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In review

Eckert, A. J., D. E. Harwood, B. M. Lind, E. M. Hobson, A. Delfino Mix, P. E. Maloney, and C. J. Friedline. The genetic architecture of local adaptation II: The QTL landscape of water-use efficiency for foxtail pine (Pinus balfouriana Grev. & Balf.). Posted to bioRxiv with doi:

Menon, M., J. Swenson, E. Moler, A. Whipple, K. M. Waring, and A. J. Eckert. Variation in gene expression patterns across a conifer hybrid zone highlights the architecture of adaptive evolution under novel selective pressures.


Peach, L. R., K. M. Waring, P. Z. Fule, A. J. Eckert, M. Menon, and J. Swenson. 2023. Drought-induced growth phenotypes are associated with genetic variation across a white pine hybrid zone. Canadian Journal of Forest Research. In press. doi: 

Eckert, A. J. and D. B. Neale. 2023. Probing the dark matter of environmental associations yields novel insights into the architecture of adaptation. New Phytologist 237: 1479-1482. doi:


Bolte, C. E., T. M. Faske, C. J. Friedline, and A. J. Eckert. 2022. Divergence amid recurring gene flow: complex demographic histories for two North American pine species (Pinus pungens and P. rigida) fit growing expectations among forest trees. Tree Genetics & Genomes 18: 35. doi:

de Miguel, M., I. Rodriguez-Quillon, M. Heuertz, A. Hurel, D. Grivet, J. Jaramillo-Correa, G. Vendramin, C. Plomion, J. Majada, R. Alia, A. J. Eckert, and S. C. Gonzalez-Martinez. 2022. Polygenic adaptation and negative selection across traits, years and environments in a long-lived plant species (Pinus pinaster Ait., Pinaceae). Molecular Ecology 31: 2089-2105. doi:


Caballero, M., E. Lauer, J. Bennett, S. Zaman, S. McEvoy, J. Acosta, C. Jackson, L. Townsend, A. Eckert, R. W. Whetten, C. Loopstra, J. Holliday, M. Mandal, J. L. Wegrzyn, and F. Isik. 2021. Toward genomic selection in Pinus taeda: Integrating resources to support array design in a complex conifer genome. ​Applications in Plant Sciences 9: e11439. doi:

Menon, M., J. C. Bagley, G. F. M. Page, A. V. Whipple, A. W. Schoettle, C. J. Still, C. Wehenkel, K. Waring, L. Flores-Renteria, S. A. Cushman, and A. J. Eckert. 2021. Adaptive evolution in a conifer hybrid zone is driven by a mosaic of recently introgressed and background genetic variants. Communications Biology 4: 160. doi:



Leal-Sáenz, A., K. M. Waring, M. Menon, S. A. Cushman, A. Eckert, L. Flores-Rentería, C. J. Hernández-Díaz, C. A. López-Sánchez, J. H. Martínez-Guerrero, and C. Wehenkel. 2020. Morphological differences in Pinus strobiformis across latitudinal and elevational gradients. Frontiers in Plant Science 11: 1600. doi:

Leal-Sáenz et al. (2020) is also part of the Forests and Their Interactions with the Environment research topic.

Bagley, J. C., N. M. Heming, E. E. Gutierrez, U. K. Devisetty, K. E. Mock, A. J. Eckert, and S. H. Strauss. 2020. Genotyping-by-sequencing and ecological niche modeling illuminate phylogeography, admixture, and Pleistocene range dynamics in quaking aspen (Populus tremuloides). Ecology & Evolution 10: 4609-4629. doi:

Landguth, E. L., B. R. Forester, A. J. Eckert, A. J. Shirk, M. Menon, A. Whipple, and S. A. Cushman. 2020. Modeling multilocus selection in an individual-based, spatially-explicit landscape genetics framework. Molecular Ecology Resources 20: 605-615. doi:

Interview with the lead author, Dr. Erin Landguth, at the Molecular Ecology Resources blog site is located here.

