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Description
Well-established model systems exist in four out of the seven major classes of vertebrates. These include the mouse, chicken, frog and zebrafish. Noticeably missing from this list is a reptilian model organism for comparative studies between the vertebrates and for studies of biological processes unique to reptiles. To help fill in this gap the green anole lizard, Anolis carolinensis, is being adapted as a model organism. Despite the recent release of the complete genomic sequence of the A. carolinensis, the lizard lacks some resources to aid researchers in their studies. Particularly, the lack of transcriptomic resources for lizard has made it difficult to identify genes complete with alternative splice forms and untranslated regions (UTRs). As part of this work the genome annotation for A. carolinensis was improved through next generation sequencing and assembly of the transcriptomes from 14 different adult and embryonic tissues. This revised annotation of the lizard will improve comparative studies between vertebrates, as well as studies within A. carolinensis itself, by providing more accurate gene models, which provide the bases for molecular studies. To demonstrate the utility of the improved annotations and reptilian model organism, the developmental process of somitogenesis in the lizard was analyzed and compared with other vertebrates. This study identified several key features both divergent and convergent between the vertebrates, which was not previously known before analysis of a reptilian model organism. The improved genome annotations have also allowed for molecular studies of tail regeneration in the lizard. With the annotation of 3' UTR sequences and next generation sequencing, it is now possible to do expressional studies of miRNA and predict their mRNA target transcripts at genomic scale. Through next generation small RNA sequencing and subsequent analysis, several differentially expressed miRNAs were identified in the regenerating tail, suggesting miRNA may play a key role in regulating this process in lizards. Through miRNA target prediction several key biological pathways were identified as potentially under the regulation of miRNAs during tail regeneration. In total, this work has both helped advance A. carolinensis as model system and displayed the utility of a reptilian model system.
ContributorsEckalbar, Walter L (Author) / Kusumi, Kenro (Thesis advisor) / Huentelman, Matthew (Committee member) / Rawls, Jeffery (Committee member) / Wilson-Rawls, Norma (Committee member) / Arizona State University (Publisher)
Created2012
Description
A global warming of two degrees Celsius is predicted to drive almost half the world's lizard populations to extinction. Currently, the Phoenix metropolitan region in Arizona, USA, is an average of 3 oC warmer than the surrounding desert. Using a bare lot as a control, I placed copper lizard models with data loggers in several vegetation and irrigation treatments that represent the dominant backyard landscaping styles in Phoenix (grassy mesic with mist irrigation, drip irrigated xeric, unirrigated native, and a hybrid style known as oasis). Lizard activity time in summer is currently restricted to a few hours in un-irrigated native desert landscaping, while heavily irrigated grass and shade trees allow for continual activity during even the hottest days. Maintaining the existing diversity of landscaping styles (as part of an ongoing mitigation strategy targeted at humans) will be beneficial for lizards.
Fourteen native lizard species inhabit the desert surrounding Phoenix, AZ, USA, but only two species persist within heavily developed areas. This pattern is best explained by a combination of socioeconomic status, land cover, and location. Lizard diversity is highest in affluent areas and lizard abundance is greatest near large patches of open desert. The percentage of building cover has a strong negative impact on both diversity and abundance. Despite Phoenix's intense urban heat island effect, which strongly constrains the potential activity and microhabitat use of lizards in summer, thermal patterns have not yet impacted their distribution and relative abundance at larger scales.
Fourteen native lizard species inhabit the desert surrounding Phoenix, AZ, USA, but only two species persist within heavily developed areas. This pattern is best explained by a combination of socioeconomic status, land cover, and location. Lizard diversity is highest in affluent areas and lizard abundance is greatest near large patches of open desert. The percentage of building cover has a strong negative impact on both diversity and abundance. Despite Phoenix's intense urban heat island effect, which strongly constrains the potential activity and microhabitat use of lizards in summer, thermal patterns have not yet impacted their distribution and relative abundance at larger scales.
