Computational protocol: Volatility in the effective size of a freshwater gastropod population

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Protocol publication

[…] The Quarterman Park Duck Pond (32.87822, −79.98077) was constructed from a marshy embayment of the Cooper River in the early 20th century. For most of its history, it was tidally influenced and slightly brackish, but recent drainage improvements have rendered it entirely fresh, fed by local runoff. Its area at present is approximately 1.0 hectare, and depth is no more than 2 m.The pond is maintained by city personnel at irregular intervals and has been kept free of macrophytic vegetation in recent years. Water temperatures can rise above 35°C during summer months, depressing dissolved oxygen to low levels, despite city efforts at artificial aeration. Its population of P. acuta reaches maximum density on allochthonous leaves and debris floating at the eastern (windward) end of the pond, at the drain.We visited the pond each spring from 2009 to 2015, beginning in March, examining debris at the eastern end to qualitatively assess snail densities. If the apparent census size was sufficient to yield several hundred snails with reasonable effort, an annual sample was taken. Otherwise, we postponed the sample and returned a few weeks later. Approximately 150–200 P. acuta were ultimately sampled every spring, with one exception. The exception was 2012, when the snail population never reached an abundance at which it could be sampled, from March to August.Snails collected at each sampling year were returned to the laboratory and frozen individually in 80–160 μl of tris tissue buffer for analysis of allozyme polymorphism. We used horizontal starch gel electrophoresis in a TEB8 buffer system to resolve variation at the Est3, Isdh, and 6pgd loci and an aminopropylmorpholine pH 6 buffer system for a second examination of Isdh and 6pgd. Details regarding our electrophoretic methods, including a description of our equipment and recipes for all stains and buffers employed, have been published by Dillon () and Dillon and Wethington ().Allele frequencies and tests of fit to Hardy–Weinberg expectation were calculated using GenePop version 4.5.1 (Raymond & Rousset, ; Rousset, ). Values of F IS were computed using the method of Weir and Cockerham (), and exact p‐values were by the Markov chain method.NeEstimator v2.01 is freely available software designed to estimate effective population size using three single‐sample methods and three‐two‐sample (moment‐based temporal) methods (Do et al., ). Among the single‐sample methods, Gilbert and Whitlock () reported that the linkage disequilibrium (LDNe) method of Waples and Do () consistently returned the lowest root square mean error across the range of effective population numbers simulated, absent migration.The three‐two‐sample methods implemented by NeEstimator 2.01 employ the standard temporal method (ST) of Waples (), with different approaches to computing standardized allele frequency variance: the Fc of Nei and Tajima (), the Fk of Pollak (), and the Fs of Jorde and Ryman (). The simulations of Gilbert and Whitlock () suggested that all three of these two‐sample methods perform with equivalent efficiency. Thus, we elected to estimate the effective population size of the Quarterman Park P. acuta population using four approaches: LDNe, STFc, STFk, and STFs. Jackknife methods were used to calculate 95% confidence intervals (CI) for all N e estimates. […]

Pipeline specifications

Software tools Genepop, NeEstimator
Application Population genetic analysis
Organisms Physella acuta