Ecology and Evolutionary Biology Commons^™

Notes On Bird Species In Bamboo In Northern Madre De Dios, Peru, Including The First Peruvian Record Of Acre Tody-Tyrant (Hemitriccus Cohnhafti), Michael G. Harvey, Daniel F. Lane, Justin Hite, Ryan S. Terrill, Sheila Figueroa Ramírez, Brian Tilston Smith, John Klicka, Walter Vargas Campos

Occasional Papers of the Museum of Natural Science, Louisiana State University

In the southwestern Amazon Basin, large areas of habitat are comprised predominantly of Guadua bamboo. Many bird species occur in or specialize on Guadua-dominated habitats, but little is known about the taxonomy, distribution, and evolutionary history of this avian assemblage. During 2011, we surveyed the surroundings of Iberia, an area with many large Guadua stands in the southern Peruvian Amazon. We found many Guadua specialist bird species and discovered a surprising Andean element to the local avifauna. We present information on Guadua specialists, Andean species, birds of open habitats, and avian migration and reproduction. We provide accounts for species …

Nocturnal Homing In The Tropical Amblypygid Phrynus Pseudoparvulus (Class Arachnida, Order Amblypygi), Eileen Hebets, E.J. Gering, Verner P. Bingman, Daniel D. Wiegmann

Eileen Hebets Publications

Arthropods are renowned for their navigational capabilities, with numerous examples known from insects and crustaceans. Early studies of amblypygids (Class Arachnida, Order Amblypygi) also suggest complex nocturnal navigation, despite their apparent lack of visual adaptations to the low-light conditions of a tropical understory. In a series of two studies, we use the tropical amblypygid, Phrynus pseudoparvulus, to assess their nocturnal homing ability. Our first experiment displaced and tracked resident and nonresident individuals. Resident individuals, displaced up to 4.5 m from their home refuges and released onto their home tree, were more likely to return to their previously occupied refuge than …

The Complete Plastid Genome Sequence Of Iris Gatesii (Section Oncocyclus), A Bearded Species From Southeastern Turkey, Carol A. Wilson

Aliso: A Journal of Systematic and Floristic Botany

Iris gatesii is a rare bearded species in subgenus Iris section Oncocyclus that occurs in steppe communities of southeastern Turkey. This species is not commonly cultivated, but related species in section Iris are economically important horticultural plants. The complete plastid genome is reported for I. gatesii based on data generated using the Illumina HiSeq platform and is compared to genomes of 16 species selected from across the monocotyledons. This Iris genome is the only known plastid genome available for order Asparagales that is not from Orchidaceae. The I. gatesii plastid genome, unlike orchid genomes, has little gene loss and rearrangement …

Sudden Aspen Decline Report For Spruce Beetle Epidemic And Aspen Decline Management Response Eis, Jim Worrall, Suzanne Marchetti, Gerald E. Rehfeldt

Aspen Bibliography

Aspen is an important component of GMUG’s forests. Over 288,000 ha (712,000 acres) of aspendominated forest type (TAA) occur across the GMUG (Table 1). Just over half (55%) of the aspen forest type is outside wilderness and roadless areas.

Detection Of Predator Cues Alters Mating Tactics In Male Wolf Spiders, Dustin J. Wilgers, Daniel Wickwire, Eileen Hebets

Eileen Hebets Publications

Males of the wolf spider, Rabidosa punctulata, exhibit condition-dependent alternative mating tactics, whereby small, poor condition males engage in multimodal courtship while large, good condition males adopt a direct mount tactic that forgoes courtship. This study explores the possibility that tactic-specific costs can help explain this unintuitive pattern of mating tactic expression. Specifically, we hypothesize that courtship signaling is costly with respect to eavesdropping by predators and that males can alter their tactic expression based upon the perceived environmental predation risk. We test this by first examining the risk of predation associated with different mating tactics. We use a …

