1
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McLaren TH, Tomback DF, Grevstad N, Wunder MB, Wehtje W, Walker LE, Smith DW. Clark's nutcracker forest community visitation: Whitebark pine maintains a keystone seed disperser. Ecol Evol 2023; 13:e10813. [PMID: 38145018 PMCID: PMC10739129 DOI: 10.1002/ece3.10813] [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: 08/23/2023] [Revised: 11/14/2023] [Accepted: 11/24/2023] [Indexed: 12/26/2023] Open
Abstract
Clark's nutcrackers (Nucifraga columbiana) are obligate seed dispersers for whitebark pine (Pinus albicaulis), but they frequently use other conifer seed resources because of annual variability in cone production or geographic variation in whitebark pine availability. Whitebark pine is declining from several threats including white pine blister rust, leading to potential population declines in the nutcracker and the pine. We hypothesize that where there are few additional seed resources, whitebark pine becomes the key and limiting resource supporting nutcracker populations. We investigated how nutcrackers use coniferous forest community types within Yellowstone National Park to determine potential seed resources and the importance of whitebark pine. We established sites representing five forest community types, including whitebark pine, lodgepole pine (P. contorta), Engelmann spruce (Picea engelmannii), limber pine (P. flexilis), and Douglas-fir (Pseudotsuga menziesii). Each transect annually generated nutcracker point counts, conifer cone production indices, community composition data, and seed resource use observations. We compared hierarchical distance sampling models, estimating nutcracker density and its relationship to forest community type, seed harvesting time-period, year, study site, and cone seed energy. We found cone production varied across years indicating annual variability in energy availability. Nutcracker density was best predicted by forest community type and survey time-period and was highest in whitebark pine stands during the mid-harvesting season. Nutcracker density was comparatively low for all other forest community types. This finding underscores the importance of whitebark pine as a key seed resource for Clark's nutcracker in Yellowstone National Park. The decline of whitebark pine potentially leads to a downward spiral in nutcrackers and whitebark pine, arguing for continued monitoring of nutcrackers and implementation of restoration treatments for whitebark pine.
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Affiliation(s)
- Thomas H. McLaren
- Department of Integrative BiologyUniversity of Colorado DenverDenverColoradoUSA
- Present address:
Klamath Bird ObservatoryAshlandOregonUSA
| | - Diana F. Tomback
- Department of Integrative BiologyUniversity of Colorado DenverDenverColoradoUSA
| | - Nels Grevstad
- Department of Mathematics and StatisticsMetropolitan State University of DenverDenverColoradoUSA
| | - Michael B. Wunder
- Department of Integrative BiologyUniversity of Colorado DenverDenverColoradoUSA
| | | | - Lauren E. Walker
- Yellowstone National ParkYellowstone Center for ResourcesYellowstone National ParkWyomingUSA
- Present address:
United States Geological SurveyEastern Ecological Science CenterLaurelMarylandUSA
| | - Douglas W. Smith
- Yellowstone National ParkYellowstone Center for ResourcesYellowstone National ParkWyomingUSA
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Gill NS, Turner MG, Brown CD, Glassman SI, Haire SL, Hansen WD, Pansing ER, St Clair SB, Tomback DF. Limitations to Propagule Dispersal Will Constrain Postfire Recovery of Plants and Fungi in Western Coniferous Forests. Bioscience 2022. [DOI: 10.1093/biosci/biab139] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Abstract
Many forest species are adapted to long-interval, high-severity fires, but the intervals between severe fires are decreasing with changes in climate, land use, and biological invasions. Although the effects of changing fire regimes on some important recovery processes have previously been considered, the consequences for the dispersal of propagules (plant seeds and fungal spores) in forest communities have not. We characterize three mechanisms by which changing fire regimes disrupt propagule dispersal in mesic temperate, boreal, and high-elevation forests: reduced abundance and altered spatial distributions of propagule source populations, less effective dispersal of propagules by wind, and altered behavior of animal dispersers and propagule predators. We consider how disruptions to propagule dispersal may interact with other factors that are also influenced by fire regime change, potentially increasing risk of forest conversion. Finally, we highlight urgent research topics regarding how dispersal limitation may shape twenty-first century forest recovery after stand-replacing fire.
