The Biology Department Faculty maintain active research labs, collaborating with Puget Sound undergraduate research students, as well as scholars across the country and around the world. Below are some of the most recent publications from our faculty. To learn more about an individual faculty member's lab, or to see complete lists of publications, please explore our faculty research pages.
Gene duplication and polyploidization are genetic mechanisms that instantly add genetic material to an organism's genome on which evolution can then act. In this paper we describe how the two light receptor genes phytochrome B1 and B2 have diverged since their duplication both in their phenotypic functions and their transcriptional regulation of gene networks in response to light.
Carlson, KD, Bhogale, S, Anderson, D, Zaragoza-Mendoza, A, Madlung, A. Subfunctionalization of phytochrome B1/B2 leads to differential auxin and photosynthetic responses. (2020) Plant Direct 4(2): e00205.
In this study we examined the distribution of epiphytic bryophytes in bigleaf maple trees in the Olympic temperate rainforest along with the factors that drive their distribution. We found differences in epiphyte communities between the trunks and branches with more species found on the trunk. Structural features of the tree, including branch size, height, and moss depth, influenced epiphyte distributions more than microclimate.
Woods, C. L., L. M. Nevins, and E. J. Didier. (2019). Structural heterogeneity of trees influences epiphyte distributions in a northern temperate rainforest. Journal of Vegetation Science 30:1134-1142.
In this paper, we describe our findings that the plant-specific light receptor phytochrome appears to have functions even in the dark. Additionally, we show that phytochrome plays a role in the balancing of sucrose distribution in the germinating seedling.
Microbes are the basis of the plankton communities and marine food webs. In order to grow and support their metabolism, these microbes require nutrients typically found dissolved in seawater. However, in the open ocean, away from land and coasts, the supply of a key nutrient for microbes, phosphate, can be very scarce and yet microbes have adapted to live in these ecosystems. This study uses metagenomics data to quantify genes that allow marine microbes to scavenge phosphate from organic compounds containing phosphorus. One of the genes quantified codes for an enzyme known as the carbon-phosphorus lyase which has evolved mainly in bacteria to breakdown phosphorus-containing compounds known as phosphonates. A key finding of this study was that the carbon-phosphorus lyase genes were highly selected for in parts of the ocean that contain very little phosphate. This result is relevant to understanding the role of the ocean in climate, because one of the byproducts released during phosphonate degradation is the greenhouse gas methane. The results of this study suggest that when the supply of phosphate is very low in oceanic waters, the potential release of methane by bacteria may increase.
The presence of humans can profoundly change landscapes. In the South Gondar region of the northern highlands in Ethiopia, the last remaining forests are small fragments of 5 ha that surround churches. These forests are protected by the Ethiopian Orthodox Tewahido church, and are integral to their livelihoods and cultural heritage. In this paper we examined the influence of human presence on forest integrity and found that human disturbance negatively affected forest diversity and regeneration potential. Forest management strategies focusing on reducing trail systems and clearings within forests and conserving large trees as seed sources could benefit both the forest and church communities.
A nomadic vine in the light-limited understory showed a response to nutrient addition that suggests nutrient limitation. Thus, limitation by multiple factors seems to be the rule rather than the exception in many plant groups.
Woods, C. L., S. J. DeWalt, C. L. Cardelús, K. E. Harms, J. B. Yavitt, and S. J. Wright. (2018). Fertilization influences the nutrient acquisition strategy of a hemiepiphytic aroid in a lowland tropical forest understory. Plant and Soil.
Female striped plateau lizards express ornaments that may advertise the quality of the female and her future offspring to potential mates. In this paper, a senior thesis student and I asked whether males pay attention to this ornament and alter their behavior accordingly. By placing two males together with an ornamented female, we found that males perform more male-male display behaviors more quickly when in the presence of large-ornamented female. We discuss these results in the context of sexual selection on female traits and male mate choice.
Paterson, J.E., S.L. Weiss and G. Blouin-Demers. In press. Experimental removal reveals only weak interspecific competition between two coexisting lizards. Canadian Journal of Zoology
So far, the marine bacterial species known to metabolize a marine natural product known as methylphosphonate accomplish this through the carbon-phosphorus lyase enzyme, a mechanism that releases the greenhouse gas methane as a byproduct. This study describes an alternative pathway by which the marine photosynthetic bacterium Prochlorococcusmetabolizes methylphosphonate. The new pathway consists of oxidizing methylphosphonate into formate and phosphate, avoiding the release of methane. This result is relevant to our understanding of the role of marine phosphonates and oceanic microbes in climate, because it demonstrates that not all methylphosphonate in the ocean is degraded into methane. Some of it must be converted to formic acid, a compound that can be easily utilized by other marine microbes as fuel for cellular processes or as a biomass building block.
In this paper I present a lab exercise I developed and tested with my students in here at the University of Puget Sound. I show results from assessing in what ways the exercise furthered student learning in bioinformatics and discuss the overall state of bioinformatics instruction in undergraduate Biology education.
