scholarly journals A comparison of abundance estimates from extended batch‐marking and Jolly–Seber‐type experiments

2013 ◽  
Vol 4 (2) ◽  
pp. 210-218 ◽  
Author(s):  
Laura L. E. Cowen ◽  
Panagiotis Besbeas ◽  
Byron J. T. Morgan ◽  
Carl J. Schwarz
Keyword(s):  
Abundance Estimates ◽  
Batch Marking

Abundance Estimates of Guiana Dolphins (Sotalia guianensis; Van Bénéden, 1864) Inhabiting an Estuarine System in Southeastern Brazil

2019 ◽  
Vol 45 (1) ◽  
pp. 56-65 ◽  
Author(s):  
Aline B. de Mello ◽  
Julia M. B. Molina ◽  
Maja Kajin ◽  
Marcos C. de O. Santos
Keyword(s):  
Southeastern Brazil ◽  
Estuarine System ◽  
Sotalia Guianensis ◽  
Abundance Estimates

Bridled Quail-dove Geotrygon mystacea population assessment after hurricanes Irma and Maria, St. Eustatius, Caribbean Netherlands

2021 ◽  
pp. 1-12
Author(s):  
FRANK F. RIVERA-MILÁN ◽  
HANNAH MADDEN ◽  
KEVIN VERDEL
Keyword(s):  
National Park ◽  
Food Limitation ◽  
Distance Sampling ◽  
Population Status ◽  
Management Actions ◽  
Abundance Estimates ◽  
Detection Mode ◽  
Limited Food ◽  
Seed Eating ◽  
Free Ranging

Summary Structural vegetation damage and food limitation are important effects of major hurricanes, particularly for fruit/seed-eating, forest-dependent Caribbean birds with restricted distributions and small populations, such as the Bridled Quail-dove Geotrygon mystacea. Motivated by the lack of abundance estimates, corrected for detection probability, we conducted distance-sampling surveys inside and outside the Quill National Park each May in 2016-2019. Detection mode was the most important covariate, with others receiving no support from the data. Detectability of available single individuals and clusters of individuals within 60 m of transect centrelines averaged 0.957 ± 0.114 standard error for audio detections, 0.434 ± 0.052 for visual detections, and 0.693 ± 0.064 for detection modes combined. Availability averaged 0.475 ± 0.138 and the product of detectability and availability averaged 0.329 ± 0.098. Density averaged 1.459 ± 0.277 individuals ha-1 and population size averaged 642 ± 122 individuals in 440 ha. Density did not differ along and away from forest trails, but was higher inside than outside the park and at elevations within 201-400 m than 100-200 m and 401-600 m. Density declined by 76% after hurricanes Irma and Maria in 2017. We suggest that major hurricanes together with free-ranging livestock overgrazing degraded foraging habitats, limited food supply, and caused a population bottleneck. Our methodology can be implemented across the distribution range to assess population status and trends and evaluate the result of management actions at key conservation sites. Bridled Quail-dove populations probably were declining on most islands before the 2017 hurricanes and population status warrants revision.

scholarly journals Temporal trends in stock origin and abundance of juvenile herring (Clupea harengus) in the Irish Sea

2009 ◽  
Vol 66 (8) ◽  
pp. 1749-1753 ◽  
Author(s):  
Nóirín Burke ◽  
Deirdre Brophy ◽  
Pieter-Jan Schön ◽  
Pauline A. King
Keyword(s):  
Temporal Trends ◽  
Clupea Harengus ◽  
Irish Sea ◽  
First Year ◽  
Juvenile Abundance ◽  
Abundance Estimates ◽  
Otolith Microstructure Analysis ◽  
Celtic Sea ◽  
The Irish Sea ◽  
First Year Of Life

Abstract Burke, N., Brophy, D., Schön, P-J., and King, P. A. 2009. Temporal trends in stock origin and abundance of juvenile herring (Clupea harengus) in the Irish Sea. – ICES Journal of Marine Science, 66: 1749–1753. Celtic Sea herring (Clupea harengus) larvae partly disperse into the Irish Sea, where they mix with the resident stock during their first year of life. This affects the reliability of the use of acoustic estimates of juvenile abundance on the Irish Sea nursery grounds as a recruitment index for use in stock predictions. Otolith microstructure analysis can be used to distinguish between autumn-spawned and winter-spawned individuals. Because winter spawners do not occur in the Irish Sea, this component can be assigned to Celtic Sea immigrants. We used this method to estimate the proportion of winter-spawned individuals in samples of age-1 herring from the western Irish Sea over a 10-year period (1993–2003), and subtracted a corresponding proportion from the acoustic age-1 abundance estimates. The adjusted index for autumn-spawned (supposedly Irish Sea) juveniles was significantly correlated with the abundance of age-3 fish from the same year class in commercial catches and in the acoustic surveys (p < 0.05 and <0.01, respectively), whereas the correlations for unadjusted indices were not significant. These findings are discussed in relation to the monitoring and assessment of herring in the two areas.

scholarly journals Boreal bird abundance estimates within different energy sector disturbances vary with point count radius

The Condor ◽  
2016 ◽  
Vol 118 (2) ◽  
pp. 376-390 ◽  
Author(s):  
Erin Bayne ◽  
Lionel Leston ◽  
C. Lisa Mahon ◽  
Péter Sólymos ◽  
Craig Machtans ◽  
...  
Keyword(s):  
Energy Sector ◽  
Bird Abundance ◽  
Point Count ◽  
Abundance Estimates

