Evolution Commons^™

Mixing It Up: The Impact Of Episodic Introgression On The Evolution Of High-Latitude Mesocarnivores, Jocelyn P. Colella

Biology ETDs

At high latitudes, climatic oscillations have triggered repeated episodes of organismal divergence by geographically isolating populations. For terrestrial species, extended isolation in glacial refugia – ice-free regions that enable terrestrial species persistence through glacial maxima – is hypothesized to stimulate allopatric divergence. Alternatively, upon glacial recession, divergent populations expanded from independent glacial refugia and often contacted other diverging populations. In the absence of reproductive isolating mechanisms, this biogeographic process may trigger hybridization and ultimately, gene flow between divergent taxa. My dissertation research aims to understand how these episodic periods of isolation and contact have impacted the evolution of high latitude …

Solanum Plastisexum, An Enigmatic New Bush Tomato From The Australian Monsoon Tropics Exhibiting Breeding System Fluidity., Angela J. Mcdonnell, Heather B. Wetreich, Jason T. Cantley, Peter Jobson, Christopher T. Martine

Faculty Journal Articles

A bush tomato that has evaded classification by solanologists for decades has been identified and is described as a new species belonging to the Australian “Solanum dioicum group” of the Ord Victoria Plain biogeographic region in the monsoon tropics of the Northern Territory. Although now recognised to be andromonoecious, S. plastisexum Martine & McDonnell, sp. nov. exhibits multiple reproductive phenotypes, with solitary perfect flowers, a few staminate flowers or with cymes composed of a basal hermaphrodite and an extended rachis of several to many staminate flowers. When in fruit, the distal rachis may abcise and drop. A member of …

Differentiating Black Bears (Ursus Americanus) And Brown Bears (U. Arctos) Using Linear Tooth Measurements And Identification Of Ursids From Oregon Caves National Monument, Emily Bogner

Electronic Theses and Dissertations

North American black bears and brown bears can be difficult to distinguish in the fossil record due to similar dental and skeletal morphologies. Challenges identifying ursid material from Oregon Caves National Monument (ORCA) called for an accurate tool to distinguish the species. This study utilized a large database of lower tooth lengths and ratios in an attempt to differentiate black and brown bears in North America. Further, this project examined how these linear measurements differ geographically. Analysis of variance (ANOVA) found significant differences between black and brown bears from across North America for every variable studied. Stepwise discriminant analyses (DA) …

Phylogeny Of The Australian Solanum Dioicum Group Using Seven Nuclear Genes: Testing Symon’S Fruit And Seed Dispersal Hypotheses., Christopher T. Martine, Ingrid E. Jordon-Thaden, Angela J. Mcdonnell, Jason T. Cantley, Daniel S. Hayes, Morgan D. Roche, Emma S. Frawley, Ian S. Gilman, David C. Tank

Faculty Journal Articles

The dioecious and andromonoecious Solanum taxa (the “S. dioicum group”) of the Australian Monsoon Tropics have been the subject of phylogenetic and taxonomic study for decades, yet much of their basic biology is still unknown. This is especially true for plant-animal interactions, including the influence of fruit form and calyx morphology on seed dispersal. We combine field/greenhouse observations and specimen-based study with phylogenetic analysis of seven nuclear regions obtained via a microfluidic PCR-based enrichment strategy and high-throughput sequencing, and present the first species-tree hypothesis for the S. dioicum group. Our results suggest that epizoochorous trample burr seed …

Co-Occurrence Of Manganese Oxidase Genes Indicates Lateral Transfer Between Classes Of Proteobacteria, Jacob Olichney

