Geology topics

Ronald A. Van Den Bussche

Publications and source records attributed to Ronald A. Van Den Bussche.

10 recordsLinked to original sources

USGS2023

A 37 K SNP array for the management and conservation of Golden Eagles (Aquila chrysaetos)

We describe the development of a custom 37 K Affymetrix Axiom myDesign single nucleotide polymorphism (SNP) array for a culturally and ecologically important apex predator, the golden eagle ( Aquila chrysaetos ). Using this SNP array, we performed population genomic analysis on 154 individuals of known natal localities and detected three genetic clusters that we designated as Taiga/High Arctic, Great Basin, and Rocky Mountains/Great Plains. Each of these clusters appears to display clinal variation within these geographic regions. After determining genetic structure, we performed an assignment test of 32 individuals, five of which were siblings of individuals used in the assessment of genetic structure, three had associated telemetry data, and the remaining individuals were of unknown natal locations. Using this array, four siblings were correctly assigned to the same geographic region as their sibling and the genetic assignment of the radio telemetered birds agreed with the expected movement patterns displayed by these individuals. For the remaining individuals, we were able to assign all but five individuals to one of the three genetic clusters. Our genetic assignments illustrates the utility of this SNP array to accurately assign most individuals to predesignated geographical regions. While further compiling genetic and other data types, we can increase the power of this tool for identifying those breeding populations that may need assistance due to anthropogenic stressors that negatively impact their population viability. The use of this genetic resource will help substantiate decisions by multiple conservation groups that seek to preserve the natural population structure of the golden eagle.

Conservation Genetics↗

USGS2022

Lithology and disturbance drive cavefish and cave crayfish occurrence in the Ozark Highlands ecoregion

Diverse communities of groundwater-dwelling organisms (i.e., stygobionts) are important for human wellbeing; however, we lack an understanding of the factors driving their distributions, making it difficult to protect many at-risk species. Therefore, our study objective was to determine the landscape factors related to the occurrence of cavefishes and cave crayfishes in the Ozark Highlands ecoregion, USA. We sampled cavefishes and cave crayfishes at 61 sampling units using both visual and environmental DNA surveys. We then modeled occurrence probability in relation to lithology and human disturbance while accounting for imperfect detection. Our results indicated that occurrence probability of cave crayfishes was negatively associated with human disturbance, whereas there was a weak positive relationship between cavefish occurrence and disturbance. Both cavefishes and cave crayfishes were more likely to occur in limestone rather than dolostone lithology. Our results indicate structuring factors are related to the distribution of these taxa, but with human disturbance as a prevalent modifier of distributions for cave crayfishes. Limiting human alteration near karst features may be warranted to promote the persistence of some stygobionts. Moreover, our results indicate current sampling efforts are inadequate to detect cryptic species; therefore, expanding sampling may be needed to develop effective conservation actions.

Arkansas, Missouri, Oklahoma↗

USGS2019

Using environmental DNA (eDNA) to assess the presence of cavefish and cave crayfish populations in caves of the Ozark Highlands

Many cavefishes and cave crayfishes are considered of conservation concern; however, sampling these species is inherently difficult given their occupied environments. The goal of our project was to verify the presence of select karst organisms while developing the foundation for sampling approaches that might be useful to conservation and management agencies. Our project objectives were to develop assays to amplify deoxyribonucleic acid (DNA) from several species of Ozark cavefishes and cave crayfishes and complete an initial surveillance of locations across the Ozark Highlands using environmental DNA (eDNA). Using DNA either provided by agency cooperators or that we extracted from tissue samples, we PCR amplified and then sequenced the Cytochrome Oxidase 1 (CO1) gene for cave crayfishes and the NADH Dehydrogenase Subunit 2 (ND2) gene for cavefishes. We developed species-specific primers and probes for five cave crayfishes and two cavefishes. From February 2017 to May 2017, we sampled 1–5 sampling units from 42 caves, wells, and springs (i.e., sites) using eDNA and traditional visual surveys. We measured physicochemical parameters at each sampling unit to estimate detection probability associated with both techniques. We also calculated two occupancy covariates for each site using geospatial data. We successfully amplified Troglichthys rosae DNA from the environment and detected DNA representing this species at 24 of 40 sites. At 16 of the sites where we detected T. rosae DNA, we did not visually observe the species. Although our assay for Typlichthys eigenmanni successfully amplified the target DNA from the environment, it also resulted in false absences where the species was visually confirmed. Using eDNA to detect cave crayfishes was much more difficult. The assay for Cambarus subterraneus did not work for eDNA samples and we were unable to pick up DNA from the environment, even at locations where it was visually confirmed. Alternatively, the eDNA surveys worked well for C. tartarus and we were able to amplify DNA at every site where it was visually observed. Our assay for C. aculabrum was based on a single sample obtained from GenBank, and did not amplify eDNA from field samples. Lastly, our eDNA results from samples in the known range of Orconectes stygocaneyi suggested the species may be found at an additional cave. Detection using eDNA based on our O. stygocaneyi assay was likely low because it was designed from a pseudogene; however, positive eDNA samples were sequenced to confirm species-specific DNA. Detection probability of both cavefishes and cave crayfishes varied by survey technique and was influenced by water volume, water clarity, water velocity, and substrate. Detection of cavefishes and cave crayfishes via visual surveys decreased when water volume increased, whereas detection using eDNA increased with greater water volume. Detection between taxa using either sample method was highest in habitats classified by fine substrates, except for eDNA detection of crayfishes which was greatest in coarse substrates. Detection of cavefishes increased with water clarity, but detection of cave crayfishes increased with turbidity. Detection probability of both cavefishes and crayfishes using eDNA increased slightly with water velocity, but decreased with visual surveys as water velocity increased. Occupancy by both taxa was positively related to particular geologic series. Crayfish occupancy was negatively related to fine-scale anthropogenic disturbance (i.e., 500-m buffer around the site), whereas crayfish showed no relationship with disturbance. Our results suggest possible range extensions, provide insights to factors driving detection using both sample techniques, and suggest areas where recharge zones may be shared among caves. Future efforts focused on a comprehensive evaluation of genetic diversity among cave crayfishes to improve assay design could improve detection and the applicability of eDNA as a supplemental and non-invasive sampling approach.

