Life Sciences Commons^™

A Phylogenetic Analysis Of The Population Dynamics Of A Captive Colony Of Diploptera Punctata., Nick Peterson

Theses/Capstones/Creative Projects

The unique milk production of Diploptera punctata makes this species a promising model species in entomology for studying the evolution of milk production and for insect endocrinology. Despite this, the genetic diversity of captive populations of the species is not well studied. To better evaluate the captive diversity and population dynamics of Diploptera punctata at UNO we extracted the DNA of 20 random individuals and amplified their DNA using 4 different primers before cleaning the amplified products and sequencing the genes of the samples for use in both individual and concatenated phylogenetic trees. Our results indicate the UNO colony of …

Genealogical Vs Phylogenetic Mutation Rates: Answering A Challenge, Robert Carter

Proceedings of the International Conference on Creationism

There is a discrepancy between the mutation rate we can measure today and the rate at which evolution is supposed to have proceeded. The former is sometimes called the genealogical mutation rate, for it is obtained by comparing individuals whom we know to be related. The latter is sometimes called the phylogenetic mutation rate. It is calculated by counting the fixed differences between two species and dividing by the estimated time since their common ancestor. Genealogical mutation rates are generally several orders of magnitude faster than phylogenetic estimates. This causes problems for the evolutionary model. For example, using the genealogical …

Phylogenomics Reveals The History Of Host Use In Mosquitoes, John Soghigan, Charles Sither, Silvia Andrade Justi, Gen Morinaga, Brian K. Cassel, Christopher J. Vitek, Todd P. Livdahl, Siyang Xia, Andrea Gloria-Soria, Jeffrey R. Powell, Thomas Zavortink, Christopher M. Hardy, Nathan D. Burkett-Cadena, Lawrence E. Reeves, Richard C. Wilkerson, Robert R. Dunn, David K. Yeates, Maria Anice Sallum, Brian D. Byrd, Michelle D. Trautwein, Yvonne-Marie Linton, Michael H. Reiskind, Brian M. Wiegmann

Biology

Mosquitoes have profoundly affected human history and continue to threaten human health through the transmission of a diverse array of pathogens. The phylogeny of mosquitoes has remained poorly characterized due to difficulty in taxonomic sampling and limited availability of genomic data beyond the most important vector species. Here, we used phylogenomic analysis of 709 single copy ortholog groups from 256 mosquito species to produce a strongly supported phylogeny that resolves the position of the major disease vector species and the major mosquito lineages. Our analyses support an origin of mosquitoes in the early Triassic (217 MYA [highest posterior density region: …

Dna Barcoding Indicates Multiple Invasions Of The Freshwater Snail Melanoides Tuberculata Sensu Lato In Florida, Lori Tolley-Jordan, Michael A. Chadwick, Jimmy K. Triplett

Research, Publications & Creative Work

Melanoides tuberculata sensu lato (Thiaridae) are polymorphic female-clonal snails of Asian and African origins that have invaded freshwaters worldwide, including those in Florida. Although the snails have been documented in Florida for at least 70 years, no studies have investigated whether the observed distribution is due to a single introduction or multiple independent invasions. Here, cytochrome oxidase I was used to measure genetic diversity within and among sites in Florida and compare genetic diversity between Florida and other regions of the world. We also examined the relationship between shell morphology and haplotype diversity to determine if shell morphs can serve …

The Phylogeny Predicts Potential New Sources Of Antibiotics From Plants, Malini Anna Prasad, Jeanmaire Molina

Discovery Day

The evolution and spread of antibiotic resistance has been the greatest threat to successful antibiotic treatment, and hence the driving force behind the search for new therapies. None of our modern pharmaceutical antibiotics have been developed from plants, albeit plants have been used since antiquity in traditional medicine to fight bacterial infections. We phylogenetically analyzed 138 plant species with antibacterial activity and found 5 plant families that are disproportionately important, with confamilials exerting similar antibacterial mechanisms, as expected due to common ancestry. Myrtaceae (guava family) was shown to inhibit quorum sensing, disrupting bacterial communication implicated in pathogenicity, due to its …

A Combined Microscopy And Single-Cell Sequencing Approach Reveals The Ecology, Morphology, And Phylogeny Of Uncultured Lineages Of Zoosporic Fungi, Kensuke Seto, D. Rabern Simmons, C. Alisha Quandt, Thijs Frenken, Alden C. Dirks, Rebecca A. Clemons, Katelyn M. Mckindles, R. Michael L. Mckay, Timothy Y. James

