The Giant Gartersnake (Thamnophis gigas) is a low density visually evasive species with a low detection probability based on standard field survey methods (e.g., traps, visual census). Habitat loss ...has resulted in extirpations or serious declines for T. gigas populations throughout the southern two thirds of its historic range. Uncertainty regarding its current distribution and occupancy present management challenges for the species. Enhancing survey sensitivity through development of environmental DNA sampling (eDNA) methods would improve compliance monitoring under the Endangered Species Act, recovery planning for T. gigas, and evaluation of California's Central Valley tule marsh habitat on which this species depends. To address these needs, we designed and validated diagnostic quantitative Polymerase Chain Reaction (qPCR) assays for identifying portions of the Cytochrome B (CytB) and the Nicotinamide adenine dinucleotide (NADH) dehydrogenase subunit 4 (ND4) genes of the T. gigas mitochondrial genome. The designed ND4 qPCR assay was not specific to T. gigas DNA and amplified DNA from a closely related and spatially co-occurring Thamnophis species (T.s. fitchi). The CytB T. gigas qPCR assay proved specific to a species level with a sensitivity that reliably detected T. gigas DNA at a concentration of 2.0x10-5 ng μL-1. To assess detection range, coordinated field sampling was conducted at aquatic sites with an observed and documented population of T. gigas. The T. gigas qPCR assay reliably detected DNA from samples taken 300m downstream from the known source. We then used environmental eDNA sampling and qPCR analysis to augment unsuccessful trap surveys in the southern range of T. gigas and detected DNA in 28 of the 52 locations sampled, confirming that T. gigas was still present at some sites where physical trapping failed to identify presence. QPCR-based DNA detection coupled with eDNA sampling methods provides an effective means to obtain critical population metrics from this otherwise cryptic, federally protected and hard to study organism, offering great promise for elucidating patterns of occupancy with greater efficiency and at far less cost than trapping methods, particularly where detection probabilities are low.
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Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Quantifiable measurement of habitat restoration effects on salmonid reproductive performance is limited, although it is necessary for evaluating whether population responses follow management ...actions. We investigated using close‐kin mark‐recapture methods to partition restoration effects within standard monitoring metrics of juvenile emigrants leaving the natal reach. This approach allowed for statistical comparison of relative juvenile capture rates (recruitment) from Chinook Salmon (Oncorhynchus tshawytscha) naturally reproducing in gravel augmented (restored) and nonaugmented (unrestored) reaches of a highly managed California River. Genetic parentage techniques linked adult females that had spawned in augmented and nonaugmented spawning habitats with juvenile Chinook Salmon sampled the following spring at a trap located below the natal spawning area. Successful recruitment was documented from both augmented and nonaugmented habitats, with no statistical difference between the two habitat types. The capture rate per adult female was low (0.19–0.24 juveniles/female) compared to rates observed in other systems. Within the juvenile collections, most females in the study had 0 or 1 offspring observed; however, one female that spawned in a restored habitat had 25 offspring recovered at the trap. We modeled juvenile capture rates in relation to a range of biological and environmental variables including spawning habitat site, spawning habitat treatment (augmented and nonaugmented), annual spawner abundance, year spawned, female fork length, spawning and hatch day, and flow maximum and variance. There was an inverse relationship between annual adult abundance (escapement obtained from carcass surveys) and recruitment (juvenile recoveries at trap), suggesting habitat limitation may be creating density‐dependent effects. Additionally, female body size was positively associated with recruitment, while spawning day and mean daily temperature were inversely associated with recruitment, suggesting that both biological and environmental factors independent of habitat influenced reproduction potential. This study provides evidence that habitat restoration could have an additive (incremental) positive effect on recruitment rate, informing hatchery management and restoration activities related to population recovery.
