Resolving allele dosage in duplicated loci using genotyping‐by‐sequencing data: A path forward for population genetic analysis
Advanced Search
Select up to three search categories and corresponding keywords using the fields to the right. Refer to the Help section for more detailed instructions.

Search our Collections & Repository

For very narrow results

When looking for a specific result

Best used for discovery & interchangable words

Recommended to be used in conjunction with other fields

Dates

to

Document Data
Library
People
Clear All
Clear All

For additional assistance using the Custom Query please check out our Help Page

i

Resolving allele dosage in duplicated loci using genotyping‐by‐sequencing data: A path forward for population genetic analysis

Filetype[PDF-721.46 KB]



Details:

  • Journal Title:
    Molecular Ecology Resources
  • Personal Author:
  • NOAA Program & Office:
  • Description:
    Whole‐genome duplications have occurred in the recent ancestors of many plants, fish and amphibians. Signals of these whole‐genome duplications still exist in the form of paralogous loci. Recent advances have allowed reliable identification of paralogs in genotyping‐by‐sequencing (GBS) data such as that generated from restriction‐site‐associated DNA sequencing (RADSeq); however, excluding paralogs from analyses is still routine due to difficulties in genotyping. This exclusion of paralogs may filter a large fraction of loci, including loci that may be adaptively important or informative for population genetic analyses. We present a maximum‐likelihood method for inferring allele dosage in paralogs and assess its accuracy using simulated GBS, empirical RADSeq and amplicon sequencing data from Chinook salmon. We accurately infer allele dosage for some paralogs from a RADSeq data set and show how accuracy is dependent upon both read depth and allele frequency. The amplicon sequencing data set, using RADSeq‐derived markers, achieved sufficient depth to infer allele dosage for all paralogs. This study demonstrates that RADSeq locus discovery combined with amplicon sequencing of targeted loci is an effective method for incorporating paralogs into population genetic analyses.
  • Keywords:
  • Source:
    Molecular Ecology Resources, 18(3), 570-579
  • DOI:
  • ISSN:
    1755-098X;1755-0998;
  • Format:
  • Publisher:
  • Document Type:
  • Rights Information:
    Accepted Manuscript
  • Compliance:
    Library
  • Main Document Checksum:
  • Download URL:
  • File Type:

Supporting Files

  • No Additional Files
More +

You May Also Like

Checkout today's featured content at repository.library.noaa.gov

Version 3.26.1