Comparing the Performance of Microsatellites and RADseq in Population Genetic Studies: Analysis of Data for Pike (Esox lucius) and a Synthesis of Previous Studies

Sunde, Johanna; Yıldırım, Yeşerin; Tibblin, Petter; Forsman, Anders

doi:10.3389/fgene.2020.00218

Cited by 99 publications

(126 citation statements)

References 104 publications

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“…However, in comparison to the SSRs, SNP markers exhibited lower within population genetic diversity but afforded higher resolutive power for describing fine-scale population genetic structure. Such overall concordance between SNPs and SSRs, but taking into account the difference in resolutive power between these two types of marker, has been reported in other recent studies of marine and freshwater organisms, including kelp [48], brown trout [71], coral reef-associated fish [72], and pike [73].…”

Section: Comparison Of Resolutive Power Between Two Types Of Utilisedsupporting

confidence: 77%

Seascape Genomics of the Sugar Kelp Saccharina latissima Along the North Eastern Atlantic Latitudinal Gradient

Guzinski¹,

Ruggeri²,

Ballenghien³

et al. 2020

Preprint

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Temperature is one of the most important range-limiting factors for many seaweeds. Driven by the recent climatic changes, rapid northward shifts of species’ distribution ranges can potentially modify the phylogeographic signature of Last Glacial Maximum such as increased genetic diversity at lower latitudes. To explore this question in detail in the kelp Saccharina latissima, we used microsatellites and double digest RAD-sequencing derived SNPs on S. latissima sporophytes sampled within 11 sites spanning the entire European Atlantic latitudinal range of this species. In addition, we checked for statistical correlation between genetic marker allele frequencies and three environmental proxies (sea surface temperature, salinity, and water turbidity). Our findings revealed that genetic diversity was significantly higher for the northern localities compared to the southern ones in contrast to the expected phylogeographic pattern. This suggests that the southernmost S. latissima populations are negatively affected by the recent climatic changes but also that the recolonization of S. latissima range following the LGM may have occurred from northerly refugia. Seven SNPs and 12 microsatellite alleles were found to be significantly associated with at least one of the three environmental variables. We discuss the potential adaptive functions of the genes associated with the outlier markers and the importance of these markers for successful conservation and aquaculture strategies for S. latissima in this age of rapid global change.

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Section: Comparison Of Resolutive Power Between Two Types Of Utilisedsupporting

confidence: 77%

Seascape Genomics of the Sugar Kelp Saccharina latissima Along the North Eastern Atlantic Latitudinal Gradient

Guzinski¹,

Ruggeri²,

Ballenghien³

et al. 2020

Preprint

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“…This may be due to the greater probability of identifying conserved restriction site linked markers in genome-wide RADseq studies as opposed to meaningful biological differences. Thus, the relative differences between populations are likely to be more important than specific values (Sunde et al, 2020). Indeed, the trend observed between ecogeographic groups here was similar to the previous SSR study (Sifres et al, 2011).…”

Section: Characterizing Population Differentiation In S Habrochaitessupporting

confidence: 89%

“…Both the observed and expected heterozygosity values per accession were lower using RAD-seq than SSRs (Fig. 3A), a trend that has been observed previously (Sunde et al, 2020). This may be due to the greater probability of identifying conserved restriction site linked markers in genome-wide RADseq studies as opposed to meaningful biological differences.…”

Section: Characterizing Population Differentiation In S Habrochaitessupporting

confidence: 67%

“…The RAD-seq results provide a less biased estimation of population structure than a previous analysis based on fewer AFLP and SSR markers (Sifres et al, 2011), which also tend to be faster evolving than genome-wide SNP loci (Sunde et al, 2020). Our results show eight different population clusters across the species range, which have been substantially influenced by variations in geography.…”

Section: Discussionmentioning

confidence: 60%

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Migration through a major Andean ecogeographic disruption as a driver of genotypic and phenotypic diversity in a wild tomato species

