Troubleshooting Ne inflation in gl.stairway2

[Krishna Pavan Kumar Komanduri]

Hi dartR community,

I am using gl.stairway2 to estimate recent demographic history and test for a population bottleneck in the past 100 years.

gl.stairway2(My_genlight,
             stairway.path = stairway.path.exe,
             mu = 8e-10,
             gentime = 1,
             run=T,
             nreps = 200,
             parallel=4,
             L=1.8e6,
             minbinsize =5)

I am currently using the following parameters:

- Generation time: 1 year (since my species reaches sexual maturity at 0.57 years and breeds the following season).
- Mutation rate: 8e-10 (potential frog mutation rate derived from literature).
- L (callable sites): 1.8e6
L was calculated using: [loci (monomorphic + polymorphic) * mean read length (60 bp based on TrimmedSequence mean)]

However, I am encountering very high values for both the estimated Ne and time (years/generations), and this appears to be a scaling issue with L, as these values reach reasonable scales when L is increased to 1e7.

To put my current L value into context, the genome size of the closest species, Litoria verreauxii alpina, is 2.77 Gb. An L of 1.8e6 would mean a coverage of roughly 0.06% of the entire genome.

If I understand correctly, DArT pre-filters SNPs before sharing the data. And so I was wondering if calculating L directly from the received genlight object inherently underestimates the true sequence space surveyed? I noticed the Kioloa tutorial on Effective Population Size advises against this type of calculation and recommends using the length of the chromosome.

Question: If calculating L directly from the genlight object is not appropriate for DArT data, could anyone recommend how to find a more realistic L value or how to estimate the length of the chromosome for species without a sequenced genome?

I would really appreciate any insights. Thank you!

Regards,
Krishna


P.S. I am new to population genetic analysis and dartRverse, so apologies for any oversight.