ContributorsAckley, Jeffrey (Author) / Wu, Jianguo (Thesis advisor) / Sullivan, Brian (Thesis advisor) / Myint, Soe (Committee member) / DeNardo, Dale (Committee member) / Angilletta Jr., Michael (Committee member) / Arizona State University (Publisher)
Created2015
Description
Basilisk lizards are often studied for their unique ability to run across the surface of
water. Due to the complicated fluid dynamics of this process, the forces applied on the
water’s surface cannot be measured using traditional methods. This thesis presents a
novel technique of measuring the forces using a fluid dynamic force platform (FDFP),
a light, rigid box immersed in water. This platform, along with a motion capture
system, can be used to characterize the kinematics and dynamics of a basilisk lizard
running on water. This could ultimately lead to robots that can run on water in a
similar manner.
water. Due to the complicated fluid dynamics of this process, the forces applied on the
water’s surface cannot be measured using traditional methods. This thesis presents a
novel technique of measuring the forces using a fluid dynamic force platform (FDFP),
a light, rigid box immersed in water. This platform, along with a motion capture
system, can be used to characterize the kinematics and dynamics of a basilisk lizard
running on water. This could ultimately lead to robots that can run on water in a
similar manner.
ContributorsSweeney, Andrew Joseph (Author) / Marvi, Hamidreza (Thesis advisor) / Lentink, David (Committee member) / Lee, Hyunglae (Committee member) / Arizona State University (Publisher)
Created2019
Description
While a number of vertebrates, including fishes, salamanders, frogs, and lizards, display regenerative capacity, the process is not necessarily the same. It has been proposed that regeneration, while evolutionarily conserved, has diverged during evolution. However, the extent to which the mechanisms of regeneration have changed between taxa still remains elusive. In the salamander limb, cells dedifferentiate to a more plastic state and aggregate in the distal portion of the appendage to form a blastema, which is responsible for outgrowth and tissue development. In contrast, no such mechanism has been identified in lizards, and it is unclear to what extent evolutionary divergence between amniotes and anamniotes has altered this mechanism. Anolis carolinensis lizards are capable of regenerating their tails after stress-induced autotomy or self-amputation. In this investigation, the distribution of proliferating cells in early A. carolinensis tail regeneration was visualized by immunohistochemistry to examine the location and quantity of proliferating cells. An aggregate of proliferating cells at the distal region of the regenerate is considered indicative of blastema formation. Proliferating cell nuclear antigen (PCNA) and minichromosome maintenance complex component 2 (MCM2) were utilized as proliferation markers. Positive cells were counted for each tail (n=9, n=8 respectively). The percent of proliferating cells at the tip and base of the regenerating tail were compared with a one-way ANOVA statistical test. Both markers showed no significant difference (P=0.585, P=0.603 respectively) indicating absence of a blastema-like structure. These results suggest an alternative mechanism of regeneration in lizards and potentially other amniotes.
ContributorsTokuyama, Minami Adrianne (Author) / Kusumi, Kenro (Thesis director) / Wilson-Rawls, Jeanne (Committee member) / Menke, Douglas (Committee member) / Barrett, The Honors College (Contributor) / Department of Chemistry and Biochemistry (Contributor) / School of Life Sciences (Contributor)
Created2014-05
Description
The effects of biocontrol and the potential risks associated with them are of interest to many researchers. In the Virgin River area of Nevada, natural resource managers have done studies of various removal techniques on the non-native Tamarix spp. strands. One such area of focus is the use of biocontrol in the form of the tamarisk leaf beetle (Diorhabda spp.), and the resulting changes in the environment from the defoliation of the trees. Previous studies have shown that removal of the plants can potentially be beneficial to lizards. But do changes in the environment change the amount of food available? We were interested to see if the amount of arthropod biomass from these areas had a relationship with the lizard abundance. Taking arthropod collection data from the Virgin River, we compared it with arthropod data over several years, before and after Diorhabda was introduced in 2010. Arthropod biomass data was obtained by taking the collected arthropods and drying them in an oven and weighing them. Results show that there is no correlation between the arthropod numbers or biomass with the amount of lizards in the area, that biomass was greatest after biocontrol introduction, and biomass was highest in mixed Tamarix and native tree strands versus just Tamarix strands. In conclusion, arthropod numbers and biomass have shown to be a poor indicator of lizard abundance, and factors such as temperature changes in the environment might be a better indicator of the changing abundance of lizards.