Madlung, A. Assessing an effective undergraduate module teaching applied bioinformatics to biology students. (2018) PLoS Computational Biology 14(1): e1005872. https://doi.org/10.1371/journal.pcbi.1005872
Does class size matter? Puget Sound was part of a multi-institution study to determine the effect of class size on performance in Introductory Biology class rooms. We found that as class sizes decreases, so does the gender gap in performance on high stakes exams. We also found that women tend to perform better than men on non-exam assignments, regardless of class size. These findings have important implications for equitable pedagogy and caps on classroom sizes.
Ballen, C.J., S. Aguillon, R. Brunelli, A.G. Drake, D. Wassenberg, S.L. Weiss, K.R. Zamudio, and S. Cotner. 2018. Do small classes in higher education reduce performance gaps in STEM? BioScience biy056
It seems obvious to dog owners that dogs understand what tone of voice means. But what about when tone of voice is the only piece of information that a dog gets – no facial expression, no gestures, no words??? What researchers at the University of Puget Sound found may surprise you!
Colbert–White, E.N., Tullis, A., Andresen, D.R., Parker, K.M.* and Patterson, K.E.*
Can dogs use vocal intonation as a social referencing cue in an object choice task? Animal Cognition. 2018 Mar;21(2):253-265.
Developing a series of colorful and engaging elementary school exercises to promote the idea that some viruses can fight disease, as well appreciate the microbial world.
Breitbart, M., Malki, K., Sawaya, N.A., Bonnain, C., and M.O. Martin (2018). “Elementary Student Outreach Activity Demonstrating the Use of ‘Phage Therapy Heroes’ to Combat Bacterial Infections.” J. Microbiol. Bio. Education. 19(1). pii: 19.1.30. doi: 10.1128/jmbe.v19i1.1407
As trees increase in size, they create microhabitats that enable more and more epiphyte species to accumulate in the tree crown. This paper examines epiphyte succession at two scales: the inner crown whereby it follows replacement models and the entire tree crown whereby it follows a species accumulation model.
Woods, C. L. (2017) Primary ecological succession in vascular epiphytes: the species accumulation model. Biotropica 49:452-460.
In this paper we tested the hypothesis that allopolyploidization (the hybridization of two different species concurrent with genome duplication) not only is a pathway to instant speciation, but, possibly due to the genomic shock during the initial polyploid formation, might create diversity early on in the evolution of the new species. We identify a large number of stress-response related genes, including genes responding to drought stress, that are differentially expressed between sister populations of the same cross. We conclude that allopolyploidy might allow these sister populations to functionally diverge from each other – for example in dry versus wet conditions - and might provide a mechanism for niche specialization as a first step towards speciation.
Carlson, KD, Fernandez-Pozo, N, Bombarely, A, Pisupati, R., Mueller, LA, Madlung, A. Natural variation in stress response gene activity in the allopolyploid Arabidopsis suecica. (2017) BMC Genomics 18:653 doi.org/10.1186/s12864-017-4067-x
In the south Gondar region of northern Ethiopia the remaining forests are protected because they surround churches and are an integral component of the Ethiopian Orthodox Tewahido church. We found that these forests have persisted on the landscape and increased in area over the past 50 years. However, forests have a high degree of human presence and some were increasing due to the planting of exotic Eucalyptus, which could compromise their continued persistence on the landscape.
Cardelús, C. L., P. Scull, A. Wassie Eshete, C.L. Woods, P. Klepeis E. Kent and I. Orlowska. (2017) Shadow conservation and the persistence of church forests in Northern Ethiopia. Biotropica 49:726-733.
The extremely large claw possessed by male fiddler crabs helps make them more attractive to females, thereby enhancing their reproductive success. But surely this massive claw – sometimes reaching up to 50% of the total body mass of the animal — costs a considerable amount of metabolic energy to carry around (imagine a 150 lb human carrying a 75 lb backpack!). Turns out, researchers at the University of Puget Sound found that this is not the case.
Tullis, A. and Straube, C.H.T.* The metabolic cost of carrying a sexually selected trait in the male fiddler crab Uca pugilator. Journal of Experimental Biology. 220: 3641-3648.
The first published genome of Ensifer, a predator of Gram positive bacteria. Though related to beneficial alpha proteobacteria, Ensifer has a number of interesting properties, including predation, synthesis of exopolysaccharide, and "tracking motility.
Williams, L.E., Baltrus, D.A., O’Donnell, S.D., Skelly, T.J., and M.O. Martin (2017). “Complete Genome Sequence of the Predatory Bacterium Ensifer adhaerens Casida A.” Genome Announc. 5: e01344-17.
The church community has built walls around some of their sacred forests in northern Ethiopia. Walls benefited the seedlings of many tree species but some trees will require facilitated regeneration.
Woods, C. L., C. L. Cardelús, P. S. Scull, A. Wassie, M. Baez*, and P. Klepeis. (2017) Stone walls and sacred forest conservation in Ethiopia. Biodiversity and Conservation 26:209-221.