Ecology and Evolutionary Biology Commons^™

A Novel Method Of Microsatellite Genotyping-By-Sequencing Using Individual Combinatorial Barcoding, Salla Vartia, Jose L. Villanueva-Cañas, John Finarelli, Edward D. Farrell, Patrick C. Collins, Graham M. Hughes, Jeanette E.L. Carlson, David T. Gauthier, Philip Mcginnity, Thomas F. Cross, Richard D. Fitzgerald, Luca Mirimin, Fiona Crispie, Paul D. Cotter, Jens Carlsson

Biological Sciences Faculty Publications

This study examines the potential of next-generation sequencing based 'genotyping-by-sequencing' (GBS) of microsatellite loci for rapid and cost-effective genotyping in large-scale population genetic studies. The recovery of individual genotypes from large sequence pools was achieved by PCR-incorporated combinatorial barcoding using universal primers. Three experimental conditions were employed to explore the possibility of using this approach with existing and novel multiplex marker panels and weighted amplicon mixture. The GBS approach was validated against microsatellite data generated by capillary electrophoresis. GBS allows access to the underlying nucleotide sequences that can reveal homoplasy, even in large datasets and facilitates cross laboratory transfer. GBS …

The Microbiome In Light Of Host Evolution, Alexander M. Waldrop Jr.

Theses and Dissertations

Recent advances in sequencing technologies have provided an unprecedented window in the unseen biological world. Accompanying this revolution is a growing appreciation for the ubiquity and diversity of beneficial interactions between animals and the microbes they carry. Given the symbiotic roles of microbes in host nutrition, immunity, behavior, development, and nearly every other facet of host biology, it is becoming increasingly clear that any understanding of hosts and their evolution would be incomplete without also considering the microbial dimension. Yet despite the growing body of evidence that many of these partnerships are rooted deep in evolutionary time, the majority of …

Pain-Capable Neural Substrates May Be Widely Available In The Animal Kingdom, Edgar T. Walters

Animal Sentience

Neural and behavioral evidence from diverse species indicates that some forms of pain may be generated by coordinated activity in networks far smaller than the cortical pain matrix in mammals. Studies on responses to injury in squid suggest that simplification of the circuitry necessary for conscious pain might be achieved by restricting awareness to very limited information about a noxious event, possibly only to the fact that injury has occurred, ignoring information that is much less important for survival, such as the location of the injury. Some of the neural properties proposed to be critical for conscious pain in mammals …

Biogeographical Patterns In The Hard-Tick Genus Amblyomma Koch 1844 (Acari: Ixodidae), Matthew H. Seabolt

College of Graduate Studies: Theses & Dissertations

Amblyomma Koch is a genus of hard-ticks with approximately 130 species. Its geographical range is typical for organisms with a Gondwanan origin. A majority of these species are endemic to the Neo- and Afrotropical regions, with the remaining taxa dispersed throughout Southeast Asia, Australia and the Pacific islands. Based on this distribution, we hypothesize that the genus dispersal patterns will mirror the fragmentation and continental drift of the Gondwanan supercontinent. Maximum parsimony, maximum likelihood, Bayesian inference and node-dating analyses of nuclear 18S rDNA gene sequences reveal a more recent origin and radiation patterns within the genus and suggest that Amblyomma …

Fish Pain: An Inconvenient Truth, Culum Brown

Animal Sentience

Whether fish feel pain is a hot political topic. The consequences of our denial are huge given the billions of fish that are slaughtered annually for human consumption. The economic costs of changing our commercial fishery harvest practices are also likely to be great. Key outlines a structure-function analogy of pain in humans, tries to force that template on the rest of the vertebrate kingdom, and fails. His target article has so far elicited 34 commentaries from scientific experts from a broad range of disciplines; only three of these support his position. The broad consensus from the scientific community is …

Pain And Fish Welfare, Eliane Gonçalves-De-Freitas

Animal Sentience

The evolutionary approach of Key’s (2016) target article, generically comparing humans with fish of all kinds, is simplistic. The author ignores published research on structural and molecular aspects of pain in fish. The target article reads more like a selective polemic against fish welfare than an even-handed analysis.

