Genetics and Genomics Commons^™

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 …

Characterization Of 24 Microsatellite Loci In Delta Smelt, Hypomesus Transpacificus, And Their Cross-Species Amplification In Two Other Smelt Species Of The Osmeridae Family, Kathleen M. Fisch, Jessica Lynn Petersen, Melinda R. Baerwald, John K. Pedroia, Bernie May

Department of Animal Science: Faculty Publications

We characterized 24 polymorphic tetranucleotide microsatellite loci for delta smelt (Hypomesus transpacificus) endemic to the San Francisco Bay Estuary, California, USA. Screening of samples (n = 30) yielded two to 26 alleles per locus with observed levels of heterozygosity ranging from 0.17 to 1.0. Only one locus deviated from Hardy–Weinberg equilibrium, suggesting these individuals originate from a single panmictic population. Linkage disequilibrium was found in two pairs of loci after excluding the locus out of Hardy–Weinberg equilibrium. Twenty-two primer pairs cross-amplified in wakasagi smelt (Hypomesus nipponensis), and 15 primer pairs cross-amplified in longfin smelt ( …

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.

2009 Report : A Multi-Refuge Program To Evaluate The Effect Of Ungulate Browsing On Habitat, Richard B. Keigley, Jeffrey Warren, Wayne J. King

Aspen Bibliography

No abstract provided.

An Aspen Success Story : 2009 Aspen Monitoring Report, James L. Robertson

Aspen Bibliography

No abstract provided.

Primate Phylogenomics: Developing Numerous Nuclear Non-Coding, Non-Repetitive Markers For Ecological And Phylogenetic Applications And Analysis Of Evolutionary Rate Variation, Zuogang Peng, Navin Elango, Derek E. Wildman, Soojin V. Yi

Wayne State University Associated BioMed Central Scholarship

Abstract

Background

Genetic analyses are often limited by the availability of appropriate molecular markers. Markers from neutrally evolving genomic regions may be particularly useful for inferring evolutionary histories because they escape the constraints of natural selection. For the majority of taxa however, obtaining such markers is challenging. Advances in genomics have the potential to alleviate the shortage of neutral markers. Here we present a method to develop numerous markers from putatively neutral regions of primate genomes.

Results

We began with the available whole genome sequences of human, chimpanzee and macaque. Using computational methods, we identified a total of 280 potential …

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 …

Letter From The Dean, Lalit Verma

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

No abstract provided.

Pervasive Hitchhiking At Coding And Regulatory Sites In Humans, James J. Cai, J. Michael Macpherson, Guy Sella, Dmitri A. Petrov

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Much effort and interest have focused on assessing the importance of natural selection, particularly positive natural selection, in shaping the human genome. Although scans for positive selection have identified candidate loci that may be associated with positive selection in humans, such scans do not indicate whether adaptation is frequent in general in humans. Studies based on the reasoning of the MacDonald–Kreitman test, which, in principle, can be used to evaluate the extent of positive selection, suggested that adaptation is detectable in the human genome but that it is less common than in Drosophila or Escherichia coli. Both positive and purifying …

Ecological Genomics Of Nematode Community Interactions: Model And Non-Model Approaches, Michael A. Herman, Joseph D. Coolon, Kenneth L. Jones, Timothy Todd

School of Biological Sciences: Faculty Publications

The effects of human-induced environmental change are evident at multiple levels of biological organization. To date, most environmental change studies have focused on effects at the ecosystem, community, and organismal levels. However, the ultimate controls of biological responses are located in the genome. Thus, genetic and genomic studies of organismal responses to environmental changes are necessary. Recent advances in genome analysis now make such analyses possible. In this chapter we describe a research approach and program that can begin to span this gap by using genome-enabled approaches to characterize organismal changes and then employing a genetically tractable model organism to …

Geographic Variation In Malarial Parasite Lineages In The Common Yellowthroat (Geothlypis Trichas), K. M. Pagenkopp, John Klicka, K. L. Durrant, J. C. Garvin, R. C. Fleischer

Ornithology Program (HRC)

Our current understanding of migration routes of many birds is limited and researchers have employed various methods to determine migratory patterns. Recently, parasites have been used to track migratory birds. The objective of this study was to determine whether haemosporidian parasite lineages detect significant geographic structure in common yellowthroats (Geothlypis trichas). We examined liver tissue or blood from 552 birds sampled from multiple locations throughout the continental United States, southern Canada, and the Bahamas. We found a 52.7% overall prevalence of haematozoan infection. We identified 86.1% of these infections to genus: 81% were Plasmodium; 5% were Haemoproteus …

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 …

Marketing Of Forest Reproductive Material: The Use Of Microsatellites For Identification Of Registered Tree Clones In Finland, Leena Koviuranta, Kari Leinonen, Pertti Pulkkinen

Aspen Bibliography

According to the current legislation on the marketing of forest reproductive material, tree clones marketed in the EU must have certain traits which make them identifiable, and these traits must have been accepted and registered by an official body. Due to this obligation, there is a need for reliable, functional and practicable methods for specifying these distinctive characters. We have developed a clone identification method for European and hybrid aspens and curly birch, based on nuclear microsatellites, which can be used for determining the distinctive characters mentioned in the directive. For aspens, we have used 18 loci, of which nine …

Micrornas And The Advent Of Vertebrate Morphological Complexity, Alysha M. Heimberg, Lorenzo F. Sempere, Vanessa N. Moy, Phillip C. J. Donoghue, Kevin J. Peterson

