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- All Subjects: Evolution
- Creators: Kusumi, Kenro
- Creators: Lynch, Michael
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
Many factors are at play within the genome of an organism, contributing to much of the diversity and variation across the tree of life. While the genome is generally encoded by four nucleotides, A, C, T, and G, this code can be expanded. One particular mechanism that we examine in this thesis is modification of bases—more specifically, methylation of Adenine (m6A) within the GATC motif of Escherichia coli. These methylated adenines are especially important in a process called methyl-directed mismatch repair (MMR), a pathway responsible for repairing errors in the DNA sequence produced by replication. In this pathway, methylated adenines identify the parent strand and direct the repair proteins to correct the erroneous base in the daughter strand. While the primary role of methylated adenines at GATC sites is to direct the MMR pathway, this methylation has also been found to affect other processes, such as gene expression, the activity of transposable elements, and the timing of DNA replication. However, in the absence of MMR, the ability of these other processes to maintain adenine methylation and its targets is unknown.
To determine if the disruption of the MMR pathway results in the reduced conservation of methylated adenines as well as an increased tolerance for mutations that result in the loss or gain of new GATC sites, we surveyed individual clones isolated from experimentally evolving wild-type and MMR-deficient (mutL- ;conferring an 150x increase in mutation rate) populations of E. coli with whole-genome sequencing. Initial analysis revealed a lack of mutations affecting methylation sites (GATC tetranucleotides) in wild-type clones. However, the inherent low mutation rates conferred by the wild-type background render this result inconclusive, due to a lack of statistical power, and reveal a need for a more direct measure of changes in methylation status. Thus as a first step to comparative methylomics, we benchmarked four different methylation-calling pipelines on three biological replicates of the wildtype progenitor strain for our evolved populations.
While it is understood that these methylated sites play a role in the MMR pathway, it is not fully understood the full extent of their effect on the genome. Thus the goal of this thesis was to better understand the forces which maintain the genome, specifically concerning m6A within the GATC motif.
To determine if the disruption of the MMR pathway results in the reduced conservation of methylated adenines as well as an increased tolerance for mutations that result in the loss or gain of new GATC sites, we surveyed individual clones isolated from experimentally evolving wild-type and MMR-deficient (mutL- ;conferring an 150x increase in mutation rate) populations of E. coli with whole-genome sequencing. Initial analysis revealed a lack of mutations affecting methylation sites (GATC tetranucleotides) in wild-type clones. However, the inherent low mutation rates conferred by the wild-type background render this result inconclusive, due to a lack of statistical power, and reveal a need for a more direct measure of changes in methylation status. Thus as a first step to comparative methylomics, we benchmarked four different methylation-calling pipelines on three biological replicates of the wildtype progenitor strain for our evolved populations.
While it is understood that these methylated sites play a role in the MMR pathway, it is not fully understood the full extent of their effect on the genome. Thus the goal of this thesis was to better understand the forces which maintain the genome, specifically concerning m6A within the GATC motif.
ContributorsBoyer, Gwyneth (Author) / Lynch, Michael (Thesis director) / Behringer, Megan (Committee member) / Geiler-Samerotte, Kerry (Committee member) / School of Life Sciences (Contributor) / Department of Psychology (Contributor) / Barrett, The Honors College (Contributor)
Created2020-05
Description
Within the primate lineage, skeletal traits that contribute to inter-specific anatomical variation and enable varied niche occupations and forms of locomotion are often described as the result of environmental adaptations. However, skeletal phenotypes are more accurately defined as complex traits, and environmental, genetic, and epigenetic mechanisms, such as DNA methylation which regulates gene expression, all contribute to these phenotypes. Nevertheless, skeletal complexity in relation to epigenetic variation has not been assessed across the primate order. In order to gain a complete understanding of the evolution of skeletal phenotypes across primates, it is necessary to study skeletal epigenetics in primates. This study attempts to fill this gap by identifying intra- and inter-specific variation in primate skeletal tissue methylation in order to test whether specific features of skeletal form are related to specific variations in methylation. Specifically, methylation arrays and gene-specific methylation sequencing are used to identify DNA methylation patterns in femoral trabecular bone and cartilage of several nonhuman primate species. Samples include baboons (Papio spp.), macaques (Macaca mulatta), vervets (Chlorocebus aethiops), chimpanzees (Pan troglodytes), and marmosets (Callithrix jacchus), and the efficiencies of these methods are validated in each taxon. Within one nonhuman primate species (baboons), intra-specific variations in methylation patterns are identified across a range of comparative levels, including skeletal tissue differences (bone vs. cartilage), age cohort differences (adults vs. juveniles), and skeletal disease state differences (osteoarthritic vs. healthy), and some of the identified patterns are evolutionarily conserved with those known in humans. Additionally, in all nonhuman primate species, intra-specific methylation variation in association with nonpathological femur morphologies is assessed. Lastly, inter-specific changes in methylation are evaluated among all nonhuman primate taxa and used to provide a phylogenetic framework for methylation changes previously identified in the hominin lineage. Overall, findings from this work reveal how skeletal DNA methylation patterns vary within and among primate species and relate to skeletal phenotypes, and together they inform our understanding of epigenetic regulation and complex skeletal trait evolution in primates.
