Patterns of genetic divergence in the Rio Grande cooter (Pseudemys gorzugi), a riverine turtle inhabiting an arid and anthropogenically modified system.

The lower Rio Grande and Pecos River of the southwest United States have been heavily modified by human activities, profoundly impacting the integrity of their aquatic wildlife. In this context, we focused our study on the population genomics of the Rio Grande Cooter (Pseudemys gorzugi), a freshwater turtle of increasing conservation concern, residing in these two rivers and their tributaries. The genetic data revealed two distinct populations: one in the Pecos and Black Rivers of New Mexico and another in the Rio Grande and Devils River of Texas, with admixed individuals identified at the confluence of the Rio Grande and Pecos River. In addition to having a smaller geographic range, we found lower observed heterozygosity, reduced nucleotide diversity, and a smaller effective population size (Ne) in New Mexico population. Our results depict a significant isolation-by-distance pattern across their distribution, with migration being notably infrequent at river confluences. These findings are pivotal for future conservation and restoration strategies, emphasizing the need to recognize the unique needs of each population.

Distribution and prevalence of Sin Nombre hantavirus in rodent species in eastern New Mexico.

Orthohantaviruses are diverse zoonotic RNA viruses. Small mammals, such as mice and rats are common chronic, asymptomatic hosts that transmit the virus through their feces and urine. In North America, hantavirus infection primarily causes hantavirus cardiopulmonary syndrome (HCPS), which has a mortality rate of nearly 36%. In the United States of America, New Mexico (NM) is leading the nation in the number of HCPS-reported cases (N = 129). However, no reported cases of HCPS have occurred within eastern NM. In this study, we assessed the prevalence of Sin Nombre virus (SNV) in rodent assemblages across eastern NM, using RT-qPCR. We screened for potential rodent hosts in the region, as well as identified areas that may pose significant infection risk to humans. We captured and collected blood and lung tissues from 738 rodents belonging to 23 species. 167 individuals from 16 different species were positive for SNV RNA by RT-qPCR, including 6 species unreported in the literature: Onychomys leucogaster (Northern grasshopper mouse), Dipodomys merriami (Merriam's kangaroo rat), Dipodomys ordii (Ord's kangaroo rat), Dipodomys spectabilis (Banner-tailed kangaroo rat), Perognathus flavus (Silky pocket mouse), and Chaetodipus hispidus (Hispid pocket mouse). The infection rates did not differ between sexes or rodent families (i.e., Cricetidae vs. Heteromyidae). Generalized linear model showed that disturbed habitat types positively influenced the prevalence of SNV at sites of survey. Overall, the results of this study indicate that many rodent species in east New Mexico have the potential to maintain SNV in the environment, but further research is needed to assess species specific infectivity mechanisms and potential risk to humans.

Amplification and sequencing of entire tick mitochondrial genomes for a phylogenomic analysis.

The mitochondrial genome (mitogenome) has proven to be important for the taxonomy, systematics, and population genetics of ticks. However, current methods to generate mitogenomes can be cost-prohibitive at scale. To address this issue, we developed a cost-effective approach to amplify and sequence the whole mitogenome of individual tick specimens. Using two different primer sites, this approach generated two full-length mitogenome amplicons that were sequenced using the Oxford Nanopore Technologies' Mk1B sequencer. We used this approach to generate 85 individual tick mitogenomes from samples comprised of the three tick families, 11 genera, and 57 species. Twenty-six of these species did not have a complete mitogenome available on GenBank prior to this work. We benchmarked the accuracy of this approach using a subset of samples that had been previously sequenced by low-coverage Illumina genome skimming. We found our assemblies were comparable or exceeded the Illumina method, achieving a median sequence concordance of 99.98%. We further analyzed our mitogenome dataset in a mitophylogenomic analysis in the context of all three tick families. We were able to sequence 72 samples in one run and achieved a cost/sample of ~ $10 USD. This cost-effective strategy is applicable for sample identification, taxonomy, systematics, and population genetics for not only ticks but likely other metazoans; thus, making mitogenome sequencing equitable for the wider scientific community.

Effects of salinization on the occurrence of a long-lived vertebrate in a desert river.

