Ecology and Evolutionary Biology Commons^™

Phylogenomic Discordance Suggests Polytomies Along The Backbone Of The Large Genus Solanum, Edeline Gagnon, Rebeccca Hilgenhof, Andrés Orejuela, Angela J. Mcdonnell, Gaurav Sablok, Xavier Aubriot, Leandro Giacomin, Yuri Gouvêa, Thamyris Bragionis, João Renato Stehmann, Lynn Bohs, Steven Dodsworth, Christopher T. Martine, Péter Poczai, Sandra Knapp, Tiina Särkinen

Faculty Journal Articles

Premise of the study

Evolutionary studies require solid phylogenetic frameworks, but increased volumes of phylogenomic data have revealed incongruent topologies among gene trees in many organisms both between and within genomes. Some of these incongruences indicate polytomies that may remain impossible to resolve. Here we investigate the degree of gene-tree discordance in Solanum, one of the largest flowering plant genera that includes the cultivated potato, tomato, and eggplant, as well as 24 minor crop plants.

Methods

A densely sampled species-level phylogeny of Solanum is built using unpublished and publicly available Sanger sequences comprising 60% of all accepted species (742 spp.) …

Population Structure Of A Federally Endangered Plant (Astragalus Jaegerianus Munz, Fabaceae) With Limited Range Using Microsatellites, Sueann Neal

Electronic Theses, Projects, and Dissertations

Studies on population genetics examine the relationship and effects of population structure, migration, gene flow and demographic history, and are therefore important in the conservation of endangered species. Astragalus jaegerianus, a critically federally endangered species found in a geographically restricted range is investigated to determine population structure and genetic variation. Previous research on A. jaegerianus focused on DNA sequence data for cpDNA and nrDNA showed no variation. Further research on A. jaegerianus utilizing AFLP’s on the whole genome indicated substantial gene diversity and population structure consistent with geographically widespread species. AFLP research is a cost-effective process to identify levels …

Temperate Eurasian Origins Of Hawaiian Chenopodium (Amaranthaceae) Plus Description Of A New Species Endemic To Moloka‘I, Jason T. Cantley, Angela J. Mcdonnell, J Branson, S R. Long, W Garnett, Christopher T. Martine

Faculty Journal Articles

Chenopodium taxa of Hawai‘i are tetraploids distinguished from other members of the circumglobally distributed genus by minute morphological characters. Because of these reasons, the geographic origin of Hawaiian Chenopodium has remained unclear. Across the Hawaiian Archipelago, Chenopodium taxa are morphologically variable and grow in highly disparate xeric habitats, especially in terms of precipitation, temperature, wind, salt spray, and solar irradiation. Habitats include dry subalpine shrublands, sandy beach strand of atolls in the Northwest Hawaiian Islands, dry forests, and precipitously tall sea cliffs of northwestern Moloka‘i. From the Moloka‘i sea cliffs, which are battered by high energy winds, salt spray, and …

Geographic Population Structure And Taxonomic Identity Of Rhinichthys Osculus, The Santa Ana Speckled Dace, As Elucidated By Nuclear Dna Intron Sequencing, Liane Raynette Greaver

Electronic Theses, Projects, and Dissertations

Rhinichthys osculus (Cyprinidae), the speckled dace, is the most widely distributed freshwater fish in the western United States. The southern California populations of R. osculus are identified as the Santa Ana speckled dace (SASD), though the SASD has not yet been formally recognized as a distinct taxon. Current mtDNA analysis performed in the Metcalf Lab has shown a reciprocally monophyletic relationship among three California regions; southern, central coast, and Owens Valley. Similarly, microsatellite genotyping has shown significant levels of geographic population structure. The purpose of this study was to provide nuclear DNA sequence data to determine the taxonomic status of …

Frogs Hiding In Plain Sight: Phylogenetic Systematics Of Myanmar’S Occidozyga Species Complex, And The Identification Of A Novel Species, Allison Bogisich

Master's Theses

Different species can be difficult to distinguish from one another when they are morphologically similar. Such cryptic species are the reason many anuran species go undetected. For this study, the taxonomic identity of the Occidozyga complex across Myanmar was investigated. An integrated approach was used combining molecular, morphological and phylogeographic data to better assess its taxonomy. Results indicate the presence of three new candidate species within Occidozyga, and three evolutionarily significant unit (ESU) lineages. Two mitochondrial gene fragments (16S, COI) and one nuclear gene fragment (Rhodopsin) were examined from DNA isolated from forty-seven preserved specimens from the California Academy …

Tropical Trees As Islands: Diversity Accumulation Of Armored Scale Insects (Hemiptera: Diaspididae) On Trees As A Function Of Forest Age, Hannah Shapiro

Undergraduate Honors Theses

Armored scale insects (Hemiptera: Diaspididae) are some of the most invasive insects in the world. These cryptic plant parasites are most often encountered in managed agricultural ecosystems, but very little is known about their distribution, abundance, and diversity in tropical rainforest canopies, where they are likely to have their highest diversity. Because these ubiquitous insects are extreme generalists with undirected dispersal, their diversity (alpha and beta) accumulation can conceivably be modeled according to tenets derived from island biogeography theory. For example, one expectation is that older established trees should boast a higher species diversity and abundance than younger ones. Other …

Genetic Analyses Determine Connectivity Among Cave And Surface Populations Of The Jamaican Endemic Freshwater Crab Sesarma Fossarum In The Cockpit Country, Manuel Stemmer, Christoph D. Schubart

International Journal of Speleology

The Jamaican freshwater crab Sesarma fossarum (Decapoda: Brachyura: Sesarmidae) is endemic to western central Jamaica where it occurs in cave and surface streams of karst regions. In the present study, we examine the population genetic structure of the species, providing evidence for intraspecific differentiation and genetic substructure among twelve sampled populations. Interestingly, crabs from caves appear genetically undistinguishable from representatives of nearby surface waters, despite previously observed and described morphometric differentiation. In contrast, genetic isolation takes place among populations from rivers and caves belonging to different watersheds. In one case, even populations from different tributaries of the same river were …

Molecular Systematics Of The Subfamily Phasiinae (Diptera: Tachinidae), Jeremy Daniel Blaschke

Masters Theses

The subfamily Phasiinae (Diptera: Tachinidae) is composed of obligate endoparasitoid flies that attack heteropteran insects, many of which are important agricultural pests. To lay a foundation for future studies in phasiine life history and their potential for use as biological control agents, the phylogenetic relationships within Phasiinae were explored using nucleotide sequences of two genes, CAD and LGL. A total of 63 taxa for CAD and 73 taxa for LGL were included in the analyses, representing 58 genera. Maximum likelihood inference methods were employed to reconstruct phylogenetic relationships in separate analyses of each gene and in a combined dataset. Phylogenetic …

Freshwater Fishes Of Shipstern Nature Reserve, Caspar F. A. Bijleveld

Physiology Faculty Research Publications

A survey of fishes in and around Shipstern Nature Reserve in Northern Belize, Central America, was carried out over a period of eight months, from February to September 1990. Its purpose was to establish a preliminary list of the fishes of Shipstern Nature Reserve, including descriptions, distribution and collecting data and additionally to describe some of the habitats in which the fishes were found. This study focuses on fishes considered to be freshwater species. These occurred for the greater part in brackish habitats. Nevertheless, a few fish considered as marine species were caught in the waters of the reserve and …