scholarly journals Airborne LiDAR and Aerial Imagery to Assess Potential Burrow Locations for the Desert Tortoise (Gopherus agassizii)

2017 ◽  
Vol 9 (5) ◽  
pp. 458 ◽  
Author(s):  
◽  
◽  
◽  
Keyword(s):  
Airborne Lidar ◽  
Aerial Imagery ◽  
Gopherus Agassizii ◽  
Desert Tortoise

The effect of research activities and winter precipitation on voiding behaviour of Agassiz’s desert tortoises (Gopherus agassizii)

2014 ◽  
Vol 41 (8) ◽  
pp. 641 ◽  
Author(s):  
Mickey Agha ◽  
Mason O. Murphy ◽  
Jeffrey E. Lovich ◽  
Joshua R. Ennen ◽  
Christian R. Oldham ◽  
...  
Keyword(s):  
Stress Responses ◽  
Handling Time ◽  
Winter Precipitation ◽  
Contact Period ◽  
Gopherus Agassizii ◽  
Desert Tortoise ◽  
Defensive Strategy ◽  
Survivorship Analysis ◽  
Research Activities

Context There is little information available on how research activities might cause stress responses in wildlife, especially responses of threatened species such as the desert tortoise (Gopherus agassizii). Aims The present study aims to detect behavioural effects of researcher handling and winter precipitation on a natural population of desert tortoises in the desert of Southwestern United States, over the period 1997 to 2014, through extensive assessments of capture events during multiple research studies, and capture–mark–recapture survivorship analysis. Methods Juvenile and adult desert tortoises were repeatedly handled with consistent methodology across 18 years during 10 study seasons. Using a generalised linear mixed-effects model, we assessed the effects of both research manipulation and abiotic conditions on probability of voiding. Additionally, we used a Cormack–Jolly–Seber model to assess the effects of winter precipitation and voiding on long-term apparent survivorship. Key results Of 1008 total capture events, voiding was recorded on 83 (8.2%) occasions in 42 different individuals. Our top models indicated that increases in handling time led to significantly higher probabilities of voiding for juveniles, females and males. Similarly, increases in precipitation resulted in significantly higher probabilities of voiding for juveniles and females, but not for males. Tortoise capture frequency was negatively correlated with voiding occurrence. Cormack–Jolly–Seber models demonstrated a weak effect of winter precipitation on survivorship, but a negligible effect for both voiding behaviour and sex. Conclusions Handling-induced voiding by desert tortoises may occur during common research activities and years of above average winter precipitation. Increased likelihood of voiding in individuals with relatively low numbers of recaptures suggested that tortoises may have perceived researchers initially as predators, and therefore voided as a defensive strategy. Voiding does not appear to impact long-term survivorship in desert tortoises at this site. Implications This study has demonstrated that common handling practices on desert tortoise may cause voiding behaviour. These results suggest that in order to minimise undesirable behavioural responses in studied desert tortoise populations, defined procedures or protocols must be followed by the investigators to reduce contact period to the extent feasible.

Urban Thematic Mapping by Integrating LiDAR Point Cloud with Colour Imagery

GEOMATICA ◽  
2011 ◽  
Vol 65 (4) ◽  
pp. 375-385 ◽  
Author(s):  
Haiyan Guan ◽  
Jonathan Li ◽  
Michael A. Chapman
Keyword(s):  
Urban Areas ◽  
Point Cloud ◽  
Local Variation ◽  
Airborne Lidar ◽  
Aerial Imagery ◽  
Building Detection ◽  
Thematic Mapping ◽  
Airborne Lidar Data ◽  
Spectral Channels ◽  
Height Data

This paper presents an effective approach to integrating airborne lidar data and colour imagery acquired simultaneously for urban mapping. Texture and height information extracted from lidar point cloud is integrated with spectral channels of aerial imagery into an image segmentation process. Then, the segmented polygons are integrated with the extracted geometric features (height information between first- and lastreturn, eigenvalue-based local variation and filtered height data) and spectral features (line segments) into a supervised classifier. The results for two different urban areas in Toronto, Canada, demonstrated that a satisfactory overall accuracy of 84.96% and Kappa of 0.76 were achieved in Scene I, while a building detection rate of 92.11%, comission error of 2.10% and omission error of 9.25% were obtained in Scene II.

