Friday, March 30, 2012
Cryptic genetic variation promotes rapid evolutionary adaptation in an RNA enzyme (Hayden et al, Nature, 2011)
Tuesday, March 20, 2012
Reptiles had major evolutionary novelty: development of amniotic egg, which enabled breeding outside of the water. Until recently, only available genomes from the reptilian lineage were coming from the birds, therefore this paper and accompanying data provides a very valuable resource for further analysis of amniote evolution.The different aspects of lizard genome that were considered:
- transposable elements
- microchromosomes and synteny
- GC content
- sex determination system
- egg protein evolution
- adaptive radiation/ecology
Around 30 percent of the lizard genome consists of transposable elements. It is fascinating that unlike in mammals and birds, there is much higher variety of active elements in the lizard genome, but also low rate of their accumulation. When the authors compared the mammalian conserved elements with the lizard genome, they found that several of these elements originate from transposable elements found in the lizard genome. The authors used the term exaptation to describe the process how certain mobile elements that were active in the amniote ancestor have putative function in mammals (most probably as regulatory elements). During the discussion we agreed that this term is not so appropriate since it would imply that the mobile elements had a function in the genome from the beginning (the time of insertion), which is not the case.
Another suprising finding in the paper is high synteny between chicken and lizard chromosomes, 19 out of 22 (anchored) chicken chromosomes are each syntenic to a single lizard chromosome over their entire length, whereas only 6 human chromosomes are syntenic to a single opossum chromosome. These findings are in contrast to what would be expected when considering the time of the divergence, 148 million years for human-opossum versus 280 million years since chicken-lizard divergence. The authors did not discuss putative reasons why this is the case. Moreover, it is characteristic for the reptiles to have microchromosomes. Amazingly, all lizard’s microchromosomes align to microshromosomes in the chicken implying that these chromosomes probably emerged in the reptile ancestor.
When looking at the GC content in the lizard genome there is local variation. However, when comparing syntenic regions from lizard, chicken and human, it is obvious that lizard genome lacks GC isochores. It is interesting to see that the mean GC content in all three species is very similar, but the lizard has more homogenous distribution.
It was known previously that this particular anole species has genetic sex determination, but it was not known which system was used XY or ZW. By performing FISH analysis, authors could see that X chromosome is present in 2 copies in female and one in the male indicating XY system. Unfortunately, they were not able to determine the Y chromosome, although they hypothesis it exists since males and females have the same number of chromosomes. Moreover, they did not identify lizard sex determining gene.
There were 17 172 protein-coding genes found in the lizard genome. It was found that the lizard has lineage specific duplications of various egg proteins. When comparing egg proteins vs. non-egg proteins in orthologues between the chicken and the lizard, dN/dS ratio is higher for the egg proteins suggesting reduced purifying selection and/or positive selection. This finding is not so surprising since it was previously known that sex and reproduction related proteins are one of the fastest evolving proteins. Additionally, 11 opsin genes were found supporting the notion that the lizards have excellent colour vision which is very important in sexual selection and species recognition.
Anole lizard represents a textbook case of adaptive evolution. By designing primers based on the sequenced genome, researches sampled 20 kb sequence datasets from protein coding and noncoding regions from 93 species of anoles. The analyses of these sequences confirmed previous notion based on morphological and molecular data that ecomorphs evolved independently on each island. Moreover, it shed light on the order of colonization events that took place.
Although in the beginning of the discussion there was an opinion that maybe the article addressed many different topics without going into depth, after discussing further the general opinion was changed. Since it is a genome paper, there is already a great effort invested in assembling the genome and conveying basic analysis. This article went even further adding a lot of additional analysis and experiments to contribute to our understanding of lizards, reptiles and consequently the amniote evolution.Alföldi, J., Di Palma, F., Grabherr, M., Williams, C., Kong, L., Mauceli, E., Russell, P., Lowe, C., Glor, R., Jaffe, J., Ray, D., Boissinot, S., Shedlock, A., Botka, C., Castoe, T., Colbourne, J., Fujita, M., Moreno, R., ten Hallers, B., Haussler, D., Heger, A., Heiman, D., Janes, D., Johnson, J., de Jong, P., Koriabine, M., Lara, M., Novick, P., Organ, C., Peach, S., Poe, S., Pollock, D., de Queiroz, K., Sanger, T., Searle, S., Smith, J., Smith, Z., Swofford, R., Turner-Maier, J., Wade, J., Young, S., Zadissa, A., Edwards, S., Glenn, T., Schneider, C., Losos, J., Lander, E., Breen, M., Ponting, C., & Lindblad-Toh, K. (2011). The genome of the green anole lizard and a comparative analysis with birds and mammals Nature, 477 (7366), 587-591 DOI: 10.1038/nature10390