Developing a Plant Phenology Ontology

Posted by Amanda Gallinat

The Plant Phenology Ontology 2016 Workshop participants

This month, I attended a NEON/USGS-sponsored workshop in Fort Collins, CO where the goal was to develop a plant phenology ontology. An ontology is a controlled vocabulary (with clear definitions of participants, processes, and the relationships between them) that can be used to link data across networks to facilitate comparisons and analysis. Here is an example of a simple ontology showing components of the vascular leaf:

From the Plant Ontology Consortium

Plant phenology is the perfect example of a process in need of vocabulary standardization. At the workshop, participants from large-scale ground-based observational networks such as the National Ecological Observatory Network (NEON) and the National Phenology Network (NPN), as well as participants using remote observations, discussed the different ways we record phenology:

Rob Guralnick leads the charge! Photo by Kjell Bolmgren

Our phenology terms varied widely depending on the data set! The result is that despite increasing spatial and temporal coverage of phenology observations, the different vocabularies among networks makes the task of comparing or combining these data sets immensely challenging:  

Comparing phenology data sets. Photo by Kjell Bolmgren

As a group, we defined important entities and processes involved in leaf phenology (that could be applied to all gymnosperms and angiosperms), as well as how each of those terms link to one another. We made great progress on the ontology, but there is still a lot of work to do before a full ontology is online and ready to use. After working on the leaf phenology ontology during the week, we took a stab at the reproductive phenology ontology during our last group dinner:

Jenn Yost of Cal Poly knocks out an ontology in crayon

The ultimate goal is to build an ontology that will allow researchers to integrate phenology measurements from different networks, to address important topics like the effects of climate change on phenology in different habitats, or linking species-level and canopy-level phenology. I look forward to continuing work on the plant phenology ontology with this great group of researchers! 

Reproduction Ecology

by Caitlin McDonough MacKenzie

The Primack Lab has a new member. Baby Mara was born in September 2015!

Mara has already attended the Acadia Science Symposium and the Northeast Alpine Stewardship Gathering with her parents where she enjoyed watching her mother present the preliminary results from field work in Acadia National Park. When they were not exploring Northern New England, Mara and her mother spent the fall semester at home — bonding, recovering, and growing at a relaxed pace under Boston University's graduate student parental leave policy. 

Now, Mara is gearing up for a semester of independence while her mother returns to teaching and research. Time management and efficiency have quickly developed as necessary skills in this work-life balance; eating quickly and staying caffeinated are equally important. Though honestly, the first four years of graduate school have already honed those skills — parenting just throws them into sharper relief. And of course, coming home to a giggling, happy baby makes the monotony of grading, data entry, or coding quickly fade away!

Student Research at the Arnold Arboretum

Posted by Chase Mason

At the Arnold Arboretum, three Boston University seniors are midway through a variety of new research projects at the intersection of plant physiology, ecology, genetics, and evolution. Sponsored by BU Professor Richard Primack, undergraduates Juliana Webber, Luca Russo, and Tessa Pliakas are set to begin their second semester of research with Arboretum scientist and Putnam Fellow Chase Mason.

Since September, Juliana has been examining the evolution of leaf flavonoids and other phenolics across diverse wild sunflowers (genus Helianthus) from across North America. Her results indicate large variation in secondary chemistry across wild sunflowers, and will improve our understanding of how allocation to defensive chemistry varies in response to plant adaptation to local soil and climate conditions.

At the same time, both Juliana and Luca have been examining the response of cultivated sunflower (Helianthus annuus) to hormonally-simulated insect attack. Juliana and Luca have been tracking how activating this internal plant defense response affects sunflower allocation to growth and reproduction, and leaf palatability to snails, grasshoppers, and caterpillars. In the coming months they will be examining in detail which classes of chemical defenses were most upregulated by defense induction, and together these multiple angles will tell us a great deal about trade-offs between growth, defense, and reproduction in an important oilseed crop.

In the lab, Tessa has been examining the carotenoid content of nearly a thousand samples of frozen sunflower petals, in an attempt to understand the genetic basis of flower color in cultivated sunflower. By assessing pigment concentration across an association mapping panel of several hundred sequenced sunflower lines, Tessa will begin the new year by mapping variation in petal carotenoid content to the sunflower genome, in order to describe the genetic architecture of this trait and begin the hunt for the candidate genes that determine whether sunflower petals are faint yellow, bright orange, or somewhere in between.

You can read more about Dr. Mason’s research and keep up to date on developments here.