Great Lakes Institute for Environmental Research Publications

Environmental DNA analyses of fungal communities typically reveal a much larger diversity than can be ascribed to known species. Much of this hidden diversity lies within undescribed fungal lineages, especially the early diverging fungi (EDF). Although these EDF often represent new lineages even at the phylum level, they have never been cultured, making their morphology and ecology uncertain. One of the methods to characterize these uncultured fungi is a single-cell DNA sequencing approach. In this study, we established a large data set of single-cell sequences of EDF by manually isolating and photographing parasitic fungi on various hosts such as algae, …

Morphological Trait Evolution In Solanum (Solanaceae): Evolutionary Lability Of Key Taxonomic Characters, Rebecca Hilgenhof, Edeline Gagnon, Sandra Knapp, Xavier Aubriot, Eric Tepe, Lynn Bohs, Leandro Giacomin, Yuri Gouvea, Andres Orejuela, Christopher T. Martine, Clara Ines Orozco, Iris E. Peralta, Tina Sarkinen

Faculty Journal Articles

Solanum is one of the world's largest and economically most important plant genera, including 1245 currently accepted species and several major and minor crops (e.g., tomato, potato, brinjal eggplant, scarlet eggplant, Gboma eggplant, lulo, and pepino). Here we provide an overview of the evolution of 25 key morphological traits for the major and minor clades of this giant genus based on stochastic mapping using a well-sampled recently published phylogeny of Solanum. The most evolutionarily labile traits (showing >100 transitions across the genus) relate to plant structure (growth form and sympodial unit structure), herbivore defence (glandular trichomes), pollination (corolla shape …

Comparative Genomic Analysis Of 31 Phytophthora Genomes Reveals Genome Plasticity And Horizontal Gene Transfer, Brent A. Kronmiller, Nicolas Feau, Danyu Shen, Javier F. Tabima, Shahin S. Ali, Andrew D. Armitage, Felipe Arredondo, Bryan A. Bailey, Stephanie R. Bollmann, Angela Dale, Richard J. Harrison, Kelly Hrywkiw, Takao Kasuga, Rebecca Mcdougal, Charlotte F. Nellist, Preeti Panda, Sucheta Tripathy, Nari M. Williams, Wenwu Ye, Yuanchao Wang, Richard C. Hamelin, Niklaus Grünwald

Biology

Phytophthora species are oomycete plant pathogens that cause great economic and ecological impacts. The Phytophthora genus includes over 180 known species, infecting a wide range of plant hosts, including crops, trees, and ornamentals. We sequenced the genomes of 31 individual Phytophthora species and 24 individual transcriptomes to study genetic relationships across the genus. De novo genome assemblies revealed variation in genome sizes, numbers of predicted genes, and in repetitive element content across the Phytophthora genus. A genus-wide comparison evaluated orthologous groups of genes. Predicted effector gene counts varied across Phytophthora species by effector family, genome size, and plant host range. …

A Cladoxylopsid With Complex Vascular Architecture From The Early Devonian Battery Point Formation (Québec, Canada), Jessica Chu

Cal Poly Humboldt theses and projects

Cladoxylopsids are seed-free plants that formed the world’s earliest forests and gave rise to horsetails (sphenopsids), but their evolutionary origins are poorly understood. Here, I describe a new Early Devonian cladoxylopsid from the Emsian (400-395 Ma) Battery Point Formation (Québec, Canada). The structural features of this plant indicate taxonomic affinity to cladoxylalean cladoxylopsids and its phylogenetic position supports placement in genus Cladoxylon (the proposed name, Cladoxylon kespekianum sp. nov., to be formalized by peer-reviewed publication). Specimens of this plant are permineralized in calcium carbonate and were studied using the acetate peel technique with light and electron microscopy. Cladoxylon kespekianum is …

Nuclear Phylogeny And Insights Into Whole-Genome Duplications And Reproductive Development Of Solanaceae Plants, Jie Wang, Weibin Xu, Junwen Zhai, Yi Hu, Jing Guo, Caifei Zhang, Yiyong Zhao, Lin Zhang, Christopher T. Martine, Hong Ma, Chien-Hsun Huang

