Genetics Commons^™

Drafting Human Ancestry: What Does The Neanderthal Genome Tell Us About Hominid Evolution? Commentary On Green Et Al. (2010), Michael Hofreiter

Human Biology

Ten years after the first draft versions of the human genome were
announced, technical progress in both DNA sequencing and ancient DNA
analyses has allowed a research team around Ed Green and Svante Pa¨a¨bo to
complete this task from infinitely more difficult hominid samples: a few
pieces of bone originating from our closest, albeit extinct, relatives, the
Neanderthals. Pulling the Neanderthal sequences out of a sea of contaminating
environmental DNA impregnating the bones and at the same time
avoiding the problems of contamination with modern human DNA is in itself
a remarkable accomplishment. However, the crucial question in the long …

Reduced Mhc And Neutral Variation In The Galápagos Hawk, An Island Endemic, Jennifer Bollmer, Joshua Hull, Holly Ernest, José Sarasola, Patricia Parker

Biology Department Faculty Works

BackgroundGenes at the major histocompatibility complex (MHC) are known for high levels of polymorphism maintained by balancing selection. In small or bottlenecked populations, however, genetic drift may be strong enough to overwhelm the effect of balancing selection, resulting in reduced MHC variability. In this study we investigated MHC evolution in two recently diverged bird species: the endemic Galápagos hawk (Buteo galapagoensis), which occurs in small, isolated island populations, and its widespread mainland relative, the Swainson's hawk (B. swainsoni).ResultsWe amplified at least two MHC class II B gene copies in each species. We recovered only three different sequences from 32 Galápagos …

Phenotypic And Genetic Characterization Of Wildland Collections Of Western And Searls Prairie Clovers For Rangeland Revegetation In The Western Usa, Kishor Bhattarai

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Western prairie clover [Dalea ornata (Douglas ex Hook.) Eaton & J. Wright] is a perennial legume that occurs in the northern Great Basin, Snake River Basin, and southern Columbia Plateau, whereas Searls prairie clover [Dalea searlsiae (A. Gray) Barneby], also a perennial legume, occurs in the southern Great Basin and surrounding areas. Understanding the genetic and ecotypic variation of these prairie clovers is a prerequisite for developing populations suitable for rangeland revegetation in the western USA. DNA sequences of internal transcribed spacer (ITS/5.8S) and trnK/matK were used to study the phylogeny of these species. The species were distinguished …

Reconstructing Species Responses To Past Climatic Changes Using Niche Modeling And Genetic Data, Tereza Jezkova

UNLV Theses, Dissertations, Professional Papers, and Capstones

Glacial – interglacial cycles have a pronounced impact on species distributions and genetic structure. Many species shift their distributions to lower latitudes and altitudes during the colder glacial periods and expand northwards and up the elevation during warmer interglacial periods. Some species however are capable of adapting to changing environment which allows them to persist in place despite climatic changes. I explored how climatic changes after the last glacial maximum (LGM) effected two species inhabiting the deserts of western North America: one mammal (Chisel-toothed Kangaroo Rat, Dipodomys microps) and one reptile (Desert Horned Lizard, Phrynosoma platyrhinos). I used …

Plastic And Genetic Determination Of Population, Community, And Ecosystem Properties In Freshwater Environments, Leigh C. Latta Iv

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The hierarchy of biological organization, from molecules to ecosystems, describes the relationships among various biological systems. Of particular interest is assessing how the factors that primarily determine the nature of one hierarchical level also have transcendent qualities that affect the ecology and evolution of higher hierarchical levels. The goal of this dissertation was to use a bottom-up approach to examine the transcendent effects of two factors that strongly determine the nature of their associated level of biological organization. The first, phenotypic plasticity, is a primary factor that determines the phenotype of an individual. The second factor, genetic diversity, largely determines …

Genomic Perspectives On Evolution In Bracken Fern, Joshua P. Der

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The fern genus Pteridium comprises a number of closely related species distributed throughout the world. Collectively they are called bracken ferns and have historically been treated as a single species, Pteridium aquilinum. Bracken is notorious as a toxic weed that colonizes open fields and poisons livestock. Bracken is also easily cultured and has become one of the most intensively studied ferns. Bracken has been used as a model system for the study of the fern life cycle, fern gametophyte development, the pheromonal mechanism of sex determination, toxicology, invasion ecology, and climate change. This dissertation places bracken within a global …