Hidden Diversity In Sardines: Genetic And Morphological Evidence For Cryptic Species In The Goldstripe Sardinella, Sardinella Gibbosa (Bleeker, 1849), Rey C. Thomas, Demian A. Willette, Kent E. Carpenter, Mudjekeewis D. Santos

Biological Sciences Faculty Publications

Cryptic species continue to be uncovered in many fish taxa, posing challenges for fisheries conservation and management. In Sardinella gibbosa, previous investigations revealed subtle intra-species variations, resulting in numerous synonyms and a controversial taxonomy for this sardine. Here, we tested for cryptic diversity within S. gibbosa using genetic data from two mitochondrial and one nuclear gene regions of 248 individuals of S. gibbosa, collected from eight locations across the Philippine archipelago. Deep genetic divergence and subsequent clustering was consistent across both mitochondrial and nuclear markers. Clade distribution is geographically limited: Clade 1 is widely distributed in the central Philippines, while …

Endogenous Ros Levels In C. Elegans Under Exogenous Stress Support Revision Of Oxidative Stress Theory Of Life-History Tradeoffs, Samson W. Smith, Leigh C. Latta Iv, Dee R. Denver, Suzanne Estes

Biology Faculty Publications and Presentations

Background: The oxidative stress theory of life-history tradeoffs states that oxidative stress caused by damaging free radicals directly underpins tradeoffs between reproduction and longevity by altering the allocation of energetic resources between these tasks. We test this theory by characterizing the effects of exogenous oxidative insult and its interaction with thermal stress and diet quality on a suite of life-history traits and correlations in Caenorhabditis elegans nematodes. We also quantify demographic aging rates and endogenous reactive oxygen species (ROS) levels in live animals.

Results: Our findings indicate a tradeoff between investment in reproduction and antioxidant defense (somatic maintenance) consistent with …

Recognition Of Two New Species Of Freshwater Crabs From The Seychelles Based On Molecular Evidence (Potamoidea: Potamonautidae)., Neil Cumberlidge, Savel Regan Daniels Phd

Journal Articles

The Afrotropical freshwater crab genus Seychellum is endemic to the granitic Seychelles in the Indian Ocean (Mahé, Silhouette, Praslin, La Digue and Frégate). Here we describe two new cryptic species of Seychellum that represent two evolutionarily separate lineages of a previously monotypic genus. This raises to three the number of species of freshwater crabs known from Seychelles. Each species is endemic to either one island (Silhouette) or to a pair of islands (Mahé and Frégate, or Praslin and La Digue). The three species can be clearly distinguished as separate lineages by DNA analysis, haplotyping and examination of gonopod characters. The …

Lineage-Specific Transcriptional Profiles Of Symbiodinium Spp. Unaltered By Heat Stress In A Coral Host, Daniel J. Barshis, Jason T. Ladner, Thomas A. Oliver, Stephen R. Palumbi

Biological Sciences Faculty Publications

Dinoflagellates of the genus Symbiodinium form an endosymbiosis with reef building corals, in which photosynthetically derived nutrients comprise the majority of the coral energy budget. An extraordinary amount of functional and genetic diversity is contained within the coral-associated Symbiodinium, with some phylotypes (i.e., genotypic groupings), conferring enhanced stress tolerance to host corals. Recent advances in DNA sequencing technologies have enabled transcriptome-wide profiling of the stress response of the cnidarian coral host; however, a comprehensive understanding of the molecular response to stress of coral-associated Symbiodinium, as well as differences among physiologically susceptible and tolerant types, remains largely unexplored. Here, …

The Prevalence And Effect Of Wolbachia Infection On The Brown Widow Spider (Latrodectus Geometricus), Brittany Dane' Arrington