Faculty Journal Articles

Solanaceae, the nightshade family, have ∼2700 species, including the important crops potato and tomato, ornamentals, and medicinal plants. Several sequenced Solanaceae genomes show evidence for whole-genome duplication (WGD), providing an excellent opportunity to investigate WGD and its impacts. Here, we generated 93 transcriptomes/genomes and combined them with 87 public datasets, for a total of 180 Solanaceae species representing all four subfamilies and 14 of 15 tribes. Nearly 1700 nuclear genes from these transcriptomic/genomic datasets were used to reconstruct a highly resolved Solanaceae phylogenetic tree with six major clades. The Solanaceae tree supports four previously recognized subfamilies (Goetzeioideae, Cestroideae, Nicotianoideae, …

Reassessment Of Chirita Umbrophila (Gesneriaceae) Based On Molecular And Morphological Evidence, Peng-Wei Li, James F. Smith, Debabrata Maity, Xi-Zuo Shi, Li-Hua Yang

Biology Faculty Publications and Presentations

Chirita umbrophila is a species endemic to Yunnan, China, and its exact systematic position remains a mystery since it was treated as a species with uncertain generic affiliation in the taxonomic revision of Chirita in 1985. In the present study, the phylogenetic relationships between C. umbrophila and its allied species were inferred using two nuclear ribosomal DNA regions (ETS and ITS) and three chloroplast regions (rpl16, rps16, and trnL-F). Additionally, the type locality of C. umbrophila was revisited and flowering specimens were collected and examined. Our phylogenetic analyses showed that Chirita umbrophila is imbedded in three …

Molecular Evolution And Biogeography Of The New World Eptesicus Bats, Xueling Yi

Theses and Dissertations

Molecular evolution refers to a broad field of studies ranging from microevolution (e.g., population genetics) to macroevolution (e.g., phylogeny), including the bridging field of phylogeography. In natural populations, molecular studies are also combined with biogeography that links biological diversity with geographic distributions to provide a comprehensive understanding of evolutionary processes. The field of molecular evolution has been largely advanced from early exploratory descriptions to statistical tests on biological hypotheses and integrative analyses using sophisticated modeling. However, studies of molecular evolution still face some unresolved questions and challenges, especially in non-model systems. For example, the application of new technology has largely …

Ancestral State Reconstruction Of Oviposition Techniques In New World Stick Insects, Ellie Mcgregor, Jackson Linde, Michael F. Whiting

Library/Life Sciences Undergraduate Poster Competition 2022

Phasmids, commonly known as stick bugs, are unique and interesting creatures, both phenotypically and genotypically. Their cryptic abilities are what draws most people to them, but their oviposition techniques, or how they disperse eggs, has become a new source of interest. While most phasmids are known to flick or drop their eggs from the canopy, there are several other techniques including inserting the eggs into the soil or gluing them to a substrate. New world phasmids have not been thoroughly studied, especially in understanding which technique was ancestral. The purpose of this paper was to construct a phylogenetic tree to …

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.) …

Predicting Gene Function Of Unknown Yeast Orfs Through Phylogenetic Comparative Analysis, Lewis Barr

Graduate Research Showcase

Yeast (Saccharomyces cerevisiae) has been an instrumental model system for an extraordinary diverse array of research applications for over a century now. The S. cerevisiae genome was fully sequenced in 1996, and, as a result, 6,753 potential proteins were identified. These putative proteins were established by investigating likely open reading frames within the genome. Over the past few decades, nearly 5,000 open reading frames (ORFs) and their expressed proteins have been described, and the remaining undefined open reading frames are labeled as open reading frames of unknown function (ORFans). To better understand the remaining gaps within the S. …

Identification Of A Rickettsial Endosymbiont In A Soft Tick Ornithodoros Turicata Americanus, Lichao Liu, Daniel E. Sonenshine, Hameeda Sultana, Girish Neelakanta

Biological Sciences Faculty Publications

Bacterial endosymbionts are abundantly found in both hard and soft ticks. Occidentia massiliensis, a rickettsial endosymbiont, was first identified in the soft tick Ornithodoros sonrai collected from Senegal and later was identified in a hard tick Africaniella transversale. In this study, we noted the presence of Occidentia species, designated as Occidentia-like species, in a soft tick O. turicata americanus. Sequencing and phylogenetic analyses of the two genetic markers, 16S rRNA and groEL confirmed the presence of Occidentia-like species in O. turicata americanus ticks. The Occidentia-like species was noted to be present in all developmental stages …

The Effects Of Average Annual Temperature On Flowering Times And Flower Count, Angela Copploe

Williams Honors College, Honors Research Projects

Over a course of 15 years, three different species of flowers were examined to see the relationship between the increase in average annual temperature, flowering time, and flower count.

