Evolution of the alcohol dehydrogenase gene family in diploid and tetraploid Gossypium L

Molecular data have had a profound effect on the field of plant evolutionary biology, yet the potential wealth of data stored in low-copy nuclear-encoded genes has been virtually ignored, relative to studies of chloroplast and ribosomal DNA. In this dissertation I present an analysis of a model nuclear-encoded gene family (alcohol dehydrogenase, Adh) in a model organismal system, the cotton genus (Gossypium L., Malvaceae);A combination of PCR- and Southern hybridization-based approaches was employed to isolate, sequence, and map multiple Adh gene family members. Diploid Gossypium contain at least seven Adh loci. Sequence analysis reveals extensive intron variation between loci, and one locus has lost two introns. Evolutionary rates differ between loci and between lineages. Finally, the Adh gene family appears dynamic in that examples of gene duplication, pseudogenization, and elimination were found;We have also employed Adh genes for phylogenetic analyses. We tested the relative utility of seven noncoding cpDNA regions and a pair of homoeologous nuclear genes for resolving recent divergences, using tetraploid cottons as a model system. We sequenced over 7 kb of CPDNA per taxon, yet obtained incomplete phylogenetic resolution. We also sequenced a 1.65-kb region of a homoeologous pair of Adh genes and obtained a robust and completely resolved topology. This enhanced resolution reflects an approximately three- to six-fold increase in evolutionary rate relative to the cpDNA sequences;Finally we have exploited Adh sequences to study intraspecific genetic diversity. We estimated nucleotide diversity for a pair of homoeologous Adh loci in allotetraploid G. hirsutum. Nucleotide diversity for AdhA in Gossypium is lower than for any plant nuclear gene yet described. This low diversity appears to reflect a history severe genetic bottlenecks supplemented by an unusually slow nucleotide substitution rate and an autogamous breeding system. While not statistically supportable, the sum of the observations also suggest differential evolutionary dynamics at each of the homoeologous loci

Use of Nuclear Genes for Phylogeny Reconstruction in Plants

Molecular data have had a profound impact on the field of plant systematics, and the application of DNA-sequence data to phylogenetic problems is now routine. The majority of data used in plant molecular phylogenetic studies derives from chloroplast DNA and nuclear rDNA, while the use of low-copy nuclear genes has not been widely adopted. This is due, at least in part, to the greater difficulty of isolating and characterising low-copy nuclear genes relative to chloroplast and rDNA sequences that are readily amplified with universal primers. The higher level of sequence variation characteristic of low-copy nuclear genes, however, often compensates for the experimental effort required to obtain them. In this review, we briefly discuss the strengths and limitations of chloroplast and rDNA sequences, and then focus our attention on the use of low-copy nuclear sequences. Advantages of low-copy nuclear sequences include a higher rate of evolution than for organellar sequences, the potential to accumulate datasets from multiple unlinked loci, and bi-parental inheritance. Challenges intrinsic to the use of low-copy nuclear sequences include distinguishing orthologous loci from divergent paralogous loci in the same gene family, being mindful of the complications arising from concerted evolution or recombination among paralogous sequences, and the presence of intraspecific, intrapopulational and intraindividual polymorphism. Finally, we provide a detailed protocol for the isolation, characterisation and use of low-copy nuclear sequences for phylogenetic studies

Results of an aqueous source term model for a radiological risk assessment of the Drigg LLW Site, U.K.