The lower Pecos River located in the southwest USA, is a naturally saline river system that has been significantly altered in relatively recent years. Climate change, coupled with anthropogenic disturbances such as dam construction have led to portions of the river becoming more susceptible to increased salinization and declines in water quality. These alterations have been documented to be detrimental to multiple freshwater communities; however, there is a lack of knowledge on how these alterations influence long-lived species in the river, such as freshwater turtles, where the effects can appear over dramatically different temporal scales. The Rio Grande Cooter (Pseudemys gorzugi) is a species of concern known to occur in the Pecos River. To understand the current distribution and habitat requirements for P. gorzugi in the Pecos River, we used a single-season, single-species occupancy modeling framework to estimate occurrence while accounting for the sampling process. Day of year, water surface area, and water visibility had the greatest influence on the ability to detect the species given a sampling unit is occupied. Conductivity (a measure of salinity) had the greatest influence on the occupancy probability for the species, where sites with higher conductivity coincided with lower occupancy probabilities. This study indicates that increased salinization on the lower Pecos River is a cause for concern regarding freshwater turtle populations within the Chihuahuan Desert.

Influence of landscape condition on relative abundance and body condition of two generalist freshwater turtle species.

Anthropogenic land use changes have broad impacts on biological diversity, often resulting in shifts in community composition. While many studies have documented negative impacts on occurrence and abundance of species, less attention has been given to native species that potentially benefit from anthropogenic land use changes. For many species reaching high densities in human-dominated landscapes, it is unclear whether these environments represent higher quality habitat than more natural environments. We examined the influence of landscape ecological integrity on relative abundance and body condition of two native generalist freshwater turtle species that are prevalent in anthropogenic systems, the painted turtle (Chrysemys picta) and red-eared slider (Trachemys scripta elegans). Relative abundance was negatively associated with ecological integrity for both species, but the relationship was not strongly supported for painted turtles. Body condition was positively associated with ecological integrity for painted turtles, with no strong association for red-eared sliders. Our study suggests that both species benefitted at the population level from reduced ecological integrity, but individual-level habitat quality was reduced for painted turtles. The differing responses between these two habitat generalists could partially explain why red-eared sliders have become a widespread exotic invasive species, while painted turtles have not.

Morphometric data for five freshwater turtles in south, central, and west Texas.

From 2008 to 2013, we sampled freshwater turtle populations at 66 sites in south, central, and west Texas, USA. Sampling sites included ponds, lakes, resacas (oxbow lakes), canals, and rivers. We sampled turtle populations using baited hoop nets (66 sites) and basking traps (3 sites), and captured turtles by hand opportunistically in terrestrial habitat. We measured carapace length and width, plastron length and width, body depth, and weight of captured turtles. Excluding recaptures, we measured 356 Apalone spinifera emoryi (Texas Spiny Softshell), 24 Chelydra serpentina (Snapping Turtle), 20 Kinosternon flavescens (Yellow Mud Turtle), 47 Trachemys gaigeae (Big Bend Slider), and 1070 Trachemys scripta elegans (Red-eared Slider). Carapace length of Apalone spinifera emoryi ranged from 85 to 426 mm (mean = 182 mm). Carapace length of Chelydra serpentina ranged from 74 to 320 mm (mean = 233 mm). Carapace length of Kinosternon flavescens ranged from 64 to 147 mm (mean = 114 mm). Carapace length of Trachemys gaigeae ranged from 54 to 203 mm (mean = 141 mm). Carapace length of Trachemys scripta elegans ranged from 30 to 328 mm (mean = 171 mm). These data are useful for assessing spatial and temporal variation in size and body condition of freshwater turtles.

Detection of New World Hantavirus Antibodies in Rodents of Eastern New Mexico, USA.

Hantaviruses, causal agents of the potentially lethal hantavirus pulmonary syndrome, have widely distributed rodent hosts. Using an enzyme-linked immunosorbent assay, we tested blood from 398 wild rodents captured in eastern New Mexico, US in 2015-17 and found 42 antibody-positive samples representing six genera.

Comparison of hoop-net trapping and visual surveys to monitor abundance of the Rio Grande cooter (Pseudemys gorzugi).