Bolte, C. E., and A. J. Eckert. 2020. Determining the when, where and how of conifer speciation: a challenge arising from the study 'Evolutionary history of a relict conifer Pseudotaxus chienii'. Annals of Botany 125: v-vii. doi:

Menon, M., E. Landguth, A. Leal-Sáenz, J. Bagley, A. Schoettle, C. Wehenkel, L. Flores-Rentería, S. Cushman, K. Waring, and A. J. Eckert. 2020. Tracing the footprints of a moving hybrid zone under a demographic history of speciation with gene flow. Evolutionary Applications 13: 195-209.  doi:



Lind, B. M., M. North, P. E. Maloney, and A. J. Eckert. 2019. Effect of fire and thinning on fine scale genetic structure and gene flow in fire-suppressed populations of sugar pine (Pinus lambertiana Douglas). Forest Ecology & Management 447: 115-129. doi:

DeSaix, M. G., L. P. Bulluck, A. J. Eckert, C. B. Viverette, T. J. Boves, J. A. Reese, C. M. Tonra, and R. J. Dyer. 2019. Population assignment reveals low migratory connectivity in a weakly structured songbird. Molecular Ecology 28: 2122-2135. doi:


Friedline, C. J., T. M. Faske, E. M. Hobson, B. M. Lind, D. Parry, R. J. Dyer, D. M. Johnson, L. M. Thompson, K. L. Grayson, and A. J. Eckert. 2019. Evolutionary genomics of gypsy moth populations sampled along a latitudinal gradient. Molecular Ecology 28: 2206-2223doi:

Faske, T. M., L. M. Thompson, N. Banahene, A. Levorse, M. Quiroga-Herrera, K. Sherman, S. E. Timko, B. Yang, D. R. Gray, D. Parry, P. C. Tobin, A. J. Eckert, D. M. Johnson, and K. L. Grayson. 2019. Can gypsy moth stand the heat? A reciprocal transplant experiment with an invasive forest pest across its southern range margin. Biological Invasions 21: 1365-1378.  doi:



Banahene, N., S. K. Salem, T. M. Faske, H. M. Byrne, M. Glackin, S. J. Agosta, A. J. Eckert, K. L. Grayson, and L. M. Thompson. 2018. Thermal sensitivity of gypsy moth (Lepidoptera: Erebidae) during larval and pupal development. Environmental Entomology 47: 1623-1631. doi:

Parchman, T. L., J. P. Jahner, K. Uckele, L. M. Galland, and A. J. Eckert. 2018. RADseq approaches and applications for forest tree genetics. Tree Genetics & Genomes 14: 39. doi:

Lind, B. M., M. Menon, C. E. Bolte, T. M. Faske, and A. J. Eckert. 2018. The genomics of local adaptation in trees: Are we out of the woods yet? Tree Genetics & Genomes 14: 29. doi:

Menon, M., J. C. Bagley, C. Friedline, A. V. Whipple, A. W. Schoettle, A. Leal-Sáenz, C. Wehenkel, F. Molina-Freaner, L. Flores-Rentería, M. S. Gonzalez-Elizondo, R. A. Sniezko, S. A. Cushman, K. M. Waring, and A. J. Eckert. 2018. The role of hybridization during ecological divergence of southwestern white pine (Pinus strobiformis) and limber pine (P. flexilis). Molecular Ecology 27: 1245-1260doi:

Vangestel, C., A. J. Eckert, J. L. Wegrzyn, B. J. St. Clair, and D. B. Neale. 2018. Linking phenotype, genotype and environment to unravel cold hardiness in coastal Douglas-fir (Pseudotsuga menziesii var. menziesii). Tree Genetics & Genomes  14: 10. doi:


Grivet, D., K. Avia, A. Vaattovaarra, A. Eckert, D. Neale, O. Savolainen, and S. C. Gonzalez-Martinez. 2017. Contrasted patterns of diversity and adaptive evolution in two widespread European pines. Molecular Ecology 26: 6857-6870. doi:

Lind, B. M., C. J. Friedline, J. L. Wegrzyn, P. E. Maloney, D. R. Vogler, D. B. Neale, and A. J. Eckert. 2017. Water availability drives signatures of local adaptation in whitebark pine (Pinus albicaulis Engelm.) across fine spatial scales of the Lake Tahoe Basin, USA. Molecular Ecology 26: 3168-3185. doi:


Stevens, K. A., J. L. Wegrzyn, A. Zimin, D. Puiu, M. Crepeau, C. Cardeno, R. Paul, D. Gonzalez-Ibeas, M. Koriabine, A. E. Holtz-Morris, P. J. Martinez-Garcia, U. U. Sezen, G. Marcais, K. Jermstad, P. E. McGuire, C. A. Loopstra, J. M. Davis, A. Eckert, P. de Jong, J. A. Yorke, S. L. Salzberg, D. B. Neale, C. H. Langley. 2016. Sequence of the sugar pine megagenome. Genetics 204: 1613-1626. doi:

Talbot, B., T-W Chen, S. Zimmerman, S. Joost, A. J. Eckert, T. M. Crow, D. Semizer-Cuming, C. Seshadri, S. Manel. 2016. Combining genotype, phenotype, and environment to infer potential candidate genes. Journal of Heredity 108: 207-216. doi:

Rajora, O. P., A. J. Eckert, and J. W. R. Zinck. 2016. Single-locus versus multilocus patterns of local adaptation to climate in eastern white pine (Pinus strobus, Pinaceae). PLoS ONE 11: e0158691. doi:

Maloney, P. M., A. J. Eckert, D. R. Vogler, C. E. Jensen, A. Delfino Mix, and D. B. Neale. 2016. Landscape biology of western white pine: implications for conservation of a widely-distributed five-needle pine at its southern range limit. Forests 7: 93. doi:

Mosca, E., F. Gugerli, A. J. Eckert, and D. B. Neale. 2016. Signatures of natural selection on Pinus cembra and P. mugo along elevational gradients in the Alps. Tree Genetics & Genomes 12: 9. doi:

Sork, V. L., K. Squire, P. F. Gugger, S. Steele, E. Levy, and A. J. Eckert. 2016. Landscape genomic analysis of candidate genes for climate adaptation in a California endemic oak, Quercus lobata Nee. American Journal of Botany 103: 33-46. doi:


Rellstab, C., A. Hancock, A. Eckert, F. Gugerli, and R. Holderegger. 2015. A practical guide to environmental association analyses in landscape genomics. Molecular Ecology 24: 4348-4370. doi:

Friedline, C. J., B. M. Lind, E. M. Hobson, D. E. Harwood, A. D. Mix, P. E. Maloney, and A. J. Eckert. 2015. The genetic architecture of local adaptation I: The genomic landscape of foxtail pine (Pinus balfouriana Grev. & Balf.) as revealed from a high-density linkage map. Tree Genetics & Genomes 11: 49. doi:

Eckert, A. J., P. E. Maloney, D. R. Vogler, C. E. Jensen, A. Delfino Mix, and D. B. Neale. 2015. Local adaptation at fine spatial scales: an example from sugar pine (Pinus lambertiana, Pinaceae). Tree Genetics & Genomes 11: 42. doi:



Baker, P. A., S. C. Fritz, C. W. Dick, A. J. Eckert, B. K. Horton, S. Manzoni, C. C. Ribas, C. N. Garzione, and D. S. Battisti. 2014. The emerging field of geogenomics: constraining geological problems with genetic data. Earth-Science Reviews 135: 38-47. doi:


DeGiorgio, M., J. Syring, A. J. Eckert, A. I. Liston, R. Cronn, D. B. Neale, and N. A. Rosenberg. 2014. An empirical evaluation of species tree inference strategies using a multilocus data set from North American pines. BMC Evolutionary Biology 14: 67. doi:



Eckert, A. J., J. L. Wegrzyn, J. D. Liechty, J. M. Lee, W. P. Cumbie, J. M. Davis, B. Goldfarb, C. A. Loopstra, S. R. Palle, T. Quesada, C. H. Langley, and D. B. Neale. 2013. The evolutionary genetics of the genes underlying phenotypic associations for loblolly pine (Pinus taeda, Pinaceae). Genetics 195: 1353-1372. doi: 113.157198


Bashalkhanov, S., A. J. Eckert, and O. P. Rajora. 2013. Genetic signatures of natural selection in response to air pollution in red spruce (Picea rubens, Pinaceae). Molecular Ecology 22: 5877-5889. doi:


Eckert, A. J., A. D. Bower, K. D. Jermstad, J. L. Wegrzyn, B. J. Knauss, J. V. Syring, and D. B. Neale. 2013. Multilocus analyses reveal little evidence for lineage wide adaptive evolution within major clades of soft pines (Pinus subgenus Strobus). Molecular Ecology 22: 5635-5650. doi:


Palle, S. R., C. M. Seeve, A. J. Eckert, J. L. Wegrzyn, D. B. Neale, C. A. Loopstra. 2013. Association of loblolly pine xylem development gene expression with single nucleotide polymorphisms. Tree Physiology 33: 763-774. doi:


Sork, V. L., S. N. Aitken, R. J. Dyer, A. J. Eckert, P. Legendre, and D. B. Neale. 2013. Putting the landscape into the genomics of forest trees: approaches for understanding local adaptation and population responses to a changing climate. Tree Genetics & Genomes 9: 901-911. doi:



Mosca, E., A. J. Eckert, E. Di Pierro, D. Rocchini, N. La Porta, P. Belletti, and D. B. Neale. 2012. The geographical and environmental determinants of genetic diversity for four alpine conifers of the European Alps. Molecular Ecology 21: 5530-5545. doi:


Eckert, A. J., H. Shahi, S. L. Datwyler, and D. B. Neale. 2012. Spatially variable natural selection and the divergence between parapatric subspecies of lodgepole pine (Pinus contorta, Pinaceae). American Journal of Botany 99: 1323-1334. doi:


Chen, J., T. Kallman, X. Ma, N. Gyllenstrand, G. Zaina, M. Morgante, J. Bousquet, A. Eckert, J. Wegrzyn, D. Neale, U. Lagercrantz and M. Lascoux. 2012. Disentangling the roles of history and local selection in shaping clinal variation of allele frequencies and gene expression for photoperiodic genes in Norway spruce (Picea abies). Genetics 191: 865-881. doi:


Eckert, A. J. and R. J. Dyer. 2012. Defining the landscape of adaptive genetic diversity. Molecular Ecology 21: 2836-2838. doi:


Mosca, E., A. J. Eckert, J. D. Liechty, J. L. Wegrzyn, N. La Porta, G. G. Vendramin, and D. B. Neale. 2012. Contrasting patterns of nucleotide diversity for four conifers of Alpine European forests. Evolutionary Applications 5: 762-775. doi: .x


Eckert, A. J., J. L. Wegrzyn, W. P. Cumbie, B. Goldfarb, D. A. Huber, V. Tolstikov, O. Fiehn, and D. B. Neale. 2012. Association genetics of the loblolly pine (Pinus taeda, Pinaceae) metabolome. New Phytologist 193: 890-902. doi: 03976.x



Chancerel, E., C. Lepoittevin, G. Le Provost, Y. C. Lin, J. P. Jaramillo-Correa, A. J. Eckert, J. L. Wegrzyn, D. Zelenika, A. Boland, J. M. Frigerio, P. Chaumeil, P. Garnier-Géré, C. Boury, D. Grivet, S. C. González-Martínez, P. Rouzé, Y. Van de Peer, D. B. Neale, M. T. Cervera, A. Kremer, and C. Plomion. 2011. Development and implementation of a highly-multiplexed SNP array for genetic mapping in maritime pine. BMC Genomics 12: 368. doi:


