Rapid vertebrate speciation via isolation, bottlenecks, and drift

Speciation is often driven by selective processes like those associated with viability, mate choice, or local adaptation, and "speciation genes" have been identified in many eukaryotic lineages. In contrast, neutral processes are rarely considered as the primary drivers of speciation, especially over short evolutionary timeframes. Here, we describe a rapid vertebrate speciation event driven primarily by genetic drift. The White Sands pupfish (Cyprinodon tularosa) is endemic to New Mexico's Tularosa Basin where the species is currently managed as two Evolutionarily significant units (ESUs) and is of international conservation concern (Endangered). Whole-genome resequencing data from each ESU showed remarkably high and uniform levels of differentiation across the entire genome (global FST ≈ 0.40). Despite inhabiting ecologically dissimilar springs and streams, our whole-genome analysis revealed no discrete islands of divergence indicative of strong selection, even when we focused on an array of candidate genes. Demographic modeling of the joint allele frequency spectrum indicates the two ESUs split only ~4 to 5 kya and that both ESUs have undergone major bottlenecks within the last 2.5 millennia. Our results indicate the genome-wide disparities between the two ESUs are not driven by divergent selection but by neutral drift due to small population sizes, geographic isolation, and repeated bottlenecks. While rapid speciation is often driven by natural or sexual selection, here we show that isolation and drift have led to speciation within a few thousand generations. We discuss these evolutionary insights in light of the conservation management challenges they pose.

Structural and environmental predictors of tricolored bat presence and abundance in Texas caves

The identification of bat colonies is essential to conserve and manage these globally threatened mammals. Caves offer potential roosting locations (hibernacula) to hibernating bat species; however, identifying regions where bat-occupied caves exist can be time-consuming. In Texas, caves are often on privately owned land, creating difficulties for accessing and managing potential hibernacula. The tricolored bat (Perimyotis subflavus), a species susceptible to white-nose syndrome, hibernates in caves in the winter in Texas. We sought to identify and quantify site-specific structural and environmental features that influence the presence and abundance of overwintering tricolored bats. We surveyed caves for bats and recorded environmental and structural features of 116 caves January–February 2016, December–February 2016–2017, January–February 2018, and December–February 2018–2019. We used a zero-inflated Poisson regression to identify which features best explained the presence and abundance of tricolored bats. We found that bat presence increased as cave length decreased, and as Normalized Difference Vegetation Index (NDVI) and external vapor pressure deficit increased. Bat abundance increased as number of portals, cave length, NDVI, and external temperature increased. Combining surface data with subsurface features can assist with identifying specific karst regions and known caves within those regions for survey and management efforts.

The endangered White Sands pupfish (Cyprinodon tularosa) genome reveals low diversity and heterogenous patterns of differentiation

The White Sands pupfish (Cyprinodon tularosa), endemic to New Mexico in Southwestern North America, is of conservation concern due in part to invasive species, chemical pollution, and groundwater withdrawal. Herein, we developed a draft reference genome and use it to provide biological insights into the evolution and conservation of C. tularosa. We used our assembly to localize microsatellite markers previously used to demarcate evolutionary significant units (ESU), quantified genomic divergence and transposable element profiles between species, and compared C. tularosa genomic diversity related species. Our de novo assembly of PacBio Sequel II error-corrected reads resulted in a 1.08 Gb draft genome with a contig N50 of 1.4 Mb and 25,260 annotated protein coding genes, including 95% of the expected Actinopterygii conserved complete single-copy orthologues. Many of the C. tularosa microsatellite markers used for conservation assessments fell within, or near, genes and exhibited a pattern of increased heterozygosity near genic areas compared to those in intergenic regions. Nuclear alignments between these two species revealed 193 genes contained in rapidly diverging tracts; transposable element profiles were largely concordant and suggest a shared, rapid expansion of LINE and Gypsy elements. Genome-wide heterozygosity was markedly lower in C. tularosa compared to estimates from other related species, probably because of smaller long-term effective population sizes constrained by their isolated and limited habitat. Overall, these inferences provide new insights into C. tularosa that should help inform future management efforts.

Ten-year projection of white-nose syndrome disease dynamics at the southern leading-edge of infection in North America

Predicting the emergence and spread of infectious diseases is critical for the effective conservation of biodiversity. White-nose syndrome (WNS), an emerging infectious disease of bats, has resulted in high mortality in eastern North America. Because the fungal causative agent Pseudogymnoascus destructans is constrained by temperature and humidity, spread dynamics may vary by geography. Environmental conditions in the southern part of the continent are different than the northeast, where disease dynamics are typically studied, making it difficult to predict how the disease will manifest. Herein, we modelled WNS pathogen spread in Texas based on cave densities and average dispersal distances of hosts, projecting these results out to 10 years. We parameterized a predictive model of WNS epidemiology and its effects on bat populations with observed cave environmental data. Our model suggests that bat populations in northern Texas will be more affected by WNS mortality than southern Texas. As such, we recommend prioritizing the preservation of large overwintering colonies of bats in north Texas through management actions. Our model illustrates that infectious disease spread and infectious disease severity can become uncoupled over a gradient of environmental variation and highlight the importance of understanding host, pathogen and environmental conditions across a breadth of environments.

