Friday, 6 July 2012

Research round-up

Unfortunately there has been little activity on the blog of late, mainly due to the small matter of getting my PhD thesis handed in, submitting manuscripts to journals, and finding a job etc! Having said that, I have been somewhat busy in other parts of the Web. Boopboops now has a sister Twitter feed for science related things (@boopsboops), and I have now coded up a Website promoting my CV, publications, and research skills etc, etc.

So, in absence of anything better, and as I've been meaning to do for a while, I thought I'd write about my favourite fish papers of 2009, 2010, and 2011.



(1) Larmuseau et al. (2009) To see in different seas: spatial variation in the rhodopsin gene of the sand goby (Pomatoschistus minutus). Molecular Ecology 10.1111/j.1365-294X.2009.04331.x


I like the idea of looking at how organisms adapt to their surroundings. This study compared variation in the rhodopsin visual pigment locus with phylogeographic patterns in "neutral" mitochondrial and microsatellite markers (i.e. likely to detect any population-genetic structure), and found that in the sand goby, the two were discordant. Variation in the rhodopsin gene (RHO/RH1/RHOD) was partitioned differently and corresponded to photic environment (light penetration, water turbidity etc). There were also signs of positive selection at sites coding for amino acid changes relevant to spectral adaptation.

It's also interesting to note that rhodopsin is a commonly used marker for phylogenetic studies, which is probably due to early studies on vertebrate visual systems providing easy to use primer sets. However, I would be cautious about its use now, as these apparent convergences due to environmental conditions may not give a good indication of common ancestry for a species tree!



(2) LavouĂ© et al. (2011) Remarkable morphological stasis in an extant vertebrate despite tens of millions of years of divergence. Proceedings of the Royal Society B 10.1098/rspb.2010.1639 


If you've ever kept a tropical aquarium, you may have seen the African butterfly fish (Pantodon buchholzi) lurking in the oddball tanks. They're indeed a strange fish and are great fun to keep, clinging to the surface and greedily snapping up any insects that you feed them. Pantodon buchholzi is the species in a monotypic genus and family, known from the Niger and Congo basins.

When their mitochondrial genomes were sequenced, the researchers estimated that the two isolated populations had diverged over 50 million years ago, despite looking almost identical in terms of shape and meristics!

Evolution is taking place on the DNA clearly, but not on the external anatomy it seems. The reasons as to why and how this has happened are fascinating. The authors state "Proposed mechanisms of morphological stasis include stabilizing selection, ecological niche conservatism and genetic and developmental constraints". I look forward to further studies on this.



(3) Mims et al. (2010) Geography disentangles introgression from ancestral polymorphism in Lake Malawi cichlids. Molecular Ecology 10.1111/j.1365-294X.2010.04529.x


The cichlid flocks of the African Rift Lakes are an almost extreme opposite example to the one presented above. There is huge phenotypic diversity, but often very little in the way of molecular differences. The mbuna cichlids Labeotropheus fuelleborni and Metriaclima zebra, are quite different in appearance, but share mitochondrial DNA haplotypes typical of very recently diverged, or hybridising species. The authors also report "greater mtDNA differentiation among localities than between species".

Information from the nuclear genome can help in these situations of understanding levels of gene flow, but can have limited resolving power when not used in sufficient number. Enter NGS. Modern sequencing methods can now provide orders of magnitude more data, and with a large SNP (single nucleotide polymorphism) set, here the authors report that the two species are indeed genetically distinct, and that recent hybridisation among the two species is unlikely. Certainly a useful tool for exploring these questions further.

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