DOI: 10.5061/dryad.jdfn2z3jj
title: Phenotypic and genomic signatures of latitudinal local adaptation along with prevailing ocean current in a coastal goby

description: In the marine realm, unidirectional ocean currents often lead to high
 migration rates of marine organisms and, therefore, inhibit the formation
 of their latitudinal genetic structure. In contrast, cryptic latitudinal
 structures associated with local adaptation may frequently exist in
 widespread species generally exposed to a strong environmental
 heterogeneity. However, our understanding of the evolvability of locally
 adapted populations in open marine environments still needs to be
 completed. The coastal area along the Sea of Japan, where the Tsushima
 Warm Current flows from south to north in the Japanese Archipelago,
 provides a good model system for exploring this question. This study
 explored evidence for latitudinal local adaptation along with the
 prevailing ocean current in the ice goby Leucopsarion petersii at the
 phenotypic and genomic levels. Common garden experiments clearly showed
 genetically-based clinal variation in growth rate, strongly suggesting
 local adaptation through counter gradient selection of this
 fitness-related trait. Analyses based on reduced-representation sequencing
 revealed a slight signal of genetic differentiation between the southern
 and northern populations, although continuous historical gene flow between
 them was supported by demographic modeling. Also, whole-genome
 resequencing showed their past independent demographic history during the
 last glacial period. Thus, these results suggest that gene flow along with
 the prevailing ocean current is somewhat limited, and the populations are
 not completely panmictic. Furthermore, the selection scan based on
 low-coverage genome-wide sequencing detected putative genomic signatures
 of latitudinal adaptation of growth-related genes. Thus, our integrative
 study provided a novel example of marine local adaptation under a large
 ocean current.
description: # **Phenotypic and genomic signatures of latitudinal local adaptation
 along with prevailing ocean current in a coastal goby**
 [https://doi.org/10.5061/dryad.jdfn2z3jj](https://doi.org/10.5061/dryad.jdfn2z3jj) ## **Brief description of the data and file structure** It consists of three folders. The first is the SNP data used in the population analysis, the second is the main scripts used in this analysis, the third is the genome annotation files, and the fourth is the data from common garden experiments. Details are as follows. ### **SNP\_data.tar.gz** **RAD_all.vcf.gz** A vcf file from RAD-seq data including monomorphic sites **RAD_snp.vcf.gz** A vcf file from RAD-seq data **WGS_all.vcf.gz** A vcf file from WGS data including monomorphic sites **WGS_snp.vcf.gz** A vcf file from WGS data **angsdput.beagle.gz** A beagle file from lcWGS data ### **Scripts.tar.gz** **RAD** This directory includes scripts for population genetic analyses based on RAD-seq data **RAD_fastsimcoal** This directory includes scripts for fastsimcoal analyses based on RAD-seq data **WGS** This directory includes scripts for population genetic analyses based on WGS data **WGS_psmc** This directory includes scripts for PSMC analyses based on WGS data **Assembly** This directory includes scripts for genome assembly and gene prediction of the ice goby *Leucopsarion petersii*   ### **Gene\_prediction\_files.tar.gz** **shirouo_stringtie.gtf.fas.transdecoder.gff3** Gff3 file for the constrgenome assembly of the ice goby *Leucopsarion petersii* **shirouo_stringtie.gtf.fas.transdecoder.pep** Protein sequences for genome assembly of the ice goby *Leucopsarion petersii* ### **Common\_garden\_data.tar.gz** Please see the corresponding manuscript for all the methods for the collection and processing of data. **growth.xlsx** The file shows data about the mean larval body size (total length: mm) of each age (i.e., days post-hatching: 0, 10, 20, 30, 40, 50, and 60 days) in each rearing tank (n = 3 tanks per population per temperature) in two types of common garden experiments. ExcelSheet 1 (3_pop) contains data in the first common garden experiment with a single using rearing temperature (18°C) using three different latitudinal populations (AJ, FK, and SG; see supplementary Table S1 about population IDs). ExcelSheet 2 (2_pop) contains data in the second common garden experiment with multiple rearing temperatures (i.e., 15, 20, 25°C) using two different latitudinal populations (AJ and SG).  **development.xlsx** The file shows data about the number of dorsal and anal fin rays and dorsal and anal fin supports (i.e., pterygiophores) of each larval specimen under the common garden experiment using two different latitudinal populations (AJ and SG; see supplementary Table S1 about population IDs). Data about rearing temperature (i.e., 15, 20, 25°C), age (i.e., days post-hatching: 0, 10, 20, 30, 40, 50, and 60 days), and body size (total length: mm) are also included for each larval specimen.