Student Scholar Showcase

Pseudomonas putida GB-1 is a model organism for the study of manganese oxidation in bacteria, however, the frequency of co-localization of multiple known and suspected manganese oxidizing proteins, as well as their occurrence between species, is unknown. Eight different genes isolated from known manganese oxidizing bacteria (MnxG, MopA, McoA, PputGB1_2552, PputGB1_2553, MoxA, MofA, and Bacillus MnxG) were tested individually using BioPython and BLAST (Basic Local Alignment Search Tool) on multiple genomic databases. BLAST searches had an expect value cutoff of 1e-50, limiting gene homologs to those with high sequence similarity. The abundance of homologous genes across classes of proteobacteria point …

Comparing Feeding Accuracy Between High And Low Predation Trinidad Guppies, Lydia J. Bonnell

Honors College Theses

Efficient feeding accuracy could increase an organism’s survival. Although local adaptation in Trinidad guppies is common, the effects on accuracy are unknown. Guppies were wild caught in 2015 and 2017, filmed while capturing prey. Accuracy wasn’t different within samples but differed across samples, possibly due to the prey types used.

A Phylogenetic Analysis Of Bostrichoidea (Coleoptera) And Revisions Of The Southern African Spider Beetle Genera Meziomorphum And Eutaphroptinus (Ptinidae: Coleoptera), Olivia M. Gearner

Masters Theses & Specialist Projects

Proposals for the internal relationships and classification of the bostrichoids are currently poorly supported, and almost all are based on morphology alone. This study improves upon on previous phylogenetic analyses of the group by including more taxa using the standard genes for many phylogenetic analyses. Cytochrome C oxidase subunit 1 (CO1), 28S small subunit rRNA, and 16S small subunit rRNA mitochondrial genes were sequenced or obtained from Genbank, then analyzed using parsimony and Bayesian analyses. Topologies differed depending on genes used. A three gene tree and a two gene (28S and CO1) tree both supported relationships in which a basal …

Plant Mitochondrial Genome Evolution And Structure Has Been Shaped By Double-Strand Break Repair And Recombination, Emily Wynn

School of Biological Sciences: Dissertations, Theses, and Student Research

Plant mitochondrial genomes are large but contain a small number of genes. These genes have very low mutation rates, but genomes rearrange and expand at significant rates. We propose that much of the apparent complexity of plant mitochondrial genomes can be explained by the interactions of double-strand break repair, recombination, and selection. One possible explanation for the disparity between the low mutation rates of genes and the high divergence of non-genes is that synonymous mutations in genes are not truly neutral. In some species, rps14 has been duplicated in the nucleus, allowing the mitochondrial copy to become a pseudogene. By …

Genomics Based Approaches To Fungal Evolution, Aaron J. Robinson, Donald O. Natvig

Biology ETDs

Advances in DNA sequencing and data analysis make it possible to address questions in population genetics and evolution at the genomic level. Fungi are excellent subjects for such studies, because they are found in diverse environments, have short generation times, can be maintained in culture and have relatively small genomes. My research employed genetic approaches using a variety of sequencing technologies and methods of analysis to explore questions in fungal evolution.

In one study, I explored the genetics behind differences in thermotolerance between isolates of Neurospora discreta from Alaska and New Mexico. Isolates from the two states exhibited differences in …

Comparing Orientation Behavior And Prey Preference Of Leptasterias Spp. Between Microhabitats, Jenna C. Sanders, Margaret W. Johnson, C Sarah Cohen

STAR Program Research Presentations

Leptasterias spp. is a species complex of small, six rayed, predatory sea stars that inhabit rocky intertidal communities along the Pacific coast of North America. A developmental mode of brooding their young, rather than broadcasting for planktonic development, limits dispersal away from the natal area, and may also result in fine scale local adaptation of populations. Local adaptation may lead to morphological and behavioral differences among populations, specifically towards the most available prey. Within the rocky intertidalthere are zones of high and low wave impact which create microhabitats with their own selective forces. In areas of high wave impact, stars …

Changes In North American Mammal Niche Preferences From The Late Pleistocene To The Present, Silvia Pineda-Munoz, Anikó Tóth, S. Kathleen Lyons, Yue Wang, Jenny Mcguire

