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Neale DB, Zimin AV, Meltzer A, Bhattarai A, Amee M, Figueroa Corona L, Allen BJ, Puiu D, Wright J, De La Torre AR, McGuire PE, Timp W, Salzberg SL, Wegrzyn JL. A genome sequence for the threatened whitebark pine. G3 (Bethesda) 2024; 14:jkae061. [PMID: 38526344 PMCID: PMC11075562 DOI: 10.1093/g3journal/jkae061] [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] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 02/29/2024] [Accepted: 03/12/2024] [Indexed: 03/26/2024]
Abstract
Whitebark pine (WBP, Pinus albicaulis) is a white pine of subalpine regions in the Western contiguous United States and Canada. WBP has become critically threatened throughout a significant part of its natural range due to mortality from the introduced fungal pathogen white pine blister rust (WPBR, Cronartium ribicola) and additional threats from mountain pine beetle (Dendroctonus ponderosae), wildfire, and maladaptation due to changing climate. Vast acreages of WBP have suffered nearly complete mortality. Genomic technologies can contribute to a faster, more cost-effective approach to the traditional practices of identifying disease-resistant, climate-adapted seed sources for restoration. With deep-coverage Illumina short reads of haploid megagametophyte tissue and Oxford Nanopore long reads of diploid needle tissue, followed by a hybrid, multistep assembly approach, we produced a final assembly containing 27.6 Gb of sequence in 92,740 contigs (N50 537,007 bp) and 34,716 scaffolds (N50 2.0 Gb). Approximately 87.2% (24.0 Gb) of total sequence was placed on the 12 WBP chromosomes. Annotation yielded 25,362 protein-coding genes, and over 77% of the genome was characterized as repeats. WBP has demonstrated the greatest variation in resistance to WPBR among the North American white pines. Candidate genes for quantitative resistance include disease resistance genes known as nucleotide-binding leucine-rich repeat receptors (NLRs). A combination of protein domain alignments and direct genome scanning was employed to fully describe the 3 subclasses of NLRs. Our high-quality reference sequence and annotation provide a marked improvement in NLR identification compared to previous assessments that leveraged de novo-assembled transcriptomes.
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Affiliation(s)
- David B Neale
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
- Whitebark Pine Ecosystem Foundation, Missoula, MT 59808, USA
| | - Aleksey V Zimin
- Department of Biomedical Engineering and Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Amy Meltzer
- Department of Biomedical Engineering and Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Akriti Bhattarai
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Maurice Amee
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
| | | | - Brian J Allen
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
- University of California Cooperative Extension, Central Sierra, Jackson, CA 95642, USA
| | - Daniela Puiu
- Department of Biomedical Engineering and Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Jessica Wright
- USDA Forest Service, Pacific Southwest Research Station, Davis, CA 95618, USA
| | | | - Patrick E McGuire
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - Winston Timp
- Department of Biomedical Engineering and Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Steven L Salzberg
- Department of Biomedical Engineering and Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21218, USA
- Departments of Computer Science and Biostatistics, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Jill L Wegrzyn
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA
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2
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Kovalenko V, Doser JW, Bate LJ, Six DL. Paired acoustic recordings and point count surveys reveal Clark's nutcracker and whitebark pine associations across Glacier National Park. Ecol Evol 2024; 14:e10867. [PMID: 38274862 PMCID: PMC10808773 DOI: 10.1002/ece3.10867] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 12/28/2023] [Accepted: 01/05/2024] [Indexed: 01/27/2024] Open
Abstract
Global declines in tree populations have led to dramatic shifts in forest ecosystem composition, biodiversity, and functioning. These changes have consequences for both forest plant and wildlife communities, particularly when declining species are involved in coevolved mutualisms. Whitebark pine (Pinus albicaulis) is a declining keystone species in western North American high-elevation ecosystems and an obligate mutualist of Clark's nutcracker (Nucifraga columbiana), an avian seed predator and disperser. By leveraging traditional point count surveys and passive acoustic monitoring, we investigated how stand characteristics of whitebark pine in a protected area (Glacier National Park, Montana, USA) influenced occupancy and vocal activity patterns in Clark's nutcracker. Using Bayesian spatial occupancy models and generalized linear mixed models, we found that habitat use of Clark's nutcracker was primarily supported by greater cone density and increasing diameter of live whitebark pine. Additionally, we demonstrated the value of performing parallel analyses with traditional point count surveys and passive acoustic monitoring to provide multiple lines of evidence for relationships between Clark's nutcracker and whitebark pine forest characteristics. Our findings allow managers to gauge the whitebark pine conditions important for retaining high nutcracker visitation and prioritize management efforts in whitebark pine ecosystems with low nutcracker visitation.
