29 June 2011
28 June 2011
The staphylinid subfamily Pselaphinae is a species rich group of roughly 9,000 species. This subfamily was once considered a family of its own. The life history of Pselaphinae are poorly known though most are thought to be predaceous. Pselaphinae are called ant-loving beetles because many species are inquilines of ant nests but many other species are found in leaf litter and other organic detritus. The one pictured below was extracted from a berlese funnel loaded with decaying wood. The wood was from a local park in Arligton, Texas. The photo was taken using a microscope in our lab and the attached nikon ccd. Once I took the picture I followed a lot of the directions that were given in a recent article in the Scarab Newsletter by Jocelyn Gill
. She does a great job describing the process that she uses to producer her photos for Henry Howden. She describes the whole process step by step in Photoshop. However, I was able to follow along and do most of what she mentions using GIMP.
09 June 2011
His team collected a pair of beetles from a population known to exhibit phosphine resistance and began line breading them. After 4 generations these beetles were split into two pools. One pool was exposed to phosphine and 20 of those that survived were pooled and sequenced. The other pool of beetles were sequenced without testing for phosphine resistance. The idea behind this method is that the gene of importance will be segregating in the untested population but fixed in the selected population. This means that you can compare the SNP frequency in the two pools ideally you would see 100% in the tested population and some smaller frequency in the untested population.
The actual picture that you get when you look at the data can be a bit more complicated. It ends up that at least in this case there are a lot of random SNPs that segregated in one pool or the other to avoid this complication he used a sliding window analysis with a width of 300 bp to identify regions that are important in the phenotype of interest.
The end of this story is that David and his group were able to identify 2 loci responsible for the posphine resistance. As an added benefit this research even helped improve what we know about the Tribolium castaneum genome. It ends up that the one of the SNPs mapped to one of the unassigned contigs. Thanks to this research we know exactly were this contig belongs.
Today was the last day of the International Tribolium Meeting and tonight we had the opener for the Arthropod Genomics Symposium Meeting. It was opened up with a talk by Kevin Hackett from the USDA he talked about the strategy behind the 5,000 arthropod genome project. This was kind of a cool speech. No power point or anything just 30 minutes of what he thinks we could gain by banding together and organizing our efforts as much as possible. He ended it with a couple of sci-fi refs which is never a bad thing.
However, by far my favorite talk was from Daniel Bopp from the University of Zurich. He discussed what he has uncovered about the determination of sex in coleoptera (tribolium). His results showed that much of the same machinery seems to be used in tribolium as is used in drosophila, with some signifigant changes for instance in sxl. What was really exciting to me was that his talk gave me some ideas about what might be underlying the odd distribution of sex chromosomes in coleoptera.
Fun first day at my first conference!
07 June 2011
I think that Arthropod Genomics will be pretty cool. We are going to have two days of just Tribolium talk (it’s the model organism in our lab) and then the rest of the time will be broader with people studying everything you can imagine. It will also be nice to meet more people and be able to start connecting faces to all the names that I read in papers. I hope to make posts most days giving a recap of the most interesting research that I hear about. I'm off to Kansas City.
04 June 2011
David and Wayne Maddison the developers behind MacClade and Mesquite are shifting their efforts away from MacClade which will not work under MacOS X Lion. Because of this they have decided to release MacClade for free. This a great phylogenetics software that is largely gui driven and is a little easier to learn than some of the more common command line only alternatives out there. The manual by itself is actually a pretty handy resource since it includes a lot of theory as well as examples.
03 June 2011
I read an interesting paper from this book today. The book Natural Selection and Beyond: The Intellectual Legacy of Alfred Russel Wallace looks like a really great collection of papers. I feel like I know as much about Wallace as your average biologist but looking at the table of contents and reading the introduction shows me that there was a lot more to this man than what we often remember.
Thanks to the generosity of the author (Andrew Berry), I have read the first paper “Ardent Beetle-hunters”: Natural History, Collecting and the Theory of Evolution. The title of the paper comes from a speech that Wallace gave on the 1st July 1908 at a meeting of the Linnean Society. Wallace credited this commonality between he and Darwin as being key in their independent development of natural selection as the process driving evolution. The author points out that both of these scientist were more than just your typical naturalists. Wallace and Darwin were gifted and were able to learn to recognize an amazing breadth of biological diversity with great rapidity. Both naturalists also had the experience of learning a limited temporal fauna which could act as a framework for organizing the vast number of new species they would discover when they traveled. I think that Wallace makes an important point in his speech when he says that he and Darwin were “collectors ... of a speculative turn of mind...constantly led to think upon the why and the how of all this wonderful variety” This ability to ask the right question is so important in science. Often a groundbreaking research begins not as an amazing epiphany but an insightful question that you struggle to answer. That struggle which in the case of natural selection lasted for years with Darwin can then lead to an amazing epiphany.
Berry's conclusion is that it was the fortuitous combination of a natural gift, exposure to a diverse group organisms (beetle collecting) and an ability to synthesize information that led to the great discoveries of Darwin and Wallace. Berry also reminds us that this pattern is not unique it is the pattern of a number of great biologists like E.O. Wilson and Ernst Mayr.
Finally the paper includes a quote that I love. It is from T.H. Huxley who after reading Origin said “How extremely stupid not to have thought of that!” If a scientist like Huxley can feel that way then maybe I should feel a little better as I struggle to come up with an amazing groundbreaking dissertation topic.
02 June 2011
The National Academies Press is making a great many of their titles available free as PDF files. For a poor grad student like myself this is awesome. I have already downloaded my first book: Systematics and the Origin of Species: On Ernst Mayr's 100th Anniversary. The site also has a lot of other really good books like the In the Light of Evolution series. I hope you find something good to read.
01 June 2011
I will sit for my comps in a little less than a year. At my school PhD comps include a written and a oral portion. About six weeks before the big date each person on my committee of five professors will give me two questions. In theory one of these will be closely related to my own research interests while the other will be a broader question. I'll have a few weeks to compose my answers to these questions which I will then return to my committee members. After they have had a chance to review my answers we will have the oral portion of the exam. Lately these seem to run around two hours. The questions that you are asked in this portion can be over just about anything but usually are weighted towards the students research interests.
To get ready for this I have made up a reading and study list to try and make sure that I know everything that I personally feel a person with a PhD in biology should know. I am probably over doing it but when else am I ever going to get to study so much across such a broad range of topics. Since I have a full year to prepare I can really cover an amazing amount of information.
Each morning I am reading and summarizing two article from my reading list. My list has about 250 articles plus another 40 or so book chapters. I put it together from reading groups and classes that I have had over the last year as well scouring a lot of online resources like:
(I'll post it later this week once it is cleaned up and alphabetized)
I am also reviewing Campbell and Reece a few hours each week. My main goal with it is to be able to explain most of the real groundbreaking experiments that allowed us to reach the level of understanding that we have today. I also feel like it covers some of the basic processes that are outside of my research area but that I should still be able to explain to someone else (photosynthesis, gene regulation, etc.)
On the entomology front I am reading two books. Each evening I read either Biology of Coleoptera by Crowson or The Evolution of Insects by Grimaldi and Engel.
I hope that this level of preparation is a bit more than most at my school and that it will allow me to fly through comps with no problem. I'd love to hear how anyone else who has already been through this process prepared for comps and how you felt about it once it was all said and done.