Question: Tool for bottleneck analysis in genetics
0
gravatar for flogin
5 months ago by
flogin150
FioCruz/Brazil
flogin150 wrote:

Hello folk,

I'm wondering if have any tool to compute bottleneck events using as input an alignment file (for example, with 200+ sequences of the same gene from different individuals).

I know that have several softwares, as DNAsp that we can make several evolutionary tests as Tajima, Fu and Li's or Linkage Disequilibrium, and that we can use the results of these tests to infer a bottleneck event, but, have a specific tool, or another test that we can perform to evaluate bottleneck events?

I have as input the sequences of an intragenic region from several individuals of the same specie from different locations (more than 100 individuals per location).

tool genetics bottleneck • 175 views
ADD COMMENTlink written 5 months ago by flogin150
2
gravatar for h.mon
5 months ago by
h.mon28k
Brazil
h.mon28k wrote:

With just one small genomic region, you can't infer bottlenecks, regardless of the methods or software available.

ADD COMMENTlink written 5 months ago by h.mon28k

Can this same criterion be used to a set of 8 orthologues genes?

ADD REPLYlink written 5 months ago by flogin150
1

Eight still seems like a small number. I don't know the minimum number of regions required to confidently infer bottlenecks, as I don't work very much with population genetics / genomics. It seems this paper (Distinguishing between population bottleneck and population subdivision by a Bayesian model choice procedure) has a discussion about number of sites and power of evolutionary inferences.

Nowadays, with the lowering costs of sequencing, and techniques such as GBS, RADseq and others, one can obtain genome-wide populational data.

ADD REPLYlink written 5 months ago by h.mon28k

thanks!, yeah, the NGS technologies help us with large data analysis, but this datasets cames from colaborations, and are from 300+ individuals.. so a little expansive to make whole genome analysis with this N.

ADD REPLYlink written 5 months ago by flogin150
1

With GBS / Radseq, you can sequence 300 hundred individuals in one lane of a HiSeq 2500 or NovaSeq, and get plenty of markers for genome-wide inferences. I don't have a pairwise price comparison, but with 300 individuals, as soon as you want to increase the number of markers to more than a dozen, cost differences start to dwarf and even tip to the massive sequencing side.

Considering you don't know yet how many markers you need to detect population bottlenecks, massive sequencing may be a cost-effective option.

ADD REPLYlink written 5 months ago by h.mon28k
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