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Affiliation(s)
- Vladimir Kovalenko
- Department of Ecosystem and Conservation SciencesUniversity of MontanaMissoulaMontanaUSA
- Science CenterGlacier National ParkWest GlacierMontanaUSA
| | - Jeffrey W. Doser
- Department of Integrative Biology, Ecology, Evolution and Behavior ProgramMichigan State UniversityEast LansingMichiganUSA
| | - Lisa J. Bate
- Science CenterGlacier National ParkWest GlacierMontanaUSA
| | - Diana L. Six
- Department of Ecosystem and Conservation SciencesUniversity of MontanaMissoulaMontanaUSA
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Dudney J, Latimer AM, van Mantgem P, Zald H, Willing CE, Nesmith JCB, Cribbs J, Milano E. The energy-water limitation threshold explains divergent drought responses in tree growth, needle length, and stable isotope ratios. Glob Chang Biol 2023; 29:4368-4382. [PMID: 37089078 DOI: 10.1111/gcb.16740] [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] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 02/08/2023] [Accepted: 03/16/2023] [Indexed: 05/03/2023]
Abstract
Predicted increases in extreme droughts will likely cause major shifts in carbon sequestration and forest composition. Although growth declines during drought are widely documented, an increasing number of studies have reported both positive and negative responses to the same drought. These divergent growth patterns may reflect thresholds (i.e., nonlinear responses) promoted by changes in the dominant climatic constraints on tree growth. Here we tested whether stemwood growth exhibited linear or nonlinear responses to temperature and precipitation and whether stemwood growth thresholds co-occurred with multiple thresholds in source and sink processes that limit tree growth. We extracted 772 tree cores, 1398 needle length records, and 1075 stable isotope samples from 27 sites across whitebark pine's (Pinus albicaulis Engelm.) climatic niche in the Sierra Nevada. Our results indicated that a temperature threshold in stemwood growth occurred at 8.4°C (7.12-9.51°C; estimated using fall-spring maximum temperature). This threshold was significantly correlated with thresholds in foliar growth, as well as carbon (δ13 C) and nitrogen (δ15 N) stable isotope ratios, that emerged during drought. These co-occurring thresholds reflected the transition between energy- and water-limited tree growth (i.e., the E-W limitation threshold). This transition likely mediated carbon and nutrient cycling, as well as important differences in growth-defense trade-offs and drought adaptations. Furthermore, whitebark pine growing in energy-limited regions may continue to experience elevated growth in response to climate change. The positive effect of warming, however, may be offset by growth declines in water-limited regions, threatening the long-term sustainability of the recently listed whitebark pine species in the Sierra Nevada.
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Affiliation(s)
- Joan Dudney
- Environmental Studies Program, Santa Barbara, California, USA
- Bren School of Environmental Science & Management, UC Santa Barbara, Santa Barbara, California, USA
| | - Andrew M Latimer
- Department of Plant Sciences, University of California, Davis, California, USA
| | - Phillip van Mantgem
- U.S. Geological Survey, Western Ecological Research Center, Sacramento, California, USA
| | - Harold Zald
- USDA Forest Service, Pacific Northwest Research Station, Corvallis, Oregon, USA
| | - Claire E Willing
- Department of Biology, Stanford University, Stanford, California, USA
- School of Environmental and Forest Sciences, University of Washington, Seattle, Washington, USA
| | | | - Jennifer Cribbs
- Department of Plant Sciences, University of California, Davis, California, USA
| | - Elizabeth Milano
- U.S. Geological Survey, Western Ecological Research Center, Sacramento, California, USA
- USDA Forest Service, Rocky Mountain Research Station, Moscow, Idaho, USA
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Howe M, Carroll A, Gratton C, Raffa KF. Climate-induced outbreaks in high-elevation pines are driven primarily by immigration of bark beetles from historical hosts. Glob Chang Biol 2021; 27:5786-5805. [PMID: 34428326 DOI: 10.1111/gcb.15861] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 05/11/2021] [Revised: 07/19/2021] [Accepted: 08/02/2021] [Indexed: 06/13/2023]
Abstract
