Microsatellite Development and First Population Size Estimates for the Groundwater Isopod Proasellus walteri

Abstract

Effective population size (N e) is one of the most important parameters in, ecology, evolutionary and conservation biology; however, few studies of N e in surface freshwater organisms have been published to date. Even fewer studies have been carried out in groundwater organisms, although their evolution has long been considered to be particularly constrained by small N e. In this study, we estimated the contemporary effective population size of the obligate groundwater isopod: Proaselluswalteri (Chappuis, 1948). To this end, a genomic library was enriched for microsatellite motifs and sequenced using 454 GS-FLX technology. A total of 54,593 reads were assembled in 10,346 contigs or singlets, of which 245 contained candidate microsatellite sequences with suitable priming sites. Ninety-six loci were tested for amplification, polymorphism and multiplexing properties, of which seven were finally selected for N e estimation. Linkage disequilibrium and approximate Bayesian computation methods revealed that N e in this small interstitial groundwater isopod could reach large sizes (> 585 individuals). Our results suggest that environmental conditions in groundwater, while often referred to as extreme, are not necessarily associated with small N e.

Inferring long-term effective population size with Mutation-Selection models

“…In particular, in mammals, the inferred variation in N e correlates negatively with body size and, more generally, Figuet et al (2017). Similarly, in isopods, smaller effective population sizes are inferred in subterranean species, again, as expected (Capderrey et al, 2013).…”

“…As another case study, we analysed a group of isopod species that have made multiple independent transitions to subterranean environments. The transition from a terrestrial to a subterranean lifestyle is typically associated with a global life-history and ecological syndrome characterized by a loss of vision, longer generation times and, most interestingly, smaller population sizes, due to a lower carrying capacity of the subterranean environment (Capderrey et al, 2013). Protein coding DNA sequence alignments and qualitative life-history traits such as habitat (surface or underground), pigmentation (depigmented, partially depigmented or pigmented) and ocular structure (anophthalmia, microphthalmia, or ocular) are available for these species (Eme et al, 2013;Saclier et al, 2018).…”

Inferring Long-Term Effective Population Size with Mutation–Selection Models

“…As another case study, we analyzed a group of isopod species that have made multiple independent transitions to subterranean environments. The transition from a terrestrial to a subterranean lifestyle is typically associated with a global life-history and ecological syndrome characterized by a loss of vision, longer generation times and, most interestingly, smaller population sizes, due to a lower carrying capacity of the subterranean environment ( Capderrey et al 2013 ). Protein coding DNA sequence alignments and qualitative LHTs, such as habitat (surface or underground), pigmentation (depigmented, partially depigmented or pigmented), and ocular structure (anophthalmia, microphthalmia, or ocular) are available for these species ( Eme et al 2013 ; Saclier et al 2018 ).…”

Geomorphic influence on intraspecific genetic differentiation and diversity along hyporheic corridors

“…Genotyping was performed using a set of seven microsatellite markers (Capderrey et al, ) developed from an enriched library of genomic DNA sequenced on a 454 FLX sequencer (454 Life Sciences/Roche Applied Biosystems, Nutley, NJ, USA). PCR multiplexes and conditions, genotyping mixes and electrophoresis, as well as allele scoring followed Capderrey et al (2013a).…”

“…Chapman et al (2003), we developed a multiplex PCR scheme using one genus-specific forward primer (16S-ProaF1: 5 0 -CCTATGAGTC GTTTAAATGGCCGCA-3 0 ; Calvignac, Konecny,Malard, & Douady, 2011) and two species-specific reverse primers (16S-Pwalt-R458: 5 0 -CTATCTATATATATATTTGCTTATATAGGG-3 0 , 16S-Psyna-R217: 5 0 -TAAAGTTTTATAGGGTCTTATCGTCCA-3 0 , for P. walteri and P. synaselloides complex respectively) targeting the 16S mitochondrial DNA. Reverse primers were designed in such a way that PCR products were different in size (458 and 217 bp for P. walteri and P. synaselloides complex respectively) and could be differentiated by electrophoresis on 1.5% agarose gels.Genotyping was performed using a set of seven microsatellite markers(Capderrey et al, 2013a) developed from an enriched library of genomic DNA sequenced on a 454 FLX sequencer (454 Life Sciences/Roche Applied Biosystems, Nutley, NJ, USA). PCR multiplexes and conditions, genotyping mixes and electrophoresis, as well as allele scoring followed Capderrey et al (2013a).…”