Ecology And Genetics Of Philodina Megalotrocha (Rotifera, Bdelloidea) From Chihuahuan Desert Populations, Lina Kamel Hamdan

Open Access Theses & Dissertations

The Chihuahuan Desert is a unique region with high biodiversity. There is a high degree endemism of freshwater biota, but relatively few studies have been focused on zooplankton. Bdelloid rotifers are one component of these ecosystems and often dominate very temporary habitats. Bdelloids are usually assumed to be cosmopolitan species due to their potentially high dispersal rates. Distribution records of the bdelloid P. megalotrocha extend from North America to New Zealand. However, little is known about its ecology or genetics. The aims of this study are to: 1) determine whether the distribution of P. megalotrocha in the Chihuahuan Desert is …

Systematics Of The Genus Ptychadena Boulenger, 1917 (Anura: Ptychadenidae) From Democratic Republic Of The Congo, Katrina Marie Weber

Open Access Theses & Dissertations

This thesis increases the scope of previous phylogenetic analyses that revealed high levels of genetic differentiation within the anuran genus Ptychadena. Herein, I increase sampling of Central African populations of Ptychadena by over six times to examine their relationships to other African populations and to search for cryptic species. This study represents the most comprehensive molecular phylogeny of Ptychadena to date. A total of three mitochondrial (12S, 16S, and cyt b) and two nuclear (RAG1 and rhodopsin) genes were sequenced for 67 specimens of Ptychadena. Maximum parsimony, maximum likelihood, and Bayesian analyses were conducted. These analyses revealed …

Fisheries Management Paper No.245 - Aquaculture Of Coral, Live Rocks And Associated Products. Aquaculture Policy, Department Of Fisheries, Western Australia

Fisheries Management Papers

Aquarium enthusiasts use corals, live rock and associated products (e.g. live sand) for display and to maintain healthy water quality conditions in their marine aquariums. There is a large and growing market for these products. While the wild harvest fisheries for aquarium products in Western Australia are sustainably managed, output is capped, so increased product is needed to meet the market demand. With a trend towards the capping of wild harvest and additional pressures, such as the introduction of Marine Parks and other marine protected areas, the aquaculture of these products is set for industry development and expansion.

The large …

Thirty-Seven Additional Microsatellite Loci In The Pacific Lion-Paw Scallop (Nodipecten Subnodosus) And Cross-Amplification In Other Pectinids, Jessica Lynn Petersen, Ana M. Ibarra, Bernie May

Department of Animal Science: Faculty Publications

We characterized 37 new microsatellite markers in the Pacific lion-paw scallop (Nodipecten subnodosus) and tested for cross-amplification in four other species. Genetic diversity was estimated using 24 individuals from the Lagoon Ojo de Liebre, B.C.S., Mexico. Allelic richness varied from 5 to 27 alleles per locus and the average expected heterozygosity was 0.76. Ten loci exhibited significant departure from Hardy–Weinberg equilibrium likely due to the presence of null alleles. Sixteen of these markers cross-amplified in closely related N. nodosus, while little or no amplification was observed in three Argopecten species.

Letter From The Dean, Lalit Verma

Discovery, The Student Journal of Dale Bumpers College of Agricultural, Food and Life Sciences

No abstract provided.

Estrogenic Compounds Downstream From Three Small Cities In Eastern Nebraska: Occurrence And Biological Effect, Marlo K. Sellin, Daniel D. Snow, Debbie L. Akerly, Alan S. Kolok

Biology Faculty Publications

Recent studies have detected estrogenic compounds in surface waters in North America and Europe. Furthermore, the presence of estrogenic compounds in surface waters has been attributed, in some cases, to the discharge of wastewater treatment plant (WWTP) effluent. The primary objective of the current study was to determine if WWTP effluent contributes estrogens to the surface waters of Nebraska. A second objective of this study was to determine if estrogens were found in concentrations sufficient enough to manifest feminizing effects on fish. These objectives were satisfied by deploying polar organic chemical integrative samplers (POCIS) and caged fathead minnows at eight …

Ecotypic Variation In Elymus Elymoides Subspecies Brevifolius Race C In The Northern Intermountain West, Matthew C. Parsons

