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United States Department of Agriculture Forest Service.

Genetic and Silvicultural Foundations for Management

PUBLICATIONS

Publications for the Genetic and Silvicultural Foundations for Management Team are listed under the following sections:

 

     

RECENT PUBLICATIONS
Pub.
No.
Author/Year/Title/Outlet
748 Weitemier, K., S.C. Straub, R.C. Cronn, M. Fishbein, R. Schmickl, A. McDonnell, A. Liston, 2014. Hyb-Seq: Combining target enrichment and genome skimming for plant phylogenomics. Appl Plant Sci, Aug 29;2(9)
747b Bruner, D.M., D.K. Brauer, J.L. Snider, C.A. Harrington, P.A. Moore Jr., 2014. Phenological responses of juvenile pecan and white oak on an upland site. Agroforest Syst 88:141–155.
747 Owusu, S.A., M. Staton , T.N. Jennings, S. Schlarbaum, M.V. Coggeshall , J.Romero-Severson , J.E. Carlson and O. Gailing, 2014. Development of genomic microsatellites in Gleditsia triacanthos (Fabaceae) using illumina sequencing. Applications in Plant Sciences 2013 1 ( 12 ): 1300050.
746 St. Clair, J.B., 2014. The development of forest seed zones in the Pacific Northwest of the United States. In Bozzana, M., R. Jalonen, E. Thomas, D. Boshier, L. Gallo, S. Cavers, S. Bordacs
745

Hayden, K.J., M. Garbelotto, B.J. Knaus, R.C. Cronn, H. Rai and J.W. Wright, 2014. Dual RNA-seq of the plant pathogen Phytophthora ramorum and its tanoak host. Tree Genetics & Genomes DOI 10.1007/s11295-014-0698-0.

744 DeGiorgio, M., J. Syring, A.J. Eckert, A. Liston, R. Cronn, D.B. Neale and N.A. Rosenberg, 2014. An empirical evaluation of two-stage species tree inference strategies using a multilocus dataset from North American pines. BMC Evolutionary Biology 2014, 14:67 http://www.biomedcentral.com/1471-2148/14/67.
743 Bower, A.D., J.B.St. Clair, and V. Erickson, 2014. Generalized provisional seed zones for native plants. Ecological Applications, 24(5), 2014, pp. 913–919.
742 Rehfeldt, G.E.,B. C. Jaquish, J. López-Upton, C. Sáenz-Romero , J. B. St Clair, L.P. Leites, and D.G. Joyce, 2014. Comparative genetic responses to climate for the varieties of Pinus ponderosa and Pseudotsuga menziesii: Realized climate niches. Forest Ecology and Management 324 (2014) 126–137. Part1, part 2, and part 3.
741c Kilkenny, F.F., J.B. St. Clair, and M. Horning, 2013. Climate change and the future of seed zones  In: Haase, D. L.; Pinto, J. R.; Wilkinson, K. M., technical coordinators. National Proceedings: Forest and Conservation Nursery Associations - 2012. Proceedings RMRS-P-69. Fort Collins, CO: U.S. Department of Agriculture, Forest Service, Rocky Mountain Research Station. p. 87-89.
741b St. Clair, J.B, F. Kilkenny, R.C. Johnson, N.L. Shaw, and G. Weaver, 2013. Genetic variation in adaptive traits and seed transfer zones for Pseudoroegneria spicata (bluebunch wheatgrass) in the northwestern United States. Evol Appl. 2013 Sep;6(6):933-48. doi: 10.1111/eva.12077. Epub 2013 Jun 6. .
741 Gilmore, B., N. Bassil, B. Knaus, A. Nyberg, D. Smith, D.L. Marney, and K. Hummer, 2013. Microsatellite Marker development in Peony using Next Generation Sequencing. J. Amer. Soc. Hort. Sci. 138(1):64–74.
740 Ross-Davis, A.L, J. E. Stewart, J. W. Hanna, M.-S. Kim, B. J. Knaus, R. Cronn, H. Rai, B. A. Richardson, G. I. McDonald and N. B. Klopfenstein, 2013. Transcriptome of an Armillaria root disease pathogen reveals candidate genes involved in host substrate utilization at the host–pathogen interface. Forest Pathology 43 (2013) 468–477.
739 Jennings, T.N, B. J. Knaus , K. Alderman , P.E. Hennon , D. V. D' Amore , and R.Cronn, 2013. Microsatellite Primers for the Pacific Northwest Conifer Callitropsis nootkatensis (Cupressaceae). Applications in Plant Sciences 2013 1 ( 9 ): 1300025
738 Straub, S.C.K., R. C. Cronn, C. Edwards, M. Fishbein, and A. Liston, 2013. Horizontal Transfer of DNA from the Mitochondrial to the Plastid Genome and Its Subsequent Evolution in Milkweeds (Apocynaceae). Genome Biol. Evol. 5(10):1872–1885.
736 Holub, S.M., T.A. Terry, C.A. Harrington, R.B. Harrison, R. Meade, 2013. Tree growth ten years after residual biomass removal, soil compaction, tillage, and competing vegetation control in a highly-productive Douglas-fir plantation. Forest Ecology and Management 305, 60–66.
735 Rai, H.S., K.E. Mock, B.A. Richardson, R.C. Cronn, K.J. Hayden, J.W. Wright, B.J. Knaus, and P.G. Wolf, 2013. Transcriptome characterization and detection of gene expression differences in aspen (Populus tremuloides). Tree Genetics & Genomes 9:1031–1041
734 Ross-Davis, A. L., Stewart, J. E., Hanna, J. W., Kim, M.-S., Knaus, B. J., Cronn, R., Rai, H., Richardson, B. A., McDonald, G. I., Klopfenstein, N. B. , 2013. Transcriptome of an Armillaria root disease pathogen reveals candidate genes involved in host substrate utilization at the host–pathogen interface. Forest Pathology, 43: 468–477. doi: 10.1111/efp.12056