Seasonal Reproductive Cycle of the Desert Tortoise (Gopherus agassizii) in the Eastern Mojave Desert

1994 ◽  
Vol 8 ◽  
pp. 72 ◽  
Author(s):  
David C. Rostal ◽  
Valentine A. Lance ◽  
Janice S. Grumbles ◽  
Allison C. Alberts
Keyword(s):  
Reproductive Cycle ◽  
Mojave Desert ◽  
Gopherus Agassizii ◽  
Desert Tortoise

scholarly journals Improved draft of the Mojave Desert tortoise genome, Gopherus agassizii, version 1.1

2017 ◽  
Author(s):  
Timothy H Webster ◽  
Greer A. Dolby ◽  
Melissa Wilson Sayres ◽  
Kenro Kusumi
Keyword(s):  
Threatened Species ◽  
Mojave Desert ◽  
Gene Annotation ◽  
Draft Genome ◽  
Gopherus Agassizii ◽  
Desert Tortoise ◽  
Draft Genome Assembly ◽  
Initial Release ◽  
Exogenous Sequence ◽  
Mojave Desert Tortoise

Exogenous sequence contamination presents a challenge in first-draft genomes because it can lead to non-contiguous, chimeric assembled sequences. This can mislead downstream analyses reliant on synteny, such as linkage-based analyses. Recently, the Mojave Desert Tortoise (Gopherus agassizii) draft genome was published as a resource to advance conservation efforts for the threatened species and discover more about chelonian biology and evolution. Here, we illustrate steps taken to improve the desert tortoise draft genome by removing contaminating sequences—actions that are typically carried out after the initial release of a draft genome assembly. We used information from NCBI’s Vecscreen output to remove intra-scaffold contamination and trim heading and trailing Ns. We then reordered and renamed scaffolds, and transferred the gene annotation onto this assembly. Finally, we describe the tools developed for this pipeline, freely available on Github (https://github.com/thw17/G_agassizii_reference_update), which facilitate post-assembly processing of other draft genomes. The new gopAga1.1 genome has an N50 of 251 KB, L50 of 2592 scaffolds, and its annotation retains 17,201 of the original 20,172 genes that were unaffected by the scaffold processing.

scholarly journals Improved draft of the Mojave Desert tortoise genome, Gopherus agassizii, version 1.1

2018 ◽  
Author(s):  
Timothy H Webster ◽  
Greer A Dolby ◽  
Melissa A Wilson Sayres ◽  
Kenro Kusumi
Keyword(s):  
Threatened Species ◽  
Mojave Desert ◽  
Gene Annotation ◽  
Draft Genome ◽  
Gopherus Agassizii ◽  
Desert Tortoise ◽  
Draft Genome Assembly ◽  
Initial Release ◽  
Exogenous Sequence ◽  
Mojave Desert Tortoise

Exogenous sequence contamination presents a challenge in first-draft genomes because it can lead to non-contiguous, chimeric assembled sequences. This can mislead downstream analyses reliant on synteny, such as linkage-based analyses. Recently, the Mojave Desert Tortoise (Gopherus agassizii) draft genome was published as a resource to advance conservation efforts for the threatened species and discover more about chelonian biology and evolution. Here, we illustrate steps taken to improve the desert tortoise draft genome by removing contaminating sequences—actions that are typically carried out after the initial release of a draft genome assembly. We used information from NCBI’s Vecscreen output to remove intra-scaffold contamination and trim heading and trailing Ns. We then reordered and renamed scaffolds, and transferred the gene annotation onto this assembly. Finally, we describe the tools developed for this pipeline, freely available on Github (https://github.com/thw17/G_agassizii_reference_update), which facilitate post-assembly processing of other draft genomes. The new gopAga1.1 genome has an N50 of 251 kb, L50 of 2592 scaffolds, and its annotation retains 17,201 of the original 20,172 genes that were unaffected by the scaffold processing.

scholarly journals Characterizing a New England Saltmarsh with NASA G-LiHT Airborne Lidar