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Little information is available on the extent of local adaptation for many native grass species. This is the case for squirreltail (Elymus section Sitanion), despite this group's prevalence and importance in rangeland restoration efforts. I evaluated 32 populations of E. elymoides ssp. brevifolius race C, a phylogenetic subdivision of bottlebrush squirreltail (E. elymoides) centered in the northern Intermountain West, for phenotypic variables and neutral genetic markers to measure their association with geographical origin. Phenotypic traits were measured in common field and greenhouse environments, and genetic diversity was assessed using Amplified Fragment Length Polymorphism. Three factors were extracted from the phenotypic …

The Dynamic Evolutionary History Of The Bananaquit (Coereba Flaveola) In The Caribbean Revealed By A Multigene Analysis, Eva Bellemain, Eldredge Bermingham, Robert Ricklefs

Biology Department Faculty Works

BackgroundThe bananaquit (Coereba flaveola) is a small nectivorous and frugivorous emberizine bird (order Passeriformes) that is an abundant resident throughout the Caribbean region. We used multi-gene analyses to investigate the evolutionary history of this species throughout its distribution in the West Indies and in South and Middle America. We sequenced six mitochondrial genes (3744 base pairs) and three nuclear genes (2049 base pairs) for forty-four bananaquits and three outgroup species. We infer the ancestral area of the present-day bananaquit populations, report on the species' phylogenetic, biogeographic and evolutionary history, and propose scenarios for its diversification and range expansion.ResultsPhylogenetic concordance between …

Ancient Dna Identification Of Early 20th Century Simian T-Cell Leukemia Virus Type 1, Sebastien Calvignac, Jean-Michel Terme, Shannon M. Hensley, Pierre Jalinot, Alex D. Greenwood, Catherine Hanni

Biological Sciences Faculty Publications

The molecular identification of proviruses from ancient tissues (and particularly from bones) remains a contentious issue. It can be expected that the copy number of proviruses will be low, which magnifies the risk of contamination with retroviruses from exogenous sources. To assess the feasibility of paleoretrovirological studies, we attempted to identify proviruses from early 20th century bones of museum specimens while following a strict ancient DNA methodology. Simian T-cell leukemia virus type 1 sequences were successfully obtained and authenticated from a Chlorocebus pygerythrus specimen. This represents the first clear evidence that it will be possible to use museum specimens to …

Speciation Within Bonneted Bats (Genus Eumops): The Complexity Of Morphological, Mitochondrial, And Nuclear Data Sets In Systematics, Molly M. Mcdonough, Loren K. Ammerman, Robert M. Timm, Hugh H. Genoways, Peter A. Larsen, Robert J. Baker

University of Nebraska State Museum: Mammalogy Papers

We phylogenetically analyze 705 base pairs of the cytochrome-b gene and 351 amplified fragment length polymorphism (AFLP) bands from populations of the karyotypically variable Wagner’s bonneted bat, Eumops glaucinus, and the Florida bonneted bat, Eumops floridanus (Chiroptera: Molossidae). Three karyotypes have been documented across the range of E. glaucinus, and we report that the karyotype from Cuba is morphologically similar to that from Jamaica. A 4th karyotype is present in specimens from western Ecuador. Three distinct lineages are present in both the cytochrome-b and AFLP trees. One lineage is restricted to western Ecuador and exhibits cytochrome-b …

High Rate Of Recent Transposable Element–Induced Adaptation In Drosophila Melanogaster, Josefa Gonzalez, Kapa Lenkov, Mikhail Lipatov, J. Michael Macpherson, Dmitri A. Petrov

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Although transposable elements (TEs) are known to be potent sources of mutation, their contribution to the generation of recent adaptive changes has never been systematically assessed. In this work, we conduct a genome-wide screen for adaptive TE insertions in Drosophila melanogaster that have taken place during or after the spread of this species out of Africa. We determine population frequencies of 902 of the 1,572 TEs in Release 3 of the D. melanogaster genome and identify a set of 13 putatively adaptive TEs. These 13 TEs increased in population frequency sharply after the spread out of Africa. We argue that …

Simpler Mode Of Inheritance Of Transcriptional Variation In Male Drosophila Melanogaster, Marta Wayne, Marina Telonis-Scott, Lisa Bono, Lawrence G. Harshman, Artyom Kopp, Sergey V. Nuzhdin, Lauren Mcintyre

