First Advisor

Daniel J. Ballhorn

Term of Graduation

Spring 2021

Date of Publication


Document Type


Degree Name

Doctor of Philosophy (Ph.D.) in Biology





Physical Description

1 online resource (ix, 114 pages)


Red alder (Alnus rubra Bong.) is the dominant hardwood tree species in the Pacific Northwest. Red alders are only found in western North America, generally within 200 km of the coast and below 1000 m in elevation--although there are several disjunct populations in the northern Rocky Mountains in Idaho. Commonly a riparian species, the shade intolerant red alder generates most of the leaf litter in the streams and rivers it occupies which has been shown to greatly influence the decomposer communities. This, in turn, has a cascading effect throughout the entire riparian ecosystem greatly influencing multiple levels of the food chain. Red alders also aid in stream cooling by shading areas with its canopy which has been shown to reduce diel temperature swings. This reduction improves survivability in ecologically and economically important salmonid fish species (e.g. Coho Salmon, Rainbow Trout) in which the fry require cool freshwater streams and rivers for juvenile growth and development. When not occupying riparian habitat, red alder is a pioneer species that is well suited to occupy recently disturbed areas (e.g. timber harvesting, fire damage), or areas with poor soil conditions where essential nutrients may be limited. The success of red alder as an early successional species is facilitated by the symbiotic relationship it forms with the N2-fixing actinorhizal bacteria Frankia alni. In this mutualism, Frankia bacteria fix nitrogen for red alder and in return they receive photosynthetic products produced by their symbiotic host. The process of bacterial nitrogen-fixation can be very expensive for the host plant since as much as 40% of all photoassimilates produced are funneled to the Frankia symbionts for this process. Red alders usually associate with specific strains of Frankia--which exhibit low diversity over large special scales--with the choice being controlled primarily by the host. Resultantly, alders are able to improve soil conditions which has been shown to improve growth and success of other valuable tree species in the Pacific Northwest (e.g. Douglas fir, big leaf maple). Initially considered a nuisance weed or a pest species by local logging operations due to the enumerable red alder seedlings that occupy freshly logged areas, red alder has become one of the most commercially valuable species in the Pacific Northwest. The quick growth, short lifespan (< 100 years), and beautiful red tinted wood--paired with red alder's ability to fix nitrogen thereby eliminating the need for chemical fertilizers--has made red alder one of the most commercially valuable species in the Pacific Northwest with plantations in several states, and up into Canada as well.

Despite the invaluable ecosystem services and the high commercial value of red alder, very little is known about their genetics. In particular, studies utilizing next generation sequencing (NGS) technology are lacking. To help narrow the knowledge gap in red alder genetics I used a high-density single nucleotide polymorphism profile generated by genotype by sequencing to help fill in the gaps of knowledge in phylogeography and local adaptation to environmental conditions, and selection of specific Frankia strains as well. I use a suite of relatively recently developed bioinformatics programs to look for population structure in red alder, and then utilize these data to calculate dispersal dates into the disjunct populations in Idaho. I was able to identify four sub-populations of red alder (2 coastal, 2 inland), and five separate dates at which I estimate red alder was able to disperse into the inland range. This helped clear up ambiguities in the timing and number of times that red alder was able to disperse into the inland disjunct populations.

A combination of microscopy and statistical analysis was then used to look for polyploidy in red alder, and determine if polyploidy is common in the species. Diploid and tetraploid cytotypes were identified, and the distribution throughout the range was relatively even. Finally, the disjunct populations encounter different abiotic conditions than those on the coast. This, as well as the lack of regular gene flow into the disjunct inland populations provide a good system for studying local adaptation via association studies in red alder. I also utilized association studies to look for markers involved in Frankia selection as well. I identified five marker SNPs as candidate loci for local adaptation to environmental variables. I was also able to identify two marker SNPs as candidate loci for selection of specific Frankia genotypes by the novel approach of using the Frankia genotype as a red alder phenotype in a genome wide association study. This finding has significant potential for future crop improvement approaches.

Future studies should look at the entire distribution of red alder including Canada, California, and the rest of the disjunct populations in Idaho. It is likely that more sub-populations and many more dispersal events inland would be identified. Particularly, the Frankia association study could be ran on thousands of SNPs in hundreds of individuals covering the whole range of red alder's distribution. If more detail could be elucidated on the genetics involved in this selection process it may be possible to engineer common crop species with the ability to form symbiotic associations to fix nitrogen for said crop species. This would eliminate the need for the addition of chemical fertilizers which have been shown to have a devastating effect on freshwater ecosystems.


© 2021 Jacob Brent Loveless

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