Elizabeth P. Dolan

The Pecos pupfish, Cyprinodon pecosensis , is an imperilled freshwater fish found in arid regions of Texas and New Mexico (USA). The species faces multiple challenges to persistence including reductions in suitable habitat, water shortages, as well as hybridization and competition with an introduced congener (sheepshead minnow, C. variegatus ). As part of the current management strategy, refuge populations, seeded with non‐introgressed individuals collected from Texas, are maintained at the Fort Worth Zoo and on private property in West Texas. Therefore, assessments of standing genetic variation within and among wild and refuge populations and levels of admixture in the wild are critical for future conservation and management planning. Fin clips were acquired in 10 locations in the wild, five in Texas, five in New Mexico and from two refuge populations in Texas (one maintained by Fort Worth Zoo and another on a private property in West Texas). In Texas, non‐introgressed C. pecosensis were found in the wild at only one location Upper Salt Creek (USC); all other locations were composed of admixed individuals or non‐introgressed C. variegatus . No admixed individuals were found in New Mexico. Significant genetic heterogeneity was detected between all locations of non‐introgressed C. pecosensis , including the refuge populations, and estimates of divergence between Texas locations (USC and refuge populations) and New Mexico locations were relatively large ( F _ST : 0.23–0.32). Estimates of contemporary effective population size for USC and the two refuge populations were less than 50, but greater than 500 for all New Mexico populations. In summation, while New Mexico populations look secure, the data suggest that C. pecosensis in Texas is currently imperilled by the threat of hybridization, as well as potential loss of genetic diversity on contemporary time scales. Deep divergence between Texas (including refuge populations) and New Mexico suggests that further study would be needed prior to any management plans that would involve assisted gene flow between the regions.

Combined analyses of molecular and morphological data support a revised classification of Notropis stramineus comprising five distinct evolutionary lineages, two for which names are available, Notropis stramineus (Cope, 1865) and N. missuriensis (Cope, 1871), herein redescribed, and three for which no names are available, here formally described as new species. Four of these clades comprise a species complex, here termed the N. stramineus species complex, while these four clades, in addition to N. procne , N. topeka , N. chihuahua and the fifth clade form a monophyletic group here termed the N. stramineus species group. Notropis lucifer sp. nov. , sister taxon of N. chihuahua , is distributed in the Colorado River and Rio Grande basins of Texas (USA), where it is distributed in the Devils River, and presumably also in Pinto Creek; based on distribution, populations in tributaries of the Rio Grande in Mexico are tentatively also assigned to this species. Notropis lucifer sp. nov. can be distinguished from other members of the N. stramineus species group primarily by coloration in life and pigmentation patterns which are still visible after preservation. Notropis oblitus sp. nov. is found in several Gulf Slope streams in Texas, including the upper reaches of Nueces, San Antonio, and Guadalupe River basins, though likely absent from the Colorado River basin. This species can be distinguished from other members by head shape, eye size and pigmentation patterns. Notropis multicorniculatus sp. nov. is found in the western portions of the Arkansas, Canadian and Red River basins in parts of Texas, Oklahoma, and Kansas, and likely also Arkansas and Colorado, as well as the Pecos River (New Mexico), where it is likely non-native. This species can be distinguished from other members of the species complex by comparatively larger and more abundant tubercles in males and differences in body shape. Comments are provided regarding the genus Miniellus , which has been recently suggested to comprise 21 species, including N. stramineus .

The Leon Springs pupfish, Cyprinodon bovinus , is federally listed as endangered and currently confined to spring-fed pools on the Diamond Y Spring Preserve in Pecos County, Texas, USA. A refuge population is maintained by U.S. Fish and Wildlife Service in Dexter, New Mexico, USA because of ongoing threats from hybridization with the introduced congener, the sheepshead minnow, C. variegatus. To inform continued conservation and management planning for this species, a comprehensive conservation genomics study using double digest restriction-site associated DNA sequencing was performed. No evidence of contemporary hybridization or recent introgression between C. bovinus and C. variegatus was found. The refuge population was significantly differentiated from wild samples collected at two locations, and the two wild populations (less than 1 km apart) also exhibited significant heterogeneity in allele frequencies. Estimates of within population diversity were smaller for wild locations than the refuge population. Correspondingly, the wild populations’ contemporary effective population size estimates were smaller than the refuge’s effective population size estimates (145–262 versus 679). Temporal analyses, involving genetic data collected from samples obtained in 2013, suggest an increased magnitude of drift acting on the wild populations relative to the reserve population. Based on the results of this study, it appears that steps taken in the early 2000s to eradicate genetically admixed individuals from the wild populations were successful. However, habitat fragmentation and small effective population sizes of the wild populations have led to accelerated drift and decreasing levels of within population genetic diversity. This may jeopardize the long-term persistence of C. bovinus .

Gambusia nobilis is a federally endangered species found across a fragmented distribution within the Pecos River Drainage of Texas and New Mexico, USA. Drought, human water usage, and potential hybridization and competition with introduced congeners threaten species persistence. Therefore, a population genomics study was conducted to provide critical information for conservation planning. Unsupervised clustering suggested hierarchical structure, with a primary K = 3, and deep divergences were detected among samples grouped into the Leon Creek watershed, the Toyah Creek watershed, and water bodies within the Bitter Lake National Wildlife Refuge ( F’ _ST = 0.55–0.76 for putatively neutral data). Phylogenetic analyses showed three distinct clades corresponding to these groups, with divergence times estimated to be in the last 50 000 years. Complimentary morphological analyses detected differences among the three groups, including features of male colour pattern, and the number of caudal-fin rays in both sexes. Taken as a whole, the results indicate that the endangered G. nobilis comprises three species (two of which are named herein as G. pyrros n. sp. and G. echelleorum n. sp.), rather than one, and the study highlights the daunting yet critical task of documenting species diversity during a period of unprecedented diversity loss.