The Argentine Black and White Tegu (Salvator merianae, formerly Tupinambis merianae) is a large lizard from South America. Now established and invasive in southern Florida, and it poses threats to ...populations of many native species. Models suggest much of the southern United States may contain suitable temperature regimes for this species, yet there is considerable uncertainty regarding either the potential for range expansion northward out of tropical and subtropical zones or the potential for the species establishing elsewhere following additional independent introductions. We evaluated survival, body temperature, duration and timing of winter dormancy, and health of wild-caught tegus from southern Florida held in semi-natural enclosures for over a year in Auburn, Alabama (> 900 km northwest of capture location). Nine of twelve lizards emerged from winter dormancy and seven survived the greater-than-one-year duration of the study. Average length of dormancy (176 d) was greater than that reported in the native range or for invasive populations in southern Florida and females remained dormant longer than males. Tegus grew rapidly throughout the study and the presence of sperm in the testes of males and previtellogenic or early vitellogenic follicles in female ovaries at the end of our study suggest the animals would have been capable of reproduction the following spring. The survival and overall health of the majority of adult tegus in our study suggests weather and climate patterns are unlikely to prevent survival following introduction in many areas of the United States far from their current invasive range.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
As legless predators, snakes are unique in their ability to immobilize and kill their prey through the process of constriction, and yet how this pressure incapacitates and ultimately kills the prey ...remains unknown. In this study, we examined the cardiovascular function of anesthetized rats before, during and after being constricted by boas (Boa constrictor) to examine the effect of constriction on the prey's circulatory function. The results demonstrate that within 6 s of being constricted, peripheral arterial blood pressure (PBP) at the femoral artery dropped to 1/2 of baseline values while central venous pressure (CVP) increased 6-fold from baseline during the same time. Electrocardiographic recordings from the anesthetized rat's heart revealed profound bradycardia as heart rate (fH) dropped to nearly half of baseline within 60 s of being constricted, and QRS duration nearly doubled over the same time period. By the end of constriction (mean 6.5±1 min), rat PBP dropped 2.9-fold, fH dropped 3.9-fold, systemic perfusion pressure (SPP=PBP-CVP) dropped 5.7-fold, and 91% of rats (10 of 11) had evidence of cardiac electrical dysfunction. Blood drawn immediately after constriction revealed that, relative to baseline, rats were hyperkalemic (serum potassium levels nearly doubled) and acidotic (blood pH dropped from 7.4 to 7.0). These results are the first to document the physiological response of prey to constriction and support the hypothesis that snake constriction induces rapid prey death due to circulatory arrest.
We introduce artemis, a new package for the R statistical programming environment designed to analyze quantitative polymerase chain reaction (qPCR) data from environmental DNA studies. The artemis ...package directly addresses several challenges for analyzing eDNA survey data, including the censorship of data generated by qPCR analysis. The performance of artemis models is compared with commonly used regression approaches using both simulated and experimental data. We demonstrate that the models in artemis have several favorable characteristics compared with standard regression approaches, yielding more accurate estimates, less bias, and better prediction performance while offering similar ease of use. Lastly, we discuss trade‐offs and considerations for choosing the most appropriate analysis approach for eDNA survey data.
We introduce artemis, a new package for the R statistical programming environment designed to analyze quantitative polymerase chain reaction (qPCR) data from environmental DNA studies. The artemis package directly addresses several challenges for analyzing eDNA survey data, including the censorship of data generated by qPCR analysis. The performance of artemis models is compared with commonly used regression approaches using both simulated and experimental data.
Due to the challenges associated with monitoring in riverine environments, unbiased and precise spawner abundance estimates are often lacking for populations of Pacific salmon Oncorhynchus spp. ...listed under the Federal Endangered Species Act. We investigated genetic approaches to estimate the 2009 spawner abundance for a population of Columbia River Chinook Salmon Oncorhynchus tshawytscha via genetic mark–recapture and rarefaction curves. The marks were the genotyped carcasses collected from the spawning area during the first sampling event. The second sampling event consisted of a collection of juveniles from a downstream migrant trap located below the spawning area. The parents that assigned to the juveniles through parentage analysis were considered the recaptures, which was a subset of the genotypes captured in the second sample. Using the Petersen estimator, the genetic mark–recapture spawner abundance estimates based on the binomial and hypergeometric models were 910 and 945 Chinook Salmon, respectively. These results were in agreement with independently derived spawner abundance estimates based on redd counts, area-under-the-curve methods, and carcass tagging based on the Jolly–Seber model. Using a rarefaction curve approach, which required only the juvenile offspring sample, our estimate of successful breeders was 781 fish. Our genetic-based approaches provide new alternatives to estimate adult Pacific salmon abundance in challenging environmental conditions or for populations with poor or unknown estimates of precision. Received December 7, 2012; accepted July 17, 2013
The dynamic Quaternary geology of the Pacific Ring of Fire created substantial challenges for biogeography. Fish life history and population genetic variation were shaped by climate change, repeated ...formation and subsidence of ice sheets, sea-level change, volcanism and tectonics, isostatic rebound, and now human activities. It is widely recognized in Chinook salmon (Oncorhynchus tshawytscha) that parallel evolution and phenotypic plasticity have obscured range-wide patterns of lifehistory segregation with evolutionary lineage, yet the idea of the lineages themselves persists. We employed a large, internationally standardized, microsatellite data set to explore population structure at coast-wide scale and test for two divergent lineages, whether or not related to life history. We found at least 27 distinct lineages. However, relationships among groups were poorly resolved--essentially a star phylogeny. We found pervasive isolation by distance among groups, complicating cluster analysis. Only in the interior Columbia River (east of the Cascade Mountains) is there a deep genetic bifurcation that supports both the two-lineage hypothesis and the life-history segregation hypothesis. This broad-scale perspective helps reconcile different views of Chinook salmon phylogeography and life-history distribution.