College of Graduate Studies: Theses & Dissertations

Wolbachia was recently identified in the Brown Widow Spider (Latrodectus geometricus). This symbiont has not previously been found in this genus, therefore the consequences on the host’s population dynamics are unknown. The frequency of endosymbiont infection can provide insight into the population dynamics of the host as this bacteria is known to alter host life history. In my 1^st chapter I determine the prevalence of Wolbachia pipentis infection in in the Brown Widow Spider (Latrodectus geometricus) from five locations in the Southeastern United States. Infection frequency differed significantly among sampling locations, ranging from 20% to …

Epistasis In Predator-Prey Relationships, Iuliia Inozemtseva

College of Graduate Studies: Theses & Dissertations

Epistasis is the interaction between two or more genes to control a single phenotype. We model epistasis of the prey in a two-locus two-allele problem in a basic predator- prey relationship. The resulting model allows us to examine both population sizes as well as genotypic and phenotypic frequencies. In the context of several numerical examples, we show that if epistasis results in an undesirable or desirable phenotype in the prey by making the particular genotype more or less susceptible to the predator or dangerous to the predator, elimination of undesirable phenotypes and then genotypes occurs.

Concordant Phylogenetic Patterns Inferred From Mitochondrial And Microsatellite Dna In The Giant Clam Tridacna Crocea, Timery S. Deboer, Ma Rio Abdon Naguit, Mark V. Erdmann, Maria Carmen A. Ablan-Lagman, Ambariyanto, Kent E. Carpenter, Abdul Hamid A. Toba, Paul H. Barber

Biological Sciences Faculty Publications

The boring giant clam, Tridacna crocea Lamarck, 1819, is a CITES-listed bivalve that is declining due to overharvest and environmental degradation. Previous molecular studies in the Coral Triangle using mitochondrial DNA indicated the presence of deep phylogenetic divergence and strong phylogeographic structure across this region, suggesting the possibility of multiple cryptic species. In the present study, we compare data from non-recombining mitochondrial (mtDNA; cytochrome oxidase subunit 1, COI) and eight microsatellite loci to better understand patterns of genetic structure and species boundaries in T. crocea populations across Indonesia and the Philippines. Microsatellite loci and mtDNA data from 618 individuals representing …

Causes And Consequences Of Female Mate Choice In Drosophila Melanogaster: A Hemiclonal Analysis, Hannah Me Tennant

Theses and Dissertations (Comprehensive)

One of Darwin’s greatest questions, the reason why females prefer elaborate sexually selected male traits and displays, was elucidated by the Fisherian coevolution of male traits and female preferences. While variation in male attractiveness and ornamentation has received much attention, there has been little attempt to evaluate the causes and consequences of intraspecific variation in components of female preference. Furthermore, demonstrating a genetic basis to female preference does not answer the question of how within-population genetic variation is maintained.

Understanding the sources of variation in potential mating interactions between males and females is important because this variation determines the strength …

The Distribution Of Fitness Effects Of Spontaneous Mutations In Vibrio Fischeri, Chelsea K. Jones

Honors Theses and Capstones

Mutations are the ultimate source of the biological diversity on which natural selection acts, but the vast majority of these mutations are harmful. As such, mutations lead to disease states like cancer, extinction of small populations, and can drive pathogen evolution. Unfortunately, because mutations are rare and past studies have been subject to detection biases, very little is known about the distribution of fitness effects from naturally occurring mutations. In this study, we used mutation accumulation and full genome sequencing to capture naturally occurring mutations before they were exposed to the sieve of natural selection in Vibrio fischeri. We …

The Roles Of Phenotypic Plasticity And Genotypic Specialization In High Altitude Adaptation, Danielle M. Tufts

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

In vertebrates living at high altitude, arterial hypoxemia may be ameliorated by reversible changes in the oxygen-carrying capacity of the blood (regulated by erythropoiesis) and/or changes in blood–oxygen affinity (regulated by allosteric effectors of hemoglobin function). These hematological traits often differ between taxa that are native to different elevational zones, but it is often unknown whether the observed physiological differences reflect fixed, genetically based differences or environmentally induced acclimatization responses (phenotypic plasticity). Here, we report measurements of hematological traits related to blood–O₂ transport in populations of deer mice (Peromyscus maniculatus) that are native to high- and low-altitude …