A radionuclide source term model has been developed which simulates the biogeochemical evolution of the Drigg low level waste (LLW) disposal site. The DRINK (DRIgg Near field Kinetic) model provides data regarding radionuclide concentrations in groundwater over a period of 100,000 years, which are used as input to assessment calculations for a groundwater pathway. The DRINK model also provides input to human intrusion and gaseous assessment calculations through simulation of the solid radionuclide inventory. These calculations are being used to support the Drigg post closure safety case. The DRINK model considers the coupled interaction of the effects of fluid flow, microbiology, corrosion, chemical reaction, sorption and radioactive decay. It represents the first direct use of a mechanistic reaction-transport model in risk assessment calculations

Cryptic Repeated Genomic Recombination During Speciation in Gossypium gossypioides

The Mexican cotton Gossypium gossypioides is a perplexing entity, with conflicting morphological, cytogenetic, and molecular evidence of its phylogenetic affinity to other American cottons. We reevaluated the evolutionary history of this enigmatic species using 16.4 kb of DNA sequence. Phylogenetic analyses show that chloroplast DNA (7.3 kb), nuclear ribosomal internal transcribed spacers (ITS; 0.69 kb), and unique nuclear genes (8.4 kb) yield conflicting resolutions for G. gossypioides. Eight low-copy nuclear genes provide a nearly unanimous resolution of G. gossypioides as the basalmost American diploid cotton, whereas cpDNA sequences resolve G. gossypioides deeply nested within the American diploid clade sister to Peruvian G. raimondii, and ITS places G. gossypioides in an African (rather than an American) clade. These data, in conjunction with previous evidence from the repetitive fraction of the genome, implicate a complex history for G. gossypioides possibly involving temporally separated introgression events from genetically divergent cottons that are presently restricted to different hemispheres. Based on repetitive nuclear DNA, it appears that G. gossypioides experienced nuclear introgression from an African species shortly after divergence from the remainder of the American assemblage. More recently, hybridization with a Mexican species may have resulted in cpDNA introgression, and possibly a second round of cryptic nuclear introgression. Gossypium gossypioides provides a striking example of the previously unsuspected chimeric nature of some plant genomes and the resulting phylogenetic complexity produced by multiple historical reticulation events

Intron Size and Genome Size in Plants

It has long been known that genomes vary over a remarkable range of sizes in both plants (Bennett, Cox, and Leitch 1997) and animals (Gregory 2001). It also has become evident that across the broad phylogenetic sweep, genome size may be correlated with intron size (Deutsch and Long 1999; Vinogradov 1999; McLysaght et al. 2000), suggesting that some component of genome size evolution takes place within genes. Examples include humans and pufferfish (Fugu), where comparisons of 199 introns in 22 orthologous genes showed that introns in Fugu were on average eight times as small as those in humans, consistent with their ratio of genome sizes (McLysaght et al. 2000). Similarly, Deutsch and Long (1999) tabulated intron sizes across a broad phylogenetic spectrum of eukaryotes and noted a general but weak correlation with genome size, with humans having the most and longest introns (mean of 3.4 kbp) among the 10 taxa studied. Intron size is also correlated with genome size in Drosophila (Moriyama, Petrov, and Hartl 1998), showing that the correlation may extend to more recent divergences

U.S. Pacific Marine Mammal Stock Assessments

Under the 1994 amendments to the Marine Mammal Protection Act, the National Marine Fisheries Service (NMFS) and the U.S. Fish and Wildlife Service (USFWS) were required to produce stock assessment reports for all marine mammal stocks in waters within the U.S. Exclusive Economic Zone. This document contains the stock assessment reports for the U.S. Pacific marine mammal stocks under NMFS jurisdiction. Marine mammal species which are under the management jurisdiction of the USFWS are not included in this report. A separate report containing background, guidelines for preparation, and .a summary of all stock assessment reports is available from the NMFS Office of Protected Resources. This report was prepared by staff of the Southwest Fisheries Science Center, NMFS and the Alaska Fisheries Science Center, NMFS. The information presented here was compiled primarily from published sources, but additional unpublished information was included where it contributed to the assessments. The authors wish to thanks the members of the Pacific Scientific Review Group for their valuable contributions and constructive criticism: Hannah Bernard, Robin Brown, Mark Fraker, Doyle Hanan, John Heyning, Steve Jeffries, Katherine Ralls, Michael Scott, and Terry Wright. Their comments greatly improved the quality of these reports, We also thanks the Marine Mammal Commission, The Humane Society of the United States, The Marine Mammal Center, The Center for Marine Conservation, and Friends of the Sea Otter for their careful reviews and thoughtful comments. Special thanks to Paul Wade of the Office of Protected Resources for his exhaustive review and comments, which greatly enhanced the consistency and technical quality of the reports. Any ommissions or errors are the sole responsibility of the authors. This is a working document and individual stock assessment reports will be updated as new information becomes available and as changes to marine mammal stocks and fisheries occur; therefore, each stock assessment report is intended to be a stand alone document. The authors solicit any new information or comments which would improve future stock assessment reports. This is Southwest Fisheries Science Center Technical Memorandum NOAA-TM-NMFS-SWFSC- 219, July 1995. 11

