scholarly journals Development of demographic models to analyze populations with multi-year data—Using Agassiz’s Desert Tortoise (Gopherus agassizii) as a case study

2021 ◽  
Author(s):  
Kristin H. Berry ◽  
Julie L. Yee
Keyword(s):  
Gopherus Agassizii ◽  
Desert Tortoise ◽  
Demographic Models

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.

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 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

Case Study: Using Soil Survey to Help Predict Sonoran Desert Tortoise Population Distribution and Densities

Rangelands ◽  
2017 ◽  
Vol 39 (3-4) ◽  
pp. 97-111
Author(s):  
Robert D. Stager ◽  
Elno Roundy ◽  
Gary Brackley ◽  
Steve Leonard ◽  
Leon Lato
Keyword(s):  
Sonoran Desert ◽  
Population Distribution ◽  
Soil Survey ◽  
Desert Tortoise
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