4.7 Review

Characterizing genic and nongenic molecular markers: comparison of microsatellites and SNPs

Journal

MOLECULAR ECOLOGY RESOURCES
Volume 13, Issue 3, Pages 377-392

Publisher

WILEY
DOI: 10.1111/1755-0998.12071

Keywords

Gasterosteus aculeatus; genetic variability; heterozygosity; population divergence

Funding

  1. Academy of Finland [134728, 129662]
  2. LUOVA graduate school
  3. Population Genetics Graduate School
  4. European Community [217246]
  5. BONUS, the joint Baltic Sea research and development programme (BALTGENE)
  6. Academy of Finland (AKA) [129662] Funding Source: Academy of Finland (AKA)

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The implications of transitioning to single nucleotide polymorphism (SNPs) from microsatellite markers (MSs) have been investigated in a number of population genetics studies, but the effect of genomic location on the amount of information each type of marker reveals has not been explored in detail. We developed novel SNP markers flanking 1kb regions of 13 genic (within gene or <1kb away from gene) and 13 nongenic (>10kb from annotated gene) MSs in the threespine stickleback genome to obtain comparable data for both types of markers. We analysed patterns of genetic diversity and divergence on various geographic scales after converting the SNP loci within each genomic region into haplotypes. Marker type (SNP haplotype or MS) and location (genic or nongenic) significantly affected most estimates of population diversity and divergence. Between-lineage divergence was significantly higher in SNP haplotypes (genic and nongenic), however, within-lineage divergence was similar between marker types. Most divergence and diversity measures were uncorrelated between markers, except for population differentiation which was correlated between MSs and SNP haplotypes (both genic and nongenic). Broad-scale population structure and assignment were similarly resolved by both marker types, however, only the MSs were able to delimit fine-scale population structuring, particularly when genic and nongenic markers were combined. These results demonstrate that estimates of genetic variability and differentiation among populations can be strongly influenced by marker type, their genomic location in relation to genes and by the interaction of these two factors. This highlights the importance of having an awareness of the inherent strengths and limitations associated with different molecular tools to select the most appropriate methods for accurately addressing various ecological and evolutionary questions.

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