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Affiliation(s)
- Nathan S Gill
- Texas Tech University, Lubbock, Texas, United States
| | - Monica G Turner
- University of Wisconsin–Madison, Madison, Wisconsin, United States
| | - Carissa D Brown
- Memorial University, St. John's, Newfoundland and Labrador, Canada
| | | | - Sandra L Haire
- Haire Laboratory for Landscape Ecology, Tucson, Arizona, United States
| | | | | | | | - Diana F Tomback
- University of Colorado Denver, Denver, Colorado, United States
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Pansing ER, Tomback DF, Wunder MB. Climate‐altered fire regimes may increase extirpation risk in an upper subalpine conifer species of management concern. Ecosphere 2020. [DOI: 10.1002/ecs2.3220] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- Elizabeth R. Pansing
- Department of Integrative Biology University of Colorado Denver CB 171, P.O. Box 173364 Denver Colorado80204USA
| | - Diana F. Tomback
- Department of Integrative Biology University of Colorado Denver CB 171, P.O. Box 173364 Denver Colorado80204USA
| | - Michael B. Wunder
- Department of Integrative Biology University of Colorado Denver CB 171, P.O. Box 173364 Denver Colorado80204USA
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Williams TJ, Tomback DF, Grevstad N, Broms K. Temporal and energetic drivers of seed resource use by Clark's nutcracker, keystone seed disperser of coniferous forests. Ecosphere 2020. [DOI: 10.1002/ecs2.3085] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Affiliation(s)
- Tyler J. Williams
- Department of Integrative Biology University of Colorado Denver Denver Colorado 80217 USA
| | - Diana F. Tomback
- Department of Integrative Biology University of Colorado Denver Denver Colorado 80217 USA
| | - Nels Grevstad
- Department of Mathematical and Computer Sciences Metropolitan State University of Denver Denver Colorado 80217 USA
| | - Kristin Broms
- Neptune and Company 1435 Garrison Street Denver Colorado 80215 USA
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Degrassi AL, Brantley S, Levine CR, Mohan J, Record S, Tomback DF, Ellison AM. Loss of foundation species revisited: conceptual framework with lessons learned from eastern hemlock and whitebark pine. Ecosphere 2019. [DOI: 10.1002/ecs2.2917] [Citation(s) in RCA: 9] [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: 11/05/2022] Open
Affiliation(s)
- Allyson L. Degrassi
- Department of Department of Environment and Society Shenandoah University 1460 University Drive Winchester Virginia 22601 USA
| | - Steven Brantley
- Joseph W. Jones Ecological Research Center 3988 Jones Center Drive Newton Georgia 39870 USA
| | - Carrie R. Levine
- Conservation Science Partners, Inc. 11050 Pioneer Trail, Suite 202 Truckee California 96161 USA
| | - Jacqueline Mohan
- Odum School of Ecology University of Georgia Athens 140 E. Green Street Athens Georgia 30602 USA
| | - Sydne Record
- Department of Biology Bryn Mawr College 101 North Merion Avenue Bryn Mawr Pennsylvania 19010 USA
| | - Diana F. Tomback
- Department of Integrative Biology, CB 171 University of Colorado Denver P.O. Box 173364 Denver Colorado 80217 USA
- Whitebark Pine Ecosystem Foundation P.O. Box 17943 Missoula Montana 59808 USA
| | - Aaron M. Ellison
- Harvard Forest Harvard University 324 North Main Street Petersham Massachusetts 01366 USA
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6
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Lea MV, Syring J, Jennings T, Cronn R, Bruederle LP, Neale JR, Tomback DF. Development of nuclear microsatellite loci for Pinus albicaulis Engelm. (Pinaceae), a conifer of conservation concern. PLoS One 2018; 13:e0205423. [PMID: 30335779 PMCID: PMC6193661 DOI: 10.1371/journal.pone.0205423] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Accepted: 09/25/2018] [Indexed: 12/24/2022] Open
Abstract
Pinus albicaulis (whitebark pine) is a widely-distributed but rapidly declining high elevation western North American tree and a candidate for listing under the U.S. Endangered Species Act. Our objectives were to develop reliable nuclear microsatellite markers that can be used to assess within-population genetic diversity as well as seed and pollen migration dynamics, and to validate markers using two geographically proximal P. albicaulis populations. We identified 1,667 microsatellite-containing sequences from shotgun DNA libraries of P. albicaulis. Primer pairs were designed for 308 unique microsatellite-containing loci, and these were evaluated for PCR amplification success and segregation in a panel of diploid needle tissue. DNA was extracted with an SDS protocol, and primers were screened through gel electrophoresis. Microsatellites were genotyped through fluorescent primer fragment analysis. Ten novel and 13 transferred loci were found to be reproducible in analyses based on 20 foliage samples from each of two locations: Henderson Mountain, Custer Gallatin National Forest, Montana, and Mt. Washburn, Yellowstone National Park, Wyoming (USA). Transferred loci had higher numbers of alleles and expected heterozygosities than novel loci, but also revealed evidence for a higher frequency of null alleles. Eight of the 13 transferred loci deviated significantly from Hardy-Weinberg Equilibrium, and showed large positive FIS values that were likely inflated by null alleles. Mantel’s tests of transferred and novel markers showed no correlation between genetic and geographic distances within or among the two sampled populations. AMOVA suggests that 91% of genetic variability occurs within populations and 9% between the two populations. Studies assessing genetic diversity using these microsatellite loci can help guide future management and restoration activities for P. albicaulis.
