scholarly journals Precipitation quantity and timing affect native plant production and growth of a key herbivore, the desert tortoise, in the Mojave Desert

2017 ◽  
Vol 4 (1) ◽  
Author(s):  
Melia G. Nafus ◽  
Tracey D. Tuberville ◽  
Kurt A. Buhlmann ◽  
Brian D. Todd
2021 ◽  
Vol 41 (2) ◽  
Author(s):  
Todd C. Esque ◽  
Lesley A. DeFalco ◽  
Gayle L. Tyree ◽  
K. Kristina Drake ◽  
Kenneth E. Nussear ◽  
...  

1994 ◽  
Vol 8 ◽  
pp. 72 ◽  
Author(s):  
David C. Rostal ◽  
Valentine A. Lance ◽  
Janice S. Grumbles ◽  
Allison C. Alberts

2017 ◽  
Vol 26 (12) ◽  
pp. 1030 ◽  
Author(s):  
Andrew H. Lybbert ◽  
Justin Taylor ◽  
Alysa DeFranco ◽  
Samuel B. St Clair

Wildfire can drastically affect plant sexual reproductive success in plant–pollinator systems. We assessed plant reproductive success of wind, generalist and specialist pollinated plant species along paired unburned, burned-edge and burned-interior locations of large wildfires in the Mojave Desert. Flower production of wind and generalist pollinated plants was greater in burned landscapes than adjacent unburned areas, whereas specialist species responses were more neutral. Fruit production of generalist species was greater in burned landscapes than in unburned areas, whereas fruit production of wind- and specialist-pollinated species showed no difference in burned and unburned landscapes. Plants surviving in wildfire-disturbed landscapes did not show evidence of pollination failure, as measured by fruit set and seed:ovule ratios. Generalist- and specialist-plant species established in the interior of burned landscapes showed no difference in fruit production than plants established on burned edges suggesting that pollination services are conserved with increasing distance from fire boundaries in burned desert landscapes. Stimulation of plant reproduction in burned environments due to competition release may contribute to the maintenance of pollinator services and re-establishment of the native plant community in post-fire desert environments.


2017 ◽  
Vol 27 (2) ◽  
pp. 429-445 ◽  
Author(s):  
Daniel F. Shryock ◽  
Caroline A. Havrilla ◽  
Lesley A. DeFalco ◽  
Todd C. Esque ◽  
Nathan A. Custer ◽  
...  

2017 ◽  
Author(s):  
Timothy H Webster ◽  
Greer A. Dolby ◽  
Melissa Wilson Sayres ◽  
Kenro Kusumi

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.


2018 ◽  
Author(s):  
Timothy H Webster ◽  
Greer A Dolby ◽  
Melissa A Wilson Sayres ◽  
Kenro Kusumi

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.


2020 ◽  
Vol 12 (2) ◽  
pp. 3917-3925
Author(s):  
Greer A Dolby ◽  
Matheo Morales ◽  
Timothy H Webster ◽  
Dale F DeNardo ◽  
Melissa A Wilson ◽  
...  

Abstract Toll-like receptors (TLRs) are a complex family of innate immune genes that are well characterized in mammals and birds but less well understood in nonavian sauropsids (reptiles). The advent of highly contiguous draft genomes of nonmodel organisms enables study of such gene families through analysis of synteny and sequence identity. Here, we analyze TLR genes from the genomes of 22 tetrapod species. Findings reveal a TLR8 gene expansion in crocodilians and turtles (TLR8B), and a second duplication (TLR8C) specifically within turtles, followed by pseudogenization of that gene in the nonfreshwater species (desert tortoise and green sea turtle). Additionally, the Mojave desert tortoise (Gopherus agassizii) has a stop codon in TLR8B (TLR8-1) that is polymorphic among conspecifics. Revised orthology further reveals a new TLR homolog, TLR21-like, which is exclusive to lizards, snakes, turtles, and crocodilians. These analyses were made possible by a new draft genome assembly of the desert tortoise (gopAga2.0), which used chromatin-based assembly to yield draft chromosomal scaffolds (L50 = 26 scaffolds, N50 = 28.36 Mb, longest scaffold = 107 Mb) and an enhanced de novo genome annotation with 25,469 genes. Our three-step approach to orthology curation and comparative analysis of TLR genes shows what new insights are possible using genome assemblies with chromosome-scale scaffolds that permit integration of synteny conservation data.


2019 ◽  
Vol 12 (1) ◽  
pp. 293 ◽  
Author(s):  
Monika Egerer ◽  
Jacob Cecala ◽  
Hamutahl Cohen

Across urban environments, vegetated habitats provide refuge for biodiversity. Gardens (designed for food crop production) and nurseries (designed for ornamental plant production) are both urban agricultural habitats characterized by high plant species richness but may vary in their ability to support wild pollinators, particularly bees. In gardens, pollinators are valued for crop production. In nurseries, ornamental plants rarely require pollination; thus, the potential of nurseries to support pollinators has not been examined. We asked how these habitats vary in their ability to support wild bees, and what habitat features relate to this variability. In 19 gardens and 11 nurseries in California, USA, we compared how local habitat and landscape features affected wild bee species abundance and richness. To assess local features, we estimated floral richness and measured ground cover as proxies for food and nesting resources, respectively. To assess landscape features, we measured impervious land cover surrounding each site. Our analyses showed that differences in floral richness, local habitat size, and the amount of urban land cover impacted garden wild bee species richness. In nurseries, floral richness and the proportion of native plant species impacted wild bee abundance and richness. We suggest management guidelines for supporting wild pollinators in both habitats.


2017 ◽  
Vol 7 (17) ◽  
pp. 7010-7022 ◽  
Author(s):  
Giancarlo Sadoti ◽  
Miranda E. Gray ◽  
Matthew L. Farnsworth ◽  
Brett G. Dickson

PLoS ONE ◽  
2020 ◽  
Vol 15 (8) ◽  
pp. e0238202
Author(s):  
Cindy Xu ◽  
Greer A. Dolby ◽  
K. Kristina Drake ◽  
Todd C. Esque ◽  
Kenro Kusumi

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