The Interrelationships Of Placental Mammals And The Limits Of Phylogenetic Inference, James E. Tarver, Mario Dos Reis, Siavash Mirarab, Raymond J. J. Moran, Sean Parker, Joseph E. O'Reilly, Benjamin L. King, Mary J. O'Connell, Robert J. Asher, Tandy Warnow, Kevin J. Peterson, Philip C.J. Donoghue, Davide Pisani

Dartmouth Scholarship

Placental mammals comprise three principal clades: Afrotheria (e.g., elephants and tenrecs), Xenarthra (e.g., armadillos and sloths), and Boreoeutheria (all other placental mammals), the relationships among which are the subject of controversy and a touchstone for debate on the limits of phylogenetic inference. Previous analyses have found support for all three hypotheses, leading some to conclude that this phylogenetic problem might be impossible to resolve due to the compounded effects of incomplete lineage sorting (ILS) and a rapid radiation. Here we show, using a genome scale nucleotide data set, microRNAs, and the reanalysis of the three largest previously published amino acid …

Essential Questions, Imsa Biology Team

Evolution

In order to understand the current state of biological life and how it has changed over time, the following questions must be addressed:

Evidence Of Evolution 1: Structures, Imsa Biology Team

Evolution

In order to investigate linage, evolutionary history, and common ancestry, you need to be familiar with the following structures.

Mechanisms And Speciation 1: The Modern Synthesis, Imsa Biology Team

Evolution

The Modern Synthesis or Synthetic Theory of Evolution is an explanation of evolution that is based on modern genetic principles. According to the Modern Synthesis (a.k.a. Neo-Darwinism):

Evolution Practice 1, Imsa Biology Team

Evolution

Answer the following questions using information from the handouts, and examples from the LAB

Evolution Practice 2, Imsa Biology Team

Evolution

Evolution Problems

Genetic Drift Simulation, Imsa Biology Team

Evolution

Genetic drift can be defined as a random fluctuation in gene frequency. More specifically, it tells us that different alleles may increase or decrease in a population in proportion to one another over time, just by chance, rather than due to any fitness advantage.

Evidence Of Evolution 3: Evolutionary Evidence And Inferences Lab: A Discussion Guide, Imsa Biology Team

Evolution

This lab activity was designed to provide you with opportunities to make inferences and draw conclusions about evolution and the common ancestry of various animals based on their anatomical characteristics and comparative anatomy. You will be given tasks to accomplish or questions to answer at each of 11 stations. In order to do this successfully, you must make careful observations of the specimens on display.

Evidence Of Evolution 2: Definitions For Evolutionary Evidence Lab, Imsa Biology Team

Evolution

This lab activity was designed to provide you with opportunities to make inferences and draw conclusions about evolution and the common ancestry of various animals based on their anatomical characteristics and comparative anatomy. You will be given tasks to accomplish or questions to answer at each of 11 stations. In order to do this successfully, you must make careful observations of the specimens on display. You must also know the following definitions before beginning this activity:

Mechanisms And Speciation 2: Evolution On The Web Questions, Imsa Biology Team

Evolution

The website below, sponsored by UC Berkeley, is a reliable source for information about evolution. This will give you the introductory information about the mechanisms of Evolution.

An Exploration Of The Phylogenetic Placement Of Recently Discovered Ultrasmall Archaeal Lineages, Jeffrey M. O'Brien

Honors Scholar Theses

In recent years, several new clades within the domain Achaea have been discovered. This is due in part to microbiological sampling of novel environments, and the increasing ability to detect and sequence uncultivable organisms through metagenomic analysis. These organisms share certain features, such as small cell size and streamlined genomes. Reduction in genome size can present difficulties to phylogenetic reconstruction programs. Since there is less genetic data to work with, these organisms often have missing genes in concatenated multiple sequence alignments. Evolutionary Biologists have not reached a consensus on the placement of these lineages in the archaeal evolutionary tree. There …

Evolution And Otitis Media: A Review, And A Model To Explain High Prevalence In Indigenous Populations, Mahmood F. Bhutta

Human Biology Open Access Pre-Prints

Inflammation of the middle ear (otitis media) comprises a group of disorders that are highly prevalent in childhood, and indeed are amongst the most common disorders of childhood. Otitis media is also heritable, and has effects on fecundity. This means that otitis media is subject to evolution, yet the evolutionary selection forces that may determine susceptibility to otitis media have never been adequately explored.