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Affiliation(s)
- Marian V. Lea
- Department of Integrative Biology, University of Colorado Denver, Denver, Colorado, United States of America
| | - John Syring
- Department of Biology, Linfield College, McMinnville, Oregon, United States of America
| | - Tara Jennings
- Pacific Northwest Research Station, United States Department of Agriculture, Forest Service, Corvallis, Oregon, United States of America
| | - Richard Cronn
- Pacific Northwest Research Station, United States Department of Agriculture, Forest Service, Corvallis, Oregon, United States of America
| | - Leo P. Bruederle
- Department of Integrative Biology, University of Colorado Denver, Denver, Colorado, United States of America
| | | | - Diana F. Tomback
- Department of Integrative Biology, University of Colorado Denver, Denver, Colorado, United States of America
- * E-mail:
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Pansing ER, Tomback DF, Wunder MB, French JP, Wagner AC. Microsite and elevation zone effects on seed pilferage, germination, and seedling survival during early whitebark pine recruitment. Ecol Evol 2017; 7:9027-9040. [PMID: 29152195 PMCID: PMC5677468 DOI: 10.1002/ece3.3421] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 07/27/2017] [Accepted: 08/03/2017] [Indexed: 11/13/2022] Open
Abstract
Tree recruitment is a spatially structured process that may undergo change over time because of variation in postdispersal processes. We examined seed pilferage, seed germination, and seedling survival in whitebark pine to determine whether 1) microsite type alters the initial spatial pattern of seed caches, 2) higher abiotic stress (i.e. higher elevations) exacerbates spatial distribution changes, and 3) these postdispersal processes are spatially clustered. At two study areas, we created a seed distribution pattern by burying seed caches in microsite types frequently used by whitebark pine's avian seed disperser (Clark's nutcracker) in upper subalpine forest and at treeline, the latter characterized by high abiotic environmental stress. We monitored caches for two years for pilferage, germination, and seedling survival. Odds of pilferage (both study areas), germination (northern study area), and survival (southern study area) were higher at treeline relative to subalpine forest. At the southern study area, we found higher odds of 1) pilferage near rocks and trees relative to no object in subalpine forest, 2) germination near rocks relative to trees within both elevation zones, and 3) seedling survival near rocks and trees relative to no object at treeline. No microsite effects were detected at the northern study area. Findings indicated that the microsite distribution of seed caches changes with seed/seedling stage. Higher odds of seedling survival near rocks and trees were observed at treeline, suggesting abiotic stress may limit safe site availability, thereby shifting the spatial distribution toward protective microsites. Higher odds of pilferage at treeline, however, suggest rodents may limit treeline recruitment. Further, odds of pilferage were higher near rocks and trees relative to no object in subalpine forest but did not differ among microsites at treeline, suggesting pilferage can modulate the spatial structure of regeneration, a finding supported by limited clustering of postdispersal processes.