Lawrence G. Harshman Publications

Sexual selection drives faster evolution in males. The X chromosome is potentially an important target for sexual selection, because hemizygosity in males permits accumulation of alleles, causing tradeoffs in fitness between sexes. Hemizygosity of the X could cause fundamentally different modes of inheritance between the sexes, with more additive variation in males and more nonadditive variation in females. Indeed, we find that genetic variation for the transcriptome is primarily additive in males but nonadditive in females. As expected, these differences are more pronounced on the X chromosome than the autosomes, but autosomal loci are also affected, possibly because of X-linked …

A Simple And Improved Pcr-Based Technique For White-Tailed Deer (Odocoileus Virginianus) Sex Identification, Alec R. Lindsay Ph. D., Jerrold L. Belant

Faculty Works

We describe a simple single-reaction technique for identifying the sex of white-tailed deer (Odocoileus virginianus) based on the PCR amplification of a zinc-finger intron using one pair of primers. Although Sry-coamplification confirmed sex identities, use of the Sry marker was unnecessary due to dimorphic alleles on the X and Y chromosomes at the zinc-finger locus. Insertions in intron 7 of the Y-linked allele (417 bp) make it nearly twice as long as the X-linked allele (236 bp) and thus the amplification products are easily discernable by simple agarose gel electrophoresis. The relatively short size of these products makes them useful …

Shark Bay Prawn And Scallop Fisheries. Draft Review Report, Department Of Fisheries Western Australia

Fisheries Management Papers

In recent times, the Department of Fisheries has received representations from both sectors about the ongoing interaction of the fisheries and their respective management settings. As a result, a decision was made to comprehensively review the fisheries, taking into account matters of fishery sustainability and gear interactions, together with industry economics and market considerations. The review has also addressed research requirements to ensure an appropriate scientific basis for decision-making into the future.

Microarray Challenges In Ecology, Jan E. Kammenga, Michael A. Herman, N. Joop Ouborg, Loretta Johnson, Rainer Bretling

School of Biological Sciences: Faculty Publications

Microarrays are used to measure simultaneously the amount of mRNAs transcribed from many genes. They were originally designed for gene expression profiling in relatively simple biological systems, such as cell lines and model systems under constant laboratory conditions. This poses a challenge to ecologists who increasingly want to use microarrays to unravel the genetic mechanisms underlying complex interactions among organisms and between organisms and their environment. Here, we discuss typical experimental and statistical problems that arise when analyzing genome-wide expression profiles in an ecological context. We show that experimental design and environmental confounders greatly influence the identification of candidate genes …

Sensory Genes And Mate Choice: Evidence That Duplications, Mutations, And Adaptive Evolution Alter Variation In Mating Cue Genes And Their Receptors, Lisa Horth

Biological Sciences Faculty Publications

Fascinating new data, revealed through gene sequencing, comparative genomics, and genetic engineering, precisely establish which genes are involved in mate choice and mating activity—behaviors that are surprisingly understudied from a genetic perspective. Discussed here are some of the recently identified visual and chemosensory genes that are involved in mate choice and mating behavior. These genes’ products are involved in the production, transmission, and receipt of crucial sensory mate-choice cues that affect fitness. This review exposes newfound evidence that alternative splicing, gene-expression pattern changes, and molecular genetic variation in sensory genes are crucial for both intra- and interspecific mate choice and …

Evaluating Genetic Viability Of Pronghorn In Wind Cave National Park, Jonathan A. Jenks, Christopher N. Jacques, Jaret D. Sievers, Robert W. Klaver, R. Terry Bowyer, Daniel E. Roddy

The Prairie Naturalist

The pronghorn (Antilocapra americana) was reintroduced into Wind Cave National Park, South Dakota, in 1914 and thus, has inhabited the Park for almost a century. A decline in the population has raised concern for the continued existence of pronghorn inside Wind Cave National Park. Historically, pronghorn numbers reached greater than 300 individuals in the 1960's but declined to about 30 individuals by 2002. The primary objective of our study was to evaluate genetic characteristics of pronghorn to determine if reduced heterozygosity contributed to the decline of pronghorn in Wind Cave National Park. Microsatellite DNA was collected from 75 …

Chironomid Hemoglobin Genetic Diversity As An Indicator Of The New Jersey Hackensack Meadowlands Wetland Health, Lene Marie De Coursin Jacobs