ContributorsPicciano, Melanie Erin (Author) / Bateman, Heather (Thesis director) / Barnard, James (Committee member) / Barrett, The Honors College (Contributor) / School of Letters and Sciences (Contributor)
Created2014-05
Description
Damage to the central nervous system due to spinal cord or traumatic brain injury, as well as degenerative musculoskeletal disorders such as arthritis, drastically impact the quality of life. Regeneration of complex structures is quite limited in mammals, though other vertebrates possess this ability. Lizards are the most closely related organism to humans that can regenerate de novo skeletal muscle, hyaline cartilage, spinal cord, vasculature, and skin. Progress in studying the cellular and molecular mechanisms of lizard regeneration has previously been limited by a lack of genomic resources. Building on the release of the genome of the green anole, Anolis carolinensis, we developed a second generation, robust RNA-Seq-based genome annotation, and performed the first transcriptomic analysis of tail regeneration in this species. In order to investigate gene expression in regenerating tissue, we performed whole transcriptome and microRNA transcriptome analysis of regenerating tail tip and base and associated tissues, identifying key genetic targets in the regenerative process. These studies have identified components of a genetic program for regeneration in the lizard that includes both developmental and adult repair mechanisms shared with mammals, indicating value in the translation of these findings to future regenerative therapies.
ContributorsHutchins, Elizabeth (Author) / Kusumi, Kenro (Thesis advisor) / Rawls, Jeffrey A. (Committee member) / Denardo, Dale F. (Committee member) / Huentelman, Matthew J. (Committee member) / Arizona State University (Publisher)
Created2015
Description
Agassiz’s desert tortoise (Gopherus agassizii) is a long-lived species native to the Mojave Desert and is listed as threatened under the US Endangered Species Act. To aid conservation efforts for preserving the genetic diversity of this species, we generated a whole genome reference sequence with an annotation based on deep transcriptome sequences of adult skeletal muscle, lung, brain, and blood. The draft genome assembly for G. agassizii has a scaffold N50 length of 252 kbp and a total length of 2.4 Gbp. Genome annotation reveals 20,172 protein-coding genes in the G. agassizii assembly, and that gene structure is more similar to chicken than other turtles. We provide a series of comparative analyses demonstrating (1) that turtles are among the slowest-evolving genome-enabled reptiles, (2) amino acid changes in genes controlling desert tortoise traits such as shell development, longevity and osmoregulation, and (3) fixed variants across the Gopherus species complex in genes related to desert adaptations, including circadian rhythm and innate immune response. This G. agassizii genome reference and annotation is the first such resource for any tortoise, and will serve as a foundation for future analysis of the genetic basis of adaptations to the desert environment, allow for investigation into genomic factors affecting tortoise health, disease and longevity, and serve as a valuable resource for additional studies in this species complex.
Data Availability: All genomic and transcriptomic sequence files are available from the NIH-NCBI BioProject database (accession numbers PRJNA352725, PRJNA352726, and PRJNA281763). All genome assembly, transcriptome assembly, predicted protein, transcript, genome annotation, repeatmasker, phylogenetic trees, .vcf and GO enrichment files are available on Harvard Dataverse (doi:10.7910/DVN/EH2S9K).
ContributorsTollis, Marc (Author) / DeNardo, Dale F (Author) / Cornelius, John A (Author) / Dolby, Greer A (Author) / Edwards, Taylor (Author) / Henen, Brian T. (Author) / Karl, Alice E. (Author) / Murphy, Robert W. (Author) / Kusumi, Kenro (Author)
Created2017-05-31
Description
Traumatic injury to the central nervous or musculoskeletal system in traditional amniote models, such as mouse and chicken, is permanent with long-term physiological and functional effects. However, among amniotes, the ability to regrow complex, multi-tissue structures is unique to non-avian reptiles. Structural regeneration is extensively studied in lizards, with most species able to regrow a functional tail. The lizard regenerated tail includes the spinal cord, cartilage, de novo muscle, vasculature, and skin, and unlike mammals, these tissues can be replaced in lizards as adults. These studies focus on the events that occur before and after the tail regrowth phase, identifying conserved mechanisms that enable functional tail regeneration in the green anole lizard, Anolis carolinensis. An examination of coordinated interactions between peripheral nerves, Schwann cells, and skeletal muscle reveal that reformation of the lizard neuromuscular system is dependent upon developmental programs as well as those unique to the adult during late stages of regeneration. On the other hand, transcriptomic analysis of the early injury response identified many immunoregulatory genes that may be essential for inhibiting fibrosis and initiating regenerative programs. Lastly, an anatomical and histological study of regrown alligator tails reveal that regenerative capacity varies between different reptile groups, providing comparative opportunities within amniotes and across vertebrates. In order to identify mechanisms that limit regeneration, these cross-species analyses will be critical. Taken together, these studies serve as a foundation for future experimental work that will reveal the interplay between reparative and regenerative mechanisms in adult amniotes with translational implications for medical therapies.