Delineation Of Undescribed, Morphologically Cryptic Cave Beetles Of The Pseudanophthalmus Pubescens Species-Group (Coleoptera: Carabidae: Trechinae), Jedidiah John Nixon

Masters Theses & Specialist Projects

The genus Pseudanophthalmus Jeannel is a widespread and extremely diverse taxon of troglobiont beetle endemic to the karst of eastern North America, with its distribution centered in Tennessee and Kentucky. Despite lying near the heart of this region, the pubescens species-group was thought to contain many undescribed species. In this study, the validities of several of the late Dr. Thomas Barr’s unpublished putative new species in the pubescens-group were tested both morphologically and molecularly. Body measurements (length and width for head, thorax, and abdomen), as well as male genital morphology were compared to see if they reflected theorized species limits.. …

Phylogeny And Taxonomy Of Synechococcus–Like Cyanobacteria, Jiri Komarek, Jeffrey R. Johansen, Jan Smarda, Otakar Strunecký

2020 Faculty Bibliography

Unicellular cyanobacteria constitute a substantial, ecologically important part of freshwater and marine microflora. Solitary, elongated cyanobacterial cells without apparent slime envelopes and dividing in a single plane perpendicular to the longitudinal axis were traditionally classified into the genus Synechococcus. The type species originates from a freshwater benthic habitat while a number of other Synechococcus–like species were described from diverse environments. Morphologically similar, unicellular populations of “Synechococcus” belong to the most abundant oxygen evolving prokaryotes inhabiting freshwater and oceanic picoplanktic communities. Other species from extreme thermal habitats were described from temperatures over 70 °C. Recent molecular analyses, particularly the 16S rRNA …

A Generic Classification Of The Thelypteridaceae, Susan E. Fawcett

Graduate College Dissertations and Theses

The Thelypteridaceae is among the largest fern families, with over 1000 species, and comprises about 10% of all fern diversity. The family is cosmopolitan and most diverse near the equator, although species range as far north as Greenland and Alaska, and as far south as southern New Zealand. The generic classification of the Thelypteridaceae has been the subject of much controversy among authors. Proposed taxonomic systems have varied from recognizing more than 1000 species in the family within a single genus, Thelypteris, to systems favoring upwards of 30 genera. Insights on intrafamilial relationships have been gained from recent phylogenetic studies, …

From Gondwana To Gaarlandia: Molecular Phylogenetics And Historical Biogeography Of Spiders, Lisa Chamberland

Graduate College Dissertations and Theses

The distributions of Earth’s flora and fauna are shaped by a myriad of biotic and abiotic factors including dispersal capacity, and the geologic histories of landscapes. The relative importance of long-distance (overland or overwater) dispersal and vicariance, or the subsequent separations of populations via physical barriers (e.g. mountains, rivers, oceans) in shaping the disjunct distribution of taxa, are the two main biogeographic hypotheses used to explain disjunct distributions. This research explored the evolutionary histories of spiders to test how long-distance dispersal and vicariance have generated species diversity and distributions are shaped on local and global scales. In the first part …

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 …

Phylogeny Of Terrestrial Isopods Based On The Complete Mitochondrial Genomes, Subvert The Monophyly Of Oniscidea, Rui Zhang, Ruru Chen, Jianmei An, Carlos A. Santamaria

Integrative Biology Faculty and Staff Publications

Background: Oniscidea is the only truly terrestrial taxon within the Crustacea, and vital to soil formation. However, the monophyly of suborder Oniscidea has been in dispute since 1995, with different studies disagreeing on whether the coastal Ligiidae are included within the suborder. To clarify the phylogenetic hypothesis of suborder Oniscidea, we sequenced the complete mitochondrial genomes of Ligia exotica (Roux, 1828) and Mongoloniscus sinensis (Dollfus, 1901).