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Affiliation(s)
| | - Diana F. Tomback
- Department of Integrative BiologyUniversity of Colorado DenverDenverCOUSA
| | - Michael B. Wunder
- Department of Integrative BiologyUniversity of Colorado DenverDenverCOUSA
| | - Joshua P. French
- Department of Mathematical and Statistical SciencesUniversity of Colorado DenverDenverCOUSA
| | - Aaron C. Wagner
- Department of Integrative BiologyUniversity of Colorado DenverDenverCOUSA
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8
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Baker MC, Thompson DB, Sherman GL, Cunningham MA, Tomback DF. ALLOZYME FREQUENCIES IN A LINEAR SERIES OF SONG DIALECT POPULATIONS. Evolution 2017; 36:1020-1029. [PMID: 28567817 DOI: 10.1111/j.1558-5646.1982.tb05470.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/1981] [Revised: 11/29/1981] [Indexed: 11/30/2022]
Affiliation(s)
- Myron Charles Baker
- Department of Zoology and Entomology, Colorado State University, Fort Collins, Colorado, 80523
| | - Daniel B Thompson
- Department of Zoology and Entomology, Colorado State University, Fort Collins, Colorado, 80523
| | - Gregory L Sherman
- Department of Zoology and Entomology, Colorado State University, Fort Collins, Colorado, 80523
| | - Michael A Cunningham
- Department of Zoology and Entomology, Colorado State University, Fort Collins, Colorado, 80523
| | - Diana F Tomback
- Department of Zoology and Entomology, Colorado State University, Fort Collins, Colorado, 80523
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9
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Tomback DF, Blakeslee SC, Wagner AC, Wunder MB, Resler LM, Pyatt JC, Diaz S. Whitebark pine facilitation at treeline: potential interactions for disruption by an invasive pathogen. Ecol Evol 2016; 6:5144-57. [PMID: 27551372 PMCID: PMC4984493 DOI: 10.1002/ece3.2198] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [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: 10/25/2015] [Revised: 04/14/2016] [Accepted: 04/26/2016] [Indexed: 11/26/2022] Open
Abstract
In stressful environments, facilitation often aids plant establishment, but invasive plant pathogens may potentially disrupt these interactions. In many treeline communities in the northern Rocky Mountains of the U.S. and Canada, Pinus albicaulis, a stress‐tolerant pine, initiates tree islands at higher frequencies than other conifers – that is, leads to leeward tree establishment more frequently. The facilitation provided by a solitary (isolated) P. albicaulis leading to tree island initiation may be important for different life‐history stages for leeward conifers, but it is not known which life‐history stages are influenced and protection provided. However, P. albicaulis mortality from the non‐native pathogen Cronartium ribicola potentially disrupts these facilitative interactions, reducing tree island initiation. In two Rocky Mountain eastern slope study areas, we experimentally examined fundamental plant–plant interactions which might facilitate tree island formation: the protection offered by P. albicaulis to leeward seed and seedling life‐history stages, and to leeward krummholz conifers. In the latter case, we simulated mortality from C. ribicola for windward P. albicaulis to determine whether loss of P. albicaulis from C. ribicola impacts leeward conifers. Relative to other common solitary conifers at treeline, solitary P. albicaulis had higher abundance. More seeds germinated in leeward rock microsites than in conifer or exposed microsites, but the odds of cotyledon seedling survival during the growing season were highest in P. albicaulis microsites. Planted seedling survival was low among all microsites examined. Simulating death of windward P. albicaulis by C. ribicola reduced shoot growth of leeward trees. Loss of P. albicaulis to exotic disease may limit facilitation interactions and conifer community development at treeline and potentially impede upward movement as climate warms.
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Affiliation(s)
- Diana F Tomback
- Department of Integrative Biology Campus Box 171 University of Colorado Denver PO Box 173364 Denver Colorado 80217
| | - Sarah C Blakeslee
- Department of Integrative Biology Campus Box 171 University of Colorado Denver PO Box 173364 Denver Colorado 80217
| | - Aaron C Wagner
- Department of Integrative Biology Campus Box 171 University of Colorado Denver PO Box 173364 Denver Colorado 80217
| | - Michael B Wunder
- Department of Integrative Biology Campus Box 171 University of Colorado Denver PO Box 173364 Denver Colorado 80217
| | - Lynn M Resler
- Department of Geography Virginia Tech 115 Major Williams Hall (0115) Blacksburg Virginia 24061
| | - Jill C Pyatt
- Department of Integrative Biology Campus Box 171 University of Colorado Denver PO Box 173364 Denver Colorado 80217
| | - Soledad Diaz
- Department of Integrative Biology Campus Box 171 University of Colorado Denver PO Box 173364 Denver Colorado 80217
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10
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Keane RE, Holsinger LM, Mahalovich MF, Tomback DF. Evaluating future success of whitebark pine ecosystem restoration under climate change using simulation modeling. Restor Ecol 2016. [DOI: 10.1111/rec.12419] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Robert E. Keane
- Missoula Fire Sciences Laboratory; U.S. Forest Service, Rocky Mountain Research Station; 5775 Hwy 10 West Missoula MT 59808 U.S.A
