Distribution of tiger salamanders in northern Sonora, Mexico: comparison of sampling methods and possible implications for an endangered subspecies

2021 ◽  
pp. 1-11
Author(s):  
Blake R. Hossack ◽  
Julio Alberto Lemos-Espinal ◽  
Brent H. Sigafus ◽  
Erin Muths ◽  
Gerardo Carreón Arroyo ◽  
...  
Keyword(s):  
Management Practices ◽  
Introgressive Hybridization ◽  
Environmental Dna ◽  
Tiger Salamander ◽  
Limited Information ◽  
Occupancy Models ◽  
Imperfect Detection ◽  
Tiger Salamanders ◽  
Land And Water Management ◽  
The Usa

Abstract Many aquatic species in the arid USA-Mexico borderlands region are imperiled, but limited information on distributions and threats often hinders management. To provide information on the distribution of the Western Tiger Salamander (Ambystoma mavortium), including the USA-federally endangered Sonoran Tiger Salamander (Ambystoma mavortium stebbinsi), we used traditional (seines, dip-nets) and modern (environmental DNA [eDNA]) methods to sample 91 waterbodies in northern Sonora, Mexico, during 2015-2018. The endemic Sonoran Tiger Salamander is threatened by introgressive hybridization and potential replacement by another sub-species of the Western Tiger Salamander, the non-native Barred Tiger Salamander (A. m. mavortium). Based on occupancy models that accounted for imperfect detection, eDNA sampling provided a similar detection probability (0.82 [95% CI: 0.56-0.94]) as seining (0.83 [0.46-0.96]) and much higher detection than dip-netting (0.09 [0.02-0.23]). Volume of water filtered had little effect on detection, possibly because turbid sites had greater densities of salamanders. Salamanders were estimated to occur at 51 sites in 3 river drainages in Sonora. These results indicate tiger salamanders are much more widespread in northern Sonora than previously documented, perhaps aided by changes in land and water management practices. However, because the two subspecies of salamanders cannot be reliably distinguished based on morphology or eDNA methods that are based on mitochondrial DNA, we are uncertain if we detected only native genotypes or if we documented recent invasion of the area by the non-native sub-species. Thus, there is an urgent need for methods to reliably distinguish the subspecies so managers can identify appropriate interventions.

scholarly journals Validating metabarcoding-based biodiversity assessments with multi-species occupancy models: a case study using coastal marine eDNA

2019 ◽  
Author(s):  
Beverly McClenaghan ◽  
Zacchaeus G. Compson ◽  
Mehrdad Hajibabaei
Keyword(s):  
Model Comparison ◽  
Environmental Dna ◽  
Model Assessment ◽  
Occupancy Models ◽  
Ecological Inference ◽  
Biodiversity Data ◽  
Imperfect Detection ◽  
Coastal Marine ◽  
Species Occupancy

AbstractEnvironmental DNA (eDNA) metabarcoding is an increasingly popular method for rapid biodiversity assessment. As with any ecological survey, false negatives can arise during sampling and, if unaccounted for, lead to biased results and potentially misdiagnosed environmental assessments. We developed a multi-scale, multi-species occupancy model for the analysis of community biodiversity data resulting from eDNA metabarcoding; this model accounts for imperfect detection and additional sources of environmental and experimental variation. We present methods for model assessment and model comparison and demonstrate how these tools improve the inferential power of eDNA metabarcoding data using a case study in a coastal, marine environment. Using occupancy models to account for factors often overlooked in the analysis of eDNA metabarcoding data will dramatically improve ecological inference, sampling design, and methodologies, empowering practitioners with an approach to wield the high-resolution biodiversity data of next-generation sequencing platforms.

scholarly journals Shifting up a gear with iDNA: from mammal detection events to standardized surveys

2018 ◽  
Author(s):  
Jesse F Abrams ◽  
Lisa Hoerig ◽  
Robert Brozovic ◽  
Jan Axtner ◽  
Alex Crampton-Platt ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Ad Hoc ◽  
Environmental Dna ◽  
Camera Trap ◽  
Camera Traps ◽  
Occupancy Models ◽  
Imperfect Detection ◽  
Mammal Species ◽  
Occupancy Model ◽  
Cost Efficient

