Concordant geographic and genetic structure revealed by genotyping‐by‐sequencing in a New Zealand marine isopod

Abstract

Population genetic structure in the marine environment can be influenced by life‐history traits such as developmental mode (biphasic, with distinct adult and larval morphology, and direct development, in which larvae resemble adults) or habitat specificity, as well as geography and selection. Developmental mode is thought to significantly influence dispersal, with direct developers expected to have much lower dispersal potential. However, this prediction can be complicated by the presence of geophysical barriers to dispersal. In this study, we use a panel of 8,020 SNPs to investigate population structure and biogeography over multiple spatial scales for a direct‐developing species, the New Zealand endemic marine isopod Isocladus armatus. Because our sampling range is intersected by two well‐known biogeographic barriers (the East Cape and the Cook Strait), our study provides an opportunity to understand how such barriers influence dispersal in direct developers. On a small spatial scale (20 km), gene flow between locations is extremely high, suggestive of an island model of migration. However, over larger spatial scales (600 km), populations exhibit a clear pattern of isolation‐by‐distance. Our results indicate that I. armatus exhibits significant migration across the hypothesized barriers and suggest that large‐scale ocean currents associated with these locations do not present a barrier to dispersal. Interestingly, we find evidence of a north‐south population genetic break occurring between Māhia and Wellington. While no known geophysical barrier is apparent in this area, it coincides with the location of a proposed border between bioregions. Analysis of loci under selection revealed that both isolation‐by‐distance and adaption may be contributing to the degree of population structure we have observed here. We conclude that developmental life history largely predicts dispersal in the intertidal isopod I. armatus. However, localized biogeographic processes can disrupt this expectation, and this may explain the potential meta‐population detected in the Auckland region.

Intraspecific genetic variation matters when predicting seagrass distribution under climate change

“…It is of great importance to consider species dispersal ability into SDMs when estimating climate change impacts (Araújo et al, 2006; Guisan et al, 2017). Given that species move across transregional barriers in marine environments (Pearman et al, 2020; Robinson et al, 2011) and the relatively high dispersal ability of T . hemprichii (Lacap et al, 2002), we estimated range size change under an unlimited dispersal scenario, which assumes that species have unrestricted dispersal ability and can disperse to any suitable area (Araújo et al, 2006; Zhang, Mammola, Liang, et al, 2020).…”

“…It is of great importance to consider species dispersal ability into SDMs when estimating climate change impacts (Araújo et al, 2006;Guisan et al, 2017). Given that species move across transregional barriers in marine environments (Pearman et al, 2020;Robinson et al, 2011) and the relatively high dispersal ability of T.…”

Commonly used Hardy-Weinberg equilibrium filtering schemes impact population structure inferences using RADseq data

“…We further found a significant reduction in STRUCTURE-inferred average nucleotide distance for the New Zealand isopod when comparing the ‘Out Any’ filter approach with ‘No Filter’ or ‘Out All’, while our comparable simulations showed no effect of this filter on inferred population structure via STRUCTURE. The discrepancies between the simulated and isopod analyses likely arise from the fact that simulations do not encapsulate the full complexity of real populations: Our simulations do not consider selection, while the isopod dataset was based on morphotypes thought to be under selection (Pearman et al, 2020; Wells & Dale, 2018).…”

“…In order to validate our results against empirical data and across multiple SNP calling pipelines, we selected three publicly available datasets as they represented a range of organisms, with a range of population structure: A DArTseq (Diversity Arrays Technology sequencing) dataset of a New Zealand isopod ( Isocladus armatus ) (Pearman et al, 2020), and two RADseq datasets of the New Zealand fur seal ( Arctocephalus forsteri ) (Dussex et al, 2018) and the Plains zebra ( Equus quagga ) (Larison et al, 2021). For the isopod dataset, the DArTseq genotypes were provided by diversityarrays™, who generated them using their proprietary SNP calling software with a de novo assembly (SRA: PRJNA643849, https://osf.io/kjxbm/).…”

Long read sequencing reveals atypical mitochondrial genome structure in a New Zealand marine isopod

“…We extracted DNA from one individual for Nanopore sequencing using a modified Qiagen DNEasy Blood and Tissue protocol, developed for I. armatus (Pearman et al, 2020). We extracted DNA from a second individual for Illumina sequencing using a modified Promega Wizard protocol.…”