ContributorsHousman, Genevieve (Author) / Stone, Anne (Thesis advisor) / Quillen, Ellen (Committee member) / Kusumi, Kenro (Committee member) / Stojanowski, Christopher (Committee member) / Arizona State University (Publisher)
Created2017
Description
The modern tetraploid species Gossypium barbadense L. (AD2) traces its origins to an allopolyploidy event between diploid progenitors G. raimondii (DT Genome, Americas) and G. herbaceum (AT Genome, Asia/Africa). In this study, nine fiber-related genes consisting of seven MYB transcription factors, a cellulose synthase homolog, and a tubulin homolog were resequenced across 54 G. barbadense lines spanning the wild-to-domesticated spectrum. Tests for nucleotide diversity (π), linkage disequilibrium (LD), and Tajima’s D were performed to examine the extent to which evolutionary forces have acted on these nine loci in G. barbadense. Results indicated that the AT-genome loci had significantly higher levels of diversity and lower levels of LD relative to homoelogous loci from the DT-genome. Additionally, all loci showed signatures of a population size expansion after a bottleneck or selective sweep and/or purifying selection. As previously shown for a sister tetraploid taxa (G. hirsutum), gene conversion resulting from a DT-genome allele invasion into the AT-genome likely explains the higher levels of diversity and lower levels of intragenic LD in the AT-genome. Given the relatively very low level of genetic diversity in elite lines, introduction of novel alleles from wild, land race, or obsolete lines into modern Pima cotton breeding programs is needed to expand the narrow gene pool of G. barbadense for continual yield improvements.
ContributorsNadon, Brian Davis (Author) / Gaxiola, Roberto (Thesis director) / Kusumi, Kenro (Committee member) / Dyer, John (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor)
Created2013-05
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
The morphological characteristics of organisms are intricately linked to their ecological features. As a result, species with similar ecological niches may exhibit shared morphological traits due to convergent evolution. Some genomic features could be relevant to influencing the occurrence of convergence evolution. Anoles, with over 400 species, are an excellent model for studying this process. Within Anolis, groups of species that have evolved similar morphological traits and ecological adaptations in response to specific environmental niches are described as ecomorphs. One ecomorph, the crown-giant anoles, has independently evolved large body sizes and adapted to arboreal habitats, predominantly occupying the upper canopy layer of forests. The objective of this study was to explore the convergent evolution of morphological traits in crown giant anoles, by comparing the osteological traits of two crown giants, Anolis frenatus, and A. equestris, to four non-crown giant species from different ecomorphs, A. auratus, A. carolinensis, A. biporcatus, and A. sagrei. The analysis indicated an absence of convergence in most morphological traits except for body size (SVL). Additionally, this study explored the potential role of transposable elements (TEs) as a genomic feature shaping the morphological diversity of crown giant anoles. The genes located within TE-rich regions on the genome were identified across selected Anolis species. An enrichment of genes associated with regulation and developmental processes was detected in regions with high TE abundance for all analyzed species, but not exclusive to crown giants. The results suggest that crown giants seem to only converge in their substantial body size and that the variability in other morphological characteristics could be attributed to some other ecological features or the phylogenetic relationships of each species. Moreover, TEs may play a role in facilitating morphological evolution and adaptability in all Anolis species, as they could influence gene expression and regulatory pathways. This highlights the need for further investigation into the genomic mechanisms determining convergent evolution.
