Paul Fine, Professor

Closed (1) Molecular phylogenetics of Protium (Burseraceae)

Closed. This professor is continuing with Fall 2018 apprentices on this project; no new apprentices needed for Spring 2019.

In this project, We aim to assess the evolutionary history of a widespread tropical plant lineage (Protium, Burseraceae). We have sampled many populations from different habitats throughout South America in order to investigate habitat-mediated speciation in tropical trees.



A major component of this project is the processing of plant leaf samples via DNA extraction and library prep for Next Generation Sequencing. As part of this project, the apprentice will have the opportunity to learn techniques in DNA extraction and DNA quantification. Furthermore, students will also have the opportunity to learn about population genetics and phylogenetics. As part of the DNA team, the student is expected to work at least 6 hours a week (ideally 8 hours a week) on sample processing, sample sorting, DNA extraction, DNA quantification and data entry. The main bulk of this work will be done at the Fine Lab and the Evolutionary Genetics Lab (VLSB).

Day-to-day supervisor for this project: Gabriel Damasco, Graduate Student

Qualifications: A strong interest in plants or evolutionary biology is required! Previous experience in molecular techniques is desired, but not essential.

Weekly Hours: 6-8 hrs

Related website: http://ib.berkeley.edu/labs/fine/Site/home.html

Closed (2) Molecular phylogenetics and phylogeography of the beaked hazelnuts (Corylus cornuta, Betulaceae)

Closed. This professor is continuing with Fall 2018 apprentices on this project; no new apprentices needed for Spring 2019.

The California hazelnut (Corylus cornuta var. californica), which occurs on the North American west coast has been considered to be the same species as the beaked hazelnut which ranges from Alberta to northern Michigan. However, it has several morphological differences. In this project, we will extract and sequence DNA from populations throughout the range of this taxon and determine the evolutionary relationships among populations and infer the historical biogeography.

extract DNA, PCR, and prepare PCR products for sequencing. Help to analyze sequencing results. participate in evaluating the taxonomy of the different hazelnut populations.

Qualifications: a strong interest in botany and molecular phylogenetic methods is required! past experience with DNA extraction or PCR is desirable.

Weekly Hours: 6-8 hrs

Closed (3) The role of climate and geology on the phylogenetic beta diversity patterns of Amazonian tree communities

Closed. This professor is continuing with Fall 2018 apprentices on this project; no new apprentices needed for Spring 2019.

In this project we aim to investigate the role of climatic variables and geology as drivers of lineages turnover of Amazon trees at a regionals and landscape scale. To date we have sampled every single individual above 10 cm of diameter at breast high in 80 one hectare plots in Ecuadorian Amazonia and we have taken soils samples as well. Together with climatic data from wordclim (an online database) we will use this information to investigate whether the climatic envelope or geology are the main driver of phylogenetic turnover in Amazon tree communities.

The student will help to sort botanical specimens as well as extract DNA, PCR, and prepare PCR products for sequencing. Help to analyze sequencing results. The student will gain training in Amazonian tree species identification based on dried sterile specimens and at the same time will learn methods for phylogenetic and beta diversity analysis.

Day-to-day supervisor for this project: Juan E. Guevara, Ph.D. candidate

Qualifications: A strong interest in botany and molecular phylogenetic methods is required, past experience with DNA extraction or PCR is desirable.

Weekly Hours: 6-8 hrs

Closed (4) Identification of tropical trees using drone images

Closed. This professor is continuing with Fall 2018 apprentices on this project; no new apprentices needed for Spring 2019.

We are experimenting with a new machine-learning technology to try to identify canopy trees using drone imagery. These techniques can be used to help estimate population sizes of trees important for human use or trees that have endangered conservation status.

We will learn how to use a program called qGIS and draw shapes around canopies of tropical trees. We will make a training dataset and see how well a new machine-learning program is able to automatically identify individuals of the same species. Students will analyze large screen images and pinpoint the GPS coordinates of known trees and draw shapes around the tree canopies.

Qualifications: interest in remote sensing or tropical tree identification.

Weekly Hours: 3-5 hrs

Related website: http://ib.berkeley.edu/labs/fine/Site/home.html