Sampling related individuals within ponds biases estimates of population structure in a pond‐breeding amphibian

Abstract

Effective conservation and management of pond‐breeding amphibians depends on the accurate estimation of population structure, demographic parameters, and the influence of landscape features on breeding‐site connectivity. Population‐level studies of pond‐breeding amphibians typically sample larval life stages because they are easily captured and can be sampled nondestructively. These studies often identify high levels of relatedness between individuals from the same pond, which can be exacerbated by sampling the larval stage. Yet, the effect of these related individuals on population genetic studies using genomic data is not yet fully understood. Here, we assess the effect of within‐pond relatedness on population and landscape genetic analyses by focusing on the barred tiger salamanders (Ambystoma mavortium) from the Nebraska Sandhills. Utilizing genome‐wide SNPs generated using a double‐digest RADseq approach, we conducted standard population and landscape genetic analyses using datasets with and without siblings. We found that reduced sample sizes influenced parameter estimates more than the inclusion of siblings, but that within‐pond relatedness led to the inference of spurious population structure when analyses depended on allele frequencies. Our landscape genetic analyses also supported different models across datasets depending on the spatial resolution analyzed. We recommend that future studies not only test for relatedness among larval samples but also remove siblings before conducting population or landscape genetic analyses. We also recommend alternative sampling strategies to reduce sampling siblings before sequencing takes place. Biases introduced by unknowingly including siblings can have significant implications for population and landscape genetic analyses, and in turn, for species conservation strategies and outcomes.

‘Mainland-island’ population structure of a terrestrial salamander in a forest-bocage landscape with little evidence for in situ ecological speciation

“…30 27 and the more or less frequent sampling of full-and half-siblings in our study cannot be excluded. However, excluding all but one members of a family group is not exempt from problems neither and will cause other biases 78,79 . Considering the moderate number of markers and alleles in either of the two data sets we tested for the presence of full-siblings in the material at two levels.…”

Gene flow and climate‐associated genetic variation in a vagile habitat specialist

“…Multiple larval samples were often collected from single or adjacent A. dracunculus plants. Full‐sibling relationships between individuals are therefore probable due to females ovipositing multiple eggs on single plants, which may bias inferences of genetic divergence and population structure (O'Connell, Mulder, Maldonado, Currie, & Ferraro, 2019). To identify full sibs, we used the package “SNPRelate” (Zheng et al., 2012) implemented in the R environment (v3.5.1; R Core Team) to estimate kinship coefficients for all pairs of sequenced individuals.…”

Riverine barriers to gene flow in a salamander with both aquatic and terrestrial reproduction

“…We sampled during rainy nights of early spring (from March to April of 2019) and autumn (October and November of 2018 and 2019), thus matching the peaks of activity of adult re salamanders in northern Spain (Velo-Antón and . We sampled adults to prevent spurious estimates of genetic structure arising from an excessive sampling of related individuals because larvae and, to a less extent juveniles, are often spatially clustered (Wang, 2018;O'Connell et al, 2019). We collected toe clips from a total of 311 individuals (191 larviparous and 120 pueriparous salamanders) in 11 localities (mean ± SD: 28 ± 10.5 individuals per locality).…”

“…We performed ten independent runs for K = 2 and each run was set to 500,000 iterations with a burn-in period of 10 %. Moreover, the inclusion of related individuals in the analyses may overestimate population genetic structure (Wang, 2018;O'Connell et al, 2019). Accordingly, we removed an individual from each pair of rst-order relatives (R TRI ≥ 0.5, parent-offspring and full-sibs) in those localities that showed some evidence of genetic structure between riversides.…”