Results: Like most metazoan, the complete mitogenomes of two species with circular double strands. The structure and characters of mitogenomes of these two species are analyzed. The constructed phylogenetic analyses show that Oniscidea is …

Phylogeny Of The Subfamilies Of Ichneumonidae (Hymenoptera), Andrew M.R. Bennett, Sophie Cardinal, Ian D. Gauld, David B. Wahl

Biology Faculty Publications

A combined morphological and molecular phylogenetic analysis was performed to evaluate the subfamily relationships of the parasitoid wasp family Ichneumonidae (Hymenoptera). Data were obtained by coding 135 morphological and 6 biological characters for 131 exemplar species of ichneumonids and 3 species of Braconidae (the latter as outgroups). The species of ichneumonids represent all of the 42 currently recognized subfamilies. In addition, molecular sequence data (cytochrome oxidase I “DNA barcoding” region, the D2 region of 28S rDNA and part of the F2 copy of elongation factor 1-alpha) were obtained from specimens of the same species that were coded for morphology (1309 …

Cytochrome P450 Protein Family 4 Conservation And Diversification Among Flies, Kevin Croft

Scholars Week

Commercial fruit pests, such as flies within the Tephritidae family, have a large economic impact on the global food supply due to their ability to infest a wide range of host plants. The genus Rhagoletis, which contains the apple maggot fly, has become an important organism for understanding the process of switching and adapting to new hosts. The enzyme group responsible for this ability in Rhagoletis flies is the Cytochrome P450 proteins. This superfamily of proteins is also known to help organisms deal with various environmental stressors, such as detoxification of plant defensive compounds or insecticides. The Rhagoletis zephyria (the …

Morpho-Molecular Characterization Of The Litostomatean Predatory Ciliate Phialina Pupula (Müller, 1773) Foissner, 1983 (Haptoria, Lacrymariidae), Ľubomír Rajter, William Bourland, Peter Vďačný

Biology Faculty Publications and Presentations

The morphology and phylogenetic position of a haptorian ciliate, Phialina pupula (Müller, 1773) Foissner, 1983, isolated from microaerobic sandy sediments of the floodplain area of the Boise River, Idaho, U.S.A., were studied using live observation, protargol impregnation, scanning electron microscopy, and the 18S rRNA gene as well as the ITS region. The Boise population of P. pupula is characterized by a size of about 60–130 × 20–50 μm, an elliptical macronucleus with a single micronucleus, highly refractive dumbbell-shaped inclusions scattered throughout the cytoplasm and concentrated in the anterior body half, a single subterminal/terminal contractile vacuole, about 10 μm long rod-shaped …

Phylogenetic Origins For Severe Acetaminophen Toxicity In Snake Species Compared To Other Vertebrate Taxa, Peter Van Den Hurk, Harold M.I. Kerkkamp

Publications

While it has been known for a while that some snake species are extremely sensitive to acetaminophen, the underlying mechanism for this toxicity has not been reported. To investigate if essential detoxification enzymes are missing in snake species that are responsible for biotransformation of acetaminophen in other vertebrate species, livers were collected from a variety of snake species, together with samples from alligator, snapping turtle, cat, rat, and cattle. Subcellular fractions were analyzed for enzymatic activities of phenol-type sulfotransferase and UDP‑glucuronosyltransferase, total glutathione S‑transferase, and N‑acetyltransferase. The results showed that none of the snake species, together …

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 …

Ancient Origins Of A Diverse Stygofaunal Group: The Australian Bathynellidae (Crustacea), Giulia Perina

Theses: Doctorates and Masters

Research on subterranean fauna on all continents has highlighted often high levels of endemism, for both troglobionts (terrestrial subterranean organisms) and stygobionts (organisms living in groundwater). In Australia, particularly in the arid zones of Western Australia, a rich hypogean assemblage has been discovered in the past few decades, largely due to surveys required as part of environmental impact assessments for, and imposed conditions on, mining operations. Bathynellidae (Crustacea) are part of the stygofaunal community, but to-date they are poorly understood, mainly because their conservative morphology, small size and delicate exoskeleton make their dissection, observation and study very difficult. Additionally, the …

Mitochondrial Dna Sequence Alignments For Phylogenetic Analysis Of The Shrimp Genus Farfantepenaeus, Laura Timm, S. Simon, Heather Bracken-Grissom Dr.

DEEPEND Datasets

This dataset includes 12S, 16S, and COI sequence data. Sequences were obtained from the eight recognized species of Farfantepenaeus: F. aztecus, F. brasiliensis, F. brevirostris, F. californiensis, F. duorarum, F. isabelae, F. notialis, and F. subtilis. Also included are several sequences from species of Litopenaeus, which serve as outgroup(s).