| | - Lisa M. Holsinger
- Missoula Fire Sciences Laboratory; U.S. Forest Service, Rocky Mountain Research Station; 5775 Hwy 10 West Missoula MT 59808 U.S.A
| | - Mary F. Mahalovich
- U.S. Forest Service, Northern, Rocky Mountain, Southwestern, and Intermountain Regions, Forestry Sciences Laboratory; Moscow ID 83844 U.S.A
| | - Diana F. Tomback
- Department of Integrative Biology; University of Colorado Denver; Denver CO 80202 U.S.A
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11
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Samano S, Tomback DF. Cone opening phenology, seed dispersal, and seed predation in southwestern white pine (Pinus strobiformis) in southern Colorado. Écoscience 2016. [DOI: 10.1080/11956860.2003.11682780] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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12
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Tomback DF, Schoettle AW, Chevalier KE, Jones CA. Life on the edge for limber pine: Seed dispersal within a peripheral population. Écoscience 2016. [DOI: 10.2980/i1195-6860-12-4-519.1] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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13
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Smith-Mckenna EK, Resler LM, Tomback DF, Zhang H, Malanson GP. Topographic influences on the distribution of white pine blister rust inPinus albicaulistreeline communities. Écoscience 2015. [DOI: 10.2980/20-3-3599] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Castoe TA, Poole AW, de Koning APJ, Jones KL, Tomback DF, Oyler-McCance SJ, Fike JA, Lance SL, Streicher JW, Smith EN, Pollock DD. Correction: Rapid Microsatellite Identification from Illumina Paired-End Genomic Sequencing in Two Birds and a Snake. PLoS One 2015; 10:e0136465. [PMID: 26291821 PMCID: PMC4546336 DOI: 10.1371/journal.pone.0136465] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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15
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Card DC, Schield DR, Reyes-Velasco J, Fujita MK, Andrew AL, Oyler-McCance SJ, Fike JA, Tomback DF, Ruggiero RP, Castoe TA. Two low coverage bird genomes and a comparison of reference-guided versus de novo genome assemblies. PLoS One 2014; 9:e106649. [PMID: 25192061 PMCID: PMC4156343 DOI: 10.1371/journal.pone.0106649] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 08/07/2014] [Indexed: 12/04/2022] Open
Abstract
As a greater number and diversity of high-quality vertebrate reference genomes become available, it is increasingly feasible to use these references to guide new draft assemblies for related species. Reference-guided assembly approaches may substantially increase the contiguity and completeness of a new genome using only low levels of genome coverage that might otherwise be insufficient for de novo genome assembly. We used low-coverage (∼3.5-5.5x) Illumina paired-end sequencing to assemble draft genomes of two bird species (the Gunnison Sage-Grouse, Centrocercus minimus, and the Clark's Nutcracker, Nucifraga columbiana). We used these data to estimate de novo genome assemblies and reference-guided assemblies, and compared the information content and completeness of these assemblies by comparing CEGMA gene set representation, repeat element content, simple sequence repeat content, and GC isochore structure among assemblies. Our results demonstrate that even lower-coverage genome sequencing projects are capable of producing informative and useful genomic resources, particularly through the use of reference-guided assemblies.
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Affiliation(s)
- Daren C. Card
- Department of Biology, The University of Texas at Arlington, Arlington, Texas, United States of America
| | - Drew R. Schield
- Department of Biology, The University of Texas at Arlington, Arlington, Texas, United States of America
| | - Jacobo Reyes-Velasco
- Department of Biology, The University of Texas at Arlington, Arlington, Texas, United States of America
| | - Matthew K. Fujita
- Department of Biology, The University of Texas at Arlington, Arlington, Texas, United States of America
| | - Audra L. Andrew
- Department of Biology, The University of Texas at Arlington, Arlington, Texas, United States of America
| | - Sara J. Oyler-McCance
- United States Geological Survey – Fort Collins Science Center, Fort Collins, Colorado, United States of America
| | - Jennifer A. Fike
- United States Geological Survey – Fort Collins Science Center, Fort Collins, Colorado, United States of America
| | - Diana F. Tomback
- Department of Integrative Biology, University of Colorado Denver, Denver, Colorado, United States of America
| | - Robert P. Ruggiero
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Todd A. Castoe
- Department of Biology, The University of Texas at Arlington, Arlington, Texas, United States of America
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Keith Barker F, Oyler-McCance S, Tomback DF. Blood from a turnip: tissue origin of low-coverage shotgun sequencing libraries affects recovery of mitogenome sequences. ACTA ACUST UNITED AC 2013; 26:384-8. [DOI: 10.3109/19401736.2013.840588] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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17