School of Biological Sciences: Presentations

Human population has exponentially grown since the last glaciation, especially across temperate areas with easy access to water sources, excluding mammal species from their former habitats. Thus, we anticipate a change in environmental niche preferences for temperature and precipitation as increased human population forces mammal species into more extreme climates within their environmental tolerances. For our study, we collected species occurrences from 20,000 ybp to the present for 59 North American mammal species. We inferred temperature and precipitation for each location using paleoclimate simulations (CCSM3). Overall, we found that mammals now live in areas that are warmer and dryer on …

Multiple Connections Between Amazonia And Atlantic Forest Shaped The T Phylogenetic And Morphological Diversity Of Chiasmocleis Mehely, 1904 (Anura: Microhylidae: Gastrophryninae), Rafael O. De Sá, João Filipe Riva Tonini, Hannah Van Huss, Alex Long, Travis Cuddy, Mauricio C. Forlani, Pedro L.V. Peloso, Hussam Zaher, Célio F.B. Haddad

Biology Faculty Publications

Chiasmocleis is the most species-rich genus of Neotropical microhylids. Herein, we provide the first comprehensive multilocus phylogeny for the genus, including all but 3 of the 34 recognized species and multiple individuals per species. We discuss cryptic speciation, species discovery, patterns of morphological evolution, and provide a historical biogeographic analysis to account for the current distribution of the genus. Diversification of Chiasmocleis from other New World microhylids began during the Eocene, app. 40 mya, in forested areas, and current diversity seems to be a product of recurrent connections between the Atlantic Forest and Amazonia. Small-sized species evolved independently three times …

Symbiotic Bacteria Can Colonize Closely-Related, But Not Distantly-Related Species Of Its Host Dictyostelium Discoideum, Rory Vu Mather

Undergraduate Research Symposium Posters

Some of the closest interactions between organisms can be found within symbioses, where different individuals live in close physiological contact and either benefit or harm the other. A powerful kind of benefit comes when bacterial symbionts produce amino acids or provide digestive capabilities outside the host’s ability, in essence taking advantage of the other’s genetic catalog. One such symbiosis is that of the social amoeba Dictyostelium discoideum and its bacterial symbionts Burkholderia agricolaris, Burkholderia hayleyella, and Burkholderia bonneia. In this symbiosis, Burkholderia provide the capability of carrying food bacteria to their host, an advantageous trait when bacterial food is rare. …

Ecology, Monogamy, And The Evolution Of Animal Families, Jacqueline Rae Dillard

Theses and Dissertations--Biology

Family-living has been recognized as a necessary prerequisite for the evolution of advanced cooperative societies, yet the evolutionary and ecological processes that drive the coupling of different forms of cooperation in family-based societies are still poorly understood. In my dissertation, I investigate the correlated evolution of parental care, monogamy, and cooperative breeding in a variety of family-based taxa. I explore the mating and social behavior of family-living beetles with incipient cooperation to better understand the factors driving these social traits. Specifically, I evaluate different causes of extra-pair mating in socially monogamous beetles, the potential benefits that young adult offspring may …

Spatial Genetic Structure And Local Adaptation Within And Among Foxtail Pine (Pinus Balfouriana Subsp. Balfouriana) Populations Located In The Klamath Mountains, California, Rebecca D. Piri

Theses and Dissertations

Foxtail pine (Pinus balfouriana) is a subalpine conifer endemic to California, notably separated into two disjunct subspecies. Previous studies have described the northern subspecies,Pinus balfouriana subsp. balfouriana,as having an uncommonly high level of genetic differentiation and no discernible spatial patterns in phenotypic variation. This study seeks to characterize the spatial genetic structure and patterns of selection of the northern subspecies (Pinus balfouriana subsp. balfouriana) using genome-wide data and to identify the influence of ecology and environment on the unique genetic patterns. I show that genetic differentiation among populations is much less than previously estimated …

