Discordant phylogeographic patterns in ecologically similar sympatric sister species: Revisiting the null hypothesis of comparative phylogeography

Unravelling the complex factors underlying the current geographic patterns of biodiversity is a fundamental goal of biogeography and phylogeography. Comparative phylogeographic studies of co-distributed species have often addressed this issue by attributing observed differences in population structures to differences in interpretable traits between species. However, this approach implicitly relies on the largely untested assumption that species sharing similar ecological, spatial, and phylogenetic contexts should exhibit similar population structures. Herein, we revisited this null hypothesis of phylogeography by comparing the population structures of two sympatric sister species with high ecological similarity using high-throughput genomic data. With extensive sampling and advanced genomic analyses, we revealed the fine-scale population structure of Chaenogobius gulosus, enabling a direct comparison with the well-documented phylogeography of C. annularis. Our findings indicate that the..., We obtained mitochondiral sequence data (154 samples from 26 locations) and ddRAD-seq data (88 samples from 21 locations) for Chaenogobius gulosus, a coastal goby species inhabiting the Japanese Archipelago. For comparison, we also used the published data for C. annularis as necessary. Our analyses included generation of the pseudo-reference sequence for C. gulosus, population genetic analysis, and Bayesian demographic inference, and demographic modeling., , # Discordant phylogeographic patterns in ecologically similar sympatric sister species: Revisiting the null hypothesis of comparative phylogeography

[https://doi.org/10.5061/dryad.t4b8gtjcb](https://doi.org/10.5061/dryad.t4b8gtjcb)

## Description of the data and file structure

The resources in this link encompass scripts, genotyping data, and analysis results used to examine the phylogeographic structure of two closely related goby species, *Chaenogobius gulosus* and *C. annularis*. These resources are based on mitochondrial DNA and double-digested restriction-site associated sequence (ddRAD-seq) data for both species collected from multiple locations in Japan.

### Brief description of the data and file structure

#### scripts.tar.gz

The scripts used in this study (bash, python, perl, R).

These scripts are categorized into the following 4 contents, which are hierarchized within each directory.

01.mtDNA analysis

02.pseudoreference generation

03.ddRADseq genotyping

04.ddRADseq a...,