Warming temperatures are allowing native insect herbivores to expand into regions that previously exceeded their thermal tolerance, encounter new host species, and pose significant threats to native communities. However, the dynamics of these expansions remain poorly understood, particularly in the extent to which outbreaks remain reliant on emigration from historical hosts or are driven by local reproduction within novel hosts in the expanded range. We tested these non-mutually exclusive hypotheses using spatially explicit data on mountain pine beetle (Dendroctonus ponderosae), which historically undergoes intermittent outbreaks in low-elevation lodgepole pine (Pinus contorta), but is now causing severe mortality in a high-elevation endangered species, whitebark pine (Pinus albicaulis). We compiled data from 2000 to 2019 across British Columbia, Canada, at 1-km2 resolution, and analyzed spatiotemporal patterns of beetle infestations, lodgepole pine distributions, expansion into habitats dominated by whitebark pine, and the likelihood of future outbreaks in all pine communities under simulated conditions. Overall, we found strong support for the hypothesis of emigration from the historical host species continuing to be a major driver of outbreaks in the more recently accessed host. First, beetle population pressure was consistently the best predictor of infestation severity in both lodgepole and whitebark pine, and appeared to be mostly unidirectional from lodgepole to whitebark pine. Second, infestations in lodgepole pine were of a longer duration than those in whitebark pine, which appeared too brief to sustain transitions from endemic to eruptive dynamics. Furthermore, resource depletion appears to drive emigration from lodgepole pine, whereas in whitebark pine drought appears to favor establishment of immigrants although bioclimatic factors and stand structure preclude self-sustaining outbreaks. Finally, we project that most pine in British Columbia will be at risk in the event of a new major outbreak. We describe implications for conserving and protecting whitebark pine and to other climate-driven range expansions.
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Affiliation(s)
- Michael Howe
- Department of Entomology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Allan Carroll
- Department of Forest & Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Claudio Gratton
- Department of Entomology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Kenneth F Raffa
- Department of Entomology, University of Wisconsin-Madison, Madison, Wisconsin, USA
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Maher CT, Millar CI, Affleck DLR, Keane RE, Sala A, Tobalske C, Larson AJ, Nelson CR. Alpine treeline ecotones are potential refugia for a montane pine species threatened by bark beetle outbreaks. Ecol Appl 2021; 31:e2274. [PMID: 33617144 DOI: 10.1002/eap.2274] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 09/09/2020] [Accepted: 10/05/2020] [Indexed: 06/12/2023]
Abstract
Warming-induced mountain pine beetle (Dendroctonus ponderosae; MPB) outbreaks have caused extensive mortality of whitebark pine (Pinus albicaulis; WBP) throughout the species' range. In the highest mountains where WBP occur, they cross alpine treeline ecotones (ATEs) where growth forms transition from trees to shrub-like krummholz, some of which survived recent MPB outbreaks. This observation motivated the hypothesis that ATEs are refugia for WBP because krummholz growth forms escape MPB attack and have the potential to produce viable seed. To test this hypothesis, we surveyed WBP mortality along transects from the ATE edge (locally highest krummholz WBP) downslope into the forest and, to distinguish if survival mechanisms are unique to ATEs, across other forest ecotones (OFEs) from the edge of WBP occurrence into the forest. We replicated this design at 10 randomly selected sites in the U.S. Northern Rocky Mountains. We also surveyed reproduction in a subset of ATE sites. Mortality was nearly absent in upper ATEs (mean ± SE percent dead across all sites of 0.03% ± 0.03% 0-100 m from the edge and 14.1% ± 1.7% 100-500 m from the edge) but was above 20% along OFEs (21.4 ± 5.2% 0-100 m and 32.4 ± 2.7% 100-500 m from the edge). We observed lower reproduction in upper ATEs (16 ± 9.9 cones/ha and 12.9 ± 5.3 viable seeds/cone 0-100 m from the edge) compared to forests below (317.1 ± 64.4 cones/ha and 32.5 ± 2.5 viable seeds/cone 100-500 m from the edge). Uniquely high WBP survival supports the hypothesis that ATEs serve as refugia because krummholz growth forms escape MPB attack. However, low reproduction suggests ATE refugia function over longer time periods. Beyond our WBP system, we propose that plant populations in marginal environments are candidate refugia if distinct phenotypes result in reduced disturbance impacts.
