Gene flow and habitat heterogeneity shape coexistence dynamics of Arctic charr morphs in connected lakes

Sympatric morphs provide valuable systems for studying incipient divergence despite incomplete reproductive isolation. In connected waterbodies with spatially heterogeneous habitats, one or more morphs may form metapopulation structures, generating eco-evolutionary dynamics unlike those in single lakes. We studied the phenotypic and genome-wide differentiation in Arctic charr (Salvelinus alpinus) in two Icelandic lakes (Thingvallavatn, known to harbour four distinct morphs, and a smaller downstream lake, Ulfljotsvatn), using geometric morphometrics, diet analysis, genome-wide SNPs acquired via double digest Restriction-site Associated DNA sequencing (ddRADseq) and two morph-associated mitochondrial markers. Our analyses confirm a single origin of charr polymorphism in this system, with all morphs present in both lakes. Relative morph abundances differ between the lakes: PL-charr dominate in Thingvallavatn, whereas LB-charr are most abundant in Ulfljotsvatn. Three morphs, large- (LB-), s..., , , # Gene flow and habitat heterogeneity shape coexistence dynamics of Arctic charr morphs in connected lakes

Dataset DOI: [10.5061/dryad.9cnp5hqvv](https://doi.org/10.5061/dryad.9cnp5hqvv)

## Description of the data and file structure

This repository contains relevant information and files generated for Arctic Charr (*Salvelinus alpinus*) samples (N = 286) for the paper titled \"Gene flow and habitat heterogeneity shape coexistence dynamics of Arctic charr morphs in connected lakes\" (https://onlinelibrary.wiley.com/doi/10.1111/mec.70225).

## Files and variables

#### File: Basic_information_TVV-UVV_Arctic_Charr.csv

**Description:** In this file, each sample's original ID (Nr.), type, correlated DNA ID (used for sequencing data in genepopfile and MtDNA genotype), photo ID (used in the TPS file for geometric morphometrics), and other information (sampling site and sampling year) are provided. 

#### File: MtDNA_genotype_TVV-UVV_Arctic_charr.csv

**Description:** The genotype of the two ..., ,