733

Gould PJ, Harrington CA., 2013. Making the little things count: Modeling the development of understory trees in complex stands. In Density Management in the 21st Century: West Side Story. Paul D. Anderson, Kathryn L. Ronnenberg, eds. Gen. Tech. Rep. PNW-GTR-880. Portland, OR: U.S. Department of Agriculture, Forest Service, Pacific Northwest Research Station. 249 p.

732

Brodie, L.C., and D.S, DeBell, 2013. Residual densities affect growth of overstory trees and planted Douglas-fir, western hemlock, and western redcedar--results from the first decade. West. J. Appl. For. 28(3) 121-127.

731

Straub S.C.K., M. Parks, K. Weitemier, M. Fishbein, R. Cronn, A. Liston, 2013. Navigating the tip of the genomic iceberg: Next-generation sequencing for plant systematics. American Journal of Botany 99(2): 349-364.

730

Alexander A., D. Steel, B. Slikas, K. Hoekzema, C. Carraher, M. Parks, R. Cronn, C.S. Baker, 2013. Low diversity in the mitogenome of sperm whales revealed by next-generation sequencing. Genome Biology and Evolution (2013) 5 (1): 113-129. doi: 10.1093/gbe/evs126

729

Howe G.T., J. Yu., B.J. Knaus, R. Cronn, S. Kolpak, P. Dolan, W.W.Lorenz, J.F.D. Dean,. 2013. A SNP resource for Douglas-fir: de novo transcriptome assembly and SNP detection and validation. BMC Genomics. 2013 Feb 28;14:137. doi: 10.1186/1471-2164-14-137

728

Njuguna W., A. Liston., R.Cronn, T.L. Ashman, N. Bassil, 2013. Insights into Phylogeny, Sex Function and Age of Fragaria Based on Whole Chloroplast Genome Sequencing. Molecular Phylogenetics and Evolution 66(1):17-29.