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Affiliation(s)
- Colin T Maher
- WA Franke College of Forestry and Conservation, The University of Montana, 32 Campus Drive, Missoula, Montana, 59812, USA
| | - Constance I Millar
- Pacific Southwest Research Station, USDA Forest Service, 800 Buchanan Street, Albany, California, 94710, USA
| | - David L R Affleck
- WA Franke College of Forestry and Conservation, The University of Montana, 32 Campus Drive, Missoula, Montana, 59812, USA
| | - Robert E Keane
- Rocky Mountain Research Station, Missoula Fire Science Laboratory, USDA Forest Service, 5775 Highway 10 West, Missoula, Montana, 59808, USA
| | - Anna Sala
- Division of Biological Sciences, The University of Montana, 32 Campus Drive, Missoula, Montana, 59812, USA
| | - Claudine Tobalske
- Spatial Analysis Lab, Montana Natural Heritage Program, The University of Montana, 32 Campus Drive, Missoula, Montana, 59812, USA
| | - Andrew J Larson
- WA Franke College of Forestry and Conservation, Wilderness Institute, The University of Montana, 32 Campus Drive, Missoula, Montana, 59812, USA
| | - Cara R Nelson
- WA Franke College of Forestry and Conservation, The University of Montana, 32 Campus Drive, Missoula, Montana, 59812, USA
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Godfrey JM, Riggio J, Orozco J, Guzmán-Delgado P, Chin ARO, Zwieniecki MA. Ray fractions and carbohydrate dynamics of tree species along a 2750 m elevation gradient indicate climate response, not spatial storage limitation. New Phytol 2020; 225:2314-2330. [PMID: 31808954 DOI: 10.1111/nph.16361] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [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: 08/16/2019] [Accepted: 11/03/2019] [Indexed: 06/10/2023]
Abstract
Parenchyma cells in the xylem store nonstructural carbohydrates (NSC), providing reserves of energy that fuel woody perennials through periods of stress and/or limitations to photosynthesis. If the capacity for storage is subject to selection, then the fraction of wood occupied by living parenchyma should increase towards stressful environments. Ray parenchyma fraction (RPF) and seasonal NSC dynamics were quantified for 12 conifers and three oaks along a transect spanning warm dry foothills (500 m above sea level) to cold wet treeline (3250 m asl) in California's central Sierra Nevada. Mean RPF was lower for both conifer and oak species with warmer dryer ranges. RPF variability increased with elevation or in relation to associated climatic variables in conifers - treeline-dominant Pinus albicaulis had the lowest mean RPF measured (c. 3.7%), but the highest environmentally standardized variability index. Conifer RPF variability was explained by environment, increasing predominantly towards cooler wetter range edges. In oaks, NSC was explained by environment - values increasing for evergreen and decreasing for deciduous oaks with elevation. Lastly, all species surveyed appear to prioritize filling available RPF with sugar to achieve molarities that balance reasonable tensions over starch to maximize stored carbon. RPF responds to environment but is unlikely to spatially constrain NSC storage.
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Affiliation(s)
- Jessie M Godfrey
- Plant Sciences Department, University of California, Davis, CA, 95616, USA
| | - Jason Riggio
- Department of Wildlife, Fish, & Conservation Biology, University of California, Davis, CA, 95616, USA
| | - Jessica Orozco
- Plant Sciences Department, University of California, Davis, CA, 95616, USA
| | | | - Alana R O Chin
- Plant Sciences Department, University of California, Davis, CA, 95616, USA
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7
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Six DL, Vergobbi C, Cutter M. Are Survivors Different? Genetic-Based Selection of Trees by Mountain Pine Beetle During a Climate Change-Driven Outbreak in a High-Elevation Pine Forest. Front Plant Sci 2018; 9:993. [PMID: 30083173 PMCID: PMC6064936 DOI: 10.3389/fpls.2018.00993] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 06/19/2018] [Indexed: 05/20/2023]
Abstract
Increased mortality of forest trees, driven directly or indirectly by climate change, is occurring around the world. In western North America, whitebark pine, a high elevation keystone species, and lodgepole pine, a widespread ecologically and economically important tree, have experienced extensive mortality in recent climate-driven outbreaks of the mountain pine beetle. However, even in stands experiencing high levels of mortality, some mature trees have survived. We hypothesized that the outbreak acted as a natural selection event, removing trees most susceptible to the beetle and least adapted to warmer drier conditions. If this was the case, genetic change would be expected at loci underlying beetle resistance. Given we did not know the basis for resistance, we used inter-simple sequence repeats to compare the genetic profiles of two sets of trees, survivors (mature, living trees) and general population (trees just under the diameter preferred by the beetles and expected to approximate the genetic structure of each tree species at the site without beetle selection). This method detects high levels of polymorphism and has often been able to detect patterns associated with phenotypic traits. For both whitebark and lodgepole pine, survivors and general population trees mostly segregated independently indicating a genetic basis for survivorship. Exceptions were a few general population trees that segregated with survivors in proportions roughly reflecting the proportion of survivors versus beetle-killed trees. Our results indicate that during outbreaks, beetle choice may result in strong selection for trees with greater resistance to attack. Our findings suggest that survivorship is genetically based and, thus, heritable. Therefore, retaining survivors after outbreaks to act as primary seed sources could act to promote adaptation. Further research will be needed to characterize the actual mechanism(s) of resistance.