Cooperator Science Series↗

USGS2015

Population connectivity of endangered Ozark big-eared bats ( Corynorhinus townsendii ingens )

The endangered Ozark big-eared bat ( Corynorhinus townsendii ingens ) is restricted to eastern Oklahoma and western and north-central Arkansas, where populations may be susceptible to losses of genetic variation due to patchy distribution of colonies and potentially small effective population sizes. We used mitochondrial D-loop DNA sequences and 15 nuclear microsatellite loci to determine population connectivity among Ozark big-eared bat caves. Assessment of 7 caves revealed a haplotype not detected in a previous study (2002–2003) and gene flow among colonies in eastern Oklahoma. Our data suggest genetic mixing of individuals, which may be occurring at nearby swarming sites in the autumn. Further evidence of limited gene flow between caves in Oklahoma with a cave in Arkansas highlights the importance of including samples from geographically widespread caves to fully understand gene flow in this subspecies. It appears autumn swarming sites and winter hibernacula play an important role in providing opportunities for mating; therefore, we suggest protection of these sites, maternity caves, and surrounding habitat to facilitate gene flow among populations of Ozark big-eared bats.

Arkansas, Oklahoma↗

USGS2012

Mammals of Red Slough Wildlife Management Area, with comments on McCurtain County, Oklahoma

Red Slough Wildlife Management Area (RSWMA) is located in the southeastern corner of Oklahoma, McCurtain County, and represents the extreme northwestern extent of the South Central Plains (SCP) ecoregion. Previous mammal research in southeastern Oklahoma has focused mostly on the Ouachita Mountains to the north of RSWMA. As a result, of the 69 species of mammals potentially occurring in McCurtain County, only 48 species represented by 599 voucher specimens reside in natural history collections. We present results from a mammal survey of RSWMA conducted from December 2009 to August 2010. We captured 574 non-volant small mammals in 9,115 trap-nights, 11 bats in 17 net-nights, and seven salvaged meso-mammals resulting in 157 voucher specimens of 22 mammal species, including the first specimen of Castor canadensis for McCurtain County, and photographic vouchers for eight additional species from RSWMA. These results provide a baseline for future studies on RSWMA and substantially increase our natural history knowledge for many relatively under-studied mammals in southeastern Oklahoma

Oklahoma↗

USGS2011

Importance of tributary streams for rainbow trout reproduction: insights from a small stream in Georgia and a bi-genomic approach

Tributaries of tailwater fisheries in the southeastern USA have been used for spawning by stocked rainbow trout (Oncorhynchus mykiss), but their importance may have been underestimated using traditional fish survey methods such as electrofishing and redd counts. We used a bi-genomic approach, mitochondrial DNA sequences and nuclear microsatellite loci, to estimate the number of spawning adults in one small tributary (Cabin Creek) of the Chattahoochee River, Georgia, where rainbow trout are known to spawn and have successful recruitment. We extracted and analysed DNA from seven mature male rainbow trout and four juveniles that were captured in February 2006 in Cabin Creek and from 24 young-of-year (YOY) trout that were captured in April 2006. From these samples, we estimated that 24 individuals were spawning to produce the amount of genetic variation observed in the juveniles and YOY, although none of the mature males we sampled were indicated as sires. Analysis of the mitochondrial D-loop region identified four distinct haplotypes, suggesting that individuals representing four maternal lineages contributed to the offspring. Our analyses indicated that many more adults were spawning in this system than previously estimated with direct count methods and provided insight into rainbow trout spawning behavior.