Food supplementation and abundance estimation in the white-footed mouse

2006 ◽  
Vol 84 (8) ◽  
pp. 1210-1215 ◽  
Author(s):  
Pei-Jen L. Shaner
Keyword(s):  
Population Dynamics ◽  
Food Availability ◽  
Robust Design ◽  
Meta Analysis ◽  
Design Model ◽  
Food Supplementation ◽  
Abundance Estimates ◽  
Abundance Indices ◽  
Consumer Population ◽  
White Footed Mouse

Food availability often drives consumer population dynamics. However, food availability may also influence capture probability, which if not accounted for may create bias in estimating consumer abundance and confound the effects of food availability on consumer population dynamics. This study compared two commonly used abundance indices (minimum number alive (MNA) and number of animals captured per night per grid) with an abundance estimator based on robust design model as applied to the white-footed mouse ( Peromyscus leucopus (Rafinesque, 1818)) in food supplementation experiments. MNA consistently generated abundance estimates similar to the robust design model, regardless of food supplementation. The number of animals captured per night per grid, however, consistently generated lower abundance estimates compared with MNA and the robust design model. Nevertheless, the correlations between abundance estimates from MNA, number of animals captured, and robust design model were not influenced by food supplementation. This study demonstrated that food supplementation is not likely to create bias among these different measures of abundance. Therefore, there is a great potential for conducting meta-analysis of food supplementation effect on consumer population dynamics (particularly in small mammals) across studies using different abundance indices and estimators.

scholarly journals Osmotic induction improves batch marking of larval fish otoliths with enriched stable isotopes

2014 ◽  
Vol 71 (9) ◽  
pp. 2530-2538 ◽  
Author(s):  
Emmanuel de Braux ◽  
Fletcher Warren-Myers ◽  
Tim Dempster ◽  
Per Gunnar Fjelldal ◽  
Tom Hansen ◽  
...  
Keyword(s):  
Stable Isotopes ◽  
Salmo Salar ◽  
Larval Fish ◽  
Fish Larvae ◽  
Cost Effective ◽  
Industrial Applications ◽  
Chemical Markers ◽  
Potential Applications ◽  
Recent Method ◽  
Batch Marking

Abstract Otolith marking with enriched stable isotopes via immersion is a recent method of batch marking larval fish for a range of research and industrial applications. However, current immersion times and isotope concentrations required to successfully mark an otolith limit the utility of this technique. Osmotic induction improves incorporation and reduces immersion time for some chemical markers, but its effects on isotope incorporation into otoliths are unknown. Here, we tested the effects of osmotic induction over a range of different isotope concentrations and immersion times on relative mark success and strength for 26Mg:24Mg, 86Sr:88Sr and 137Ba:138Ba on Atlantic salmon (Salmo salar) larvae. 71% and 100% mark success were achieved after 1 h of immersion for 86Sr (75 µg L−1) and 137Ba (30 µg L−1) isotopes, respectively. Compared with conventional immersion, osmotic induction improved overall mark strength for 86Sr and 137Ba isotopes by 26–116%, although this effect was only observed after 12 h of immersion and predominately for 86Sr. The results demonstrate that osmotic induction reduces immersion times and the concentrations of isotope required to achieve successful marks. Osmotically induced isotope labels via larval immersion may prove a rapid and cost-effective way of batch marking fish larvae across a range of potential applications.

scholarly journals Zea mays RNA-seq estimated transcript abundances are strongly affected by read mapping bias

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Shuhua Zhan ◽  
Cortland Griswold ◽  
Lewis Lukens
Keyword(s):  
Gene Expression ◽  
Zea Mays ◽  
Reference Genome ◽  
Transcript Abundance ◽  
Gene Transcript ◽  
Rna Seq ◽  
Individual Genome ◽  
Abundance Estimates ◽  
Mapping Bias ◽  
Quantify Gene Expression

Abstract Background Genetic variation for gene expression is a source of phenotypic variation for natural and agricultural species. The common approach to map and to quantify gene expression from genetically distinct individuals is to assign their RNA-seq reads to a single reference genome. However, RNA-seq reads from alleles dissimilar to this reference genome may fail to map correctly, causing transcript levels to be underestimated. Presently, the extent of this mapping problem is not clear, particularly in highly diverse species. We investigated if mapping bias occurred and if chromosomal features associated with mapping bias. Zea mays presents a model species to assess these questions, given it has genotypically distinct and well-studied genetic lines. Results In Zea mays, the inbred B73 genome is the standard reference genome and template for RNA-seq read assignments. In the absence of mapping bias, B73 and a second inbred line, Mo17, would each have an approximately equal number of regulatory alleles that increase gene expression. Remarkably, Mo17 had 2–4 times fewer such positively acting alleles than did B73 when RNA-seq reads were aligned to the B73 reference genome. Reciprocally, over one-half of the B73 alleles that increased gene expression were not detected when reads were aligned to the Mo17 genome template. Genes at dissimilar chromosomal ends were strongly affected by mapping bias, and genes at more similar pericentromeric regions were less affected. Biased transcript estimates were higher in untranslated regions and lower in splice junctions. Bias occurred across software and alignment parameters. Conclusions Mapping bias very strongly affects gene transcript abundance estimates in maize, and bias varies across chromosomal features. Individual genome or transcriptome templates are likely necessary for accurate transcript estimation across genetically variable individuals in maize and other species.

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