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Affiliation(s)
- Diana L. Six
- Department of Ecosystem and Conservation Sciences, University of Montana, Missoula, MT, United States
| | - Clare Vergobbi
- Department of Ecosystem and Conservation Sciences, University of Montana, Missoula, MT, United States
| | - Mitchell Cutter
- Department of Biology, Whitman College, Walla Walla, WA, United States
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8
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Bullington LS, Lekberg Y, Sniezko R, Larkin B. The influence of genetics, defensive chemistry and the fungal microbiome on disease outcome in whitebark pine trees. Mol Plant Pathol 2018; 19:1847-1858. [PMID: 29388309 PMCID: PMC6638087 DOI: 10.1111/mpp.12663] [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] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Revised: 01/02/2018] [Accepted: 01/26/2018] [Indexed: 05/23/2023]
Abstract
The invasive fungal pathogen Cronartium ribicola infects and kills whitebark pine (Pinus albicaulis) throughout western North America. Whitebark pine has been proposed for listing under the Endangered Species Act in the USA, and the loss of this species is predicted to have severe impacts on ecosystem composition and function in high-elevation forests. Numerous fungal endophytes live inside whitebark pine tissues and may influence the severity of C. ribicola infection, either directly by inhibition of pathogen growth or indirectly by the induction of chemical defensive pathways in the tree. Terpenes, a form of chemical defence in pine trees, can also influence disease. In this study, we characterized fungal endophyte communities in whitebark pine seedlings before and after experimental inoculation with C. ribicola, monitored disease progression and compared fungal community composition in susceptible vs. resistant seedlings in a common garden. We analysed the terpene composition of these same seedlings. Seed family identity or maternal genetics influenced both terpenes and endophyte communities. Terpene and endophyte composition correlated with disease severity, and terpene concentrations differed in resistant vs. susceptible seedlings. These results suggest that the resistance to C. ribicola observed in natural whitebark pine populations is caused by the combined effects of genetics, endophytes and terpenes within needle tissue, in which initial interactions between microbes and hosts take place. Tree genotype, terpene and microbiome combinations associated with healthy trees could help to predict or reduce disease severity and improve outcomes of future tree breeding programmes.
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Affiliation(s)
- Lorinda S. Bullington
- MPG RanchFlorenceMT 59833USA
- Interdisciplinary Sciences, University of MontanaMissoulaMT 59801USA
| | - Ylva Lekberg
- MPG RanchFlorenceMT 59833USA
- College of Forestry and ConservationUniversity of MontanaMissoulaMT 59801USA
| | - Richard Sniezko
- USDA Forest Service, Dorena Genetic Resource CenterCottage GroveOR 97424USA
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9
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Wong CM, Daniels LD. Novel forest decline triggered by multiple interactions among climate, an introduced pathogen and bark beetles. Glob Chang Biol 2017; 23:1926-1941. [PMID: 27901296 DOI: 10.1111/gcb.13554] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [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: 03/11/2016] [Revised: 10/14/2016] [Accepted: 10/18/2016] [Indexed: 06/06/2023]
Abstract
Novel forest decline is increasing due to global environmental change, yet the causal factors and their interactions remain poorly understood. Using tree ring analyses, we show how climate and multiple biotic factors caused the decline of whitebark pine (Pinus albicaulis) in 16 stands in the southern Canadian Rockies. In our study area, 72% of whitebark pines were dead and 18% had partially dead crowns. Tree mortality peaked in the 1970s; however, the annual basal area increment of disturbed trees began to decline significantly in the late 1940s. Growth decline persisted up to 30 years before trees died from mountain pine beetle (Dendroctonus ponderosae), Ips spp. bark beetles or non-native blister rust pathogen (Cronartium ribicola). Climate-growth relations varied over time and differed among the healthy and disturbed subpopulations of whitebark pine. Prior to the 1940s, cool temperatures limited the growth of all subpopulations. Growth of live, healthy trees became limited by drought during the cool phase (1947 -1976) of the Pacific Decadal Oscillation (PDO) and then reverted to positive correlations with temperature during the subsequent warm PDO phase. In the 1940s, the climate-growth relations of the disturbed subpopulations diverged from the live, healthy trees with trees ultimately killed by mountain pine beetle diverging the most. We propose that multiple factors interacted over several decades to cause unprecedented rates of whitebark pine mortality. Climatic variation during the cool PDO phase caused drought stress that may have predisposed trees to blister rust. Subsequent decline in snowpack and warming temperatures likely incited further climatic stress and with blister rust reduced tree resistance to bark beetles. Ultimately, bark beetles and blister rust contributed to tree death. Our findings suggest the complexity of whitebark pine decline and the importance of considering multiway drought-disease-insect interactions over various timescales when interpreting forest decline.