ContributorsXu, Cindy (Author) / Kusumi, Kenro (Thesis advisor) / Newbern, Jason M (Thesis advisor) / Wilson-Rawls, Jeanne (Committee member) / Fisher, Rebecca E (Committee member) / Arizona State University (Publisher)
Created2020
Description
Spatial and temporal patterns of biodiversity are shaped, in part, by the resources available to biota, the efficiency of resource transfer through the food web, and variation in environmental conditions. Stream and riparian zones are dynamic systems connected through reciprocal resource exchange and shaped by floods, droughts, and long-term patterns in the quantity, timing, and variability of streamflow (flow regime). The interdependent nature of the stream-riparian ecosystem defies the scope of any single discipline, requiring novel approaches to untangle the controls on ecological processes. In this dissertation, I explored multiple mechanisms through which streamflow and energy flow pathways maintain the community and trophic dynamics of desert stream and riparian food webs. I conducted seasonal sampling of Arizona streams on a gradient of flow regime variability to capture fluctuations in aquatic communities and ecosystem production. I found that flow regime shapes fish community structure and the trajectory of community response following short-term flow events by constraining the life history traits of communities, which fluctuate in prevalence following discrete events. Streamflow may additionally constrain the efficiency of energy flow from primary producers to consumers. I estimated annual food web efficiency and found that efficiency decreased with higher temperature and more variable flow regime. Surprisingly, fish production was not related to the rate of aquatic primary production. To understand the origin of resources supporting aquatic and riparian food webs, I studied the contribution of aquatic and terrestrial primary production to consumers in both habitats. I demonstrated that emergent insects “recycled” terrestrial primary production back to the riparian zone, reducing the proportion of aquatic primary production in emergent insect biomass and riparian predator diet. To expand the concept of stream and riparian zones as an integrated ecosystem connected by resource cycling through the food web, I introduced a quantitative framework describing reciprocal interconnections across spatial boundaries and demonstrated strong aquatic-riparian interdependencies along an Arizona river. In this dissertation, I develop a novel perspective on the stream-riparian ecosystem as an intertwined food web, which may be vulnerable to unforeseen impacts of global change if not considered in the context of streamflow and resource dynamics.
ContributorsBaruch, Ethan Max (Author) / Sabo, John (Thesis advisor) / Bateman, Heather (Committee member) / Cease, Arianne (Committee member) / Grimm, Nancy (Committee member) / Arizona State University (Publisher)
Created2021
Description
Though the connection between terrestrial riparian consumers and the adjacent aquatic food web has been well-studied in a variety of systems, gaps with respect to several habitats remain. The Colorado River Basin represents many of these untested habitat characteristics: it contains large, controlled rivers in an arid environment that are often canyon-bound. These characteristics, however, are not unique to the Colorado River Basin. Dams and arid lands are becoming increasingly common around the world, stressing the importance of understanding the function of riparian areas within the Colorado River Basin and basins like it. Stable isotopes, including the more recent application of deuterium, can be used to elucidate trophic linkages between rivers and their riparia. Though dams may harm aquatic insect populations, it is possible that they also make aquatic insects a stable, constant food source to the riparian biological community. This dissertation demonstrates that aquatic emergent insects are a reliable, and therefore important, food source for arid land riparian consumers along regulated rivers. However, the importance of aquatic emergent insects to riparian consumers may vary across sites, even within the same river basin. To explore this variation, the diet of a common riparian lizard species Urosaurus ornatus (Ornate Tree Lizard) can be used as an indicator of cross-ecosystem connectivity. This dissertation demonstrates linkages between two differing river segments and U. ornatus, showcasing its ability as an indicator of connectivity across a diversity of systems. Within the Colorado River Basin, the Grand Canyon provides an opportunity to study a variety of riparian consumers across a gradient of habitat parameters and dam effects. This dissertation demonstrates the manifold connections between large, regulated rivers and arid riparian consumers, ranging from lizards, to bats, to, for the first time, mice. Monsoons have differing effects on river-riparian communities in this basin, potentially related to intact tributary confluences. Lastly, this dissertation demonstrates that hydropeaking reduces river-riparia connectivity by reducing aquatic insect emergence. This dissertation seeks to improve understanding of the linkages between river and their riparia to aid in the management of arid riparian areas affected by dams worldwide.
ContributorsLupoli, Christina Alexandra (Author) / Sabo, John L (Thesis advisor) / DeNardo, Dale F (Committee member) / Kennedy, Theodore A (Committee member) / Muehlbauer, Jeffrey D (Committee member) / Yackulic, Charles B (Committee member) / Arizona State University (Publisher)
Created2021