Genomic and phenotypic delimitation of species in a temperate aquatic biodiversity hotspot

Biologists have relied on morphological characteristics to identify, define, and formally describe species for the past 250 years. The advent of phylogenetic species concepts and the introduction of molecular data have spawned new species delimitation methods applicable to a wide range of eukaryotic lineages. However, these approaches heavily emphasize genomic data, often overlooking phenotypic traits. We present and implement a species delimitation approach that utilizes genome-wide markers from ddRAD-seq and meristic morphological traits, which have long been used to identify and delineate fish species. Our methodology employs unsupervised machine learning to analyze morphological data without a priori species assignments, allowing phenotypic patterns to emerge independently from genomic-based species delimitation. We apply our combined genomic and phenotypic methodology to the freshwater systems of Southeastern North America, a biodiversity hotspot where conservation efforts are hamp..., , , # Data from: Genomic and phenotypic delimitation of species in a temperate aquatic biodiversity hotspot

Dryad DOI: https://doi.org/10.5061/dryad.r4xgxd2q4

## ipyrad.tar

iPyrad parameters for ddRAD assembly

* params-Allohistium_ref.txt: ipyrad parameter file used to assemble dataset, no missing data filtering
* params-Allohistium_ref_m80p.txt: ipyrad parameter file used to assemble dataset, no missing data filtering with a min_samples_locus threshold of 80 samples (>80% samples per locus)
* params-Allohistium_ref_m90p.txt: ipyrad parameter file used to assemble dataset, no missing data filtering with a min_samples_locus threshold of 90 samples (>90% samples per locus)
* params-Allohistium_ref_m95p.txt: ipyrad parameter file used to assemble dataset, no missing data filtering with a min_samples_locus threshold of 95 samples (>95% samples per locus)

## IQTree.tar

Data, scripts, and results of IQGTree analyses

* m80p
* Allohistium_ref_m80p.phy: phylip formatted concatenated ddRAD a...,