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Affiliation(s)
- Carmen M Wong
- Department of Geography, University of British Columbia, Vancouver, BC, V6T 1Z2, Canada
| | - Lori D Daniels
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
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10
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Syring JV, Tennessen JA, Jennings TN, Wegrzyn J, Scelfo-Dalbey C, Cronn R. Targeted Capture Sequencing in Whitebark Pine Reveals Range-Wide Demographic and Adaptive Patterns Despite Challenges of a Large, Repetitive Genome. Front Plant Sci 2016; 7:484. [PMID: 27148310 PMCID: PMC4838605 DOI: 10.3389/fpls.2016.00484] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 03/25/2016] [Indexed: 05/20/2023]
Abstract
Whitebark pine (Pinus albicaulis) inhabits an expansive range in western North America, and it is a keystone species of subalpine environments. Whitebark is susceptible to multiple threats - climate change, white pine blister rust, mountain pine beetle, and fire exclusion - and it is suffering significant mortality range-wide, prompting the tree to be listed as 'globally endangered' by the International Union for Conservation of Nature and 'endangered' by the Canadian government. Conservation collections (in situ and ex situ) are being initiated to preserve the genetic legacy of the species. Reliable, transferrable, and highly variable genetic markers are essential for quantifying the genetic profiles of seed collections relative to natural stands, and ensuring the completeness of conservation collections. We evaluated the use of hybridization-based target capture to enrich specific genomic regions from the 27 GB genome of whitebark pine, and to evaluate genetic variation across loci, trees, and geography. Probes were designed to capture 7,849 distinct genes, and screening was performed on 48 trees. Despite the inclusion of repetitive elements in the probe pool, the resulting dataset provided information on 4,452 genes and 32% of targeted positions (528,873 bp), and we were able to identify 12,390 segregating sites from 47 trees. Variations reveal strong geographic trends in heterozygosity and allelic richness, with trees from the southern Cascade and Sierra Range showing the greatest distinctiveness and differentiation. Our results show that even under non-optimal conditions (low enrichment efficiency; inclusion of repetitive elements in baits), targeted enrichment produces high quality, codominant genotypes from large genomes. The resulting data can be readily integrated into management and gene conservation activities for whitebark pine, and have the potential to be applied to other members of 5-needle pine group (Pinus subsect. Quinquefolia) due to their limited genetic divergence.
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Affiliation(s)
- John V. Syring
- Department of Biology, Linfield College, McMinnvilleOR, USA
- *Correspondence: John V. Syring,
| | - Jacob A. Tennessen
- Department of Integrative Biology, Oregon State University, CorvallisOR, USA
| | - Tara N. Jennings
- Department of Botany and Plant Pathology, Oregon State University, CorvallisOR, USA
| | - Jill Wegrzyn
- Department of Ecology and Evolutionary Biology, University of Connecticut, StorrsCT, USA
| | - Camille Scelfo-Dalbey
- Jack Baskin School of Engineering, University of California, Santa Cruz, Santa CruzCA, USA
| | - Richard Cronn
- Pacific Northwest Research Station, United States Department of Agriculture, Forest Service, CorvallisOR, USA
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