727

Devine W.D., P.W. Footen, R.B. Harrison , T.A. Terry, C.A. Harrington, S.M. Holub, P.J. Gould. 2013. Estimating tree biomass, carbon, and nitrogen in two vegetation control treatments in an 11-year-old Douglas-fir plantation on a highly productive site. PNW Research Paper RP-591, Portland, OR: U.S. Department of Agriculture, Forest Service, Pacific Northwest Research Station. 38 p.

726

Devine W.D., and C.A. Harrington, 2013. Restoration release of overtopped Oregon white oak increases growth and acorn production. Forest Ecology and Management 291:87-95.

725

Curtis, R.O. 2013. True Fir Spacing and Yield Trials—20-Year Update. PNW Research Paper RP-590, Portland, OR: U.S. Department of Agriculture, Forest Service, Pacific Northwest Research Station. 40 p.

724

Parks M., R. Cronn, A. Liston, 2012. Separating the wheat from the chaff: mitigating the effects of noise in a plastome phylogenomic data set from Pinus L.(Pinaceae). BMC Evolutionary Biology 12 (1), 100.

723

Beans, C., F. F. Kilkenny , L. F. Galloway. 2012. Climate suitability and human influences combined explain the range expansion of an invasive horticultural plant. Biological Invasions 14: 2067-2078.

722

Erickson, V., C. Aubry, P. Berrang, T. Blush, A. Bower, B. Crane, T. DeSpain, D. Gwaze, J. Hamlin, M. Horning, R. Johnson, M. Mahalovich, M. Maldonado, R. Sniezko, and B. St.Clair. 2012. Genetic resource management and climate change: options for adapting National Forests to climate change. Washington, DC: USDA Forest Service, Forest Management, 19 p.

721

Gould PJ, Harrington CA, St. Clair JB. 2012. Growth phenology of coast Douglas-fir seed sources planted in diverse environments. Tree Physiology 32:1482-1496.

720

Harrington CA, Gould PG, Sniezko RA. 2012. Growth and survival of Port-Orford-cedar families on three sites on the south Oregon coast. Western Journal of Applied Forestry 27:156-158.

719

Harrington, C., L. Brodie, W. Devine, and P. Gould (prepared by Joan O’Callaghan, Science Writer). 2012. Remember redcedar! An overlooked species reveals its potential . Science Findings Issue 147, USDA Forest Service, Pacific Northwest Research Station, Portland, OR, 6 pp.

718

Parks M., Cronn R., Liston A. 2012. Separating the wheat from the chaff: mitigating the effects of noise in a plastome phylogenomic data set from Pinus L.(Pinaceae). BMC Evolutionary Biology 12 (1), 100.

717

Cronn, Richard; Knaus, Brian J.; Liston, Aaron; Maughan, Peter J.; Parks, Matthew; Syring, John V.; Udall, Joshua. 2012. Targeted enrichment strategies for next-generation plant biology. American Journal of Botany 99: 291-311.

716

Straub, Shannon CK; Fishbein, Mark; Livshultz, Tatyana; Foster, Zachary; Parks, Matthew; Weitemier,Kevin; Cronn, Richard C; Liston, Aaron. 2011. Building a model: developing genomic resources for common milkweed (Asclepias syriaca) with low coverage genome sequencing. BMC Genomics 12:211.

715

Jennings, Tara N.; Knaus, Brian J.; Kolpak, Scott; Cronn, Richard 2011. Microsatellite primers for the Pacific Northwest endemic conifer Chamaecyparis lawsoniana (Cupressaceae). American Journal of Botany: e323–e325 (doi:10.3732/ajb.1100317).

714

Bajgain, Prabin; Richardson, Bryce A.; Price, Jared C.; Cronn, Richard C.; Udall, Joshua A. 2011. Transcriptome characterization and polymorphism detection between subspecies of big sagebrush (Artemisia tridentata). BMC Genomics 12:370.

