Phenotypic and genomic signatures of latitudinal local adaptation along with prevailing ocean current in a coastal goby

Published Nov 01, 2024 on Dryad. https://doi.org/10.5061/dryad.jdfn2z3jj

Data files

Nov 01, 2024 version files 1.03 GB

Abstract

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.

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.