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Oyler-McCance SJ, Fike JA, Castoe TA, Tomback DF, Wunder MB, Schaming TD. Development and characterization of thirteen microsatellite loci in Clark’s nutcracker (Nucifraga columbiana). CONSERV GENET RESOUR 2013. [DOI: 10.1007/s12686-012-9789-0] [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: 10/27/2022]
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18
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Barringer LE, Tomback DF, Wunder MB, McKinney ST. Whitebark pine stand condition, tree abundance, and cone production as predictors of visitation by Clark's nutcracker. PLoS One 2012; 7:e37663. [PMID: 22662186 PMCID: PMC3360761 DOI: 10.1371/journal.pone.0037663] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [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: 10/11/2011] [Accepted: 04/27/2012] [Indexed: 11/22/2022] Open
Abstract
Background Accurately quantifying key interactions between species is important for developing effective recovery strategies for threatened and endangered species. Whitebark pine (Pinus albicaulis), a candidate species for listing under the Endangered Species Act, depends on Clark's nutcracker (Nucifraga columbiana) for seed dispersal. As whitebark pine succumbs to exotic disease and mountain pine beetles (Dendroctonus ponderosae), cone production declines, and nutcrackers visit stands less frequently, reducing the probability of seed dispersal. Methodology/Principal Findings We quantified whitebark pine forest structure, health metrics, and the frequency of nutcracker occurrence in national parks within the Northern and Central Rocky Mountains in 2008 and 2009. Forest health characteristics varied between the two regions, with the northern region in overall poorer health. Using these data, we show that a previously published model consistently under-predicts the proportion of survey hours resulting in nutcracker observations at all cone density levels. We present a new statistical model of the relationship between whitebark pine cone production and the probability of Clark's nutcracker occurrence based on combining data from this study and the previous study. Conclusions/Significance Our model clarified earlier findings and suggested a lower cone production threshold value for predicting likely visitation by nutcrackers: Although nutcrackers do visit whitebark pine stands with few cones, the probability of visitation increases with increased cone production. We use information theoretics to show that beta regression is a more appropriate statistical framework for modeling the relationship between cone density and proportion of survey time resulting in nutcracker observations. We illustrate how resource managers may apply this model in the process of prioritizing areas for whitebark pine restoration.
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Affiliation(s)
- Lauren E. Barringer
- Department of Integrative Biology, University of Colorado Denver, Denver, Colorado, United States of America
| | - Diana F. Tomback
- Department of Integrative Biology, University of Colorado Denver, Denver, Colorado, United States of America
| | - Michael B. Wunder
- Department of Integrative Biology, University of Colorado Denver, Denver, Colorado, United States of America
- * E-mail:
| | - Shawn T. McKinney
- National Park Service Inventory and Monitoring Program, Sierra Nevada Network, El Portal, California, United States of America
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Castoe TA, Poole AW, de Koning APJ, Jones KL, Tomback DF, Oyler-McCance SJ, Fike JA, Lance SL, Streicher JW, Smith EN, Pollock DD. Rapid microsatellite identification from Illumina paired-end genomic sequencing in two birds and a snake. PLoS One 2012; 7:e30953. [PMID: 22348032 PMCID: PMC3279355 DOI: 10.1371/journal.pone.0030953] [Citation(s) in RCA: 166] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Accepted: 12/27/2011] [Indexed: 12/01/2022] Open
Abstract
Identification of microsatellites, or simple sequence repeats (SSRs), can be a time-consuming and costly investment requiring enrichment, cloning, and sequencing of candidate loci. Recently, however, high throughput sequencing (with or without prior enrichment for specific SSR loci) has been utilized to identify SSR loci. The direct “Seq-to-SSR” approach has an advantage over enrichment-based strategies in that it does not require a priori selection of particular motifs, or prior knowledge of genomic SSR content. It has been more expensive per SSR locus recovered, however, particularly for genomes with few SSR loci, such as bird genomes. The longer but relatively more expensive 454 reads have been preferred over less expensive Illumina reads. Here, we use Illumina paired-end sequence data to identify potentially amplifiable SSR loci (PALs) from a snake (the Burmese python, Python molurus bivittatus), and directly compare these results to those from 454 data. We also compare the python results to results from Illumina sequencing of two bird genomes (Gunnison Sage-grouse, Centrocercus minimus, and Clark's Nutcracker, Nucifraga columbiana), which have considerably fewer SSRs than the python. We show that direct Illumina Seq-to-SSR can identify and characterize thousands of potentially amplifiable SSR loci for as little as $10 per sample – a fraction of the cost of 454 sequencing. Given that Illumina Seq-to-SSR is effective, inexpensive, and reliable even for species such as birds that have few SSR loci, it seems that there are now few situations for which prior hybridization is justifiable.