Determining Parentage And The Effects Of Relatedness On Play Partner Preference In Belding's Ground Squirrels, Jessica Weidenbach

Master's Theses

I investigated 1) multiple paternity in Belding’s ground squirrels (Urocitellus beldingi) and 2) social partner preferences in juvenile U. beldingi. Prior work with blood allozymes demonstrated multiple paternity in U. beldingi litters. I evaluated paternity using microsatellite DNA analysis, which is more accurate than examining blood allozymes. My results indicate that multiple paternity in U. beldingi is more extensive than previously shown, occurring in about 90% of litters with more than one juvenile, and averaging 2.95 fathers in multiply sired litters. I also evaluated the hypothesis that play and other social behavior promotes bonding among juvenile female …

Time-Dependent Random Effect Poisson Random Field Model For Polymorphism Within And Between Two Related Species, Shilei Zhou

UNLV Theses, Dissertations, Professional Papers, and Capstones

Molecular evolution is partially driven by mutation, selection, random genetic drift, or combination of the three factors. To quantify the magnitude of these genetic forces, a previously developed time-dependent fixed effect Poisson random field model provides powerful likelihood and Bayesian estimates of mutation rate, selection coefficient, and species divergence time. The assumption of the fixed effect model that selection intensity is constant within a genetic locus but varies across genes is obviously biologically unrealistic, but it serves the original purpose of making statistical inference about selection and divergence between two related species they are individually at mutation-selection-drift inequilibrium. By relaxing …

The Genetic Architecture Of Juvenile Migration In Rainbow Trout (Oncorhynchus Mykiss), Benjamin Charles Hecht

Open Access Dissertations

Animal migrations play a critical role in the health and balance of ecological systems and in the evolution and diversification of species, and this is perhaps best displayed amongst salmonid fishes (salmon, trout, and char) who exhibit variation in the propensity to migrate both within and among species. Rainbow and steelhead trout (Oncorhynchus mykiss), members of the salmonid family of fishes, capture this variation throughout their native range. Some populations and ecotypes will remain resident in freshwater habitats throughout their life history; while others have the ability to embark on tremendous marine migrations. Those that migrate undergo a suite of …

Analysis Of Uniparental Lineages In Two Villages Of Santiago Del Estero, Argentina, Seat Of “Pueblos De Indios” In Colonial Times, Maia Pauro, Angelina García, Rodrigo Nores, Darío A. Demarchi

Human Biology Open Access Pre-Prints

Based on the analysis of the mitochondrial control region and seven biallelic markers of the Y Chromosome, we investigated the genetic composition of two rural populations of southern Santiago del Estero, Argentina, that were seats in colonial times of “pueblos de indios”, a colonial practice that consisted of concentrating the indigenous populations in organized and accessible settlements, to facilitate Christianizing and policing. We found the Native American Y chromosome haplogroup Q1a3a in only 11% (3/27) of the males. Haplogroup R, common in European populations, is the most frequent haplogroup in Santiago del Estero (55%). In contrast, the persistence of Native …

Genetic Variation Of X-Strs In The Wichí Population From Chaco Province, Argentina, Laura Angela Glesmann, Pablo Francisco Martina, Cecilia Inés Catanesi

Human Biology Open Access Pre-Prints

The Wichí people from Chaco province inhabit the region called Impenetrable Chaqueño, where the climatic conditions are extreme. Besides the scarce communication with the main urban centers, the cultural patterns of the Wichí cause these communities to live in certain degree of isolation. The effect of this situation is an increased genetic differentiation from other populations, as it was observed through autosomal and Y chromosome markers. However, the genetic variation of X chromosome has not been fully analyzed yet. The patterns of allele distribution of different markers of X chromosome can be highly informative in comparative studies, because its special …