Invertebrate-derived DNA (iDNA), in combination with high throughput sequencing, has been proposed as a cost-efficient and powerful tool to survey vertebrate species. Previous studies, however, have only provided evidence that vertebrates can be detected using iDNA, but have not taken the next step of placing these detection events within a statistical framework that allows for robust biodiversity assessments. Here, we compare concurrent iDNA and camera-trap surveys. Leeches were repeatedly collected in close vicinity to 64 camera-trap stations in Sabah, Malaysian Borneo. We analyze iDNA-derived mammalian detection events in a modern occupancy model that accounts for imperfect detection and compare the results with those from occupancy models parameterized with camera-trap-derived detection events. We also combine leech-iDNA and camera-trap data in a single occupancy model. We found consistent estimates of occupancy probabilities produced by our camera-trap and leech datasets. This indicates that the metabarcoding of leech-iDNA method provides reasonable estimates of occupancy and can be a suitable method for studying and monitoring mammal species in tropical rainforests. However, we also show that a more extensive collection of leeches would be needed to assess mammal biodiversity with a similar robustness as with camera traps. As certain taxa were only detected in leeches, we see great potential in complementing camera-trap studies with the iDNA approach, as long as the collection of leeches follows a similar robust and standardized sampling scheme. Synthesis and applications: The approach we describe here is not restricted to the processing of leech samples, but can be used for the analysis of other iDNA and environmental DNA (eDNA) data. Our study is the first step to shift the application of e/iDNA studies from opportunistic ad-hoc collections to systematic surveys required for long-term wildlife populations and biodiversity monitoring programs.

Managing Water Resources, Past and Present

2004 ◽  
Keyword(s):  
Water Management ◽  
Middle Ages ◽  
Southern Africa ◽  
Management Practices ◽  
Social Groups ◽  
Water Politics ◽  
European Water ◽  
The Usa ◽  
British Experience ◽  
Over Exploitation

A multi-disciplinary analysis of the evolution of water politics and policy by an international team of distinguished experts. Water management in the Middle Ages in Europe, its evolution in the USA, the elaboration of the European Water Framework Directive, the British experience of water management, the over-exploitation of African aquifers, and the evolution of the water situation in Southern Africa are all examined. This volume underlines the fact that only an integrative and interdisciplinary understanding can lead to genuinely improved water management practices that will not benefit some social groups at the expense of others.

Maternal age at birth and daughter’s fecundability

2021 ◽  
Author(s):  
Olga Basso ◽  
Sydney K Willis ◽  
Elizabeth E Hatch ◽  
Ellen M Mikkelsen ◽  
Kenneth J Rothman ◽  
...  
Keyword(s):  
Risk Factors ◽  
Cohort Study ◽  
Maternal Age ◽  
Limited Information ◽  
Loss To Follow Up ◽  
Older Mothers ◽  
Registration Number ◽  
The Usa ◽  
Competing Interest

Abstract STUDY QUESTION Do daughters of older mothers have lower fecundability? SUMMARY ANSWER In this cohort study of North American pregnancy planners, there was virtually no association between maternal age ≥35 years and daughters’ fecundability. WHAT IS KNOWN ALREADY Despite suggestive evidence that daughters of older mothers may have lower fertility, only three retrospective studies have examined the association between maternal age and daughter’s fecundability. STUDY DESIGN, SIZE, DURATION Prospective cohort study of 6689 pregnancy planners enrolled between March 2016 and January 2020. PARTICIPANTS/MATERIALS, SETTING, METHODS Pregnancy Study Online (PRESTO) is an ongoing pre-conception cohort study of pregnancy planners (age, 21-45 years) from the USA and Canada. We estimated fecundability ratios (FR) for maternal age at the participant’s birth using multivariable proportional probabilities regression models. MAIN RESULTS AND THE ROLE OF CHANCE Daughters of mothers ≥30 years were less likely to have previous pregnancies (or pregnancy attempts) or risk factors for infertility, although they were more likely to report that their mother had experienced problems conceiving. The proportion of participants with prior unplanned pregnancies, a birth before age 21, ≥3 cycles of attempt at study entry or no follow-up was greater among daughters of mothers <25 years. Compared with maternal age 25–29 years, FRs (95% CI) for maternal age <20, 20–24, 30–34, and ≥35 were 0.72 (0.61, 0.84), 0.92 (0.85, 1.00), 1.08 (1.00, 1.17), and 1.00 (0.89, 1.12), respectively. LIMITATIONS, REASONS FOR CAUTION Although the examined covariates did not meaningfully affect the associations, we had limited information on the participants’ mother. Differences by maternal age in reproductive history, infertility risk factors and loss to follow-up suggest that selection bias may partly explain our results. WIDER IMPLICATIONS OF THE FINDINGS Our finding that maternal age 35 years or older was not associated with daughter’s fecundability is reassuring, considering the trend towards delayed childbirth. However, having been born to a young mother may be a marker of low fecundability among pregnancy planners. STUDY FUNDING/COMPETING INTEREST(S) PRESTO was funded by NICHD Grants (R21-HD072326 and R01-HD086742) and has received in-kind donations from Swiss Precision Diagnostics, FertilityFriend.com, Kindara.com, and Sandstone Diagnostics. Dr Wise is a fibroid consultant for AbbVie, Inc. TRIAL REGISTRATION NUMBER n/a

