Publications by Year: Submitted

Submitted
Ulmo Diaz, Gabriela, Augustin Engman, Bill McLarney, Carlos Lasso Alcalá, Dean A. Hendrickson, Etienne Bezault, Eric Fenteun, et al.One species, one population: panmixia in American Eel (Anguilla rostrata) extends to its tropical range of distribution.” Molecular Ecology.Abstract
The American Eel (Anguilla rostrata) has long been regarded as a panmictic fish and has been confirmed as such in the northern part of its range. In this paper, we tested for the first time whether panmixia extends to the tropical range of the species. To do so, we first assembled a reference genome (975 Mbp, 19 chromosomes) in order to support both this study and future research. To test for population structure, we estimated genotype likelihoods from low coverage whole genome sequencing of 460 American Eels, collected at 21 sampling sites (in seven geographic regions) ranging from Canada to Trinidad and Tobago. We estimated genetic distance between regions, performed ADMIXTURE-like clustering analysis and multivariate analysis, and found no evidence of population structure. In addition, two genomic regions with putative inversions were observed, both geographically widespread and present at similar frequencies in all regions. We discuss the implications of lack of genetic population structure for the species. Our results are key for the future genomic research in the American Eel and the implementation of conservation measures throughout its geographic range.
Stewart, David R., Thomas Hafen, Dean A. Hendrickson, Andrew T. Taylor, Alejandro Varela-Romero, Daniel H. Mason, Joseph C. Dysthe, et al.Development and application of environmental DNA (eDNA) markers to assess factors affecting occupancy of the endangered Yaqui Catfish and non-native Channel Catfish in the Yaqui River basin, Mexico.” Endangered Species Research, n/a, n/a.Abstract
Acquiring data on rare and threatened species can be challenging, particularly in remote areas. However, environmental DNA (eDNA) surveys offer a less effort-intensive method of detecting these species than more traditional fish sampling methods. In our study, we focused on the Yaqui Catfish (Ictalurus pricei), an endangered freshwater fish endemic to the Sonoran desert (Arizona, US and Sonora, Mexico), and the non-native Channel Catfish (Ictalurus punctatus). To detect these species, we developed and employed mitochondrial DNA markers and a stratified random sampling method. We collected water samples for eDNA detection from 35 locations in the Yaqui River basin in Mexico. Using a hierarchical Bayesian formulation of a co-occurrence model, we examined the effects of interacting species, where one species is dominant (Channel Catfish) and the other subordinate (Yaqui Catfish), while allowing for the effects of covariates to be specified on species occupancy and detection. Our best model included the influence of non-native Channel Catfish on detecting native Yaqui Catfish. Moreover, we found that detection of Channel Catfish was negatively related to water temperature and elevation, but positively related to substrate size. Occupancy of Yaqui Catfish was best explained by stream permanence (i.e., higher rates of stream discharge and low probabilities of the reach drying) and forested areas. Channel Catfish were also associated with stream permanence (i.e., low probabilities of the stream reach drying and larger upstream watershed areas) and conifer and shrub-dominated landscapes. Non-native Channel Catfish eDNA was found in all but five locations where Yaqui Catfish eDNA was detected, indicating a high likelihood of interaction and hybridization. The threat of hybridization to the already endangered Yaqui Catfish highlights the need to secure remaining populations for their long-term survival.
Turner, Thomas, Henry L. Bart Jr., Frank McCormick, Alexi Besser, Rachel Bowes, Krista D. Capps, Emily DeArmon, et al.Long-Term Ecological Research in Freshwaters Enabled by Regional Biodiversity Collections, Stable Isotope Analysis, and Environmental Informatics.” Bioscience.Abstract
Biodiversity collections are experiencing a renaissance fueled by the intersection of informatics, emerging technologies, and the extended use and interpretation of specimens and archived databases. This paper explores the potential for transformative research in ecology integrating biodiversity collections, stable isotope analysis (SIA), and environmental informatics. Like genomic DNA, SIA provides a common ‘currency’ interpreted in the context of biogeochemical principles. Integration of SIA data across collections allows for evaluation of long-term ecological change at continent-wide scales. Challenges, including analysis of sparse samples, lack of isotopic baselines, and effects of preservation remain but none are insurmountable. The general research framework proposed here interfaces with databases and observatories, such as the National Ecological Observatory Network (NEON), to provide baselines for retrospective studies and ecological forecasting. Collections and SIA add historical context to fundamental questions in freshwater ecological research, baselines for ecosystem monitoring, and a means of quantitative assessment for ecosystem restoration.