Drosophila
evolgen | November 7, 2007What happens when I mention a paper describing two more Drosophila genomes? Well, I get a comment telling me that the 12 Genomes Papers have gone live over at Nature. They have provided a nifty 12 Genomes Portal for us to navigate the articles published by Nature based on data from the 12 Genomes Project. Now, these aren't the only papers published from the 12 Genomes Project -- look for 12 Genomes Papers in the November issues of Genetics (currently not web-available), PLoS Genetics (also not up on the website), and the December issue of Genome Research.
The 12 Genomes Papers include two…
evolgen | November 7, 2007The world of genomics is changing. It was initially about sequencing the genome a single representative individual from a particular species. Now, there's a large focus on polymorphism -- that is, sequencing multiple individuals from a single species to study the genomic variation in that species. That's well under way in humans, with HapMap and various other projects designed to generate DNA polymorphism data on a genome-wide scale.
That approach has made its way to Drosophila genomics with the publication of a paper describing polymorphism across the entire genome of D. simulans, a sibling…
evolgen | October 5, 2007Previous entries:
Part 1 - Introduction
Part 2 - The Backstory
Part 3 - Obtaining Sequences
This post is part of a series exploring the evolution of a duplicated gene in the genus Drosophila. Links to the previous posts are above. Part 4 of this series (Obtaining More Sequences) can be found below.
Obtaining More Sequences
Last time we downloaded sequences for both aldolase genes from Drosophila melanogaster (see here). But, if we want to study the evolution of these genes, we need sequences from a few more species. There are now complete genome sequences available for 12 Drosophila species…
evolgen | October 3, 2007Previous entries:
Part 1 - Introduction
Part 2 - The Backstory
This post is part of a series exploring the evolution of a duplicated gene in the genus Drosophila. Links to the previous posts are above. Part 3 of this series (Obtaining Sequences) can be found below.
Obtaining Sequences
In the previous post I described the aldolase gene family, which encode proteins involved in cellular respiration. There are two aldolase genes in the Drosophila melanogaster genome. If we want to study the evolution of these genes, we can obtain the sequences from the 12 Drosophila species that have had their…
evolgen | October 1, 2007This is a repost (with some edits) of an introduction to publishing original research on blogs -- a series I am reintroducing. The original entry can be found here.
Previous entries:
Part 1 - Introduction
This post is part of a series exploring the evolution of a duplicated gene in the genus Drosophila. Links to the previous posts are above. Part 2 of this series (The Backstory) can be found below.
The Backstory
The reason you and I and all other animals (and most other forms of life) can do things (like live) is because we combine oxygen with sugars to make energy. Eventually, the oxygen…
evolgen | September 16, 2007Carl Zimmer has a post covering three recent papers on gene duplication: one on amylase variation in humans, one on whole genome duplication in yeast, and one on duplications of genes in the Drosophila arizonae reproductive tract. In all three papers, results are presented showing the importance of duplicated genes in adapting to the environment.
Now, gene duplication isn't anything new around these parts. Those who know me know that I have a bit of an interest in gene duplication. Those who don't, well, consider yourself informed that I have a bit of an interest in gene duplication.
Given…
evolgen | September 6, 2007Among my many pet peeves are when people refer to Drosophila as fruit flies (they are not). Real fruit flies (Tephritids) feed, mate, and lay their eggs on live fruit -- for this reason, many are agricultural pests (e.g., the medfly). Drosophila, on the other hand, feed on the micro-organisms found primarily on rotting fruit or other rotting plant parts. For this reason, I like to think of Drosophila as one of the most refined insects because they prefer fermented sugars (like beers and wines).
While the majority of Drosophila feed on rotting plant material, some have found an even more…
evolgen | August 31, 2007Genome rearrangements are fast becoming one of the most interesting aspects of comparative genomics (I may be slightly biased in my perspective). We have known for quite some time that genomes of different species (and even within species) differ by inversions of their chromosomes (this was first studied in Drosophila). In fact, some of the early work on the evolutionary relationships of species was done using chromosomal rearrangements. Additionally, there's a whole lot of important biological implications of rearrangements, including speciation, human disease, and the function of genes…
evolgen | July 22, 2007Mark Liberman at Language Log has been posting on genetics recently. A couple of days ago he tried to track down the origins of the components of the gene name BTBD9. The letters and numbers in the name stand for complex-tramtrack-bric-a-brac-domain 9, which are hijacked from Drosophila nomenclature. Liberman then tries to figure out the origins of the names tramtrack and bric-a-brac using FlyNome (a cool webpage that I hadn't seen before) and FlyBase. In the end, he couldn't track down the (clever) story behind either one.
I was amused by that post, and I was further impressed by Liberman's…
evolgen | June 22, 2007
Sensing and reacting to one's environment is necessary for survival. Different species have different expertise in regards to how they sense their environment. Humans, for example, have reduced olfactory abilities relative to other mammals, but excellent color vision. Cats have good night vision, but poor vision during day light. These proficiencies and deficiencies in sensory abilities hold for non-mammalian taxa as well.
