Environmental conditions experienced during larval dispersal of marine organisms can determine size-at-settlement of recruits. It is, therefore, not uncommon that larvae undergoing different dispersal histories would exhibit phenotypic variability at recruitment. Here we investigated morphological differences in recently settled southern rock lobster (Jasus edwardsii) recruits, known as pueruli, along a latitudinal and temporal gradient on the east coast of Tasmania, Australia. We further explored whether natural selection could be driving morphological variation. We used double digest restriction-site associated DNA sequencing (ddRADseq) to assess differences in genetic structure of recently settled recruits on the east coast of Tasmania over three months of peak settlement during 2012 (August, September and October). Phenotypic differences in pueruli between sites and months of settlement were observed, with significantly smaller individuals found at the northernmost site. Also, there was a lack of overall genetic divergence; however, significant differences in pairwise FST values between settlement months were observed at the southernmost study site, located at an area of confluence of ocean currents. Specifically, individuals settling into the southernmost earlier in the season were genetically different from those settling later. The lack of overall genetic divergence in the presence of phenotypic variation indicates that larval environmental history during dispersal of J. edwardsii could be a possible driver of the resulting phenotype of settlers.

Four ddRADseq libraries were prepared from genomic DNA of Jasus edwardsii pueruli samples.

Libraries were sequenced at the Australian Genome Research Facility (AGRF) on the Illumina HiSeq 2500 platform using a 100 bp single-end kit

Quality check of raw indexed data: FastQC v0.10.1

Demultiplexing: “process_radtags” protocol from Stacks v1.29

Demultiplexed libraries were filtered for bacterial and viral content using Kraken-gcc v0.10.4.

Filtered reads were processed through a custom-built “rad-loci” pipeline (https://github.com/molecularbiodiversity/rad-loci)

Individual filtered reads of all samples were aligned to the reference catalog using bwa-intel v0.7.12.

Variant calling was performed using the Genome Analysis Toolkit (GATK) v3.3_0

SNP filtering was performed in vcftools-gcc v0.1.13.