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Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
It is widely recognized that genetic diversity within species is shaped by dynamic habitats. The quantitative and molecular genetic patterns observed are the result of demographics, mutation, ...migration, and adaptation. The populations of rainbow trout Oncorhynchus mykiss in the Columbia River basin (including both resident and anadromous forms and various subspecies) present a special challenge to understanding the relative roles of those factors. Standardized microsatellite data were compiled for 226 collections (15,658 individuals) from throughout the Columbia and Snake River basins to evaluate the genetic patterns of structure and adaptation. The data were primarily from fish of the anadromous life history form, and we used a population grouping procedure based on principal components and hierarchical k‐means clustering to cluster populations into eight aggregates or groups with similar allele frequencies. These aggregates approximated geographic regions, and the two largest principal components corresponded to ancestral lineages of Sacramento redband trout O. m. stonei, coastal rainbow trout O. m. irideus, and interior Columbia River redband trout O. m. gairdneri. Genetic data were partitioned among primary aggregates (lower Columbia, middle–upper Columbia, and Snake rivers), and the magnitude of genetic divergence relative to genetic diversity was analyzed (per locus) to test for evidence of selection and subsequent signals of adaptation. Two loci showed higher divergence than expected by chance (i.e., positive selection); however, both of these loci were on the fringe of the 99% confidence level and are potential false positives. Genetic patterns were also significantly correlated with certain environmental and habitat parameters (e.g., precipitation), but the extent to which those correlations are causal as opposed to effectual remains unclear. Despite the remaining questions, these data provide a foundation for more detailed investigations of harvest, admixture, and introgression between hatchery‐ and natural‐origin fish and differences in reproductive success among individuals as well as monitoring trends in productivity.
Recent advances in molecular interrogation techniques now allow unprecedented genomic inference about the role of adaptive genetic divergence in wild populations. We used high‐throughput genotyping ...to screen a genome‐wide panel of 276 single nucleotide polymorphisms (SNPs) for the economically and culturally important salmonid Oncorhynchus mykiss. Samples included 805 individuals from 11 anadromous and resident populations from the northwestern United States and British Columbia, and represented two major lineages including paired populations of each life history within single drainages of each lineage. Overall patterns of variation affirmed clear distinctions between lineages and in most instances, isolation by distance within them. Evidence for divergent selection at eight candidate loci included significant landscape correlations, particularly with temperature. High diversity of two nonsynonymous mutations within the peptide‐binding region of the major histocompatibility complex (MHC) class II (DAB) gene provided signatures of balancing selection. Weak signals for potential selection between sympatric resident and anadromous populations were revealed from genome scans and allele frequency comparisons. Our results suggest an important adaptive role for immune‐related functions and present a large genomic resource for future studies
Recent advances in molecular interrogation techniques now allow unprecedented genomic inference about the role of adaptive genetic divergence in wild populations. We used high‐throughput genotyping to screen a genome‐wide panel of 276 single nucleotide polymorphisms (SNPs) for the economically and culturally important salmonid Oncorhynchus mykiss. Samples included 805 individuals from 11 anadromous and resident populations from the northwestern United States and British Columbia, and represented two major lineages including paired populations of each life history within single drainages of each lineage.
We used pattern recognition algorithms and image processing to identify individual Chinook salmon Oncorhynchus tshawytscha . Using melanophore spot patterns located on the dorsal head region, ...algorithms ranked all database images against each other. We coupled this technology with a graphical user interface to visually confirm or reject top-ranked algorithm results and tested this process on 295 juvenile Chinook salmon in seven photo sessions over a 251-d period. Juveniles began developing spots, identifiable in photo images, between 167 and 197 d after conception (52.7-mm fork length FL). Unique spot patterns appeared 197–232 d from conception, beginning at approximately 104-mm FL. Of 254 fish surviving the experimental period, 106 (42%) demonstrated identifiable patterns, 102 (40%) developed spots but patterns were insufficient for identification, and 46 (18%) exhibited a complete lack of spots. Spot patterns continued developing on individual fish by study end. On average, fish that developed recognizable spot patterns did so at approximately 140-mm FL. Once they did, reidentification was 100% correct in up to four subsequent trials. Patterns remained identifiable even after a 25–32% size increase over a 55-d period and as juveniles went through smoltification. Although patterns occurred at sizes typically larger than salmon observed at some California Central Valley monitoring locations, this technique provides a potentially valuable, noninvasive method of identifying individual salmon during emigration. Improved image collection techniques and use of body areas exhibiting identifiable patterns at earlier developmental stages may increase fish available for pattern identification. These results demonstrate the indexing of a large database using pattern recognition algorithms for Chinook salmon. The utility of such an approach may be valuable for addressing specific biological questions associated with mass-produced (wild and hatchery), migratory salmonids, especially as individuals develop, grow, and move through the various habitats available to them.
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