Searching for rare and secretive snakes: are camera-trap and box-trap methods interchangeable?

Abstract ContextAdvancements in camera-trap technology have provided wildlife researchers with a new technique to better understand their study species. This improved method may be especially useful for many conservation-reliant snake species that can be difficult to detect because of rarity and life histories with secretive behaviours. AimsHere, we report the results of a 6-month camera-trapping study using time lapse-triggered camera traps to detect snakes, in particular the federally listed Louisiana pinesnake (Pituophis ruthveni) in eastern Texas upland forests in the USA. MethodsSo as to evaluate the efficacy of this method of snake detection, we compared camera-trap data with traditional box-trapping data collected over the same time period across a similar habitat type, and with the same goal of detecting P. ruthveni. Key resultsNo differences in focal snake species richness were detected across the trap methods, although the snake-detection rate was nearly three times higher with camera traps than with the box traps. Detection rates of individual snake species varied with the trapping method for all but two species, but temporal trends in detection rates were similar across the trap methods for all but two species. Neither trap method detected P. ruthveni in the present study, but the species has been detected with both trap methods at other sites. ConclusionsThe higher snake-detection rate of the camera-trap method suggests that pairing this method with traditional box traps could increase the detection of P. ruthveni where it occurs. For future monitoring and research on P. ruthveni, and other similarly rare and secretive species of conservation concern, we believe these methods could be used interchangeably by saturating potentially occupied habitats with camera traps initially and then replacing cameras with box traps when the target species is detected. ImplicationsThere are financial and logistical limits to monitoring and researching rare and secretive species with box traps, and those limits are far less restrictive with camera traps. The ability to use camera-trap technologies interchangeably with box-trap methods to collect similar data more efficiently and effectively will have a significant impact on snake conservation.

External temperature and distance from nearest entrance influence microclimates of cave and culvert-roosting tri-colored bats (Perimyotis subflavus)

Many North American bat species hibernate in both natural and artificial roosts. Although hibernacula can have high internal climate stability, they still retain spatial variability in their thermal regimes, resulting in various "microclimates" throughout the roost that differ in their characteristics (e.g., temperature and air moisture). These microclimate components can be influenced by factors such as the number of entrances, the depth of the roost, and distance to the nearest entrance of the roost. Tri-colored bats are commonly found roosting in caves in winter, but they can also be found roosting in large numbers in culverts, providing the unique opportunity to investigate factors influencing microclimates of bats in both natural and artificial roost sites. As tri-colored bats are currently under consideration for federal listing, information of this type could be useful in aiding in the conservation and management of this species through a better understanding of what factors affect the microclimate near roosting bats. We collected data on microclimate temperature and microclimate actual water vapor pressure (AWVP) from a total of 760 overwintering tri-colored bats at 18 caves and 44 culverts. Using linear mixed models analysis, we found that variation in bat microclimate temperatures was best explained by external temperature and distance from nearest entrance in both caves and culverts. External temperature had a greater influence on microclimate temperatures in culverts than caves. We found that variation in microclimate AWVP was best explained by external temperature, distance from nearest entrance, and proportion from entrance (proportion of the total length of the roost from the nearest entrance) in culvert-roosting bats. Variation in microclimate AWVP was best explained by external temperature and proportion from entrance in cave-roosting bats. Our results suggest that bat microclimate temperature and AWVP are influenced by similar factors in both artificial and natural roosts, although the relative contribution of these factors differs between roost types.