Maloney, P. E., D. R. Vogler, A. J. Eckert, C. E. Jensen, and D. B. Neale. 2011. Population biology of sugar pine (Pinus lambertiana Dougl.) with reference to historical disturbances in the Lake Tahoe Basin: implications for restoration. Forest Ecology and Management 262: 770-779. doi:


Cumbie, W. P., A. J. Eckert, J. L. Wegrzyn, R. Whetten, D. B. Neale and B. Goldfarb. 2011. Association genetics of carbon isotope discrimination, height, and foliar nitrogen in a natural population of Pinus taeda L. Heredity 107: 105-114. doi:


Jermstad, K. D., A. J. Eckert, J. L. Wegrzyn, A. D. Mix, D. A. Davis, D. C. Burton and D. B. Neale. 2011. Comparative mapping in Pinus: sugar pine (Pinus lambertiana Dougl.) and loblolly pine (Pinus taeda). Tree Genetics & Genomes 7: 457-468. doi: /s11295-010-0347-1


Eckert, A. J. 2011. Seeing the forest for the trees: statistical phylogeography in a changing world. New Phytologist 189: 894-897. doi:


Palle, S. R., C. M. Seeve, A. J. Eckert, W. P. Cumbie, B. Goldfarb and C. A. Loopstra. 2011. Natural variation in expression of genes involved in xylem development in loblolly pine (Pinus taeda L.). Tree Genetics & Genomes 7: 193-206. doi:


Bower, A. D., S. C. McLane, A. J. Eckert, S. Jorgensen, A. Schoettle, S. Aitken. 2011. Conservation genetics of high elevation five-needle pines. USDA National Forest Service, Rocky Mountain Research Station Proceedings Publication RMRS-P-63.


González-Martínez S. C., S. Dillon, P. Garnier-Géré, K. Krutovsky, R. Alía, C. Burgarella, A. J. Eckert, M. R. García-Gil, D. Grivet, M. Heuertz, J. P. Jaramillo-Correa, M. Lascoux, D. B. Neale, O. Savolainen, Y. Tsumura and G. G. Vendramin. 2011. Patterns of nucleotide diversity and association mapping. In: "Conifers" (Eds. C. Plomion & J. Bousquet). Series on "Genomics of Industrial Crops" (Ed. C. Kole). Science Publishers, Inc., New Hampshire; Edenbridge Ltd., British Isles.


Jermstad, K. D., A. J. Eckert, J. L. Wegrzyn, B. B. Kinloch, A. D. Mix, D. A. Davis, D. C. Burton and D. B. Neale. 2011. A sugar pine consensus map: Comparative mapping between the Pinus subgenus Pinus and the subgenus Strobus. USDA National Forest Service, Rocky Mountain Research Station Proceedings Publication RMRS-P-63.



Quesada, T., V. Gopal, W. P. Cumbie, A. J. Eckert, J. L. Wegrzyn, D. B. Neale, B. Goldfarb, D. A. Huber, G. Casella and J. M. Davis. 2010. Association mapping of quantitative disease resistance in a natural population of loblolly pine (Pinus taeda L.). Genetics 186: 677–686. doi:


Wegrzyn, J. L., A. J. Eckert, M. Choi, J. M. Lee, B. J. Stanton, R. Sykes, M. Davis, C. J. Tsai and D. B. Neale. 2010. Association genetics of traits controlling lignin and cellulose biosynthesis in black cottonwood (Populus trichocarpa, Salicaceae) secondary xylem. New Phytologist 188: 515-532. doi:


Eckert, A. J., A. D. Bower, S. C. González-Martínez, J. L. Wegrzyn, G. Coop and D. B. Neale. 2010. Back to nature: Ecological genomics of loblolly pine (Pinus taeda, Pinaceae). Molecular Ecology 19: 3789-3805. doi:


Eckert, A. J., J. van Heerwaarden, J. L. Wegrzyn, C. D. Nelson, J. Ross-Ibarra, S. C. González-Martínez and D. B. Neale. 2010. Patterns of population structure and environmental associations to aridity across the range of loblolly pine (Pinus taeda L., Pinaceae). Genetics 185: 969-982. doi:


Eckert, A. J., M. L. Eckert and B. D. Hall. 2010. Effects of historical demography and ecological context on spatial patterns of genetic diversity within foxtail pine (Pinus balfouriana, Pinaceae) stands located in the Klamath Mountains, California. American Journal of Botany 97: 650-659. doi:


Eckert, A. J., J. D. Liechty, B. R. Tearse, B. Pande and D. B. Neale. 2010. DnaSAM: Software to perform neutrality testing for large datasets with complex null models. Molecular Ecology Resources 10: 542-545. doi:



Eckert, A. J., J. L. Wegrzyn, B. Pande, K. D. Jermstad, J. M. Lee, J. D. Liechty, B. R. Tearse, K. V. Krutovsky and D. B. Neale. 2009. Multilocus patterns of nucleotide diversity and divergence reveal positive selection at candidate genes related to cold-hardiness in coastal Douglas-fir (Pseudotsuga menziesii var. menziesii). Genetics 183: 289-298. doi: genetics.109.103895


Olmstead, R. G., M. L. Zjhra, L. G. Lohmann, S. O. Grose, and A. J. Eckert. 2009. A molecular phylogeny and classification of Bignoniaceae. American Journal of Botany 96: 1731-1743. doi:


Eckert, A. J., A. D. Bower, B. Pande, K. D. Jermstad, K. V. Krutovsky, J. B. St. Clair and D. B. Neale. 2009. Association genetics of coastal Douglas fir (Pseudotsuga menziesii var. menziesii, Pinaceae). I. Cold-hardiness related traits. Genetics 182: 1289-1302. doi: genetics.109.102350


Eckert, A. J., B. Pande, E. S. Ersoz, M. H. Wright, V. K. Rashbrook, C. M. Nicolet and D. B. Neale. 2009. High-throughput genotyping and mapping of single nucleotide polymorphisms in loblolly pine (Pinus taeda L.). Tree Genetics & Genomes 5: 225-234. doi:



Eckert, A. J. and B. C. Carstens. 2008. Does gene flow destroy phylogenetic signal? The performance of three methods for estimating a species phylogeny in the presence of gene flow. Molecular Phylogenetics and Evolution 49: 832-842. doi:


Eckert, A. J., B. R. Tearse, and B. D. Hall. 2008. A phylogeographical analysis of the range disjunction for foxtail pine (Pinus balfouriana, Pinaceae): the role of Pleistocene glaciation. Molecular Ecology 17: 1983-1997. doi:



Eckert, A. J. and M. L. Eckert. 2007. Effects of aspect, elevation, and substrate type on size class distributions of foxtail pine (Pinus balfouriana, Pinaceae) in the Klamath Mountains, California. Madroño 54: 117-125. No doi available.



Eckert, A. J. 2006. Influence of substrate type and microsite availability on the persistence of foxtail pine (Pinus balfouriana, Pinaceae) in the Klamath Mountains, California. American Journal of Botany 93: 1615-1624. doi:


Eckert, A. J. and B. D. Hall. 2006. Phylogeny, historical biogeography, and patterns of diversification for Pinus (Pinaceae) – Phylogenetic tests of fossil-based hypotheses. Molecular Phylogenetics and Evolution 40: 166-182. doi:



del Moral, R. and A. J. Eckert. 2005. Colonization of volcanic deserts from productive patches. American Journal of Botany 92: 27-36. doi:


Goetsch, L., A. J. Eckert, and B. D. Hall. 2005. The molecular systematics of Rhododendron (Ericaceae): a phylogeny based upon RPB2 gene sequences. Systematic Botany 30: 616-626. doi:



Eckert, A. J. and J. O. Sawyer. 2002. Foxtail pine importance and conifer diversity in the Klamath Mountains and southern Sierra Nevada, California. Madroño 49: 33-45. No doi available.

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