Selected Publications

We develop a novel, yet simple, Bayesian approach to combine genetic data with stable isotope data and use habitat suitability inferred from eBird occurrence data. The method is implemented in the R package gaiah, available from CRAN. We use gaiah to infer the breeding location of migratory Wilson's Warblers.
In: Methods in Ecology and Evolution online:early.
Details doi-link github dryad

We develop a procedure to reliably score tetraploid genotypes of green sturgeon using Fluidigm SNP assays. Individual alleles cannot always be resolved, but genotype categories can be. We show how such categories can be used for population assignment, inference of population structure, and individual identification.
Details doi-link github dryad

We develop a computational framework for addressing pedigree inference problems using small numbers (80-400) of single nucleotide polymorphisms (SNPs). Our approach relaxes the assumptions, which are commonly made, that sampling is complete with respect to the pedigree and that there is no genotyping error. It relies on representing the inferred pedigree as a factor graph and invoking the Sum-Product algorithm to compute and store quantities that allow the joint probability of the data to be rapidly computed under a large class of rearrangements of the pedigree structure. This allows efficient MCMC sampling over the space of pedigrees, and, hence, Bayesian inference of pedigree structure.
In: Theoretical Population Biology 107:39–51.
Details doi-link github

Recent Publications

More Publications

  • Ecological genomics predicts climate vulnerability in an endangered Southwestern songbird. (in press)

    Details

  • Genotyping-by-sequencing of genome-wide microsatellite loci reveals fine-scale harvest composition in a coastal Atlantic salmon fishery. (2018)

    Details doi-link

  • Genomic divergence across ecological gradients in the Central African rainforest songbird (Andropadus virens). (2017)

    Details doi-link dryad

  • Genetic assignment with isotopes and habitat suitability (GAIAH), a Migratory Bird Case Study. (2017)

    Details doi-link github dryad

  • Genetic and individual assignment of tetraploid green sturgeon with SNP assay data. (2017)

    Details doi-link github dryad

  • Purging putative siblings from population genetic data sets: a cautionary view. (2017)

    Details doi-link github

  • Abundance estimates and confidence intervals for the run composition of returning salmonids. (2017)

    Details doi-link github

  • parallelnewhybrid: an R package for the parallelization of hybrid detection using NEWHYBRIDS. (2017)

    Details doi-link

  • Close-kin mark-recapture. (2016)

    Details doi-link

  • Bayesian pedigree inference with small numbers of single nucleotide polymorphisms via a factor-graph representation. (2016)

    Details doi-link github

Recent & Upcoming Talks

Recent Posts

More Posts

My mind has just been blown. I have been drinking Hadley’s tidyverse Kool-aid for a couple of years now. I’m just wrapping up a seminar in UCSC’s Ecology and Evolutionary Biology Department on reproducible research. One thing that ecologists always want to do is make nice maps of their study sites. Further, spatial data is now a lot easier to come by and can provide a lot of meaninful inference.

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I used to have a virtual Windows machine set up on my Mac laptop and I would use that for compiling programs up for Windows, and testing things on the Windows side. That laptop was replaced, so I had to set up a new environment for cross compiling. My goal in this is to have to deal with Windows as little as possible, and, when I am in the Windows environment, try to use tools that are familiar (i.

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People here at the SWFSC have started using stacks to process ddRad data. They can output data from stacks in genepop format, and sometimes the want to convert that into the format that is useful for slg_pipe. I would typically have done that sort of thing using sed and awk, but I thought I would give a whirl at doing it in R. Below is a function I wrote for Martha.

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Marc Mangel is offering a course in Quantitative Fisheries at NMFS’ Southwest Fisheries Science Center (where I work). Having spent the fall delivering a course about using R to my NMFS colleagues, I thought it would be fun to sit in on Marc’s class. What a great opportunity! I just think it is the coolest thing that Marc is part of our community, and is willing to provide this enjoyable and useful education for us!

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Roy M and I were curious about how one might go about efficiently and quickly plotting big rasters like sea surface temperature data using ggplot with nice coastlines in there, etc. I had considered using ggmap. For reasons to do with the mercator projection of the base map in ggmap the word on the street is that this doesn’t work very well. I regularly crashed my whole R session trying it, too!

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Projects

Projects Under Construction

Still working on inserting info about the boatload of projects we are cooking up…

Rockfish Recruitment

Studying larval recuitment of kelp rockfish

Bird Genoscape

Mapping the flyways of America

rubias

Computationally efficient genetic stock identification in the tidyverse.

Teaching

Though my main appointment is at the National Marine Fisheries Service, I do get to teach a bit. Lately I have been teaching full-length courses or seminars in reproducible research methods and data analysis to colleagues and ecology students. I also get to guest lecture occasionally.

Quarter-courses:


Recent Guest Lectures

  • UCSC. Math 115. Graph Theory. Gave a guest lecture to Richard Montgomery’s Graph Theory course about applications of graphs in statistical inference in genetics. You can download my slides and also the accompanying narrative from GitHub. Winter 2016.


Summer Institute in Statistical Genetics


Conservation Genomics Workshop, Flathead Lake Biological Station

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