Wednesday, April 3, 2013

Biodiversity Genomics Conference, second day

Lots of talks today. After the opening words, Leo Joseph of the Australian National Wildlife Collection gave an inspiring talk about the potential of combining the resources of biological collections (animal skins, needled insects, herbaria, etc.) with Next Generation Sequencing. Specimens in these collection provide not only genomic data that can be extracted from them but also usually spatial data (where collected), temporal data (when collected) and phenotypic data that could be combined with the genotype. He also pointed out that conserved specimens with their degraded DNA are actually better usable with genomic tools than with traditional Sanger Sequencing because the former are designed to read short DNA pieces. Next, Justin Borevitz (Austr. Natl. Univ.) presented a very dense talk on his research in Arabidopsis and Australian Pelargonium, focusing on attempts to correlate genetic variation with phenotype (such as flowering time) and geographic locality to understand local adaptation.

The next session started with Graham Coop (UC Davis) who presented recent progresses in providing null models of genetic variation. Admittedly much of it was too mathematical and went over my head, but I got the general idea. When you want to know whether some genetic data signals local adaptation, the null hypothesis cannot simply be that the genes are distributed randomly. Instead, you have to account for covariance or in other words the possibility that the relevant gene copies are locally frequent due to the shared history of the local populations. For example, are Europeans light-skinned because they just happened to descend from a light-skinned ancestral population or because it is an adaptation to something? The solution is to produce a population by population covariance matrix with lots of genetic data which can be assumed to be mostly neutral, and then to compare the genetic variants of interest against it.

John Novembre (Univ. of Chicago) gave a really clear and well presented talk on four methods of increasing sophistication for spatial assignment of samples. The idea is that you have genetic information for a representative number of samples of a species across its range, e.g. all African elephants. Now customs seize a shipment of ivory from a black market in South East Asia. What analyses could you use to infer the country of origin from genetic information extracted from the seized tusks? The four methods he presented are PCA based, logistic frequency surfaces, Gaussian process based ("SCAT") and a joint analysis of genomic and isotopic data with SCAT. The first are simple but imprecise, SCAT is sophisticated but computer intensive.

Rose Andrew (Univ. of British Columbia) presented her research on incipient speciation in sunflowers. She used genomic data to examine patterns of divergence and what they mean for local selection, gene flow and isolation. The last speaker of the session was Ke Bi (UC Berkeley) who used genomic data from ca. 100 year old and contemporary chipmunk specimens to test the impact of climate change on their genetic structure; a very nice example of how museum specimens can provide the basis for cutting edge research!

In the afternoon session, Sonal Singhal (UC Berkeley) showed the pattern of genetic variability across five contact zones between species that have diverged at different times, with a clear negative correlation of introgression and time since divergence. Alan Lemmon and Emily Moriarty Lemmon (Florida State Univ.) advertised their recently published "anchored hybrid alignment" technique for rapidly producing data from hundreds of loci for ca. 100 samples for phylogenetic analysis. This was probably the talk that was most relevant for my own future research interests but, well, they have only done it for vertebrates and insects so far. Bernhard Misof (Univ. of Bonn) provided an update of the 1KITE project which is close to reaching its goal of sequencing the transcriptomes of 1,000 species of insects. The amounts of data produced in the course of the project are just mind-boggling.

Finally, Tariq Ezaz (Univ. of Canberra) presented some of his work on the evolution of sex chromosomes in lizards. Sex determination is really odd if you think about it. There are at least three systems in land vertebrates: XY, as we humans have it and where the females are XX homozygous, ZW, where the males are ZZ homozygous, and temperature dependent. In other groups of organisms, it gets even weirder, with some animals changing sex as they age, some choosing a sex depending on what the current sex ratio in their population is, and hymenopterans having haploid males. After that session ended, there were fifteen very short "lightning talks", but I had to get a few things done and missed them.

To be honest, I feel pretty overwhelmed by all the lab method wonkishness going on here. I am more interested in the phylogenetic analyses and, well, the actual organisms themselves, and my ideal situation would be to outsource the lab work part. On the other hand, I am probably the only person at the conference who could tell Pogonlepis stricta apart from Angianthus micropodiodes, or Odixia angusta from Ozothamnus rodwayi, so there is that. We all have our areas of expertise and it would be pretty boring if we all tried to be sequence capture experts...

Finally, from a purely technical perspective, the talks were generally at a very high level. Certainly variable in quality - the major problems I saw were some very overcrowded slides and the odd overly rushed presentation - but there were definitely no bad or uninteresting ones. It was also interesting to note that while one usually sees much more variability on conferences, nearly all of the speakers today used slides with a very simple black font on white background template and without any fancy logos or corporate identity nonsense. I appreciate that. One talk was white font on black background, which is harder on the eyes, but in this particular case it might be considered somewhat justified because most of the figures it showed were microscopy images with a black background.

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