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Geographic distribution of genetic diversity in populations of Rio Grande Chub Gila pandora

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Abstract

In the southwestern United States (US), the Rio Grande chub (Gila pandora) is state-listed as a fish species of greatest conservation need and federally listed as sensitive due to habitat alterations and competition with non-native fishes. Characterizing genetic diversity, genetic population structure, and effective number of breeders will assist with conservation efforts by providing a baseline of genetic metrics. Genetic relatedness within and among G. pandora populations throughout New Mexico was characterized using 11 microsatellite loci among 15 populations in three drainage basins (Rio Grande, Pecos, Canadian). Observed heterozygosity (HO) ranged from 0.71–0.87 and was similar to expected heterozygosity (0.75–0.87). Rio Ojo Caliente (Rio Grande) had the highest allelic richness (AR = 15.09), while Upper Rio Bonito (Pecos) had the lowest allelic richness (AR = 6.75). Genetic differentiation existed among all populations with the lowest genetic variation occurring within the Pecos drainage. STRUCTURE analysis revealed seven genetic clusters. Populations of G. pandora within the upper Rio Grande drainage (Rio Ojo Caliente, Rio Vallecitos, Rio Pueblo de Taos) had high levels of admixture with Q-values ranging from 0.30–0.50. In contrast, populations within the Pecos drainage (Pecos River and Upper Rio Bonito) had low levels of admixture (Q = 0.94 and 0.87, respectively). Estimates of effective number of breeders (N b ) varied from 6.1 (Pecos: Upper Rio Bonito) to 109.7 (Rio Grande: Rio Peñasco) indicating that populations in the Pecos drainage are at risk of extirpation. In the event that management actions are deemed necessary to preserve or increase genetic diversity of G. pandora, consideration must be given as to which populations are selected for translocation.

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Acknowledgments

Support was provided by the United States (US) Forest Service—Santa Fe National Forest (C. Cook) (IAG 09-IA-11031000-008), the US Bureau of Land Management (G. Gustina) (No. L09PG00403), and New Mexico Department of Game and Fish—Share with Wildlife Program. Field support was provided by R. Hansen of New Mexico Department of Game and Fish, M. Zeigler and S. Hall of New Mexico State University, Department of Fish, Wildlife and Conservation Ecology. Laboratory support was provided by R. Martin and M. Robinson, US Southwestern Aquatic Resources and Recovery Center. Additional support was provided by the Department of Fish, Wildlife and Conservation Ecology at New Mexico State University. This manuscript was substantially improved by comments from M. McPhee, R. Martin, M. Robinson, and T. Diver. Field collections were allowed under New Mexico Department of Game and Fish Authorization for Taking Protected Wildlife for Scientific and Educational Purposes Permit 3033 and New Mexico State University Institutional Animal Care and Use Committee Protocol 2011-003. Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the United States Government.

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Authors and Affiliations

  1. Department of Fish, Wildlife and Conservation Ecology, New Mexico State University, 2980 South Espiña Street, Las Cruces, NM, 88003, USA

    René Galindo

  2. Southwestern Native Aquatic Resources and Recovery Center, U.S. Fish and Wildlife Service, 7116 Hatchery Road, Dexter, NM, 88230, USA

    Wade D. Wilson

  3. New Mexico Cooperative Fish and Wildlife Research Unit, U.S. Geological Survey, 2980 South Espiña Street, Las Cruces, NM, 88003, USA

    Colleen A. Caldwell

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Correspondence to Colleen A. Caldwell.

Electronic supplementary material

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10592_2016_845_MOESM1_ESM.docx

Supplementary material 1 (DOCX 87 kb). Fig. S1 Plot of Bayesian Information Criterion (BIC) against increasing values of K (genetic clusters). This plot was used to find the optimal number of genetic clusters that best described the data and was generated using the function find.clusters in adegenet (Jombart 2008; Jombart and Ahmed 2011). This function runs the K-means sequentially with increasing values of K and compares models using BIC and plots these against increasing values of K.

10592_2016_845_MOESM2_ESM.docx

Supplementary material 2 (DOCX 16 kb). Table S1 Eleven microsatellite loci that cross-amplified with Rio Grande chub populations for characterization of genetic diversity. [PS = Primer set used to group locus for screening; Locus = Locus name; Dye = fluorescent color used to label locus; Species = Species used to develop locus; Primer Sequences = forward and reverse primer sequence; bp = base pairs; T m (oC) F/R = melting temperatures in degrees Celsius of the PCR product in forward and reverse]

10592_2016_845_MOESM3_ESM.docx

Supplementary material 3 (DOCX 55 kb). Table S2 Summary statistics of 11 microsatellite loci used to genotype Gila pandora populations throughout New Mexico. Rio Grande Drainage: Alamosa Creek (1); East Fork Jemez River (2); Jemez River (3); Rio Guadalupe (4); Rio Cebolla (5); Rio de las Vacas (6); Rito Peñas Negras (7); El Rito (8); Rio Ojo Caliente (9); Rio Vallecitos (10); Rio Pueblo de Taos (11); Canadian Drainage: Cieneguilla Creek (12); Pecos River Drainage: Pecos River (13); Upper Rio Bonito (14); Rio Peñasco (15). Number of alleles (NA), allelic richness (AR), observed heterozygosity (HO), expected heterozygosity (HE), Hardy-Weinberg (HW), and inbreeding coefficient (FIS) are provided. ‘ns’ represents non-significant and *** represents P < 0.0001.

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Galindo, R., Wilson, W.D. & Caldwell, C.A. Geographic distribution of genetic diversity in populations of Rio Grande Chub Gila pandora . Conserv Genet 17, 1081–1091 (2016). https://doi.org/10.1007/s10592-016-0845-2

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