Abundance estimates play an important part in the regulatory and conservation decision-making process. It is important to correct monitoring data for imperfect detection when using these data to track spatial and temporal variation in abundance, especially in the case of rare and elusive species. This paper presents the first attempt to estimate abundance of the Rio Grande cooter (Pseudemys gorzugi) while explicitly considering the detection process. Specifically, in 2016 we monitored this rare species at two sites along the Black River, New Mexico via traditional baited hoop-net traps and less invasive visual surveys to evaluate the efficacy of these two sampling designs. We fitted the Huggins closed-capture estimator to estimate capture probabilities using the trap data and distance sampling models to estimate detection probabilities using the visual survey data. We found that only the visual survey with the highest number of observed turtles resulted in similar abundance estimates to those estimated using the trap data. However, the estimates of abundance from the remaining visual survey data were highly variable and often underestimated abundance relative to the estimates from the trap data. We suspect this pattern is related to changes in the basking behavior of the species and, thus, the availability of turtles to be detected even though all visual surveys were conducted when environmental conditions were similar. Regardless, we found that riverine habitat conditions limited our ability to properly conduct visual surveys at one site. Collectively, this suggests visual surveys may not be an effective sample design for this species in this river system. When analyzing the trap data, we found capture probabilities to be highly variable across sites and between age classes and that recapture probabilities were much lower than initial capture probabilities, highlighting the importance of accounting for detectability when monitoring this species. Although baited hoop-net traps seem to be an effective sampling design, it is important to note that this method required a relatively high trap effort to reliably estimate abundance. This information will be useful when developing a larger-scale, long-term monitoring program for this species of concern.

Evidence of Batrachochytrium dendrobatidis Infection in Amphibians from Serbian Lowlands.

We investigated presence of Batrachochytrium dendrobatidis in the Republic of Serbia. Seven out of 88 samples (8%) tested positive, all belonging to the frog genus Pelophylax. Two positive sites were located directly on the Danube River. The Danube River could be an important disease corridor, and distribution of Batrachochytrium dendrobatidis along this river should be further explored.

Modeling Commercial Freshwater Turtle Production on US Farms for Pet and Meat Markets.

Freshwater turtles are being exploited for meat, eggs, traditional medicine, and pet trade. As a response, turtle farming became a booming aquaculture industry in the past two decades, specifically in the southeastern states of the United States of America (US) and across Southeast Asia. However, US turtle farms are currently producing turtles only for the pet trade while commercial trappers remain focused on catching the largest individuals from the wild. In our analyses we have created a biological and economic model that describes farming operations on a representative turtle farm in Louisiana. We first modeled current production of hatchling and yearling red-eared slider turtles (Trachemys scripta elegans) (i.e., traditional farming) for foreign and domestic pet markets, respectively. We tested the possibility of harvesting adult turtles from the breeding stock for sale to meat markets to enable alternative markets for the farmers, while decreasing the continued pressures on wild populations (i.e., non-traditional farming). Our economic model required current profit requirements of ~$13/turtle or ~$20.31/kg of meat from non-traditional farming in order to acquire the same profit as traditional farming, a value which currently exceeds market values of red-eared sliders. However, increasing competition with Asian turtle farms and decreasing hatchling prices may force the shift in the US toward producing turtles for meat markets. In addition, our model can be modified and applied to more desirable species on the meat market once more knowledge is acquired about species life histories and space requirements under farmed conditions.

Magnitude of the freshwater turtle exports from the US: long term trends and early effects of newly implemented harvest management regimes.

Unregulated commercial harvest remains a major threat for turtles across the globe. Due to continuing demand from Asian markets, a significant number of turtles are exported from the United States of America (US). Beginning in 2007, several southeastern states in the US implemented restrictions on the commercial harvest of turtles, in order to address the unsustainable take. We have summarized freshwater turtle exports from the US between 2002 and 2012 and demonstrated that the magnitude of turtle exports from the US remained high although the exports decreased throughout the decade. Louisiana and California were the major exporters. The majority of exports were captive bred, and from two genera, Pseudemys and Trachemys. We review the changes over the decade and speculate that the increase in export of wild turtles out of Louisiana after 2007 could be a consequence of strict regulations in surrounding states (e.g., Alabama, Florida). We suggest that if wild turtle protection is a goal for conservation efforts, then these states should work together to develop comprehensive regulation reforms pertaining to the harvest of wild turtles.