Seton Hall University Dissertations and Theses (ETDs)

Kearny Marsh located within the Hackensack Meadowlands is a freshwater wetland impacted by multiple environmental stressors from human activity. The marsh is located in the northeastern New Jersey metropolitan area. Chironomid larvae, aquatic larvae of midge fly, were analyzed from two Kearny Marsh sample sites, W9 and W22. A previous sediment analysis and toxicity study characterized heavy metal contaminants the marsh. The data results were applied in this thesis study to determine the correlation between environmental stressors and chironomid genetic diversity. Site W9 sediment was impacted by severe levels of total heavy metal contamination, whereas site W22 had just below …

Demographic Estimates From Y Chromosome Microsatellite Polymorphisms: Analysis Of A Worldwide Sample, J. Michael Macpherson, Sohini Ramachandran, Lisa Diamond, Marcus W. Feldman

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Polymorphisms in microsatellites on the human Y chromosome have been used to estimate important demographic parameters of human history. We compare two coalescent-based statistical methods that give estimates for a number of demographic parameters using the seven Y chromosome polymorphisms in the HGDP-CEPH Cell Line Panel, a collection of samples from 52 worldwide populations. The estimates for the time to the most recent common ancestor vary according to the method used and the assumptions about the prior distributions of model parameters, but are generally consistent with other global Y chromosome studies. We explore the sensitivity of these results to assumptions …

Aphytophagy In The Miletinae (Lycaenidae): Phylogeny, Ecology, And Conservation, John Mathew

Biological Sciences Theses & Dissertations

Less than 1% of all Lepidoptera are aphytophagous; of these, a considerable proportion is found in the family Lycaenidae. The aphytophagous Lycaenidae are believed to have arisen from a mutualistic template involving ant attendance. With this association firmly in place, it is a relatively simple shift to exploitation, either of the ants themselves, through active carnivory on the brood/trophallactic feeding from adults, or by carnivory on ant-tended homopterans, with little to no interference by the ants. Among lycaenids, aphytophagy has arisen several times; most spectacularly in the subfamily Miletinae, where all of the approximately 150 species are presumed or known …

Conservation And Restoration Of Pine Forest Genetic Resources In México, C. Sáenz-Romero, Amy E. Snively, R. Lindig-Cisneros

Student Published Works

Deforestation rates in México are about 670,000 ha/year. This threatens the richness of forest genetic resources in México, causing the disappearance of locally adapted populations and rare and endangered pine species. México is one of the six megadiverse countries in the world, with half of the world’s Pinus species. Pinus is one of the most economically and ecologically important forest genera in México. We suggest that delineation of seed zones and the establishment of a network of Forest Genetic Resource Conservation Units (FGRCUs), linked with forest management and ecological restoration programs will protect this valuable resource. We estimate that FGRCUs …

Inbreeding, Male Diploidy, And Complementary Sex Determination In The Solitary Wasp Euodynerus Foraminatus, Julie Kozaczka Stahlhut

Dissertations

In the insect order Hymenoptera, which includes wasps, bees, and ants, females normally develop from fertilized eggs and are diploid, while males develop from unfertilized eggs and are haploid. Underlying mechanisms of sex determination are more complex and vary among different hymenopteran taxa. One such method is single-locus complementary sex determination, or sl-CSD, in which sex is determined by a single gene locus with many alleles. In species with sl-CSD, diploid individuals that are heterozygous at the sex locus develop as normal females and hemizygous (haploid) individuals as normal males, but diploids homozygous at the sex locus will also develop …

Workshop On Sustainable Development Of Marine Fish Farming In Wa, Peter Rogers, R Fletcher

Fisheries Management Papers

The purpose of this paper is twofold. First to provide an overview of the role of government and more particularly the Department of Fisheries and second to outline government expectations for aquaculture development agencies in the implementation of sustainable development initiatives and the effect this could have on the management of aquaculture within WA.

Processes For The Allocation, Reallocation And Governance Of Resource Access In Connection With A Framework For The Future Management Of Fisheries In Western Australia, Government Of Western Australia Department Of Fisheries

Fisheries Management Papers

This paper outlines the issues associated with developing a framework to deal explicitly with the allocation, reallocation and the governance of access to the fisheries resources of Western Australia.