Rio Conchos pupfish microsatellite and mDNA data for population genetics

Understanding genetic and phylogenetic relationships among closely related species is critical for effective conservation planning. In the Rio Conchos basin of northern Mexico, Cyprinodon eximius has a widespread distribution, occurring alongside neighboring microendemic species: C. julimes, C. macrolepis. C. pachycephalus, and C. salvadori. Both the widespread C. eximius and the microendemic congeners face threats from climate change and anthropogenic habitat modification. We utilized 20 nuclear microsatellites and sequenced the mitochondrial cytochrome b region to investigate the evolutionary history and genetic structuring among these taxa. Our analyses revealed multiple genetically distinct groups within C. eximius, including strong divergence in the Devils River, Texas, population. We also found support for recognizing the microendemic populations across the basin as distinct species. However, discordance between mitochondrial and nuclear data indicates historical introgression bet..., , # Rio Conchos pupfish microsatellite and mDNA data for population genetics

Dataset DOI: [10.5061/dryad.8cz8w9h6t](https://doi.org/10.5061/dryad.8cz8w9h6t)

## Description of the data and file structure

Fish were collected with seines and minnow traps. Fin clips of these individuals were preserved in 98% ethanol for genetic analysis. 20 microsatellite markers developed for Conchos pupfish were used. 

For mtDNA, we sequenced 601-bp section of cytochrome b. We also used previously published sequences for 4 individuals. 

### Files and variables

#### File: pupfish_haplotypes.fasta

**Description:** mtDNA sequences

#### File: conchos_julimes_csv.csv

**Description:** microsatellite read lengths

##### Variables

* 12: microsatellite markers
* 379: individuals
* 12: populations

#### File: hap_info.txt

**Description:** meta data for the mtDNA sequences

##### Variables

* group: individuals
* population: sampling location, population name
* species: species name 

## Code/software

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