Levels and patterns of population genetic diversity in the red seaweedChondrus crispus(Florideophyceae): a direct comparison of single nucleotide polymorphisms and microsatellites

Abstract

Single nucleotide polymorphisms (SNPs) are predicted to supersede microsatellites as the marker of choice for population genetic studies in the near future. To date, however, very few studies have directly compared both marker systems in natural populations, particularly in non-model organisms. In the present study, we compared the utility of SNPs and microsatellites for population genetic analysis of the red seaweed Chondrus crispus (Florideophyceae). Six SNP loci yielded very different patterns of intrapopulation genetic diversity compared to those obtained using seven moderately (mean 5.2 alleles) polymorphic microsatellite loci, although Bayesian clustering analysis gave largely congruent results between the two marker classes. A weak but significant pattern of isolation-by-distance was observed across scales from a few hundred metres to approximately 200 km using the combined SNP and microsatellite data set of 13 loci. Over larger scales, however, there was little correlation between genetic divergence and geographical distance. Our findings suggest that even a moderate number of SNPs is sufficient to determine patterns of genetic diversity across natural populations, and also highlight the fact that patterns of genetic variation in seaweeds arise through a complex interplay of short-and long-term natural processes, as well as anthropogenic influence. Andreakis N, Kooistra WHCF, Procaccini G. 2008. High genetic diversity and connectivity in the polyploid invasive seaweed Asparagopsis taxiformis (Bonnemaisoniales) in the Mediterranean, explored with microsatellite alleles and multilocus genotypes. Molecular Ecology 18: 212-226. Beacham TD, McIntosh B, Wallace C. 2010. A comparison of stock and individual identification for sockeye salmon (Oncorhynchus nerka) in British Columbia provided by microsatellites and single nucleotide polymorphisms. Canadian Journal of Fisheries and Aquatic Science 67: 1274-1290. Beatty GE, Philipp M, Provan J. 2010. Unidirectional hybridization at a species' range boundary: implications for habitat tracking. Diversity and Distributions 16: 1-9. POPULATION GENETICS OF C. CRISPUS 259

Range-wide population structure of European sea bassDicentrarchus labrax

“…The power of markers required to discriminate among ‘open’ marine populations is linked to their characteristics and the degree of differentiation. Increasing the number of markers from tens of microsatellites to thousands of SNPs has enhanced the resolution and confidence in individual genotypes (Novembre et al ., ), although small numbers may suffice (Provan et al ., ), especially in the case of SNPs (Willing et al ., ). New genomic venues have been opened with a recent study of European sea bass based on 234 148 SNPs isolated through restriction enzyme associated DNA (RAD) genotyping (Tine et al ., ).…”

Fine-scale landscape genetics unveiling contemporary asymmetric movement of red panda (Ailurus fulgens) in Kangchenjunga landscape, India

“…Further, studying wildlife using genome-wide markers (e.g. GWAS— 15 , 48 ; SNPs— 15 , 49 ) is fascinating to evaluate fine scale population genetic structure and investigating loci under natural selection facilitating populations to adapt in the changing climatic conditions 50 . However, to check the immediate effects of landscape features on the genetic variability and population contiguity, the assessment of wild populations using microsatellites is still most cost effective and widely applied way to genetic monitor of free ranging populations 30 , 51 .…”

Understanding macroalgal dispersal in a complex hydrodynamic environment: a combined population genetic and physical modelling approach

“…Gene flow in macroalgae is further influenced by landscape quality between populations in addition to geographical distance and dispersal capabilities [3]. However, macroalgae can achieve long-distance gene flow via the dispersal of whole or partially detached thalli-bearing reproductive structures [8][9][10][11][12][13]. These may be rare and/or stochastic events, but they are important long-distance dispersal mechanisms connecting potentially isolated populations of macroalgae.…”