Course/workshop content:
Identifying biodiversity hot spots is crucial for ecological and evolutionary studies as well as to address urgent societal needs for effective land management and conservation in the face of global change. The field of spatial phylogenetics combines species occurrence data with molecular phylogenetics to recover information about the spatial distribution of phylogenetic diversity and endemism across a region. Going beyond standard studies of species distributions, spatial phylogenetics considers the relatedness among the species present in locations across a broader region. The core idea is to turn the tree of life into a GIS layer that can then be used with other layers for scientific studies in ecology and evolution as well as objective conservation assessments.
Incorporating evolutionary relatedness is important for multiple reasons. For example, knowledge of relationships may illuminate the origin of diversity patterns as well as the environmental drivers that shape it. Moreover, ecological and functional similarities among species are generally shaped by their common ancestry, but are also shaped by patterns of ecological co-occurrence. Spatial phylogenetics is useful to sort out these processes. In addition, (phylo)genetic diversity is assumed to increase a community's resilience to environmental change. This and related conservation priorities can be expressed using spatial phylogenetics.
The new and expanding field of spatial phylogenetics includes methods for exploring both alpha- and beta-phylodiversity on the landscape, including the use of spatial randomizations to assess statistical significance. It is suitable for use in all groups of organisms, including microbes as studied metagenomically (where species concepts are especially arbitrary).
This course/workshop will be a combination of lectures, discussions, and hands-on tutorials to explore the field of spatial phylogenetics. The first day will be dedicated to presenting and discussing relevant literature. The second day will focus on spatial and phylogenetic data gathering and cleaning and ways to combine them. The last day will focus on performing spatial phylogenetic analyses using Biodiverse and R.
The course will require personal attendance due to the large component of practical work, but some of the lectures will also be available via video.
Prior knowledge prerequisites
Basic knowledge in biodiversity science at the level of an MSc student or above is required. Course participants will further gain from having some experience with spatial and phylogenetic data acquisition and handling. Basic knowledge in R or other programming languages is recommended. As preparation for the first course day, participants should read a selection of scientific papers that we will provide. Course participants must bring their own laptop for the practicals (PM on Tuesday and Wednesday) and are welcome to bring their own datasets (an example dataset will also be provided for those who do not yet have their own to analyze).
Lecturers:
Dr. Brent Mishler, University of California, Berkeley, USA
Dr. Joel Nitta, University of Tokyo, Japan
Dr. Israel Borokini, University of California, Berkeley, USA
Additional lecturers: TBA
The course programme in brief:
Monday (June 5): Full day journal club; presenting and discussing spatial phylogenetics papers; critical thinking.
Tuesday (June 6): Workshop focusing on data gathering and cleaning for both: (A) spatial data and (B) phylogenetic data, then dealing with ways to combine them (“the OTU problem”) and to represent ranges (niche modeling vs. simple occurrence data, etc.). AM: short practical talks and discussions. PM: hands-on activities (assembling/augmenting their own datasets).
Wednesday (June 7): Workshop focusing on spatial phylogenetic analysis; alpha- and beta-diversity measures; looking for environmental drivers of special concentrations of biodiversity; conservation applications. AM: short practical talks and discussion. PM: hands-on activities (analyzing their own datasets if possible, or an example dataset to be provided) using Biodiverse and R.
Credits: The program is equivalent to 1 ECT for participants who complete an assignment graded as "pass/fail". ForBio will provide certificates for those successfully completed the course assignment.
Financial aid: ForBio will cover travel costs, accommodation, and subsistence for students/researchers affiliated to Norwegian universities. Other applicants will need to secure their own funding. There is no course fee.
Registration and selection process: Please fill in the online application here. ForBio reserves the right to give priority to PhD candidates having their research focus on relevant topics for the course.
Application Deadline: Closed
Max number of participants: 10
Target Group: PhD students, master students, postdocs, researchers
Working Language: English
Course organizers:
ForBio contact:
Micah Dunthorn, Quentin Mauvisseau
Support: This workshop is funded in part by the Peder Sather Grant Program