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Affiliation(s)
- Todd A. Castoe
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Alexander W. Poole
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - A. P. Jason de Koning
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Kenneth L. Jones
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Diana F. Tomback
- Department of Integrative Biology, University of Colorado Denver, Denver, Colorado, United States of America
| | - Sara J. Oyler-McCance
- United States Geological Survey – Fort Collins Science Center, Fort Collins, Colorado, United States of America
| | - Jennifer A. Fike
- United States Geological Survey – Fort Collins Science Center, Fort Collins, Colorado, United States of America
| | - Stacey L. Lance
- University of Georgia, Savannah River Ecology Laboratory, Aiken, South Carolina, United States of America
| | - Jeffrey W. Streicher
- Department of Biology and Amphibian and Reptile Diversity Research Center, The University of Texas at Arlington, Arlington, Texas, United States of America
| | - Eric N. Smith
- Department of Biology and Amphibian and Reptile Diversity Research Center, The University of Texas at Arlington, Arlington, Texas, United States of America
| | - David D. Pollock
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado, United States of America
- * E-mail:
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McKinney ST, Fiedler CE, Tomback DF. Invasive pathogen threatens bird-pine mutualism: implications for sustaining a high-elevation ecosystem. Ecol Appl 2009; 19:597-607. [PMID: 19425424 DOI: 10.1890/08-0151.1] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [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
Human-caused disruptions to seed-dispersal mutualisms increase the extinction risk for both plant and animal species. Large-seeded plants can be particularly vulnerable due to highly specialized dispersal systems and no compensatory regeneration mechanisms. Whitebark pine (Pinus albicaulis), a keystone subalpine species, obligately depends upon the Clark's Nutcracker (Nucifraga columbiana) for dispersal of its large, wingless seeds. Clark's Nutcracker, a facultative mutualist with whitebark pine, is sensitive to rates of energy gain, and emigrates from subalpine forests during periods of cone shortages. The invasive fungal pathogen Cronartium ribicola, which causes white pine blister rust, reduces whitebark pine cone production by killing cone-bearing branches and trees. Mortality from blister rust reaches 90% or higher in some whitebark pine forests in the Northern Rocky Mountains, USA, and the rust now occurs nearly rangewide in whitebark pine. Our objectives were to identify the minimum level of cone production necessary to elicit seed dispersal by nutcrackers and to determine how cone production is influenced by forest structure and health. We quantified forest conditions and ecological interactions between nutcrackers and whitebark pine in three Rocky Mountain ecosystems that differ in levels of rust infection and mortality. Both the frequency of nutcracker occurrence and probability of seed dispersal were strongly related to annual whitebark pine cone production, which had a positive linear association with live whitebark pine basal area, and negative linear association with whitebark pine tree mortality and rust infection. From our data, we estimated that a threshold level of approximately 1000 cones/ha is needed for a high likelihood of seed dispersal by nutcrackers (probability > or = 0.7), and that this level of cone production can be met by forests with live whitebark pine basal area > 5.0 m2/ha. The risk of mutualism disruption is greatest in northern most Montana (USA), where three-year mean cone production and live basal area fell below predicted threshold levels. There, nutcracker occurrence, seed dispersal, and whitebark pine regeneration were the lowest of the three ecosystems. Managers can use these threshold values to differentiate between restoration sites requiring planting of rust-resistant seedlings and sites where nutcracker seed dispersal can be expected.
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Affiliation(s)
- Shawn T McKinney
- College of Forestry and Conservation, University of Montana, Missoula, Montana 59812, USA.
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Muzika RM, Tomback DF, Arno SF, Keane RE. Everything You Always Wanted to Know about Whitebark Pine... Ecology 2002. [DOI: 10.2307/2680144] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Johnson SA, Bruederle LP, Tomback DF. A mating system conundrum: hybridization in Apocynum (Apocynaceae). Am J Bot 1998; 85:1316-1323. [PMID: 21685017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Based upon an intermediate morphology, Apocynum x-floribundum Greene has long been considered a hybrid involving A. androsaemifolium and A. cannabinum. The floral morphology in this genus, however, appears to prohibit both import and export of pollen, and observations of numerous insect visitors reveal that pollen is not routinely carried from flower to flower. Furthermore, reproductive success as measured by fruit set is very low in most populations. Hybridization was thus called into question, with allozyme evidence used to test the hypothesis of a hybrid origin for A. x-floribundum. Six diagnostic loci, as well as two loci exhibiting highly disparate allele frequencies, were resolved for each parent. All examined populations of A. x-floribundum were heterozygous at these loci, thus supporting the hypothesis of hybridization. Evidence from additional loci indicated that all populations tend to be strongly clonal. Observed heterozygosity was very low in the parental species, suggesting a history of inbreeding or a severe bottleneck. There was no support for earlier assumptions that some intermediates are derived from backcrosses or "secondary hybrids." Statistical analyses of plant height, leaf shape, petal length, sepal length, follicle length, seed length, and seed number per follicle supported these conclusions. The persistence and vegetative spread of hybrid clones may contribute to the illusion that hybridization is common.