Signatures Of Rapid Evolution In Urban And Rural Transcriptomes Of White-Footed Mice (Peromyscus Leucopus) In The New York Metropolitan Area, Stephen Edward Harris, Jason Munshi-South, Craig Oberfell, Rachel O'Neill

Publications and Research

Urbanization is a major cause of ecological degradation around the world, and human settlement in large cities is accelerating. New York City (NYC) is one of the oldest and most urbanized cities in North America, but still maintains 20% vegetation cover and substantial populations of some native wildlife. The white-footed mouse, Peromyscus leucopus, is a common resident of NYC’s forest fragments and an emerging model system for examining the evolutionary consequences of urbanization. In this study, we developed transcriptomic resources for urban P. leucopus to examine evolutionary changes in protein-coding regions for an exemplar “urban adapter.” We used Roche 454 …

Elk (Cervus Elaphus) Seasonal Habitat Selection In A Heterogeneous Forest Structure, Jesse N. Popp, David N.C. Mcgeachy, Josef Hamr

Aspen Bibliography

Seasonal habitat selection by the reintroduced Burwash elk population, approximately 30 km south of Sudbury, Ontario, has been analysed in order to assist in the development of future management. Twenty-five adult females were radio-collared and tracked 1–3 times a week for 3 years. The most prominent patterns included selection of intolerant hardwood forests (trembling aspen, white birch, and balsam poplar) during all seasons, while Great Lakes-St. Lawrence pines (white and red pine dominated stands) were used less than expected based on availability for all seasons. The selection patterns are likely associated with seasonal climatic conditions and forage preferences. Because the …

The Rate And Effects Of Spontaneous Mutation On Fitness Traits In The Social Amoeba, Dictyostelium Discoideum, David W. Hall, Sara Fox, Jennie J. Kuzdzal-Fick, Joan E. Strassmann, David C. Queller

Biology Faculty Research

We performed a mutation accumulation (MA) experiment in the social amoeba Dictyostelium discoideum to estimate the rate and distribution of effects of spontaneous mutations affecting eight putative fitness traits. We found that the per-generation mutation rate for most fitness components is 0.0019 mutations per haploid genome per generation or larger. This rate is an order of magnitude higher than estimates for fitness components in the unicellular eukaryote Saccharomyces cerevisiae, even though the base-pair substitution rate is two orders of magnitude lower. The high rate of fitness-altering mutations observed in this species may be partially explained by a large mutational target …

A Comprehensive And Integrative Reconstruction Of Evolutionary History For Anomura (Crustacea: Decapoda)., Heather D Bracken-Grissom, Maren E Cannon, Patricia Cabezas, Rodney M Feldmann, Carrie E Schweitzer, Shane T Ahyong, Darryl L Felder, Rafael Lemaitre, Keith A Crandall

Computational Biology Institute

BACKGROUND: The infraorder Anomura has long captivated the attention of evolutionary biologists due to its impressive morphological diversity and ecological adaptations. To date, 2500 extant species have been described but phylogenetic relationships at high taxonomic levels remain unresolved. Here, we reconstruct the evolutionary history-phylogeny, divergence times, character evolution and diversification-of this speciose clade. For this purpose, we sequenced two mitochondrial (16S and 12S) and three nuclear (H3, 18S and 28S) markers for 19 of the 20 extant families, using traditional Sanger and next-generation 454 sequencing methods. Molecular data were combined with 156 morphological characters in order to estimate the largest …

Evolution Of A Higher Intracellular Oxidizing Environment In Caenorhabditis Elegans Under Relaxed Selection, Joanna Joyner-Matos, Kiley A. Hicks, Dustin Cousins, Michelle Keller, Dee R. Denver, Charles F. Baer, Suzanne Estes