Spots & stripes: pleomorphic patterning of stem cells via p-ERK-depenendent cell chemotaxis shown by feather morphogenesis & mathematical simulation

A key issue in stem cell biology is the differentiation of homogeneous stem cells towards different fates which are also organized into desired configurations. Little is known about the mechanisms underlying the process of periodic patterning. Feather explants offer a fundamental and testable model in which multi-potential cells are organized into hexagonally arranged primordia and the spacing between primordia. Previous work explored roles of a Turing reaction–diffusion mechanism in establishing chemical patterns. Here we show that a continuum of feather patterns, ranging from stripes to spots, can be obtained when the level of p-ERK activity is adjusted with chemical inhibitors. The patterns are dose-dependent, tissue stage-dependent, and irreversible. Analyses show that ERK activity-dependent mesenchymal cell chemotaxis is essential for converting micro-signaling centers into stable feather primordia. A mathematical model based on short-range activation, long-range inhibition, and cell chemotaxis is developed and shown to simulate observed experimental results. This generic cell behavior model can be applied to model stem cell patterning behavior at large

The On-Orbit Performance of the Galaxy Evolution Explorer

We report the first year on-orbit performance results for the Galaxy Evolution Explorer (GALEX), a NASA Small Explorer that is performing a survey of the sky in two ultraviolet bands. The instrument comprises a 50 cm diameter modified Ritchey-Chretien telescope with a 1.25 degree field of view, selectable imaging and objective grism spectroscopic modes, and an innovative optical system with a thin-film multilayer dichroic beam splitter that enables simultaneous imaging by a pair of photon counting, microchannel plate, delay line readout detectors. Initial measurements demonstrate that GALEX is performing well, meeting its requirements for resolution, efficiency, astrometry, bandpass definition and survey sensitivity.Comment: This paper will be published as part of the Galaxy Evolution Explorer (GALEX) Astrophysical Journal Letters Special Issu

Multiple complementary studies clarify which co-occurring congener presents the greatest hybridization threat to a rare Texas endemic wildflower (Hibiscus dasycalyx: Malvaceae)

The Neches River Rose Mallow (Hibiscus dasycalyx) is a rare wildflower endemic to Texas that is federally protected in the U.S.A. While previous work suggests that H. dasycalyx may be hybridizing with its widespread congeners, the Halberd-leaved Rose Mallow (H. laevis) and the Woolly Rose Mallow (H. moscheutos), this has not been studied in detail. We evaluated the relative threats to H. dasycalyx posed by hybridization with H. laevis and H. moscheutos by 1) examining their relatedness to one another via modern phylogenomic methods, 2) examining their ecological (dis)similarities to one another using ecological niche modeling, and 3) looking for genomic evidence of hybrid-ization among them. Our results suggest that H. dasycalyx is very closely related and ecologically similar to H. laevis, and that H. laevis is interbreeding with H. dasycalyx in the wild. Conversely, H. moscheutos appears to be more distantly related to H. dasycalyx and more ecologi-cally dissimilar, and the two are most likely not hybridizing. For these reasons, we believe that H. laevis poses a greater threat to H. dasycalyxthan H. moscheutos. We offer some hypotheses as to why H. dasycalyx and H. laevis are coming into secondary contact where hybridization can occur