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Affiliation(s)
- S A Johnson
- Department of Biology, Campus Box 171, University of Colorado at Denver, P.O. Box 173364, Denver, Colorado 80217-3364
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Bruederle LP, Tomback DF, Kelly KK, Hardwick RC. Population genetic structure in a bird-dispersed pine, Pinus albicaulis (Pinaceae). ACTA ACUST UNITED AC 1998. [DOI: 10.1139/b97-162] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Whitebark pine (Pinus albicaulis) is the sole North American representative of Pinus subgenus Strobus section Strobi subsection Cembrae, a group of five species characterized by bird-dispersed seeds. Whereas population genetic structure has been described for several Eurasian Cembrae pines, the purpose of the present research was to quantify genetic diversity in whitebark pine and assess the distribution of genetic variation within and among populations interpreted within the context of this species' unique life history. Allozyme analyses were conducted on nine populations from the Greater Yellowstone Area. Genetic diversity, as measured by population means for percentage of loci polymorphic, number of alleles per locus, and expected heterozygosity was relatively low (i.e., 38.57, 1.66, 0.152) when compared with means reported for pines with wind-dispersed seeds. Genetic differentiation was also low (i.e., 0.025) relative to means reported for other gymnosperms including wind-dispersed pines. These populations are poorly differentiated, with the majority of all observed variation due to differences among individuals within populations. The data reported herein for whitebark pine populations are similar to those reported for other Cembrae pines and may reflect their recent evolutionary history, as well as life history, including documented bird dispersal of seeds.Key words: population genetic structure, plant evolutionary biology, bird dispersal, Pinus albicaulis, Pinaceae.
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Tomback DF, Holtmeier FK, Mattes H, Carsey KS, Powell ML. Tree Clusters and Growth Form Distribution in Pinus cembra, a Bird-Dispersed Pine. ACTA ACUST UNITED AC 1993. [DOI: 10.2307/1551920] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Affiliation(s)
- Myron C Baker
- Department of Zoology, Colorado State University, Fort Collins, CO, 80523
| | - Diana F Tomback
- Department of Biology, University of Colorado, Denver, CO, 80202
| | - Daniel B Thompson
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721
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Baker MC, Tomback DF, Thompson DB, Theimer TC, Bradley DC. Behavioral consequences of song learning: Discrimination of song types by male white-crowned sparrows. Learning and Motivation 1984. [DOI: 10.1016/0023-9690(84)90007-9] [Citation(s) in RCA: 9] [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: 11/27/2022]
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Baker MC, Baker AEM, Cunningham MA, Thompson DB, Tomback DF. REPLY TO “ALLOZYMES AND SONG DIALECTS: A REASSESSMENT”. Evolution 1984; 38:449-451. [DOI: 10.1111/j.1558-5646.1984.tb00304.x] [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: 07/11/1983] [Revised: 07/18/1983] [Indexed: 11/28/2022]
Affiliation(s)
- Myron Charles Baker
- Department of Zoology and Entomology; Colorado State University; Fort Collins Colorado 80523
| | - Ann E. M. Baker
- Department of Zoology and Entomology; Colorado State University; Fort Collins Colorado 80523
| | - Michael A. Cunningham
- Department of Zoology and Entomology; Colorado State University; Fort Collins Colorado 80523
| | - Daniel B. Thompson
- Department of Ecology and Evolutionary Biology; University of Arizona; Tucson Arizona 85721
- Department of Zoology and Entomology; Colorado State University; Fort Collins Colorado 80523
| | - Diana F. Tomback
- Department of Biology, Division of Natural and Physical Sciences; University of Colorado; Denver Colorado 80202
- Department of Zoology and Entomology; Colorado State University; Fort Collins Colorado 80523
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Baker MC, Thompson DB, Sherman GL, Cunningham MA, Tomback DF. Allozyme Frequencies in a Linear Series of Song Dialect Populations. Evolution 1982. [DOI: 10.2307/2408079] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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