DOI: 10.5061/dryad.wpzgmsbn3
title: Data from: Low bottleneck detection in long-lived species despite lost genetic diversity: a case study of tuatara and eastern massasauga rattlesnakes

description: Population bottlenecks can reduce genetic diversity and may lead to
 inbreeding depression. However, some studies have provided evidence that
 long lifespans buffer negative genetic effects of bottlenecks. Others have
 cautioned that longevity might merely mask the effects of genetic drift,
 which will still affect long-term population viability. We used
 microsatellite data from actual populations of tuatara (Sphenodon
 punctatus) and eastern massasaugas (Sistrurus catenatus) as a starting
 point for simulated population declines to evaluate the performance of
 bottleneck tests under a range of scenarios. We quantified losses in
 genetic diversity for each scenario and assessed the power of commonly
 used tests (i.e., M-ratio, heterozygosity excess, and mode-shift) to
 detect known bottlenecks in these moderate- to long-lived species.
 Declines in genetic diversity were greater in bottlenecks simulated for
 eastern massasaugas, the shorter-lived species, and mode-shift and
 heterozygosity excess tests were more sensitive to population declines in
 this species. Conversely, M-ratio tests were more sensitive to bottlenecks
 simulated in tuatara. Despite dramatic simulated population declines,
 heterozygosity excess and mode-shift tests often failed to detect
 bottlenecks in both species, even when large losses in genetic diversity
 had occurred (both allelic diversity and heterozygosity). While not
 eliminating type II error, M-ratio tests generally performed best and were
 most reliable when a critical value (Mc) of 0.68 was used. However, in
 tuatara simulations, M-ratio tests had high rates of type I error when Mc
 was calculated assuming θ = 10. Our results suggest that reliance on these
 tests could lead to misguided species management decisions.
description: The original/raw tuatarta genotypes were obtained at seven
 microsatellite loci collected from 272 individuals sampled from
 Takapourewa/Stephens Island, New Zealand between March 2003–March 2007.
 Sampling occurred at eight sites on the island and was distributed
 throughout the available remnant forest and pasture landcover
 types. For simulated tuatara and eastern massasauga
 microsatellite genotypes we used program BOTTLESIM to to simulate multiple
 bottleneck scenarios for each species. For all simulations, we performed
 1,000 iterations and set the reproductive system as dioecy with random
 mating, a 1:1 sex ratio, and 100% generational overlap.
 For simulation dataset 1, simulations varied by 1) length of time
 (<i>t</i><sub>B</sub>): 50, 100, and 200 years, 2)
 starting population size (<i>N</i><sub>0</sub>):
 estimated census population size and one order of magnitude above and
 below, and 3) bottlenecked population size
 (<i>N</i><sub>B</sub>): 20, 50, 100, 1000, and
 <i>N</i><sub>0</sub> (the lattermost
 <i>N</i><sub>B</sub> =
 <i>N</i><sub>0</sub> scenario representing a
 constant population size with no bottleneck). For eastern massasauga
 simulations, we assumed a census population size of 6,300 individuals, age
 of sexual maturity of 5 years, and longevity of 12 years. For tuatara
 simulations, we assumed a census population size of 25,000 individuals,
 age of sexual maturity of 14 years, and longevity of 80 years.
 For simulation dataset 2, we randomly selected seven loci from
 the eastern massasauga dataset. Using this reduced dataset, we conducted a
 set of simulations with the same values for
 <i>t</i><sub>B</sub> and
 <i>N</i><sub>B</sub> as described above and set
 <i>N</i><sub>0</sub> equal to estimated census
 population size. For simulation dataset 3, we simulated
 bottlenecks using the values for
 <i>t</i><sub>B</sub> and
 <i>N</i><sub>B</sub> described above and set
 <i>N</i><sub>0</sub> equal to estimated census
 population size for each species. Age of sexual maturity and longevity
 were set at 10 years and 50 years, respectively, for both
 species.
description: All datasets are in Genepop format and missing data are indicated
 with 000000.