Dartmouth Scholarship

The causal basis of vertebrate complexity has been sought in genome duplication events (GDEs) that occurred during the emergence of vertebrates, but evidence beyond coincidence is wanting. MicroRNAs (miRNAs) have recently been identified as a viable causal factor in increasing organismal complexity through the action of these ≈22-nt noncoding RNAs in regulating gene expression. Because miRNAs are continuously being added to animalian genomes, and, once integrated into a gene regulatory network, are strongly conserved in primary sequence and rarely secondarily lost, their evolutionary history can be accurately reconstructed. Here, using a combination of Northern analyses and genomic searches, we show …

Historic Genetic Structuring And Paraphyly Within The Great-Tailed Grackle, Jeffrey M. Dacosta, Walter Wehtje, John Klicka

Ornithology Program (HRC)

The Great-tailed Grackle (Quiscalus mexicanus) and Boat-tailed Grackle (Q. major) are sister species that have expanded their ranges during historical times. This expansion has created an area of sympatry between these species in Texas and Louisiana, and between distinctive Great-tailed Grackle subspecies in the southwestern United States and northern Mexico. We investigated the evolutionary histories of both species using mitochondrial DNA sequence data and modern phylogenetic methods. Our results reveal genetic structure within Great-tailed, but not Boat-tailed Grackles. Great-tailed Grackles are separated into two clades, but range expansion in the north has led to secondary contact …

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 …

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 …

Validation Case Study : Treatment Effectiveness In Aspen Vegetation Type : A Comparison Of Two Types Of Treatments On The Manti-La Sal National Forest, Diane M. Cote

Aspen Bibliography

No abstract provided.

Molecular Evolution Of The Cytochrome C Oxidase Subunit 5a Gene In Primates, Monica Uddin, Juan C. Opazo, Derek E. Wildman, Chet C. Sherwood, Patrick R. Hof, Morris Goodman, Lawrence I. Grossman

Wayne State University Associated BioMed Central Scholarship

Abstract

Background

Many electron transport chain (ETC) genes show accelerated rates of nonsynonymous nucleotide substitutions in anthropoid primate lineages, yet in non-anthropoid lineages the ETC proteins are typically highly conserved. Here, we test the hypothesis that COX5A, the ETC gene that encodes cytochrome c oxidase subunit 5A, shows a pattern of anthropoid-specific adaptive evolution, and investigate the distribution of this protein in catarrhine brains.

Results

In a dataset comprising 29 vertebrate taxa, including representatives from all major groups of primates, there is nearly 100% conservation of the COX5A amino acid sequence among extant, non-anthropoid placental mammals. The most recent common …

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 …

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 …

A Checklist Of The Amphibians And Reptiles Of México, Ernest A. Liner

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

No abstract provided.

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.

A Molecular Evaluation Of The North American “Grassland” Sparrow Clade, John Klicka, Garth M. Spellman

Ornithology Program (HRC)

Because they share several morphological and ecological characters, the North American sparrow (Emberizidae) genera Ammodramus, Passerculus, and Xenospiza have historically been considered members of a well-defined “grassland” sparrow assemblage. Relationships among the 11 members of this group have been the subject of much taxonomic debate, yet no comprehensive molecular assessment of relationships has been done. We investigated these relationships using mitochondrial DNA sequence data that included complete cytochrome-b and ND2 genes. Phylogenetic reconstructions derived via parsimony, likelihood, and Bayesian methods were congruent. The grassland sparrows, as presently configured, are polyphyletic. Pooecetes gramineus, Amphispiza belli (but not A. …

Regressive Evolution In The Mexican Cave Tetra, Astyanax Mexicanus, Meredith E. Protas, Melissa Conrad, Joshua B. Gross, Clifford Tabin, Richard Borowsky

Collected Faculty Scholarship

Cave adapted animals generally have reduced pigmentation and eyes, but the evolutionary forces driving the reductions are unknown; Darwin famously questioned the role of natural selection in eye loss in cave fishes; “As it is difficult to imagine that eyes, although useless, could be in any way injurious to animals living in darkness, I attribute their loss wholly to disuse” [1]. We studied the genetic basis of this phenomenon in the Mexican cave tetra, Astyanax mexicanus, by mapping the quantitative trait loci (QTL) determining differences in eye/lens sizes and melanophore number between cave and surface fish. In addition, we mapped …

Maptogenome: A Comparative Genomic Tool That Aligns Transcript Maps To Sequenced Genomes, Srikrishna Putta, Jeramiah J. Smith, Chuck Staben, S. Randal Voss

Biology Faculty Publications

Efforts to generate whole genome assemblies and dense genetic maps have provided a wealth of gene positional information for several vertebrate species. Comparing the relative location of orthologous genes among these genomes provides perspective on genome evolution and can aid in translating genetic information between distantly related organisms. However, large-scale comparisons between genetic maps and genome assemblies can prove challenging because genetic markers are commonly derived from transcribed sequences that are incompletely and variably annotated. We developed the program MapToGenome as a tool for comparing transcript maps and genome assemblies. MapToGenome processes sequence alignments between mapped transcripts and whole genome …

Ocpat: An Online Codon-Preserved Alignment Tool For Evolutionary Genomic Analysis Of Protein Coding Sequences, Guozhen Liu, Monica Uddin, Munirul Islam, Morris Goodman, Lawrence I. Grossman, Roberto Romero, Derek E. Wildman

Wayne State University Associated BioMed Central Scholarship

Abstract

Background

Rapidly accumulating genome sequence data from multiple species offer powerful opportunities for the detection of DNA sequence evolution. Phylogenetic tree construction and codon-based tests for natural selection are the prevailing tools used to detect functionally important evolutionary change in protein coding sequences. These analyses often require multiple DNA sequence alignments that maintain the correct reading frame for each collection of putative orthologous sequences. Since this feature is not available in most alignment tools, codon reading frames often must be checked manually before evolutionary analyses can commence.

Results

Here we report an online codon-preserved alignment tool (OCPAT) that generates …

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 …