ContributorsJohnson, Jaime (Author) / Kusumi, Kenro (Thesis director) / Araya-Donoso, Raúl (Committee member) / Dolby, Greer (Committee member) / Fisher, Rebecca (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor)
Created2024-05
Description
Regulation of transcription initiation is a critical factor in the emergence of diverse biological phenotypes, including the development of multiple cell types from a single genotype, the ability of organisms to respond to environmental cues, and the rise of heritable diseases. Transcription initiation is regulated in large part by promoter regions of DNA. The identification and characterization of cis-regulatory regions, and understanding how these sequences differ across species, is a question of interest in evolution. To address this topic, I used the model organism Daphnia pulex, a well-characterized microcrustacean with an annotated genome sequence and selected a distribution of well-defined populations geographically located throughout the Midwestern US, Oregon, and Canada. Using isolated total RNA from adult, female Daphnia originating from the selected populations as well as a related taxon, Daphnia pulicaria (200,000 years diverged from D. pulex), I identified an average of over 14,000 (n=14,471) promoter regions using a novel transcription start site (TSS) profiling method, STRIPE-seq. Through the identification of sequence architecture, promoter class, conservation, and transcription start region (TSR) width, of cis-regulatory regions across the aforementioned Daphnia populations, I constructed a system for the study of promoter evolution, enabling a robust interpretation of promoter evolution in the context of the population-genetic environment. The methodology presented, coupled with the generated dataset, provides a foundation for the study of the evolution of promoters across both species and populations.
ContributorsSnyder, Shannon (Author) / Lynch, Michael (Thesis advisor) / Harris, Robin (Committee member) / Raborn, Randolph T (Committee member) / Wideman, Jeremy (Committee member) / Arizona State University (Publisher)
Created2020
Description
Phenotypic evolution is an essential topic within the general field of evolution. Theoretically, the outcome of phenotypic evolution may be influenced by factors such as genetic background and the interaction of natural selection and genetic drift. To gain empirical evidence for testing the effects of those factors, we used eight long-term evolved Escherichia coli populations as a model system. These populations differ in terms of genetic background (different mutation rates) as well as bottleneck size (small- and large-magnitude). Specifically, we used a plate reader to measure three growth-related traits: maximum growth rate (umax), carrying capacity (Kc), and lag time (Lt) for 40 clones within each population. For each trait we quantified the change in mean per generation, the change in variance per generation, and the correlation coefficient between pairs of traits. Interestingly, we found that the small and large bottleneck populations of one background displayed clear, distinguishing trends that were not present within the populations of the other background. This leads to the conclusion that the influence of selection and drift on a population’s phenotypic outcomes is itself influenced by the genetic background of that population. Additionally, we found a strong positive correlation between umax and Kc within each of the high-mutation populations that was not consistent with our neutral expectation. However, the other two pairs did not exhibit a similar pattern. Our results provide a novel understanding in the relationship between the evolution of E. coli growth-related phenotypes and the population-genetic environment.
ContributorsGonzales, Jadon (Co-author, Co-author) / Lynch, Michael (Thesis director) / Ho, Wei-Chin (Committee member) / Geiler-Samerotte, Kerry (Committee member) / School of Life Sciences (Contributor, Contributor) / Barrett, The Honors College (Contributor)
Created2020-05
Description
Mutation rate is the rate of appearance for mutations to occur in a living organism. Studying and quantifying mutation rates and their evolution is important because mutations are the ultimate source of genetic variation and one of the reasons why evolution occurs. Much of the current research has investigated the mutational rate increase. The evolution of reduced mutation rate, which can be favored by natural selection because the accumulation of too many mutations can be deleterious and result in death, is less studied. Therefore, this study will be focused on antimutators, which are mutations that result in a lowering of the mutation rate. Using Escherichia coli K-12 str. MG1655 as a model system, the effects and reasons for how MMR- background E. coli evolves lower mutation rates were studied. Here we show that the candidate antimutator in dnaE lowers the mutation rate in an experimentally evolved population of E. coli with MMR- background by using a mutation rate assay to demonstrate the difference between populations with and without the antimutator candidate. The results also suggest the importance of an antimutator for populational survival.
ContributorsGraham, Logan (Author) / Ho, Wei-Chin (Thesis director) / Lynch, Michael (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor)
Created2022-05
Description
Different populations of evolved E.coli and their ancestors were grown in a variety of single amino acid environments to determine their ability to use that amino acid as a carbon source. Some evolved lines were able to grow in amino acids that their ancestors weren't able to. The source of this change in amino acid growth was investigated by testing uptake, searching for candidate mutations, and comparing growth rates of populations with and without certain mutations.
ContributorsKing, Lily (Author) / Ho, Wei-Chin (Thesis director) / Lynch, Michael (Committee member) / Barrett, The Honors College (Contributor) / School of Molecular Sciences (Contributor)
Created2022-05