Posts Tagged ‘drosophila’

Sean Carroll, EvoDevo @ U.O.

May 5, 2009

Sean Carroll visited the University of Oregon over the past couple days.  He’s authored hundreds of research papers and several books on the subject of evolutionary biology.  Here is a brief summary of Sean’s visit. . .

Last night, Sean gave the fifth lecture in our Darwin series.  This was a public talk (for scientists and non-scientists alike) and Sean presented material from his latest book “Remarkable Creatures.” Specifically, he focused on the harrowing stories of Wallace, Darwin, and Bates sailing around South America and the Galapagos islands.  The greatest insight from this lecture was that Wallace and Darwin independently converged on the theory of natural selection.  I think their convergence testifies to the strength of the theory.

Today, Sean gave a technical talk (for the EvoDevo crowd) titled “Endless Flies Most Beautiful: Cis-Regulatory Sequences and the Evolution of Animal Form.”  Sean focused on the central EvoDevo question: How do forms (i.e. morphologies) evolve? He thinks an examination of mosaic pleiotropy is the key to answering this question.   Historically, gene duplication was thought to be the primary mechanism by which new forms evolved.  Sean cites Susumu Ohno’s classic book “Evolution by Gene Development.” However, Sean countered Ohno’s thesis by showing evidence that evolution might actually select against gene duplication.  As an example, the evolutionary history of anthropod and tetrapod Hox genes — a gene that is known to drive some morphologies —  is a story of gene loss, not gene duplication.

Later approaches to the EvoDevo question examined the role of protein sequence evolution, and then eventually King and Wilson examined the role of protein sequence expression.  Essentially, King and Wilson reduced the question “how do forms evolve?” to the micro-question of “how do cis-regulatory elements evolve?”  For the remainder of Sean’s talk, he focused on “cis-regulatory elements as the units of evolution.”

Before the EvoDevo community was examining regulatory elements, inter-species genetic analysis was typically occuring over large taxonomic distances.  This approach proved problematic because transcription factor binding sites are rarely conserved over large phylogenetic distances.  Consequently, the EvoDevo community was forced to find new systems for study.  Sean Carroll’s lab — for example — shifted focus away from studying butterflies and began investigating pigmentation diversity in Drosophila (see Nature, Trends in Genetics, and PNAS).  Unlike butterflies, Drosophila studies offered the ability to explore evolutionary mechanisms at a deeper mechanistic/genetic level.  Among many subsequent results, Sean’s lab discovered the Tan gene locus is responsible for  mosaic pleiotropy in Drosophila Santomea’s wing pigmentation.

Based on results from the Tan gene — and several other studies — Sean concluded that regulatory sequence evolution is the more likely mechanism of morphological change than the coding sequence itself (see PLoS Biology 2005).  Sean gave several examples to support this theory, including a story about the Engrailed gene: an ancient regulatory protein that was recently co-opted to control development of Drosophila wing spots.

Overall, this was an enlightening visit and I feel fortunate to be studying at a university that can engage this caliber science.  For more information, check-out The Carroll Lab.

Summary: Metagenomics, fruit flies, and lessons learned

December 6, 2007

On November 8th, Nature published two cool articles about metagenomic studies of twelve Drosophila (“fruit flies”) species. In the the first paper (click here), The Drosophila 12 Genomes Consortium (D12GG) compared the complete genomic sequences of the twelve Drosophila species, which included the model organism species Drosophila Melanogaster. Although the twelve species are related, they exhibit a surprising amount genetic biodiversity. For example, the evolutionary distance between D. Grimshawi and D. Melanogaster is the same distance as between humans and lizards. As a side note, six months earlier (in May 2007), PLoS Genetics published a similar metagenomic comparison of Drosophila (click here for the paper). In the PLoS paper, Hahn et al. present the (somewhat obvious) conclusion: “the apparent stasis in total gene number among species has masked rapid turnover in individual gene gain and loss.”

On November 8, Nature also published this paper (click here), in which Stark et al. (including Hahn) used the data from D12GG’s research to demonstrate a truly novel insight about the connection between conserved metagenomic sequence motifs and functional elements. The result of this paper allows us to infer the presence of functional elements with a accuracy far surpassing previous methods. Specifically, Stark et al. show how to infer the following functional elements, based on a metagenomic sample:

  • Protein-coding regions: have highly constrained condon substitution regions, and indels have a bias for multiples of three.
  • RNA genes: tolerate substitutions that preserve base pairing.
  • miRNA: can be detected by looking for conserved palindromic stem sequences, which mutable loop sub-sequences between the two palindrome pieces.
  • Regulatory motifs: have high levels of genome-wide conservation.
  • Post-transcriptional motifs: are typically strand-based conservations.

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