713

Jennings, T.N.; Knaus, B.J.; Mullins, T.D.; Haig, S.M.; Cronn, R. 2011. Multiplexed microsatellite recovery using massively parallel sequencing. Molecular Ecology Resources 11: 1060–1067 (doi: 10.1111/j.1755-0998.2011.03033.x).

712

Magbanua, Z.V.; Ozkan, S.; Bartlett, B.D.; Chouvarine, P.; Saski, C.A.; Liston, A.; Cronn, R.; Nelson, C.D.; Peterson, D.G. 2011. Adventures in the Enormous: A 1.8 Million Clone BAC Library for the 21.7 Gb Genome of Loblolly Pine. PLoS ONE 6(1): e16214 (doi:10.1371/journal.pone.0016214).

711

Knaus, B.J.; Liston, A.; Pilgrim, K.; Schwartz, M.K.; Cronn, R. 2011. Mitochondrial genome sequences illuminate maternal lineages of conservation concern in a rare carnivore. BMC Ecology 11:10.

710

Parks, M.; Liston, A.; Cronn, R. 2011. Meeting the challenges of non-referenced genome assembly from short-read sequence data. Acta Horiculturae 859: 323-332.

667

Devine, Warren D.; Harrington, Timothy B.; Terry, Thomas A.; Harrison, Robert B.; Slesak, Robert A.; Peter, David H.; Harrington, Constance A.; Shilling, Carol J.; Schoenholtz, Stephen H. 2011.  Five-year vegetation control effects on aboveground biomass and nitrogen content and allocation in Douglas-fir plantations on three contrasting sites. Forest Ecology and Management 262(12):2187-2198.2.

666

St.Clair, J.B. and G.T. Howe. 2011. Strategies for conserving forest genetic resources in the face of climate change. Turkish Journal of Botany 35: 403-409.

623

Reynolds, Keith M.; Hessburg, Paul F.; Miller, Richard E.; Meurisse, Robert T. 2011. Evaluating soil risks associated with severe wildfire and ground-based logging. Gen. Tech. Rep. PNW-GTR-840. Portland, OR: U.S. Department of Agriculture, Forest Service, Pacific Northwest Research Station. 27 p.

622

Harrington, Constance A.; Devine, Warren D.  2011.  Stand development following precommercial thinning and fertilization treatments in a western redcedar ( Thuja plicata ) dominated forest. Can. J. For. Res. 41: 151-164.

621

Gould, P.J., J. Bradley St. Clair, and P.D. Anderson. 2011. Performance of full-sib families of Douglas-fir in pure-family and mixed-family deployments. Forest Ecology and Management 262:1417-1425

620

Gould, Peter J.; Harrington, Constance A.; Devine, Warren D.  2011.  Growth of Oregon white oak (Quercus garryana). Northwest Science. 85(2): 159-171.

619

Devine, Warren D.; Harrington, Constance A. 2011. Factors affecting diurnal stem contraction in young Douglas-fir. Agricultural and Forest Meteorology. 151 (2011) 414-419.

618

Chmura D.J, P.D. Anderson, G.T. Howe, C.A. Harrington, J.E. Halosky, D.L. Peterson, D.C. Shaw, J.B. St.Clair, 2011. Forest responses to climate change in the northwestern United States: Ecophysiological foundations for adaptive management. Forest Ecology and Management 261 (2011) 1121-1142

617

Gould, P.J., C.A. Harrington, J.B. St. Clair. 2011. Incorporating genetic variation into a model of budburst phenology of coast Douglas-fir (Pseudotsuga menziesii var. menziesii). Can. J. For. Res. 41: 139–150 (2011).

709

Johnson, R.; Stritch, L.; Olwell, P.; Lambert, S.; Horning, M.; Cronn, R. 2010. What are the best seed sources for ecosystem restoration on BLM and USFS Lands? Native Plants Journal. 11(2): 117-131.

708

Njuguna, W.; Liston, A.; Cronn, R.; Bassil, N. V. 2010. Multiplexed Fragaria chloroplast genome sequencing. Acta Horiculturae 859: 315-323.