Winter habitats of bats in Texas

Few studies have described winter microclimate selection by bats in the southern United States. This is of particular importance as the cold-adapted fungus, Pseudogymnoascus destructans, which causes the fatal bat disease white-nose syndrome (WNS), continues to spread into southern United States. To better understand the suitability of winter bat habitats for the growth of P. destructans in this region, we collected roost temperature and vapor pressure deficit from 97 hibernacula in six ecoregions in Texas during winter 2016-17 and 2017-18. We also measured skin temperature of Rafinesque's big-eared bats (Corynorhinus townsendii), Townsend's big-eared bats (C. townsendii), big-brown bats (Eptesicus fuscus), southeastern myotis (Myotis austroriparius), cave myotis (M. velifer), tri-colored bats (Perimyotis subflavus), and Mexican free-tailed bats (Tadarida brasiliensis) during hibernation to study their use of torpor in these habitats. We found that temperatures within hibernacula were strongly correlated with external air temperatures and were often within the optimal range of temperatures for P. destructans growth. Hibernacula and skin temperatures differed among species, with Rafinesque's big-eared bats, southeastern myotis, and Mexican free-tailed bats occupying warmer microclimates and having higher torpid skin temperatures. For species that were broadly distributed throughout Texas, hibernacula and skin temperatures differed within species by ecoregion; Tri-colored bats and cave myotis in colder, northern regions occupied colder microclimates within hibernacula and exhibited colder skin temperatures, than individuals of the same species in warmer, southern regions. These data illustrate the variability in microclimates used as hibernacula by bats in Texas and suggest similar variation in susceptibility to WNS in the state. Thus, monitoring microclimates at winter roosts may help predict where WNS may develop, and where management efforts would be most effective.

Structural and environmental predictors of presence and abundance of tri-colored bats in Texas culverts

The tri-colored bat (Perimyotis subflavus) is being reviewed for listing under the Endangered Species Act by the United States Fish and Wildlife Service. It is also listed as a species of greatest conservation need by the Texas Parks and Wildlife Department due to its susceptibility to white-nose syndrome (WNS) in other states. Several colonies of hibernating tri-colored bats have been documented roosting in culverts. Culverts are widespread in Texas as part of roadway infrastructure; thus, our objective was to understand and quantify which structural and environmental factors best explain culvert use and abundance of hibernating tri-colored bats in Texas. We selected and surveyed 207 culverts for presence of tri-colored bats using the Generalized Random Tessellation Stratified (GRTS) design and opportunistic sampling across 10 of 12 Texas level III ecoregions during the winters of 2016–2017 and 2017–2018. We recorded environmental and structural features of culverts at each site. We used a zero-inflated Poisson regression to identify which culvert features best explained presence and abundance of hibernating tri-colored bats. We found that number of culvert sections predicted presence of tri-colored bats. We also found that abundance of tri-colored bats was influenced by length of culvert, elevation, number of sections, portal height, portal obstruction, aspect, external VPD, external temperature, and NDVI. With the current threats to tri-colored bat populations, there is a need to consider management of culvert roosts. In addition, it is imperative to further investigate the potential susceptibility to WNS of culvert-roosting bats at more southern latitudes for local and regional planning efforts.

Inadequate thermal refuge constrains landscape habitability for a grassland bird species

Ecologists have long recognized the influence that environmental conditions have on abundance and range extent of animal species. We used the northern bobwhite (Colinus virginianus; hereafter bobwhite) as a model species for studying how microclimates serve as refuge against severe weather conditions. This species serves as an indicator or umbrella species for other sensitive ground-nesting, grassland obligate species. We conducted a mensurative field experiment in the rolling plains of Texas, USA, a semi-arid ecosystem on the southwestern periphery of bobwhite range, to determine whether native bunch grasses, apparently suitable for bobwhite nesting, could reduce ambient temperature below levels harmful for eggs. During the nesting season, we compared temperature and relative humidity readings at daily heat maxima (i.e., the 3 h during each day with highest temperatures) during the nesting season over the course of two years at 63 suitable nest sites paired with 63 random locations (n = 126) using two sensors at ∼10 and ∼60 cm above ground level. Mean temperature at nest height was 2.3% cooler at nest sites (35.99 °C ± 0.07 SE) compared to random locations (36.81 °C ± 0.07 SE); at ambient height, nest sites were slightly cooler (32.78 °C ± 0.06 SE) than random location (32.99 °C ± 0.06 SE). Mean relative humidity at nest sites was greater at nest height (34.53% ± 0.112 SE) and ambient height (36.22% ± 0.10 SE) compared to random locations at nest (33.35% ± 0.12 SE) and ambient height (35.75% ± 0.10 SE). Based on these results, cover at sites that appear visually suitable for nesting by bobwhites and other ground nesting birds provided adequate thermal refuge in the rolling plains by maintaining cooler, moister microclimates than surrounding non-nesting locations. Post-hoc analyses of data revealed that habitat conditions surrounding suitable nest sites strongly influenced thermal suitability of the substrate. Given that eggs of bobwhites and probably other species would experience lethal temperatures without these thermal refuges in the context of proper habitat condition, nesting vegetation is a critical component of niche space for bobwhites and other ground nesting birds in semi-arid regions. Many contemporary land uses, however, degrade or destroy bunch grasses and grassland systems, and thus decrease landscape inhabitability. Conservationists working with obligate grassland species that require bunch grasses in semi-arid regions should develop land management strategies that maximize the availability of these thermal refuges across space and time.