Testing For Cryptic Diversity And Inference Of Population Structure In The Cosmopolitan Hoplonemertean Emplectonema Gracile (Nemertea), Paul L. Delaney Iv

Theses and Dissertations

Emplectonema gracile (Johnston 1837) is a hoplonemertean of marine intertidal hard-bottom communities and is distributed throughout the Northern Hemisphere. Although possessing a planktonic larval stage in its life history, the range of such cosmopolitan marine invertebrate species is often explained by cryptic speciation and anthropogenic transport. The purpose of this study is to test for possible cryptic species using mtDNA markers (COI and 16S rDNA) and to investigate population structure in E. gracile over a portion of its geographic range using mtDNA markers and ddRADseq nuclear SNP data. The results of both phylogenetic- and tree-based species delimitation revealed that E. …

Life History Of The Coastal Tailed Frog (Ascaphus Truei) Across An Elevational Gradient, Adrian Daniel Macedo

Cal Poly Humboldt theses and projects

The life history of a species is described in terms of its growth, longevity, and reproduction. Unsurprisingly, life history traits are known to vary in many taxa across environmental gradients. In the case of amphibians, species at high elevations and latitudes tend to have shorter breeding seasons, shorter activity periods, longer larval periods, reach sexual maturity at older ages, and produce fewer and larger clutches per year.

The Coastal Tailed Frog (Ascaphus truei) is an ideal species for the study of geographic variation in life history because it ranges across most of the Pacific Northwest from northern California …

The Intrinsic Value Of Nature, Joanna E. Lambert

Animal Sentience

Treves et al. explain the need to preserve the rights of nonhuman species, human youth, and future generations. Although conservation biology has claimed to have an intrinsic valuation ethic since its inception in the 1980s, many aspects of the field have taken a decidedly anthropocentric and instrumentalist trajectory. This has important consequences for conservation-related policy and practice at all scales: local, regional, and global.

Happy Or Hangry Families: Does Kinship Mediate Cooperation And Cannibalism In Drosophila Melanogaster Larvae?, Lucas Khodaei

Theses and Dissertations (Comprehensive)

The fruit fly Drosophila melanogaster has a long history as a research model for studies on behaviour and group dynamics. When individuals are grouped in an environment and resources decrease, then they may behave co-operatively with one another or antagonistically compete. Hamilton’s Law states that if the benefit of helping a related individual out-weighs the cost to its direct fitness, then the individual’s indirect fitness will increase when they help their kin compared to helping an unrelated stranger. Yet it is unknown whether kinship mediates larval behaviour to encourage co-operation and/or lessen antagonistic behaviours between consanguineous individuals. In this thesis …

The Evolution Of Diet Breadth In Melissodes Bees (Apidae: Eucerini), Karen W. Wright

Biology ETDs

The relationship between phytophagous insects and their host plants has interested scientists since Darwinian times. Using modern phylogenetic inference, we are able to investigate these patterns using, not only the phylogenies of the insects, but the evolutionary relationships among the plants they feed on as well. The relationships between bees and the plants they pollinate were traditionally seen as mutualistic and were treated separately from the research investigating the antagonistic relationships between phytophagous insects and their host plants. However, recent phylogenetic studies have made great progress including bee-host relationships in with the larger body of work on phytophagous insects.

The …

Accumulation And Transmission Dynamics Of A Naturally-Occurring Mtdna Deletion In Caenorhabditis Briggsae, Jennifer Anne Sullins

Dissertations and Theses

Maintaining mitochondrial genome sequence integrity is essential for preserving normal mitochondrial function. Several human diseases have been associated with heteroplasmic mitochondrial genome mutations, but few genetic systems can simultaneously represent pathogenic mitochondrial genome evolution and inheritance. The nematode Caenorhabditis briggsae is one such model. Natural C. briggsae isolates are globally-distributed and phylogenetically grouped into three distinct clades, with isolates exhibiting varying levels of a large-scale mtDNA deletion, nad5∆. Furthermore, a small subset of clade II isolates exhibits putative compensatory mutations that may reduce the risk of deletion formation and accumulation in those populations. In this thesis, the author characterizes the …

