Sherlock Holmes Of Fruit Fly Genes
A Genetic Trigger For The Cambrian Explosion Unraveled
A team of scientists led by young Croatian evolutionary geneticist Tomislav Domazet-Lošo from Ruder Boškovic Institute (RBI) in Zagreb, Croatia, developed a novel methodological approach in evolutionary studies. Using the method they named ‘genomic phylostratigraphy’, its authors shed new and unexpected light on some of the long standing macroevolutionary issues, which have been puzzling evolutionary biologists since Darwin.
Tomislav Domazet-Loo, young evolutionary geneticist from Ruder Bokovic Institute in Zagreb, Croatia (Credit: Image courtesy of Rudjer Boskovic Institute)
The only direct method of research in evolutionary history involves analyzing the fossil remains of once living organisms, excavated in various localities throughout of the world. However, that approach often cannot provide the full evolutionary pathway of some species, as it requires uncovering of many fossils from various stages of its evolutionary history. As the fossil record is imperfect, the evolution research fundamentally hinges on luck factor in discovering the adequate paleontological sites.
However, the RBI team proposed a novel and interesting approach to bypass this obstacle. Namely, they suggested that the genome of every extant species carries the ‘snapshots’ of evolutionary epochs that species went trough. What’s even more important, they also developed the method which enables evolution researchers to readily convert those individual ‘snapshots’ into the full-length ‘evolutionary movie’ of a species.
Applying their new methodology on the fruit fly genomic data they tackled some of the most intriguing evolutionary puzzles – some of which distressed even Darwin himself. First, they demonstrated that parts of the living organism exposed to the environment – so called ‘ectoderm’ – are more prone to evolutionary changes. Further, they explained the evolutionary origin of the ‘germ layers’, the primary tissue forms that form during the first days after the conception of a new animal, and from which subsequently all other tissues are developed. Finally, they discovered the potential genetic trigger for the ‘Cambrian explosion’, a major global evolutionary event on the planet, when some 540 million years ago almost all animal forms known today suddenly ‘appeared’.
The first public lecture on these findings will be given by dr. Domazet-Lošo on September 4th at 5. ISABS Conference in Forensic Genetics and Molecular Anthropology, held in Split, Croatia. The groundbreaking paper fully presenting the theory of genomic phylostratigraphy will appear in the November issue of ‘Trends in genetics’, the most established monthly journal in Genetics.
Reference: Domazet-Lošo, T. et al. (2007) ‘A phylostratigraphy approach to uncover the genomic history of major adaptations in metazoan lineages’. Trends in Genetics (to appear in the November 2007 issue of the journal)
Genome Res. 2003 Oct;13(10):2213-9.
An evolutionary analysis of orphan genes in Drosophila.
Institut für Genetik der Universität zu Köln, 50931 Köln, Germany.
Orphan genes are protein-coding regions that have no recognizable homolog in distantly related species. A substantial fraction of coding regions in any genome sequenced consists of orphan genes, but the evolutionary and functional significance of orphan genes is not understood. We present a reanalysis of the Drosophila melanogaster proteome that shows that there are still between 26% and 29% of all proteins without a significant match with noninsect sequences, and that these orphans are underrepresented in genetic screens. To analyze the characteristics of orphan genes in Drosophila, we used sequence comparisons between cDNAs retrieved from two Drosophila yakuba libraries and their corresponding D. melanogaster orthologs. We find that a cDNA library from adults yields twice as many orphan genes as such a library from embryos. The orphan genes evolve on average more than three times faster than nonorphan genes, although the width of the evolutionary rate distribution is similar for the two classes. In particular, some orphan genes show very low substitution rates that are comparable to otherwise highly conserved genes. We propose a model suggesting that orphans may be involved in the evolution of adaptive traits, and that slow-evolving orphan genes may be particularly interesting candidate genes for identifying lineage-specific adaptations.
PMID: 14525923 [PubMed – indexed for MEDLINE]
J Mol Evol. 2004 Dec;59(6):771-9.
Correlated evolution of synonymous and nonsynonymous sites in Drosophila.
Institute of Cell, Animal and Population Biology, University of Edinburgh, Edinburgh, EH9 3JT, Scotland, UK.
Recent work has shown that Drosophila melanogaster genes with fast-evolving nonsynonymous sites have lower codon usage bias. This pattern has been attributed to interference between positive selection at nonsynonymous sites and weak selection on codon usage. Here we have looked for this correlation in a much larger and less biased dataset, comprising 630 gene pairs from D. melanogaster and D. yakuba. We confirmed that there is a negative correlation between the rate of nonsynonymous substitutions (d(N)) and codon bias in D. melanogaster. We then tested the interference hypothesis and other alternative explanations, including one involving gene expression. We found that d(N) indeed correlates with the level of gene expression. Given that gene expression is a strong determinant of codon bias, the relationship between d(N) and codon bias might be a by-product of gene expression. However, our tests show that none of the hypotheses we consider seem to explain the data fully.
PMID: 15599509 [PubMed – indexed for MEDLINE]