Question: A Food Web Whose Species Have Been Dna Sequenced?
gravatar for Douglas S. Stones
9.8 years ago by
Melbourne, Australia
Douglas S. Stones270 wrote:

I'm currently looking into the evolution of food webs and wonder: Is there DNA sequence data around for all species belonging to some food web? Ideally, I would like the species in this food web to have been fairly isolated on an evolutionary time scale.

I would like to find the phylogenetic tree of life for these species from their DNA and see what I can infer about their food web's history. I.e. what did the food webs of their ancestors look like?

phylogenetics dna • 2.0k views
ADD COMMENTlink modified 20 months ago by kasdfd0 • written 9.8 years ago by Douglas S. Stones270

Well, there's the human sequence, the bovine sequence; and the Lion, Tiger & Leopard genomes are currently sequenced. ;-)

ADD REPLYlink written 9.8 years ago by Michael Kuhn5.0k

And some gut microbes and the plants, animals and fungi that the above hunt.

ADD REPLYlink written 9.8 years ago by Larry_Parnell16k
gravatar for Larry_Parnell
9.8 years ago by
Boston, MA USA
Larry_Parnell16k wrote:

I find this to be an intriguing question, but at the same time, I am not sure how you would analyze the genomic data. A food web that you have for contemporary times, might not have existed in the past. For example, the human diet is very different now than it was 200 years ago and very different from that at the dawn of agriculture, ~10000 years ago. This makes me uneasy about a food web that includes human.

There is a tremendous number of organisms that have complete, nearly competed or survey genome sequence data available. Daphnia pulex was recently announced, the water flea. Salmon is done or nearly so. Such efforts will allow you to go deeper into your food web, but I feel that you will not find genome seq data for all organisms in a food web. With a good food web in hand, you can begin your search to match organism in that web with genome data by looking at NCBI's Genome page.

ADD COMMENTlink written 9.8 years ago by Larry_Parnell16k

Thanks for that. In fact, I plan to use the data to identify what diet changes are likely to have occurred in the food web as it evolved.

ADD REPLYlink written 9.8 years ago by Douglas S. Stones270

There is also the issue of the duplication of genomes of domesticated plants and some animals (chicken, eg) that would confound a food web for human. Subtle differences in the human genome are linked to diet. See, eg, Diet and the evolution of human amylase gene copy number variation. by Perry GH, Stone AC, et al. Nat Genet. 2007 39:1256-60. PMID: 17828263.

ADD REPLYlink written 9.8 years ago by Larry_Parnell16k
gravatar for Shigeta
9.8 years ago by
Berkeley, CA
Shigeta460 wrote:

I am not entirely sure if you can define the boundaries of a food web. If you think of the Biosphere II project, that was a serious attempt to create a closed eco system which could sustain human beings and it failed very quickly.

The only closed systems i have ever heard of was a sealed glass globe containing brine shimp and algae that, if left in sunlight could go on living indefinitely ( or at least quite a while). I don't think those genomes (there would be a collection of microorganisms in the water) are sequenced.

ADD COMMENTlink written 9.8 years ago by Shigeta460

Hmm... It looks like finding a decent food web is going to be the difficult part. I don't really expect 100% closed, but it would be nice to have external influences minimal.

ADD REPLYlink written 9.8 years ago by Douglas S. Stones270
gravatar for Neilfws
9.8 years ago by
Sydney, Australia
Neilfws49k wrote:

This is an unusual and interesting question. I think it might help to generalize it:

  1. Given a list of species, how can I find those that have DNA sequence?
  2. or how can I find a specific DNA sequence for a list of species?

To start with the second question: which sequence(s) do you want to use to build the tree? It's possible that a specialized database exists; for example, the SILVA rRNA database might be useful if you wanted to use 18S rDNA sequence.

For the first question, my starting point would be the NCBI. There are several ways into the problem. You might start with the taxonomy resource, by searching for species. Here, for example, is a page for zebrafish: in the box on the right are links to nucleotide sequences for that organism. Or you might want to search the Gene or Nucleotide databases using organism + gene name as a query, for example:

"Homo sapiens"[ORGN] AND GUCA2B[GENE]

Once you've identified a good search strategy you will want to automate search and retrieval, for which you'll need NCBI EUtils and some programming ability (in e.g. Perl, Ruby or Python).

ADD COMMENTlink modified 15 months ago by _r_am31k • written 9.8 years ago by Neilfws49k
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