Actuarial Senescence In A Dimorphic Bird: Different Rates Of Ageing In Morphs With Discrete Reproductive Strategies, M. L. Grunst, A. S. Grunst, Vincent A. Formica, M. L. Korody, A. M. Betuel, M. Barcelo-Serra, R. A. Gonser, E. M. Tuttle

Biology Faculty Works

It is often hypothesized that intra-sexual competition accelerates actuarial senescence, or the increase in mortality rates with age. However, an alternative hypothesis is that parental investment is more important to determining senescence rates. We used a unique model system, the white-throated sparrow (Zonotrichia albicollis), to study variation in actuarial senescence. In this species, genetically determined morphs display discrete mating strategies and disassortative pairing, providing an excellent opportunity to test the predictions of the above hypotheses. Compared to tan-striped males, white-striped males are more polygynous and aggressive, and less parental. Tan-striped females receive less parental support, and invest more into parental …

Review Of The Family Rivulidae (Cyprinodontiformes, Aplocheiloidei) And A Molecular And Morphological Phylogeny Of The Annual Fish Genus Austrolebias Costa 1998, Marcelo Loureiro, Rafael O. De Sá, Sebastián W. Serra, Felipe Alonso, Luis Esteban Krause Lanés, Matheus Vieira Volcan, Pablo Calviño, Dalton Nielsen, Alejandro Duarte, Graciela Garcia

Biology Faculty Publications

The family Rivulidae is the fourth most diverse clade of Neotropical fishes. Together with some genera of the related African family Nothobranchiidae, many rivulids exhibit a characteristic annual life cycle, with diapausing eggs and delayed embryonic development, which allows them to survive in the challenging seasonal ponds that they inhabit. Rivulidae also includes two species known as the only the self-fertilizing vertebrates and some species with internal fertilization. The first goal of this article is to review the systematics of the family considering phylogenetic relationships and synapomorphies of subfamilial clades, thus unifying information that is dispersed throughout the literature. From …

Males And Females Evolve Riskier Traits In Populations With Eavesdropping Parasitoids, Oliver M. Beckers, William E. Wagner

School of Biological Sciences: Faculty Publications

Predation and/or parasitism often limits the evolution of conspicuous male traits and female preferences because conspicuous traits can attract predators or parasites and it is costly for females to associate with males that attract predators or parasites. As a result, males and females in high-risk populations are expected to evolve safer mating behaviors compared to individuals from low-risk populations. We tested this antagonistic selection hypothesis in the field cricket Gryllus lineaticeps. Males produce chirped songs, and both female crickets and the eavesdropping parasitoid fly Ormia ochracea prefer faster chirp rates. The flies attack the field crickets late in the …

Crispr Knockouts Reveal An Endogenous Role For Ancient Neuropeptides In Regulating Developmental Timing In A Sea Anemone, Nagayasu Nakanishi, Mark Q. Martindale

Biological Sciences Faculty Publications and Presentations

Neuropeptides are evolutionarily ancient peptide hormones of the nervous and neuroendocrine systems, and are thought to have regulated metamorphosis in early animal ancestors. In particular, the deeply conserved Wamide family of neuropeptides—shared across Bilateria (e.g. insects and worms) and its sister group Cnidaria (e.g. jellyfishes and corals)—has been implicated in mediating life-cycle transitions, yet their endogenous roles remain poorly understood. By using CRISPR-Cas9-mediated reverse genetics, we show that cnidarian Wamide—referred to as GLWamide—regulates the timing of life cycle transition in the sea anemone cnidarian Nematostella vectensis. We find that mutant planula larvae lacking GLWamides transform into morphologically normal polyps …

