New view of population genetics of zooplankton: RAD‐seq analysis reveals population structure of the North Atlantic planktonic copepod Centropages typicus

Abstract

Detection of population genetic structure of zooplankton at medium-to-small spatial scales in the absence of physical barriers has remained challenging and controversial. The large population sizes and high rates of gene flow characteristic of zooplankton have made resolution of geographical differentiation very difficult, especially when using few genetic markers and assuming equilibrium conditions. Next-generation sequencing now allows simultaneous sampling of hundreds to thousands of genetic markers; new analytical approaches allow studies under nonequilibrium conditions and directional migration. Samples of the North Atlantic Ocean planktonic copepod, Centropages typicus, were analysed using restriction site-associated DNA (RAD) sequencing on a PROTON platform. Although prior studies revealed no genetic differentiation of populations across the geographical range of the species, analysis of RAD tags showed significant structure across the North Atlantic Ocean. We also compared the likelihood for models of connectivity among NW Atlantic populations under various directional flow scenarios that replicate oceanographic conditions of the sampled domain. High-density marker sampling with RAD sequencing markedly outperformed other technical and analytical approaches in detection of population genetic structure and characterization of connectivity of this high geneflow zooplankton species.

Population genetics analysis of the Nujiang catfish Creteuchiloglanis macropterus through a genome-wide single nucleotide polymorphisms resource generated by RAD-seq

“…Furthermore, potential homologs were excluded by removal of markers that exhibited heterozygosity values >0.5 66 . To avoid linkage bias for the SNP calling, only the first SNP per locus was included in the final analysis 67–71 . To maximize the detection of adaptive loci, a series of SNP datasets (Table 2) were constructed in the populations program in STACKS on the basis of genetic structure, by specifying parameters in the populations program (-p: change the number of populations that loci should be present; -M: population map, determine which groupings to use).…”

Temperature gradient affects differentiation of gene expression and SNP allele frequencies in the dominant Lake Baikal zooplankton species

“…High levels of gene flow set the limits to local adaptation (Lenormand, ), unless selection is strong and operates on few large‐effect alleles (Yeaman & Otto, ; Yeaman & Whitlock, ). Indeed, despite high levels of gene flow facilitated by currents in marine and large lake environments, large‐scale differentiation has been observed in zooplankton populations, provided that a sufficient number of SNP loci are analysed (Blanco‐Bercial & Bucklin, ). Baikal's E. baikalensis seems to be no exception: a previous mtDNA‐based study did not reveal any differentiation among Baikal's major basins (Zaidikov, Maior, Sukhanova, Kirilchik, & Naumova, ), while in the present study, we observe such differentiation at hundreds of (presumably nuclear) SNPs, both among stations within the same basin and among basins.…”

“…The question of large‐scale genetic differentiation of marine (Blanco‐Bercial & Bucklin, ; Goetze, Andrews, Peijnenburg, Portner, & Norton, ; Unal & Bucklin, ) and large lake (Vaillant, Bock, Haffner, & Cristescu, ) zooplankton remains somewhat controversial, as it is difficult to see how it can be maintained within a single body of water, even an ocean‐sized one, under the conditions of high gene flow imposed by currents, unless a very strong selection for local adaptation is operating (Lenormand, ). A consensus is forming that, while studies using a small number of segregating loci often do not reveal large‐scale genetic differentiation in marine copepods (Provan, Beatty, Keating, Maggs, & Savidge, ; Stupnikova, Kulagin, Neretina, & Mugue, ), next‐generation sequencing‐based studies do (Blanco‐Bercial & Bucklin, ).…”

Lost in parameter space: a road map for stacks

“…Restriction site‐Associated DNA sequencing (RAD‐seq) has been proven to be an effective method for identifying and screening high‐resolution polymorphism within and between populations (Lescak et al . ; Blanco‐Bercial & Bucklin ), ecotypes (Hale et al . ; Pavey et al .…”