scholarly journals Using areas of known occupancy to identify sources of variation in detection probability of raptors: taking time lowers replication effort for surveys

2016 ◽  
Vol 3 (10) ◽  
pp. 160368 ◽  
Author(s):  
Campbell Murn ◽  
Graham J. Holloway
Keyword(s):  
Detection Probability ◽  
Spatial Scales ◽  
Survey Methods ◽  
A Priori ◽  
Low Density ◽  
Occupancy Models ◽  
Imperfect Detection ◽  
Factors Affecting ◽  
Sources Of Variation ◽  
Time Of Year

Species occurring at low density can be difficult to detect and if not properly accounted for, imperfect detection will lead to inaccurate estimates of occupancy. Understanding sources of variation in detection probability and how they can be managed is a key part of monitoring. We used sightings data of a low-density and elusive raptor (white-headed vulture Trigonoceps occipitalis ) in areas of known occupancy (breeding territories) in a likelihood-based modelling approach to calculate detection probability and the factors affecting it. Because occupancy was known a priori to be 100%, we fixed the model occupancy parameter to 1.0 and focused on identifying sources of variation in detection probability. Using detection histories from 359 territory visits, we assessed nine covariates in 29 candidate models. The model with the highest support indicated that observer speed during a survey, combined with temporal covariates such as time of year and length of time within a territory, had the highest influence on the detection probability. Averaged detection probability was 0.207 (s.e. 0.033) and based on this the mean number of visits required to determine within 95% confidence that white-headed vultures are absent from a breeding area is 13 (95% CI: 9–20). Topographical and habitat covariates contributed little to the best models and had little effect on detection probability. We highlight that low detection probabilities of some species means that emphasizing habitat covariates could lead to spurious results in occupancy models that do not also incorporate temporal components. While variation in detection probability is complex and influenced by effects at both temporal and spatial scales, temporal covariates can and should be controlled as part of robust survey methods. Our results emphasize the importance of accounting for detection probability in occupancy studies, particularly during presence/absence studies for species such as raptors that are widespread and occur at low densities.

Short-term effects of timber harvest and forest edges on ground-layer mosses and liverworts

2005 ◽  
Vol 83 (6) ◽  
pp. 610-620 ◽  
Author(s):  
Cara R Nelson ◽  
Charles B Halpern
Keyword(s):  
Forest Management ◽  
Edge Effects ◽  
Management Practices ◽  
Timber Harvest ◽  
Ground Layer ◽  
Limited Information ◽  
Short Term ◽  
Before And After ◽  
Logging Effects ◽  
Structural Retention

Limited information exists on the effects of forest management practices on bryophytes, despite their importance to forest ecosystems. We examined short-term responses of ground-layer bryophytes to logging disturbance and creation of edges in mature Pseudotsuga forests of western Washington (USA). The abundance and richness of species were measured in four 1-ha forest aggregates (patches of intact forest) and in surrounding logged areas before and after structural retention harvests. One year after treatment, species richness, total cover, and frequency of most moss and liverwort taxa declined within harvest areas. Within forest aggregates, mosses did not show significant edge effects; however, richness and abundance of liverworts declined with proximity to the aggregate edge. Our results suggest that, over short time frames, 1-ha-sized aggregates are sufficient to maintain most common mosses through structural retention harvests but are not large enough to prevent declines or losses of liverworts. Thus, current standards for structural retention, which allow for aggregates as small as 0.2 ha, may be inadequate to retain the diversity and abundance of species found in mature, undisturbed forests.Key words: bryophyte, edge effects, forest borders, forest management, logging effects, structural retention harvest.