Here I undertake a critical analysis of evolutionary forces that may determine susceptibility to middle ear inflammation. These forces include those determining function of the middle ear, those affecting host immunity, and those affecting colonization by, …

The Evolution Of Body Size In The Order Siluriformes, D Cooper Campbell

Honors Theses

The evolution of body size has long been a topic of interest to biologists due to the close link between size and various aspects of an organism’s biology. Adult body size is influenced by the underlying tradeoff in energy allocation between maintenance, somatic growth and reproduction. I studied the evolution of a large group of globally distributed (primarily freshwater with some marine forms) fishes to test some basic hypotheses about the evolution of adult body size. Catfish (Siluriformes) are an excellent group for this type of research as they represent approximately 11% of fishes and species range in size from …

Some Agreement On Kin Selection And Eusociality?, David C. Queller, Stephen Rong, Xiaoyun Liao

Biology Faculty Research

The authors of "Relatedness, Conflict, and the Evolution of Eusociality" respond to objections raised by Martin Nowak and Benjamin Allen.

Evolution And Biodiversity, Timothy Henkel, Emily Croteau, Matthew Waters

Biological Sciences Grants Collections

This Grants Collection for Evolution and Biodiversity was created under a Round Four ALG Textbook Transformation Grant.

Affordable Learning Georgia Grants Collections are intended to provide faculty with the frameworks to quickly implement or revise the same materials as a Textbook Transformation Grants team, along with the aims and lessons learned from project teams during the implementation process.

Documents are in .pdf format, with a separate .docx (Word) version available for download. Each collection contains the following materials:

• Linked Syllabus
• Initial Proposal
• Final Report

Relatedness, Conflict, And The Evolution Of Eusociality, Xiaoyun Liao, Stephen Rong, David C. Queller

Biology Faculty Research

The evolution of sterile worker castes in eusocial insects was a major problem in evolutionary theory until Hamilton developed a method called inclusive fitness. He used it to show that sterile castes could evolve via kin selection, in which a gene for altruistic sterility is favored when the altruism sufficiently benefits relatives carrying the gene. Inclusive fitness theory is well supported empirically and has been applied to many other areas, but a recent paper argued that the general method of inclusive fitness was wrong and advocated an alternative population genetic method. The claim of these authors was bolstered by a …

The Influence Of Spines And Size Refuge On Predation Of Devonian Brachiopods From The Lime Creek Formation Near Rockford, Iowa, Broc S. Kokesh

Scholarly Horizons: University of Minnesota, Morris Undergraduate Journal

Brachiopods are small invertebrates that live on the seafloor and are prominent in the fossil record from 540 to 250 million years ago. An interesting feature of some species is that large spines develop on their exterior surfaces. These spines are thought to have evolved for defense against predators, but fossils are limited in how much information they contain about how organisms interact with each other. In this study, I examined wound markings on fossils of both a spiny (Atrypa rockfordensis) and spineless (Atrypa devoniana) species of brachiopod. Results show that spiny brachiopods were less frequently …

The Relationship Of Female Physical Attractiveness To Body Fatness, Guanlin Wang, Kurosh Djafarian, Chima A. Egedigwe, Asmaa El Hamdouchi, Robert Ojiambo, Harris Ramuth, Sandra Johanna Wallner-Liebmann, Sonja Lackner, Adama Diouf, Justina Sauciuvenaite, Catherine Hambly, Lobke M. Vaanholt, Mark D. Faries, John R. Speakman

Faculty Publications

Aspects of the female body may be attractive because they signal evolutionary fitness. Greater body fatness might reflect greater potential to survive famines, but individuals carrying larger fat stores may have poor health and lower fertility in non-famine conditions. A mathematical statistical model using epidemiological data linking fatness to fitness traits, predicted a peaked relationship between fatness and attractiveness (maximum at body mass index (BMI) = 22.8 to 24.8 depending on ethnicity and assumptions). Participants from three Caucasian populations (Austria, Lithuania and the UK), three Asian populations (China, Iran and Mauritius) and four African populations (Kenya, Morocco, Nigeria and Senegal) …

