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Under the radar: genetic assessment of Rio Grande Shiner (Notropis jemezanus) and Speckled Chub (Macrhybopsis aestivalis), two Rio Grande basin endemic cyprinids that have experienced recent range contractions

Citation

Osborne, Megan et al. (2020), Under the radar: genetic assessment of Rio Grande Shiner (Notropis jemezanus) and Speckled Chub (Macrhybopsis aestivalis), two Rio Grande basin endemic cyprinids that have experienced recent range contractions , Dryad, Dataset, https://doi.org/10.5061/dryad.4b8gthtb7

Abstract

The Rio Grande drainage of the southwestern United States and Mexico has undergone intense anthropogenic alteration by water diversions, extraction and associated habitat changes. These alterations have disproportionately impacted the pelagic broadcast spawning guild of minnows (pelagophils). Several Rio Grande endemic pelagophils, including the co-occurring Rio Grande Shiner (Notropis jemezanus) and Speckled Chub (Macrhybopsis aestivalis), have experienced dramatic recent range-wide declines yet have slipped under the radar of conservation efforts. The status of N. jemezanus and M. aestivalis in the Rio Grande and Pecos River was evaluated and standing genetic variation were characterized. Genetic evidence indicates that populations of both species found in the Rio Grande and Pecos River are genetically distinct. Additionally, 159 outlier loci were identified in M. aestivalis suggesting possible local adaptation in the Rio Grande and Pecos River populations. Though range-wide genetic data are limited, N. jemezanus populations in both rivers harbor considerable genetic diversity. Mitochondrial data from both taxa are consistent with a history of secondary contact between formerly isolated populations with deeply divergent haplotypes found within the Rio Grande and Pecos River populations of N. jemezanus and within the Rio Grande population of M. aestivalis. Extensive survey efforts in the lower Rio Grande and its tributaries in Texas document significant range contraction and near extirpation of N. jemezanus from this part of the basin; highlighting the need for immediate action to protect the species. 

Methods

Mitochodrial DNA sequence data collected using Sanger sequencing of DNA isolated from fin clip tissue samples. Sequences were edited and verified using Sequencher. Haplotype sequences are deposited on Genbank.

Microsatellite data collected using ABI3130 capillary sequencer and verified usign Genemapper software.

ddRAD sequence data is provided in .vcf files for Notropis jemezanus and Macrhybopsis aestivalis. Data processing steps are provided on GITHUB. Detail are provided in the associated publication.

Usage Notes

Missing values in microsatellite data are indicated by "0"

Ambiguous base calls are indicated by "n"

Funding

U.S. Fish and Wildlife Service Section 6 Cooperative Endangered Species Conservation Fund , Award: CFDA# 15.615

Texas Parks and Wildlife Department, Award: TX E-168-R-1

Texas A&M Agrilife Research, Award: TEX09452

New Mexico Department of Game and Fish-Share with Wildlife Program

New Mexico Department of Game and Fish-Share with Wildlife Program