Biology Faculty Publications and Presentations

We explored the relationship between relaxed selection, oxidative stress, and spontaneous mutation in a set of mutationaccumulation (MA) lines of the nematode Caenorhabditis elegans and in their common ancestor. We measured steady-state levels of free radicals and oxidatively damaged guanosine nucleosides in the somatic tissues of five MA lines for which nuclear genome base substitution and GC-TA transversion frequencies are known. The two markers of oxidative stress are highly correlated and are elevated in the MA lines relative to the ancestor; point estimates of the per-generation rate of mutational decay (DM) of these measures of oxidative stress are similar to …

Dna From Feces And Museum Specimens Confirms A First State Record Bird, Alec R. Lindsay Ph. D., Skye C. Haas

Faculty Works

In October 2005, a vagrant kingbird (Aves: Tyrannus sp.) appeared in Michigan’s Upper Peninsula, nearly 2000 km from the northern limit of its usual range. Using mitochondrial DNA obtained from a fecal sample deposited by the bird and mitochondrial DNA isolated from museum reference specimens, the species iden- tity of this bird was definitively confirmed as a Tropical Kingbird (T. melancholicus) rather than a Couch’s Kingbird (T. couchii). This is the first time DNA evidence has been used to establish a state bird record, and one of the few studies of any type to successfully use avian feces for DNA …

Occurrence And Genetic Diversity Of Lemon Sharks (Negaprion Brevirostris) At A Nursery Ground At The Chandeleur Islands, Louisiana., Jonathan F. Mckenzie

LSU New Orleans Theses and Dissertations

Anecdotal evidence suggested that immature lemon sharks (Negaprion brevirostris) occur at the Chandeleur Islands in southeastern Louisiana. From May 2009 to August 2011, the Nekton Research Laboratory at the University of New Orleans regularly sampled habitats at the Chandeleur Islands to confirm the presence of immature individuals of this species. During these efforts, 147 immature lemon sharks (neonates, young-of-the-year, and juveniles) were collected. Each shark was PIT tagged and a tissue sample was taken for genetic analyses. Sizes ranged from 56 – 177 cm total length. Sharks showed a preference for sandy substrate and smaller individuals showed significant preference …

Can Long-Range Pcr Be Used To Amplify Genetically Divergent Mitochondrial Genomes For Comparative Phylogenetics? A Case Study Within Spiders (Arthropoda: Araneae), Andrew G. Briscoe, Sara Goodacre, Susan E. Masta, Martin I. Taylor, Miquel A. Arnedo, David Penny, John Kenny, Simon Creer

Biology Faculty Publications and Presentations

The development of second generation sequencing technology has resulted in the rapid production of large volumes of sequence data for relatively little cost, thereby substantially increasing the quantity of data available for phylogenetic studies. Despite these technological advances, assembling longer sequences, such as that of entire mitochondrial genomes, has not been straightforward. Existing studies have been limited to using only incomplete or nominally intra-specific datasets resulting in a bottleneck between mitogenome amplification and downstream high-throughput sequencing. Here we assess the effectiveness of a wide range of targeted long-range PCR strategies, encapsulating single and dual fragment primer design approaches to provide …

Characterization Of Aebp2 Mutant Mice, Arundhati Bakshi

Honors Capstones

No abstract provided.

Parentage Analysis And Conservation Genetics Educational Material For The Eastern Hellbender Salamander, Cryptobranchus Alleganiensis Alleganiensis, Sarah A. Chudyk

Master's Projects

Populations of the Eastern hellbender salamander, Cryptobranchus alleganiensis alleganiensis, are declining, making this a species of special concern in New York State and under consideration for Federal Endangered Species listing. As a result of this decline, the New York State Department of Environmental Conservation and the Buffalo Zoo initiated a headstarting program with an egg mass found in the Allegheny River drainage. The juveniles being raised by the Zoo will be released back into the watershed and so understanding the genetic diversity and parentage of these hellbenders will inform the reintroduction efforts. Furthermore, in order to determine how to …