[Coral-List] Coral genomics and historical population sizes

Mikhail Matz matz at utexas.edu
Wed Oct 28 14:53:03 EDT 2015

Hi Tom - 

Good questions! I decided to cc this to coral-list, perhaps other people would find it informative, too.

> How can you do this unless you have samples of corals from throughout the last glacial cycle? 

 You can reconstruct past population sizes without any ancient coral samples - that’s the whole point. 

Two methods have been recently developed that can do this based on present-day genetic variation (see the “Gory details” section of our crowdfunding proposal, http://bit.ly/1VUDwuz , for the links to the original papers). Both are based on coalescent theory and have been extensively tested on human populations, for which we kind of know what happened in the past. 

The method called dadi (diffusion approximation for demographic inference) examines allele frequencies at thousands of SNPs in populations and is based on two notions:
- mutations in the genome accumulate at a rate proportional to the population size; 
- more recent mutations tend to be found at lower frequencies than older mutations.
Coalescent theory provides equations that link these things and makes it possible to fit a model to the mutation frequency data incorporating population size changes through time. Advantage of this method is that you don't need to sequence the whole genome and it does not matter where those mutations are in it; although you do have to genotype 15-20 individuals per population at 10,000+ SNPs. Our 2bRAD method is just the tool for that. 

The other method - PSMC, pairwise sequential markovian coalescent - requires just a single individual genome sequence (I know, it sounds like magic but it works). It makes use of the fact that average distance between neighboring mutations in the genome decreases when populations expand, and increases when they contract.  So it basically fits a time-resolved model to match the distribution of distances between mutations. One great advantage of this method is that you don’t need to specify what sort of pop size changes you expect to find - unlike dadi, which requires a pre-specified sequence of changes and the model finds the best-fitting time and size parameters for it. The difficulty with PSMC is that you need a whole-genome sequence, which could be fragmented but still must be separated into individual homologous chromosomes (“phased” is the term). This is why we propose to use Hi-C method that provides such information.

> And if you could reconstruct that, how would that help adaption to conditions outside that range?

I anticipate that for adaptation, the rates of environmental change rather than absolute temperature reached would have the most impact. Corals can live in the Arabian Gulf at brutally high temperatures (in summer, >33oC mean, 34-35oC max daily temperature), so we don’t seem to be nearing the absolute physiological temperature cap for corals just yet; the question is, is the present warming too fast for them to keep pace? There were some very rapid temperature changes in the Northern hemisphere since last glacial maximum, most notably the Younger Dryas, about 11,500 year ago: the temperature in Greenland increased by 7oC or more in just a few decades, https://www.ipcc.ch/ipccreports/tar/wg1/074.htm . Did this coincide with the collapse of Caribbean coral populations? If not, that would be good news. 

Of course this would not give us a complete picture for the present situation - we have other climate factors and human influences to put into the equation as well. But at least we would know that, even though the climate will inevitably continue to warm in the next few decades, region-wide ecological extinction of corals is not inevitable, and so our efforts to save reefs on the local scale can actually make a difference. 

does it make sense?..



On Oct 28, 2015, at 1:22 AM, Thomas Goreau <goreau at bestweb.net> wrote:

> Dear Misha,
> And if you could reconstruct that, how would that help adaption to conditions outside that range?
> Best wishes,
> Tom
> ate: Mon, 26 Oct 2015 17:54:56 -0500
> From: Mikhail Matz <matz at utexas.edu>
> Subject: [Coral-List] crowdfunding coral genomics
> To: coral list <coral-list at coral.aoml.noaa.gov>
> Message-ID: <AC520D7C-0171-4D7E-A0B3-28FEAC0F4C23 at utexas.edu>
> Content-Type: text/plain;	charset=us-ascii
> Dear colleagues -
> My lab has just launched a crowdfunding coral genomics project to find out how rapidly can corals adapt to climate change (http://bit.ly/1VUDwuz ).  I would tremendously appreciate if you could pass the word around. 
> Please note that we are committed to immediately releasing all the genomics data from this project for unrestricted use to the research community. Basically, I will post the links to the data on coral-list as soon as it is off the assembly pipeline. 
> Below the signature are suggested blurbs for twitter and facebook posts. Many thanks in advance!
> Misha
> --------
> Mikhail V. Matz
> Associate Professor
> University of Texas at Austin
> Department of Integrative Biology
> web http://www.bio.utexas.edu/research/matz_lab
> ---------
> Twitter:
> Can corals adapt to climate change? You can help to find out.  http://bit.ly/1VUDwuz @MikhailMatz #ReefGenomics
> Facebook:
> Can corals adapt to climate change? This is one of the most critical unknowns in reef conservation planning, very difficult to assess experimentally because of the timescales involved. @MikhailMatz team at University of Texas at Austin proposes an original solution:http://bit.ly/1VUDwuz. Using state-of-the-art genomic approaches, they will reconstruct rises and falls of Caribbean reefs in response to past climate changes over the last 100,000 years. This project is crowdfunded, so you can help this research directly. #ReefGenomics
> Thomas J. Goreau, PhD
> President, Global Coral Reef Alliance
> President, Biorock Technology Inc.
> Coordinator, Soil Carbon Alliance
> Coordinator, United Nations Commission on Sustainable Development Small Island Developing States Partnership in New Sustainable Technologies
> 37 Pleasant Street, Cambridge, MA 02139
> goreau at bestweb.net
> www.globalcoral.org
> Skype: tomgoreau
> Tel: (1) 617-864-4226
> Books:
> Geotherapy: Innovative Methods of Soil Fertility Restoration, Carbon Sequestration, and Reversing CO2 Increase
> http://www.crcpress.com/product/isbn/9781466595392
> Innovative Methods of Marine Ecosystem Restoration
> http://www.crcpress.com/product/isbn/9781466557734
> The Green Disc, New Technologies for a New Future: Innovative Methods for Sustainable Development
> http://www.greenthindisc.org
> No one can change the past, everyone can change the future

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