scholarly journals A sparse observation model to quantify species interactions in time and space

2019 ◽  
Author(s):  
Sadoune Ait Kaci Azzou ◽  
Liam Singer ◽  
Thierry Aebischer ◽  
Madleina Caduff ◽  
Beat Wolf ◽  
...  
Keyword(s):  
Species Interactions ◽  
Activity Patterns ◽  
Niche Partitioning ◽  
Camera Trap ◽  
Camera Traps ◽  
Observation Model ◽  
Occupancy Models ◽  
Time And Space ◽  
Imperfect Detection ◽  
Mobile Species

SummaryCamera traps and acoustic recording devices are essential tools to quantify the distribution, abundance and behavior of mobile species. Varying detection probabilities among device locations must be accounted for when analyzing such data, which is generally done using occupancy models. We introduce a Bayesian Time-dependent Observation Model for Camera Trap data (Tomcat), suited to estimate relative event densities in space and time. Tomcat allows to learn about the environmental requirements and daily activity patterns of species while accounting for imperfect detection. It further implements a sparse model that deals well will a large number of potentially highly correlated environmental variables. By integrating both spatial and temporal information, we extend the notation of overlap coefficient between species to time and space to study niche partitioning. We illustrate the power of Tomcat through an application to camera trap data of eight sympatrically occurring duiker Cephalophinae species in the savanna - rainforest ecotone in the Central African Republic and show that most species pairs show little overlap. Exceptions are those for which one species is very rare, likely as a result of direct competition.

scholarly journals Anemia and iron deficiency among chronic kidney disease Stages 3–5ND patients in the Chronic Kidney Disease Outcomes and Practice Patterns Study: often unmeasured, variably treated

2019 ◽  
Vol 13 (4) ◽  
pp. 613-624 ◽  
Author(s):  
Michelle M Y Wong ◽  
Charlotte Tu ◽  
Yun Li ◽  
Rachel L Perlman ◽  
Roberto Pecoits-Filho ◽  
...  
Keyword(s):  
Chronic Kidney Disease ◽  
Kidney Disease ◽  
Iron Deficiency ◽  
Management Practices ◽  
Practice Patterns ◽  
Intravenous Iron ◽  
Cross Sectional ◽  
Disease Outcomes ◽  
The Usa ◽  
Hemoglobin Measurement

Abstract Background International variation in anemia assessment and management practices in chronic kidney disease (CKD) is poorly understood. Methods We performed a cross-sectional analysis of anemia laboratory monitoring, prevalence and management in the prospective Chronic Kidney Disease Outcomes and Practice Patterns Study (CKDopps). A total of 6766 participants with CKD Stages 3a–5ND from nephrology clinics in Brazil, France, Germany and the USA were included. Results Among patients with anemia (hemoglobin <12 g/dL), 36–58% in Brazil, the USA and Germany had repeat hemoglobin measured and 40–61% had iron indices measured within 3 months of the index hemoglobin measurement. Anemia was more common in the USA and Brazil than in France and Germany across CKD stages. Higher ferritin and lower iron saturation (TSAT) levels were observed with lower hemoglobin levels, and higher ferritin with more advanced CKD. The proportion of anemic patients with ferritin <100 ng/mL or TSAT <20% ranged from 42% in Brazil to 53% in France and Germany, and of these patients, over 40% in Brazil, Germany and the USA, compared with 27% in France, were treated with oral or intravenous iron within 3 months after hemoglobin measurement. The proportion of patients with hemoglobin <10 g/dL treated with erythropoiesis-stimulating agents ranged from 28% in the USA to 57% in Germany. Conclusions Hemoglobin and iron stores are measured less frequently than per guidelines. Among all regions, there was a substantial proportion of anemic patients with iron deficiency who were not treated with iron, highlighting an area for practice improvement in CKD care.

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