Link to my github page

My github page (https://github.com/kyleaoconnell22) has a few repositories now with mostly Python scripts for manipulating data and running analyses related to target-capture projects. The primary repositories are ‘Exome Capture Probe Design‘ which is the pipeline I used to design capture probes from three transcripts of parachuting frogs (genus Rhacophorus). Next I have ‘Probe Design Plethodon‘,…

Awarded GGI Peer Grant for $9,086 to work on whipsnakes!

Along with Dr. Ed Myers at the National Museum, I was awarded a $9,000+ research grant to resolve the phylogeny of North American whipsnakes (genus Masticophis). We are using a target capture approach to sequence over 5,000 loci with complete population-level sampling to hopefully sort out what has been a very difficult phylogenetic problem. Both…

A short review on inferring ancient hybridization

The government is still shut down…so here is a post on ancient hybridization A lot of recent attention has been given in high profile journals to empirical examples of ancient hybridization. In this post I give a short background on the issue, highlight two recent papers, and then outline a few of the methods used…

The two-minute rule: a follow up to advice for graduate students

Someone pointed out to me this week that we all know how to be good writers, but the challenge is to actually apply these principles to our lives. I suppose writing is like anything else that people struggle with, like eating well or exercising. I recently listened to a great episode of the Entreleadership podcast…

Generate TreeMix input file

I struggled for several days to find an easy way to convert my sequence capture data to TreeMix format, but it turns out, it is not that hard after all. The general idea is to get your SNPs into vcf format, then use the populations script in STACKS to convert vcf to TreeMix. It’s that…

More advice for graduate students

Since writing the last post, I have had a few additional ideas about advice to graduate students. Generally, these thoughts apply to any job in the academy. Also, I acknowledge that I am a postdoc, and therefore not ultimately an expert in these things. Yet I think these ideas will keep me in good stead…

Advice to graduate students

When I finished my PhD last year, I had this amazing clarity about the three steps to finishing a successful PhD. I imagined that one day in the future, when my beard is grayer, that I would give the keynote speech at some conference and I would lay out these concise points that would help…

Research Update

Things have been moving right along at the museum! I just had a paper accepted in Ecology and Evolution about the effects of including related individuals in population and landscape genetic analyses. I will write more about this once the paper comes out! I also have another paper in review about bent-toed gecko biogeography on…

Since coming to DC

Things have been going well for me since I came to DC! Not only do my wife and I get to visit awesome museums each week, cars try to run me over less than in Texas, and the food is amazing! At the museum I was awarded the Global Genome Institute Peer Research Award for…