707

Zapiola, M.; Cronn, R.; Mallory-Smith, C. 2010. Development of novel chloroplast microsatellite markers to identify species in the Agrostis complex (Poaceae) and related genera. Molecular Ecology Resources 10: 738-740 (doi: 10.1111/j.1755-0998.2009.02828.x).

706

Whittall, J.B.; Syring, J.; Parks, M.; Buenrostro, J.; Dick, C.; Liston, A.; Cronn, R. 2010. Finding a (pine) needle in a haystack: Chloroplast genome sequence divergence in rare and widespread pines. Molecular Ecology 19(S1): 100-114 (doi: 10.1111/j.1365-294X.2009.04474.x)

665

Chmura, D.J., G.T. Howe, J.B. St.Clair, and P.D. Anderson. 2010. Adaptation of trees, forests and forestry to climate change. Sylwan 154(9): 587-602. (in Polish with English summary).

664

Chmura, D.J., G.T. Howe, J.B. St.Clair, and P.D. Anderson. 2010. The role of common garden studies in adapting forests to climate change in the Northwestern U.S. In Proceedings of the TREEBREEDEX Activity 5 Seminar "What Do Large Genetic Field Experimental Networks Across Europe Bring to the Scientific Community?", June 22-24, 2010, Sekocin Stary, Poland.

663

Harrington, C., P. Gould, and B. St.Clair (prepared by N. Parks, Science Writer). 2010. The future of spring bud burst: Looking at the possibilities. Science Findings Issue 128, USDA Forest Service, Pacific Northwest Research Station, Portland, OR, 6 pp.

662

Johnson, R.C., V.J. Erickson, N.L. Mandel, J.B. St.Clair, and K.W. Vance-Borland. 2010. Mapping genetic variation and seed zones for Bromus carinatus in the Blue Mountains of eastern Oregon, USA. Botany 88: 725-736.

661

Harrington, C.A., P.J. Gould, and J.B. St.Clair. 2010. Modeling the effects of winter environment on dormancy release of Douglas-fir. Forest Ecology and Management 259: 798-808.

660

Shafer, S.L., M.E. Harmon, R.P. Neilson, R. Seidl, B. St.Clair, and A. Yost. 2010. Chapter 5. The potential effects of climate change on Oregon’s vegetation. pp. 173-208 In Oregon Climate Assessment Report, K.D. Dello and P.W. Mote (eds). College of Oceanic and Atmospheric Sciences, Oregon State University, Corvallis, OR. (Report available at http://occri.net/ocar.)

659

St.Clair, J.B. and G.T. Howe. 2010. Ensuring forests adapted to future climates. Northwest Woodlands 26(2): 20-21,31.

658

Ye, T.Z., K.J.S. Jayawickrama, and J.B. St.Clair. 2010. Realized gain from block-plot coastal Douglas-fir trials in the northern Oregon Cascades. Silvae Genetica 59: 29-39.

616a

Fei, Songlin; Gould, Peter; Kaeser, Melanie; Steiner, Kim.  2010. Distribution and dynamics of the invasive native hay-scented fern. Weed Science. 58: 408-412.

616

Devine, Warren D.; Harrington, Constance A.; Kraft, Joseph M. 2010. Acorn storage alternatives tested on Oregon white oak. Native Plants Journal. 11(1): 65-76.

615

C.A. Harrington, Tech. Coord., 2010. A tale of two cedars: International symposium on western redcedar and yellow-cedar. Gen. Tech. Rep. PNW-GTR-828. Portland, OR: U.S. Department of Agriculture, Forest Service, Pacific Northwest Research Station. 177 p.

614

Brodie, L.C, and C.A. Harrington, 2010. Response of western redcedar to release and fertlilization in a mixed-species stand. In: A tale of two cedars: International symposium on western redcedar and yellow-cedar. C.A. Harrington Tech. Coord.. Gen. Tech. Rep. PNW-GTR-828. Portland, OR: U.S. Department of Agriculture, Forest Service, Pacific Northwest Research Station. 177 p.