Olfaction and taste have been well studied in a variety of taxa. Amongst the invertebrates, the genes responsible for olfaction and taste in Drosophila are one of the best…
evolgen | June 1, 2007In a new article in PLoS ONE, a group of researchers led by Kevin Edwards present a collection of images of Hawaiian Drosophila wings. Here's one figure from the paper showing the evolutionary relationships of a bunch of different clades and some representative wing patterns:
The authors point out that, with the availability of the Drosophila grimshawi genome sequence, biologists can now use molecular techniques to understand the genetic changes that give rise to the various pigmentation patterns.
Edwards KA, Doescher LT, Kaneshiro KY, Yamamoto D. 2007. A database of wing diversity in the…
evolgen | May 14, 2007
The Canadian research organization Genome BC has unveiled a science education website, Genomics Education. One of the features of the website is Floyd the Fruit Fly, who, we can only presume, is some sort of cartoon drosophilid. Or maybe he's a tephritid, but I highly doubt it. When you hear "fruit fly" and "genetics", you think Drosophila, even if they really aren't fruit flies.
In the accompanying illustration, we see Floyd with smelly feet. Apparently, Floyd thinks that his foot stank is due to mitosis. He then learns, via a disembodied voice backed up by a soundtrack from an early Ron…
evolgen | May 2, 2007Spring is in the air. The obvious signs are everywhere: the temperature is rising, the flowers are blooming, and everyone's writing about boners. There's this post from Darren Naish on turtle gonads, and Carl Zimmer has an article on duck phalluses (don't call them penises, as Darren explains) in the NYTimes (and a blog post advertising it). Carl's article summarizes the findings of this study. The basic story is that some ducks have really big penis-like structures (penises are unique to mammals, so a bird schlong is called a phallus), and the females have crazy reproductive organs to match…
evolgen | April 27, 2007The most recent issue of the Journal of Heredity contains a bunch of articles from a symposium on the "Genetics of Speciation" organized by Loren Rieseberg. Included in the collection is an article by Allen Orr and two of his students on speciation in Drosophila, which discusses mapping speciation genes, the role of meiotic drive in speciation, and Dobzhansky Muller incompatibilities via gene translocation (the latter two are the topics of recent papers from Orr's group -- here and here). Also in the special issue is an article from Mohamed Noor's lab on mapping inversion breakpoints between…
evolgen | April 19, 2007On yesterday's episode of Mythbusters they tested the myth that birds in a trailer decrease the weight of the trailer when the birds take flight. The 'busters put a bunch of birds into a trailer, weighed the trailer + birds, and then allowed the birds to fly in the trailer, measuring the weight every fraction of a second. The myth was rejected because, while the weight fluctuated a fair bit, the mean weight remained the same before and after the birds took flight.
When a bird (or anything else that flies) gets airborne, it must exert a downward force equal to its weight. The weight of the…
evolgen | April 18, 2007Dan Hartl was inducted into the National Academy of Sciences of the USA in 2005 for his contributions to the field of evolutionary genetics. His inaugural article as an Academy member was published this week in the Proceedings of the National Academy of Sciences (PNAS, pronounce pee-nas, hehe). Hartl and colleagues compared levels of polymorphism in 91 genes from Drosophila melanogaster with divergence from D. simulans. They were interested in determining the effect of natural selection on nonsynonymous mutations, kind of like what was done in this paper (reviewed here).
Hartl and colleagues…
evolgen | April 11, 2007Those of us who work on non-human systems often grumble about the total disregard human geneticists (that's geneticists who study humans, not humans who are geneticists) have toward non-human research (that's research on non-humans, not non-humans doing research). I get the feeling that plant biologists have the same attitude toward non-plant researchers, and I imagine there is some unwritten chain of superiority wherein you must pay respect to the researchers working on a system "above" you and ignore the research done on a system "beneath" yours -- and, yes, I realize the higher and lower…
evolgen | April 11, 2007Not all regions of the genome are equal in the eyes of evolution. For example, natural selection is more effective on genes in regions of higher recombination. We have known this for a while. The connection between recombination rate and natural selection was nicely refined when it was shown that DNA polymorphism is lower in regions of low recombination and higher in regions of high recombination (see Begun and Aquadro). This could be due to higher mutation rates in regions of high recombination (and vice versa), greater reach of selective sweeps in regions of low recombination (the…
evolgen | March 15, 2007This post is part of a series documenting Professor Steve Steve's recent visit to Philadelphia for the Drosophila Research Conference (aka, the Fly Meeting).
Professor Steve Steve had a wild Saturday night. He was quite happy to have met leaders in the fields of evo-devo, population genetics, and genomics. Of course, Steve Steve is a pioneer in popula-devo-geno-metrics, so everything that came up in discussion was old-hat to him. That said, it was definitely a night to remember. And a morning to forget.
Pictures of Steve Steve at the Sunday plenary session and on the drive home can be found…
evolgen | March 14, 2007This post is part of a series documenting Professor Steve Steve's recent visit to Philadelphia for the Drosophila Research Conference (aka, the Fly Meeting).
In the previous two installments of Steve Steve in Philly, we finally managed to meet up despite the best efforts of the staff at the Marriott to prevent our rendezvous, and we got Steve Steve up to date on the newest developments in fly pushing and Drosophila genetics. It had been quite a tiring day, so we ventured down to the hotel bar for a few drinks. Some of us were ready to hit the sack, but Steve Steve would have none if it; he…