Natural Selection On Thermal Performance In A Novel Thermal Environment, Michael L. Logan, Robert M. Cox, Ryan Calsbeek

Dartmouth Scholarship

Tropical ectotherms are thought to be especially vulnerable to climate change because they are adapted to relatively stable temperature regimes, such that even small increases in environmental temperature may lead to large decreases in physiological performance. One way in which tropical organisms may mitigate the detrimental effects of warming is through evolutionary change in thermal physiology. The speed and magnitude of this response depend, in part, on the strength of climate-driven selection. However, many ectotherms use behavioral adjustments to maintain preferred body temperatures in the face of environmental variation. These behaviors may shelter individuals from natural selection, preventing evolutionary adaptation …

Population And Demographic Structure Of Ixodes Scapularis Say In The Eastern United States., Joyce M. Sakamoto, Jerome Goddard, Jason L. Rasgon

CALS Publications

INTRODUCTION: The most significant vector of tick-borne pathogens in the United States is Ixodes scapularis Say (the blacklegged tick). Previous studies have identified significant genetic, behavioral and morphological differences between northern vs. southern populations of this tick. Because tick-borne pathogens are dependent on their vectors for transmission, a baseline understanding of the vector population structure is crucial to determining the risks and epidemiology of pathogen transmission. METHODS: We investigated population genetic variation of I. scapularis populations in the eastern United States using a multilocus approach. We sequenced and analyzed the mitochondrial COI and 16S genes and three nuclear genes (serpin2, …

Privatization And Property In Biology, Joan E. Strassmann, David C. Queller

Biology Faculty Research

Organisms evolve to control, preserve, protect and invest in their own bodies. When they do likewise with external resources they privatize those resources and convert them into their own property. Property is a neglected topic in biology, although examples include territories, domiciles and nest structures, food caching, mate guarding, and the resources and partners in mutualisms. Property is important because it represents a solution to the tragedy of the commons; to the extent that an individual exerts long-term control of its property, it can use it prudently, and even invest in it. Resources most worth privatizing are often high in …

An Examination Of The Phylogenetic Diversity Of Green Algae (Chlorophyceae) That Symbiose With Spotted Salamanders (Ambystoma Maculatum) In The Egg Stage., Crystal Xue

Honors Scholar Theses

In 1909, the species Oophila amblystomatis Lambert ex Wille was described for green algae that symbiose with salamanders in the egg stage (Wille). There are two hypotheses about the source of algae: 1) that algae enter from the surrounding water once the egg clutch is laid in a pond, and 2) that they are acquired from the maternal reproductive tract. We developed a third hypothesis developed to account for the salamander reproductive cycle. Male salamanders lay spermatophores, which are protein-filled capsules, on plant matter in and around ponds. Spermatophores are exposed to the environment before use by females in internal …

Transcriptomic Insights Into The Diplontic Life History Of Diatoms, Colton Richard Kessenich

Graduate Theses and Dissertations

An organism's life cycle is the direct result of its evolutionary history and represents a fundamental aspect of its ancestry and ecology. Yet the process of linking alternating life-history stages has proven to be challenging, if not impossible in some cases. Diatoms (Bacillariophyceae) are no exception to this challenge, and their diversity of life stages and reproductive strategies add further challenges. A central focus of diatom research has been to unravel the evolutionary events that led to their extraordinary diversity, a line of inquiry that has been greatly aided by the availability of next-generation sequence data. Yet without proper taxonomic …

Evolutionary Change In Continuous Reaction Norms, Courtney J. Murren, Heidi J. Maclean, Sarah E. Diamond, Ulrich K. Steiner, Mary A. Heskel, Corey A. Handelsman, Cameron K. Ghalambor, Josh R. Auld, Hilary S. Callahan, David W. Pfennig, Rick A. Relyea, Carl D. Schlichting, Joel Kingsolver

Biology Faculty Publications

No abstract provided.