Landis

Miller

Broz

et al. 2020

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The large number of species on our planet arises from the phenotypic variation and reproductive isolation occurring at the population level. In this study, we sought to understand the origins of such population-level variation in defensive acylsugar chemistry and mating systems in Solanum habrochaites – a wild tomato species found in diverse Andean habitats in Ecuador and Peru. Using Restriction-Associated-Digestion Sequencing (RAD-seq) of 50 S. habrochaites accessions, we identified eight population clusters generated via isolation and hybridization dynamics of 4-6 ancestral populations. Estimation of heterozygosity, fixation index, isolation by distance, and migration probabilities, allowed identification of multiple barriers to gene flow leading to the establishment of extant populations. One major barrier is the Amotape-Huancabamba Zone (AHZ) – a geographical feature in the Andes with high endemism, where the mountainous range breaks up into isolated microhabitats. The AHZ was associated with emergence of alleles for novel reproductive and acylsugar phenotypes. These alleles led to the evolution of self-compatibility in the northern populations, where alleles for novel defense-related enzyme variants were also found to be fixed. We identified geographical distance as a major force causing population differentiation in the central/southern part of the range, where S. habrochaites was also inferred to have originated. Findings presented here highlight the role of the diverse ecogeography of Peru and Ecuador in generating new, reproductively isolated populations, and enhance our understanding of the microevolutionary processes that lay a path to speciation.

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“…Genome-wide SNP data increases the number of loci compared to traditional mitochondrial or nuclear markers and a larger marker panel is expected to small scaled population structure when compared to single marker studies. The effect of an increased marker panel has been shown for example in mussels (Becking et al , 2016;Maas et al , 2018;de Leeuw et al , 2020), and fish (Bradbury et al , 2015;Lemopoulos et al , 2019;D'Aloia et al , 2020;Sunde et al , 2020). However, high resolution studies on sponges are lagging behind (Pérez-Portela and Riesgo, 2018), with notable exception of Brown et al (2014), Brown et al (2017) and Leiva et al (2019).…”

Section: Introductionmentioning

confidence: 99%

Previously unidentified genetic structure revealed for the sponge Suberites diversicolor: implications for sponge phylogeography and population genetics

Maas

Prost

Leeuw

et al. 2020

Preprint

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The relative influence of geography, oceanography and environment on gene flow within sessile marine species remains an open question. Detecting subtle genetic differentiation at small scales relevant to marine protected areas is challenging in benthic populations due to large effective population sizes, general lack of resolution in genetic markers, potential microbial associations, and because barriers to dispersal often remain elusive. We genotyped the sponge species Suberites diversicolor using double digest restriction-site associated DNA sequencing (4,826 Single Nucleotide Polymorphisms, SNPs), compared it to same individuals using single markers (COI and ITS), and used previously published data on the associated microbial communities from a subset of the same locations. Studying S. diversicolor from marine lakes at different spatial scales (1-1,400 km), along a gradient of connection to the surrounding sea, and with different environmental regimes, we did not detect strong effects of geographic distance, permeability of seascape barriers or local environments in shaping population genetic structure. All markers detected two major lineages and geographic clustering over a large spatial scale. However, with the SNP dataset we provide new evidence of strong population structure even at scales <10km (average FST = 0.56), where previously none was detected. A lack of congruence between host population structure and microbial community patterns of S. diversicolor from the same locations was observed, suggesting they are on different eco-evolutionary tracks. Our results call for a reassessment of poorly dispersing benthic organisms that were previously assumed to be highly connected based on low resolution markers.

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Comparing the Performance of Microsatellites and RADseq in Population Genetic Studies: Analysis of Data for Pike (Esox lucius) and a Synthesis of Previous Studies

Cited by 99 publications

References 104 publications

Seascape Genomics of the Sugar Kelp Saccharina latissima Along the North Eastern Atlantic Latitudinal Gradient

Seascape Genomics of the Sugar Kelp Saccharina latissima Along the North Eastern Atlantic Latitudinal Gradient

Migration through a major Andean ecogeographic disruption as a driver of genotypic and phenotypic diversity in a wild tomato species

Previously unidentified genetic structure revealed for the sponge Suberites diversicolor: implications for sponge phylogeography and population genetics

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