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Environment specific alleles related to adaptive seasonal traits and the fitness consequences of phenology for Pinus strobiformis

Swenson, Jared Karl (2021) Environment specific alleles related to adaptive seasonal traits and the fitness consequences of phenology for Pinus strobiformis. Masters thesis, Northern Arizona University.

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Rapid shifts in temperature and precipitation related to anthropogenic climate change threaten to decouple evolved responses to environmental stimuli resulting in maladaptive phenology. Asynchronous phenology could result in increased mortality in forest trees and trigger a cascade of impacts on large scale ecosystem processes. Understanding phenological responses to novel conditions and identifying the genetic architecture of phenological traits and survival can aid forest managers in identifying both vulnerable populations and populations with substantial genetic variation. Pinus strobiformis is a high elevation conifer whose disjunct and isolated distribution across the American southwest makes it particularly vulnerable to climate change. P. strobiformis contributes to biodiversity in mixed conifer forests, but species distribution models predict that suitable habitat for P. strobiformis will decrease across their current range and shift to higher latitudes and altitudes. Recent genetic analysis described the extent of a hybrid zone in New Mexico and Arizona between P. strobiformis and the more northerly distributed Pinus flexilis. These hybrid populations may possess unique allele combinations necessary for survival under combined water limitations and freezing conditions. This thesis builds upon a rapidly growing body of knowledge through an international collaborative effort across multiple universities and government agencies to understand the physiology, ecology, genetics, and resistance to invasive pathogens. In the first chapter we utilized three common gardens at Pinus strobiformis climate margins to detect genetic markers related to phenology, survival, and bud damage through both single and multi-trait genome wide association analyses. Multi-trait groupings included 1) the same trait measured at multiple time points, or longitudinal measures, of the same trait across multiple time periods, 2) different components of spring phenology bud development, and 3) traits that had significant associations with maternal seed source climate. We detected 103 SNPs related to survival, phenology, and bud damage over the span of two years. Most minor, or less common, alleles detected for traits had a negative effect on survival and variable effects on spring phenology. Using multi-trait groupings improved our ability to detect loci and identify shared genetic influences among multiple traits. Our results suggest that phenology, survival, and bud damage in Pinus strobiformis are regulated by complex genetic and environment interactions, environment specific allele sensitivities, and indirect effects of loci on multiple phenotypes. The second chapter extends the utility of the genome-wide association analyses by investigating phenological relationships with survival and the distribution of minor alleles along climate gradients. We investigated variation across years and growing conditions in phenological traits and their relationship with survival. The relationships among phenological traits and survival were used to group alleles by their garden specific effects. Alleles that increased survival under particular growing conditions at a specific time were considered favorable, whereas alleles that decreased survival were considered unfavorable. These allele distinctions are garden specific and likely do not represent alleles that are unfavorable nor favorable for Pinus strobiformis in their home range. An additional group of alleles was created for alleles that were related to spring phenological development. These groups were used to investigate the relationships among allele counts for individual maternal trees and maternal seed source climate variables and garden specific survival. Spring phenology and bud damage varied across the two study years and across gardens. Fall phenology demonstrated little variation between the high and low elevation gardens. Maternal trees with greater bud damage had lower survival at all gardens, whereas spring bud burst phenology had opposing relationships with survival at the two extreme gardens. Our results demonstrate that early growth in P. strobiformis responds to climatic shifts in context dependent ways. Maternal P. strobiformis trees with more unfavorable minor alleles and more phenology related minor alleles had lower survival. P. strobiformis families with more favorable, unfavorable or phenology related minor alleles were from seed source sites with less winter precipitation and more climate moisture deficit. This pattern suggests that Pinus strobiformis may have retained low frequency, rare alleles, through a combination of selective pressure on early season growth, stressful conditions, and seasonal moisture. Additionally, local adaptation within large highly variable maternal populations; and unequal patterns of gene flow may have contributed to the retention of these alleles. Our study contributes to the developing body of work that highlights the importance of seasonal precipitation and moisture deficit for P. strobiformis local adaptation and evolutionary history.

Item Type: Thesis (Masters)
Publisher’s Statement: © Copyright is held by the author. Digital access to this material is made possible by the Cline Library, Northern Arizona University. Further transmission, reproduction or presentation of protected items is prohibited except with permission of the author.
Keywords: allele distributions; GWAS; local adaptation; phenology; survival; Chichuahua white pine; Pinus strobiformis; Climate change; Maladaptive phenology
Subjects: Q Science > QK Botany
NAU Depositing Author Academic Status: Student
Department/Unit: Graduate College > Theses and Dissertations
College of the Environment, Forestry, and Natural Sciences > Biological Sciences
Date Deposited: 13 Jul 2022 16:29
Last Modified: 14 Jul 2022 08:30
URI: https://openknowledge.nau.edu/id/eprint/5824

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