2019 ◽  
Vol 11 (5) ◽  
pp. 509 ◽  
Author(s):  
Ian Paynter ◽  
Crystal Schaaf ◽  
Jennifer Bowen ◽  
Linda Deegan ◽  
Francesco Peri ◽  
...  
Keyword(s):  
New England ◽  
Spartina Alterniflora ◽  
Regional Scale ◽  
Satellite Observations ◽  
Airborne Lidar ◽  
Aerial Imagery ◽  
Lidar Data ◽  
Terrestrial Lidar ◽  
Airborne Lidar Data ◽  
Lidar Observations

Airborne lidar can observe saltmarshes on a regional scale, targeting phenological and tidal states to provide the information to more effectively utilize frequent multispectral satellite observations to monitor change. Airborne lidar observations from NASA Goddard Lidar Hyperspectral and Thermal (G-LiHT) of a well-studied region of saltmarsh (Plum Island, Massachusetts, United States) were acquired in multiple years (2014, 2015 and 2016). These airborne lidar data provide characterizations of important saltmarsh components, as well as specifications for effective surveys. The invasive Phragmites australis was observed to increase in extent from 8374 m2 in 2014, to 8882 m2 in 2015 (+6.1%), and again to 13,819 m2 in 2016 (+55.6%). Validation with terrestrial lidar supported this increase, but suggested the total extent was still underestimated. Estimates of Spartina alterniflora extent from airborne lidar were within 7% of those from terrestrial lidar, but overestimation of height of Spartina alterniflora was found to occur at the edges of creeks (+83.9%). Capturing algae was found to require observations within ±15° of nadir, and capturing creek structure required observations within ±10° of nadir. In addition, 90.33% of creeks and ditches were successfully captured in the airborne lidar data (8206.3 m out of 9084.3 m found in aerial imagery).

scholarly journals A Comparison of Standard Modeling Techniques Using Digital Aerial Imagery with National Elevation Datasets and Airborne LiDAR to Predict Size and Density Forest Metrics in the Sapphire Mountains MT, USA

2019 ◽  
Vol 8 (1) ◽  
pp. 24 ◽  
Author(s):  
Robert Ahl ◽  
John Hogland ◽  
Steve Brown
Keyword(s):  
Basal Area ◽  
Airborne Lidar ◽  
Model Fit ◽  
Aerial Imagery ◽  
Light Detection And Ranging ◽  
National Elevation Dataset ◽  
Modeling Techniques ◽  
High Degree ◽  
Field Plots ◽  
Degree Of Similarity

In recent years airborne Light Detection and Ranging (LiDAR) technology has received a great deal of attention. Using airborne LiDAR, analysts have successfully related height measurements to forest characteristics such as tree size, basal area, and number of trees. Similarly, National Agricultural Imagery Program (NAIP) digital aerial imagery in combination with elevation datasets such as the National Elevation Dataset (NED) have been used to estimate similar forest characteristics. Few comparisons, however, have been made between using airborne LiDAR, NAIP, and NED to estimate forest characteristics. In this study we compare airborne LiDAR, NAIP, and NAIP assisted NED based models of forest characteristics commonly used within forest management at the spatial scale of field plots and forest stands. Our findings suggest that there is a high degree of similarity in model fit and estimated values when using LiDAR, NAIP, and NAIP assisted NED predictor variables.

scholarly journals Immune and sex-biased gene expression in the threatened Mojave desert tortoise, Gopherus agassizii

PLoS ONE ◽  
2020 ◽  
Vol 15 (8) ◽  
pp. e0238202
Author(s):  
Cindy Xu ◽  
Greer A. Dolby ◽  
K. Kristina Drake ◽  
Todd C. Esque ◽  
Kenro Kusumi
Keyword(s):  
Gene Expression ◽  
Mojave Desert ◽  
Gopherus Agassizii ◽  
Desert Tortoise ◽  
Mojave Desert Tortoise

scholarly journals Mojave desert tortoise (Gopherus agassizii) thermal ecology and reproductive success along a rainfall cline

2015 ◽  
Vol 10 (3) ◽  
pp. 282-294 ◽  
Author(s):  
Annette E. SIEG ◽  
Megan M. GAMBONE ◽  
Bryan P. WALLACE ◽  
Susana CLUSELLA-TRULLAS ◽  
James R. SPOTILA ◽  
...  
Keyword(s):  
Reproductive Success ◽  
Mojave Desert ◽  
Thermal Ecology ◽  
Gopherus Agassizii ◽  
Desert Tortoise ◽  
Mojave Desert Tortoise
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