Research Data

Repository of research data used by MLML researchers. Includes data for both public access and internal use.

California Collaborative Fisheries Research Program
California Collaborative Fisheries Research Program (CCFRP) worked with central California fishing communities to develop monitoring protocols for the use of hook-and-line fishing gear, to collect baseline information on California marine protected areas (MPAs).
GenBank sequences that are believed to be the COI gene
COARBitrator_1.0.fa is a fasta file containing GenBank sequences that are believed to be the COI gene. Deflines contain GI and organism, delimited by spaces. All sequences are annotated as being either COI or a synonym, have substantial similarity to known COI sequences, and contain a COI conserved domain. Sequences were auto-curated by an adaptation of the ARBitrator algorithm (Heller et al., 2014). No representation is made regarding sensitivity or specificity of the adapted algorithm. Questions to
Monterey Harbor Invasive Species Fouling Experiment
For each experiment (corresponding to the two chapters found in the thesis), photos were taken in duplicate (or more if conditions were poor) every two weeks. Photos were taken with a Panasonic Lumix TS20 Waterproof camera. Photos were named with the date, block number, position in the block, treatment number, and time. For example, 2012-06-30 3B.3E.44.T0 is a photo of sample 44 in block 3 at time zero. In Chapter 1 the treatments were originally replicated by block (blocks had an A and B just for manageability of setup); however, analysis showed that the treatments varied too much between replicates so consider treatment number simply as sample number. In Chapter 2 not all photos were used in the analysis and were not named. They are still organized by block. In my thesis these photos were analyzed for percent bare space, species richness, and percentage of native versus non-native. Species that were visible were identified and primary cover was not accessed (ie species directly attached to substrate) in cases where there were multiple layers of cover. See thesis for more detailed methods., June 2012- April 2013