONCLUSIONS In this randomized placebo-controlled trial of a low-dose nonoxynol-9 gel, a significantly higher incidence of gonorrhea was found in the nonoxynol-9 group, but no significant differences between the groups were found for Candida, trichomonas, bacterial vaginosis, C trachomatis, syphilis, or HIV-1.
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Affiliation(s)
- B A Richardson
- Departments of Biostatistics, Epidemiology, and Medicine, University of Washington, Seattle WA 98104-2499, USA
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Nduati R, Richardson BA, John G, Mbori-Ngacha D, Mwatha A, Ndinya-Achola J, Bwayo J, Onyango FE, Kreiss J. Effect of breastfeeding on mortality among HIV-1 infected women: a randomised trial. Lancet 2001; 357:1651-5. [PMID: 11425369 PMCID: PMC3372408 DOI: 10.1016/s0140-6736(00)04820-0] [Citation(s) in RCA: 120] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND We have completed a randomised clinical trial of breastfeeding and formula feeding to identify the frequency of breastmilk transmission of HIV-1 to infants. However, we also analysed data from this trial to examine the effect of breastfeeding on maternal death rates during 2 years after delivery. We report our findings from this secondary analysis. METHODS Pregnant women attending four Nairobi city council clinics were offered HIVtests. At about 32 weeks' gestation, 425 HIV-1 seropositive women were randomly allocated to either breastfeed or formula feed their infants. After delivery, mother-infant pairs were followed up monthly during the first year and quarterly during the second year until death, or 2 years after delivery, or end of study. FINDINGS Mortality among mothers was higher in the breastfeeding group than in the formula group (18 vs 6 deaths, log rank test, p=0.009). The cumulative probability of maternal death at 24 months after delivery was 10.5% in the breastfeeding group and 3.8% in the formula group (p=0.02). The relative risk of death for breastfeeding mothers versus formula feeding mothers was 3.2 (95% CI 1.3-8.1, p=0.01). The attributable risk of maternal death due to breastfeeding was 69%. There was an association between maternal death and subsequent infant death, even after infant HIV-1 infection status was controlled for (relative risk 7.9, 95% CI 3.3-18.6, p<0.001). INTERPRETATION Our findings suggest that breastfeeding by HIV-1 infected women might result in adverse outcomes for both mother and infant.
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Affiliation(s)
- R Nduati
- Departments of Paediatrics and Medical Microbiology, PO Box 19676, University of Nairobi, Nairobi, Kenya.
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Abstract
OBJECTIVE To define the frequency and timing of breast milk transmission of HIV-1. DESIGN Meta-analysis of data abstracted from published literature. SUBJECTS Participants in prospective cohort studies of MTCT of HIV-1. Cohorts were separated on the basis of breast feeding duration. INTERVENTIONS None. MAIN OUTCOME MEASURES HIV-1 transmission rates. RESULTS Two thousand three hundred and seventy five HIV-1 infected women and their infants, 499 of whom breast fed, the estimated risk of breast milk HIV-1 transmission was 16% (95% CI: 9, 22%). Among breastfeeding infants, forty seven per cent of HIV-1 infections were attributable to breast feeding. Breast milk transmission risk was 21% (95% CI: 10, 33%) in cohorts with mean/median duration of breast feeding > or = 3 months and 13% (95% CI: 4, 21%) in cohorts with median duration of breast feeding < 2 months. In a separate analysis of 702 infants with prolonged duration of breast feeding, the risk of late postnatal transmission (infection occurring later than three to six months of age) was four per cent (95% CI 2, 5%). CONCLUSIONS This analysis suggests that breast milk transmission of HIV-1 is substantial and continues throughout the postnatal period. Early cessation of breast feeding at six months would avert some but not most infant HIV-1 infections due to breast feeding. While recently published studies showing some effectiveness of antiretrovirals early during the breast feeding period are encouraging, prevention of breast milk HIV-1 transmission needs to remain a high research priority.
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Affiliation(s)
- G C John
- Departments of Medicine, Epidemiology, and Biostatistics, University of Washington, Seattle, Washington 98195, USA
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John GC, Nduati RW, Mbori-Ngacha DA, Richardson BA, Panteleeff D, Mwatha A, Overbaugh J, Bwayo J, Ndinya-Achola JO, Kreiss JK. Correlates of mother-to-child human immunodeficiency virus type 1 (HIV-1) transmission: association with maternal plasma HIV-1 RNA load, genital HIV-1 DNA shedding, and breast infections. J Infect Dis 2001; 183:206-212. [PMID: 11120927 DOI: 10.1086/317918] [Citation(s) in RCA: 212] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2000] [Revised: 08/29/2000] [Indexed: 11/03/2022] Open
Abstract
To determine the effects of plasma, genital, and breast milk human immunodeficiency virus type 1 (HIV-1) and breast infections on perinatal HIV-1 transmission, a nested case-control study was conducted within a randomized clinical trial of breast-feeding and formula feeding among HIV-1-seropositive mothers in Nairobi, Kenya. In analyses comparing 92 infected infants with 187 infants who were uninfected at 2 years, maternal viral RNA levels >43,000 copies/mL (cohort median) were associated with a 4-fold increase in risk of transmission (95% confidence interval [CI], 2.2-7.2). Maternal cervical HIV-1 DNA (odds ratio [OR], 2.4; 95% CI, 1.3-4.4), vaginal HIV-1 DNA (OR, 2.3; 95% CI, 1.1-4.7), and cervical or vaginal ulcers (OR, 2.7; 95% CI, 1.2-5.8) were significantly associated with infant infection, independent of plasma virus load. Breast-feeding (OR, 1.7; 95% CI, 1.0-2.9) and mastitis (relative risk [RR], 3.9; 95% CI, 1.2-12.7) were associated with increased transmission overall, and mastitis (RR, 21.8; 95% CI, 2.3-211.0) and breast abscess (RR, 51.6; 95% CI, 4.7-571.0) were associated with late transmission (occurring >2 months postpartum). Use of methods that decrease infant exposure to HIV-1 in maternal genital secretions or breast milk may enhance currently recommended perinatal HIV-1 interventions.
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Affiliation(s)
- G C John
- Department of Medicine, University of Washington, Seattle, WA, USA.
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