Because of their longevity and endurance, turtles often function as indicators of environmental quality for the ecosystems they occupy. Evaluation of sublethal physical abnormalities in freshwater turtles can provide insight into the extent of environmental stressors. The lower Pecos River, located in the southwestern USA, has undergone anthropogenic disturbance through dam construction, channelization, and oil and gas extraction, with the recent megadrought further affecting water quality and availability. These stressors can be manifested in physical abnormalities and cumulatively affect the fitness of freshwater turtles in this fragile ecosystem. We examined photographs of 674 emydid turtles captured at 16 sites on the lower Pecos River in Eddy County, New Mexico, in 2020 and 2021. We looked for signs of poor body condition such as missing limbs, abnormal shell shape, and shell lesions. We also recorded cases of melanism in males and documented abnormal scutellation. Shell lesions, characterized by pitting with irregular flaking on the carapace and plastron, were the most common abnormality documented in Rio Grande cooters (Pseudemys gorzugi; mean prevalence per site = 21%) and red-eared sliders (Trachemys scripta elegans; mean prevalence per site = 32%). For P. gorzugi, the next most frequent abnormality was abnormal scutellation (mean prevalence per site = 12%), while T. s. elegans showed comparable rates of abnormal scutellation (mean prevalence per site = 11%) and “other” abnormalities (mean prevalence per site = 12%). The most severe “other” abnormality cases (e.g., abnormal shell shape and missing limbs) could be attributed to predation attempts or human-caused injuries, including heavy agricultural machinery and boat propellers. Melanism was documented in male P. gorzugi (mean prevalence per site = 10%) and male T. s. elegans (mean prevalence per site = 32%), likely representing older individuals. Despite the relatively high prevalence of milder abnormalities such as abnormal scutellation, further study is needed on their causes in the context of the lower Pecos River environmental conditions during turtle development. We emphasize the importance of assessing physical abnormalities while conducting freshwater turtle surveys and encourage future research to explore potential genetic and environmental factors that affect embryonic and post-hatching development of turtles.

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