613

Harrington, C.A. and P.J. Gould, 2010. Growth of western redcedar and yellow-cedar. In: A tale of two cedars: International symposium on western redcedar and yellow-cedar. C.A. Harrington Tech. Coord.. Gen. Tech. Rep. PNW-GTR-828. Portland, OR: U.S. Department of Agriculture, Forest Service, Pacific Northwest Research Station. 177 p.

612

Murray, M.D., 2010. Ancient yellow-cedar groves in the Olympic mountains, Washington. In: A tale of two cedars: International symposium on western redcedar and yellowcedar. C.A. Harrington Tech. Coord. Gen. Tech. Rep. PNW-GTR-828. Portland, OR: U.S. Department of Agriculture, Forest Service, Pacific Northwest Research Station. 177 p.

611

Murray, M.D., 2010. The natural range of yellow-cedar: A photographic tour of diverse locations. In: A tale of two cedars: International symposium on western redcedar and yellowcedar. C.A. Harrington Tech. Coord. Gen. Tech. Rep. PNW-GTR-828. Portland, OR: U.S. Department of Agriculture, Forest Service, Pacific Northwest Research Station. 177 p.

610

Curtis, R.O, D.S. DeBell, 2010. Silvicultural research in the Douglas-fir region. Pp. 7- 14 in: Meeting current and future conservation challenges through the synthesis of long-term silviculture and range management research. USDA Forest Service, Washington D,C. Gen. Tech. Report WO-84.

607

Wells, Gail, 2010. Great oaks from little acorns grow: Planting native oak in the Pacific Northwest. Science Findings. Issue 123 (May). 6 p.

606

Comfort, E. J.; Roberts, S. D.; Harrington, Constance A. 2010. Midcanopy growth following thinning in young-growth conifer forests on the Olympic Peninsula western Washington. Forest Ecol. Manage. 259 (2010) 1606–1614.

605

Devine, Warren D.; Harrington, Constance A. 2010. Planting native oak in the Pacific Northwest. Gen. Tech. Rep. PNW-GTR-804. Portland, OR: U.S. Department of Agriculture, Forest Service, Pacific Northwest Research Station. 25 p.

604

Gould, P.J.; Marshall, David D. 2010. Incorporation of Genetic Gain into Growth Projections of Douglas-Fir Using ORGANON and the Forest Vegetation Simulator. West. J. Appl. For. 25(2) 2010.

603

Devine, W.D.; Harrington, Constance; DeBell, Dean S., 2010. Intra-annual growth and mortality of four Populus clones in pure and mixed plantings. New Forests 39:287–299.

602

Peter, David H.; Harrington, Constance A. 2010. Reconstructed old-growth forest stand structure and composition of two stands on the Olympic Peninsula, Washington state. Res. Pap. PNW-RP-583. Portland, OR: U.S. Department of Agriculture, Forest Service, Pacific Northwest Research Station. 22 p.

602b

Miller, Richard E.; McIver, James D.; Howes, Steven W.; Gaeuman, William B. 2010. Assessment of soil disturbance in forests of the interior Columbia River basin: a critique. Assessment of soil disturbance in forests of the interior Columbia River basin: a critique. Gen. Tech. Rep. PNW-GTR-811. Portland, OR: U.S. Department of Agriculture, Forest Service, Pacific Northwest Research Station. 140 p.

602c

Curtis, Robert O., 2010. Effect of diameter limits and stand structure on relative density indices: a case study. West. J. Appl. For. 25(4) 169-175.

 

To request copies of these documents, please contact Tim Mullen at Olympia Forestry Sciences Laboratory at 360-753-7725 or fax: 360-753-7737 or email our contact.

 

 

USDA Forest Service - GenSilv Team
Last Modified: Wednesday, 19 November 2014 at 08:52:09 CST


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