Method comparison of EMIT 700 and EMIT II with RIA for drug screening

The EMIT 700 and EMIT II assays for marijuana, cocaine, opiates, barbiturates, and phencyclidine, as performed on a Hitachi 717 Analyzer, were compared with Roche Abuscreen RIA tests for high-volume drug abuse screening. The EMIT II kits offer some advantages over the EMIT 700 kits for testing large work loads. The EMIT II marijuana test in particular exhibits a calibration curve that promises improved ability to separate negative from positive samples due to the increased absorbance rate separation between the negative and cutoff calibrators. Both EMIT formulations are preferable in terms of speed and ease of analysis in comparison with our laboratory's current RIA procedures. Over 50,000 urine samples were screened by EMIT 700 and RIA and by EMIT II and RIA. The performance of both EMIT assays was approximately equivalent to RIA in terms of their ability to detect urine samples that confirmed positive for cocaine and opiates. Both EMIT assays detected approximately 90% of the urine samples screened positive by RIA and confirmed positive for marijuana. Both EMIT assays performed better than RIA in detecting confirmed-positive barbiturate samples.

New magnetic resonance imaging techniques for the detection of breast cancer

The importance of contrast agents in enhancing diagnoses from magnetic resonance images has been established in numerous cases. However, the development of a potent tissue-specific contrast agent, as a sensitive probe for early detection and investigation of the physiological characteristics of a tumor, has not yet been realized in MR imaging (MRI). In nuclear scintigraphy the technique has been demonstrated; however, the poor spacial resolution inherent to the modality and the substantial dose of radioactivity administered to the patient has hindered its widespread use. This article will review the different classes of contrast agents in MRI, with special focus on the strategies involved in the development of targeted tissue-specific MRI contrast agents for the early detection of breast cancer. The features of a new class of contrast agents for targeted MR imaging will be described. Gadolinium-containing melanin polymers (GMP's) have been synthesized as MR contrast agents in our laboratory. These GMP's demonstrate significantly higher relaxivities than any other paramagnetic contrast agents reported; consequently, they are extremely effective contrast enhancing, imaging agents by themselves. The successful coupling of these potent GMP's to a monoclonal antibody specific for breast carcinoma, the 323/A3 monoclonal antibody, suggests that in vivo tissue-specific MR imaging, at the receptor level, will become feasible in the near future.

Method comparison of EMIT II and online with RIA for drug screening

The newest formulation of the EMIT assay for drugs of abuse, EMIT II, and a new immunoassay, OnLine, using the kinetic interaction of microparticles in solution methodology, were evaluated for marijuana, cocaine, opiates, barbiturates, and phencyclidine. Both types of immunoassays were performed on an Hitachi 717 analyzer. Calibration curves, the degree of separation between negative and cutoff calibrators, precision, probability of carryover from positive to negative samples, and overall ease and speed of analysis were evaluated. EMIT II and OnLine were compared with RIA tests for the five drugs to determine each assay's ability to detect samples which confirm positive by GC/MS. The RIA and OnLine marijuana tests detected > 99% of confirmed positive samples while EMIT II detected about 90%. All three immunoassays performed equivalently for cocaine and opiates, each assay detecting at least 98% of positives. Barbiturates showed the greatest disparity with OnLine detecting 96%, EMIT II 85%, and RIA 79% of confirmed positive samples. Too few phencyclidine positive samples were detected for a method comparison study. The fully automated EMIT II and OnLine assays are preferable for a variety of reasons to our laboratory's current semi-automated RIA tests for large volume urine testing. The immunoassays offer comparable performance for some drugs but not for others.

Management of High-Level Waste Repository Siting

The selection of sites to store high-level radioactive waste will require more than technical decisions; an acceptable site must gain widespread public support. Ad hoc approaches have recently served as a stimulus to overcome institutional inertia in radioactive waste management, as exemplified by the Interagency Review Group and the State Planning Council for Radioactive Waste Management, but ad hoc approaches have not characteristically succeeded in resolving intense conflicts. Acceptable sites can best be established through traditional processes of legal and scientific advocacy, and their ultimate legitimacy will depend on the proper use of established democratic processes.

Frequencies of salivary genetic marker systems in Caucasians with an emphasis on Pm and Ph systems

Salivary genetic marker systems, especially the Pm and Ph systems, were studied in Caucasians. The gene frequencies obtained were, Pm+ = 0.14 and Pm- = 0.86. A variant polymorphic protein (Ph) present in the Japanese population was not observed in Caucasians.