River Research and Applications↗

USGS2009

Conservation genetics of the alligator snapping turtle: cytonuclear evidence of range-wide bottleneck effects and unusually pronounced geographic structure

A previous mtDNA study indicated that female-mediated gene flow was extremely rare among alligator snapping turtle populations in different drainages of the Gulf of Mexico. In this study, we used variation at seven microsatellite DNA loci to assess the possibility of male-mediated gene flow, we augmented the mtDNA survey with additional sampling of the large Mississippi River System, and we evaluated the hypothesis that the consistently low within-population mtDNA diversity reflects past population bottlenecks. The results show that dispersal between drainages of the Gulf of Mexico is rare ( F ST msat = 0.43, Φ STmtDNA = 0.98). Past range-wide bottlenecks are indicated by several genetic signals, including low diversity for microsatellites (1.1–3.9 alleles/locus; H e = 0.06–0.53) and mtDNA ( h = 0.00 for most drainages; π = 0.000–0.001). Microsatellite data reinforce the conclusion from mtDNA that the Suwannee River population might eventually be recognized as a distinct taxonomic unit. It was the only population showing fixation or near fixation for otherwise rare microsatellite alleles. Six evolutionarily significant units are recommended on the basis of reciprocal mtDNA monophyly and high levels of microsatellite DNA divergence.

Gulf of Mexico↗

USGS2008

Subspecific affinities and conservation genetics of western big-eared bats (Corynorhinus townsendii pallescens) at the edge of their distributional range

Subspecific affinities, determination of population boundaries, and levels of population connectedness are of critical importance for the development of management and conservation planning. We used variation at a mitochondrial locus and 5 biparentally inherited nuclear loci to determine partitioning of genetic variation of western big-eared bats (Corynorhinus townsendii) within and among caves occurring in a fragmented landscape of gypsum deposits in western Oklahoma. To accomplish this objective, we first performed a phylogenetic analysis based on the mitochondrial locus of western big-eared bats from a large portion of their range. This analysis indicated that western big-eared bats at the periphery of the distribution in western Oklahoma share phylogenetic affinities with the most geographically restricted subspecies, C. t. pallescens. Because C. townsendii is rare in Oklahoma and is listed as a species of special concern, this finding provides additional support for the continued protection of this species in Oklahoma. Within western Oklahoma, we failed to detect significant differentiation among any caves for the biparentally inherited microsatellite data. However, the mitochondrial locus exhibited significant levels of genetic differentiation among caves, with the highest level of differentiation occurring between caves within the disjunct distributions of gypsum (??ST = 38.76%). Although a significant amount of genetic differentiation was detected between populations on the 2 disjunct distributions of gypsum deposits, Analysis with the program Migrate suggested high levels of asymmetric gene flow among some populations. Our results provide a greater understanding of the population dynamics of western big-eared bats on the periphery of their range and highlight the importance of continued monitoring and study of this taxon. ?? 2008 American Society of Mammalogists.

Journal of Mammalogy↗

USGS2006

Genetic variation among subspecies of Least Tern (Sterna antillarum): Implications for conservation

DNA sequence variation from two nuclear introns and part of the mitochondrial cytochrome-b gene were used to Evaluate population structure among three subspecies of Least Term that nest in the United States (California [Sterna antillarum browni], Interior [S. a. athalassos], Eastern [S. a. antillarum]). Sequence variation was highest for nuclear intron XI (Gadp) within the glyceraldehyde-3-phosphate dehydrogenase gene. The second nuclear intron was fixed for the same allele in all subspecies. Fixation indices, FST and MST, for Gadp indicated genetic divergence between California and Interior subspecies. Estimates of nuclear gene flow were <4 individuals/generation, except between the Interior and Eastern subspecies (4 individuals/generation). Genetic indices for mitochondrial DNA did not differ among subspecies, and gene flows (reflecting female dispersal) ranged from 10 to 83 individuals/generation. Reservations are expressed about the validity of the current subspecific divisions and further research is required, including their taxonomic relationship to the Little Tern (Sterna albifrons).

Waterbirds↗

USGS2005

Unraveling the effects of sex and dispersal: Ozark big-eared bat (Corynorhinus townsendii ingens) conservation genetics

The Ozark big-eared bat (Corynorhinus townsendii ingens) is federally listed as endangered and is found in only a small number of caves in eastern Oklahoma and northwestern Arkansas. Previous studies suggested site fidelity of females to maternity caves; however, males are solitary most of the year, and thus specific information on their behavior and roosting patterns is lacking. Population genetic variation often provides the necessary data to make inferences about gene flow or mating behavior within that population. We used 2 types of molecular data: DNA sequences from the mitochondrial D loop and alleles at 5 microsatellite loci. Approximately 5% of the population, 24 males and 39 females (63 individuals), were sampled. No significant differentiation between 5 sites was present in nuclear microsatellite variation, but distribution of variation in maternally inherited markers differed among sites. This suggests limited dispersal of female Ozark big-eared bats and natal philopatry. Areas that experience local extinctions are unlikely to be recolonized by species that show strong site fidelity. These results provide a greater understanding of the population dynamics of Ozark big-eared bats and highlight the importance of cave protection relative to maintaining genetic integrity during recovery activities for this listed species. ?? 2005 American Society of Mammalogists.

Journal of Mammalogy↗