Contrasting gene flow at different spatial scales revealed by genotyping-by-sequencing inIsocladus armatus, a massively colour polymorphic New Zealand marine isopod

Abstract

Understanding how genetic diversity is maintained within populations is central to evolutionary biology. Research on colour polymorphism (CP), which typically has a genetic basis, can shed light on this issue. However, because gene flow can homogenise genetic variation, understanding population connectivity is critical in examining the maintenance of polymorphisms. In this study we assess the utility of genotyping-by-sequencing to resolve gene flow, and provide a preliminary investigation into the genetic basis of CP in Isocladus armatus, an endemic New Zealand marine isopod. Analysis of the genetic variation in 4,000 single nucleotide polymorphisms (SNPs) within and among populations and colour morphs revealed large differences in gene flow across two spatial scales. Marine isopods, which lack a pelagic larval phase, are typically assumed to exhibit greater population structuring than marine invertebrates possessing a biphasic life cycle. However, we found high gene flow rates and no genetic subdivision between two North Island populations situated 8 km apart. This suggests that I. armatus is capable of substantial dispersal along coastlines. In contrast, we identified a strong genetic disjunction between North and South Island populations. This result is similar to those reported in other New Zealand marine species, and is congruent with the presence of a geophysical barrier to dispersal down the east coast of New Zealand. We also found some support for a genetic basis to colouration evidenced by positive FST outlier tests, with two SNPs in particular showing strong association to the expression of a striped morph. Our study provides one of the first population genomic studies of a marine organism in New Zealand, and suggests that genotyping-by-sequencing can be a good alternative to more traditional investigations based on traditional markers such as microsatellites. Our study provides a foundation for further development of a highly tractable system for research on the evolutionary maintenance of CP.

Population structure and dispersal across small and large spatial scales in a direct developing marine isopod

“…Endemic to New Zealand, this massively colour polymorphic 80 species is found in abundance on semi-sheltered rocky shorelines throughout the country 81 (Jansen, 1971). A previous study concluded that this direct-developing isopod species can 82 exhibit high dispersal rates because no significant population divergence was found between 83 two sites separated by 11km of coastline (Wells & Dale, 2018). In contrast, strong population 84 genetic structure was evident on a much larger scale (1,000kms).…”

“…including restriction enzyme choice are described in detail in Wells and Dale (2018). DaRT 115 performs SNP calling using a proprietary pipeline.…”

“…The maximum distance between 101 individuals collected at any site did not exceed 30 m. Samples were stored at -80°C in 100% 102 ethanol until extraction. We have included previously collected samples from 2015 (see 103 (Wells & Dale, 2018) for sampling methods) to increase the number of sampled individuals 104 and the range of location. In addition, the temporal structure of this sampling may yield 105 insight into the short-term changes in allele frequencies within a population.…”

“…We extracted DNA following a modified Qiagen DNEasy Blood and Tissue protocol from 108 Wells and Dale (2018). Briefly, we used 178 µl of 0.5M EDTA and 22 µl of 20% SDS in each 109 extraction (rather than varying volumes by weight of tissue).…”

“…Isocladus armatus exhibits a wide range of colour morphs, which we refer to as striped, 523 variegated, white, unpatterned, or other (Wells and Dale 2018). During the collection of 524 individuals to quantify population structure, we collected at least 32 individuals from each 525 location ( Supplementary Table 1).…”