The Transcriptome Of The Bermuda Fireworm Odontosyllis Enopla (Annelida: Syllidae): A Unique Luciferase Gene Family And Putative Epitoky-Related Genes, Mercer R. Brugler, M. Teresa Aguado, Michael Tessler, Mark Siddall

Publications and Research

The Bermuda fireworm Odontosyllis enopla exhibits an extremely tight circalunar circadian behavior that results in an impressive bioluminescent mating swarm, thought to be due to a conventional luciferase-mediated oxidation of a light-emitting luciferin. In addition, the four eyes become hypertrophied and heavily pigmented, and the nephridial system is modified to store and release gametes and associated secretions. In an effort to elucidate transcripts related to bioluminescence, circadian or circalunar periodicity, as well as epitoky-related changes of the eyes and nephridial system, we examined the transcriptomic profile of three female O. enopladuring a bioluminescent swarm in Ferry Reach, Bermuda. …

Genomic Signatures Of Adaptive Evolution, Jessica A. Weber

Biology ETDs

Comparative genomics has revolutionized virtually all fields of biology including the study of evolution. In this dissertation, I used next-generation sequencing to explore the evolutionary histories and adaptive evolution of a diverse set of taxa. Comparisons ranged across time scales, from population-level genetic diversity studies to questions spanning the deepest branches of the metazoan lineage. Whole genome sequencing of 50 unrelated Korean individuals revealed that Koreans have a distinct genetic history from the Chinese and Japanese populations. Our Korean-specific variome database was used to identify novel disease-causing variants in the Korean population, highlighting the value of high-quality ethnic variation databases …

Systematics And Diversification Of The Pantropical Avian Order Coraciiformes, Jenna Merle Mccullough

Biology ETDs

How and why species diversify is a central theme of evolutionary biology. Species-rich, morphologically diverse, pantropical clades provide rare opportunities to explore questions about drivers of diversification in the tropics. Here, we present the first complete species tree of Coraciiformes (6 families, ~177 species of kingfishers, motmots, bee-eaters, and allies), produced with thousands of ultraconserved elements. We recovered a well-supported tree which shows that there are two clades within Coraciiformes: 1) bee-eaters sister to rollers + ground- rollers and 2) todies sister to motmots + kingfishers. We estimated the biogeographical history of the group, explored bill shape evolution with a …

Morph-Specific Patterns Of Reproductive Senescence: Connections To Discrete Reproductive Strategies, A. S. Grunst, M. L. Grunst, Vincent A. Formica, M. L. Korody, A. M. Betuel, M. Barcelo-Serra, S. Ford, R. A. Gonser, E. M. Tuttle

Biology Faculty Works

How reproductive strategies contribute to patterns of senescence in natural populations remains contentious. We studied reproductive senescence in the dimorphic white-throated sparrow, an excellent species for exploring this issue. Within both sexes the morphs use distinct reproductive strategies, and disassortative pairing by morph results in pair types with distinct parental systems. White morph birds are more colorful and aggressive than tan counterparts, and white males compete for extrapair matings, whereas tan males are more parental. Tan males and white females share parental care equally, whereas white males provide little parental support to tan females. We found morph-specific patterns of reproductive …

Radical Social Ecology As Deep Pragmatism: A Call To The Abolition Of Systemic Dissonance And The Minimization Of Entropic Chaos, Arielle Brender

Student Theses 2015-Present

This paper aims to shed light on the dissonance caused by the superimposition of Dominant Human Systems on Natural Systems. I highlight the synthetic nature of Dominant Human Systems as egoic and linguistic phenomenon manufactured by a mere portion of the human population, which renders them inherently oppressive unto peoples and landscapes whose wisdom were barred from the design process. In pursuing a radical pragmatic approach to mending the simultaneous oppression and destruction of the human being and the earth, I highlight the necessity of minimizing entropic chaos caused by excess energy expenditure, an essential feature of systems that aim …