University of California, Davis

About: University of California, Davis is a education organization based out in Davis, California, United States. It is known for research contribution in the topics: Population & Gene. The organization has 78770 authors who have published 180033 publications receiving 8064158 citations. The organization is also known as: UC Davis & UCD.

Comparative phylogeography of unglaciated eastern North America.

Abstract: Regional phylogeographical studies involving co-distributed animal and plant species have been conducted for several areas, most notably for Europe and the Pacific Northwest of North America. Until recently, phylogeographical studies in unglaciated eastern North America have been largely limited to animals. As more studies emerge for diverse lineages (including plants), it seems timely to assess the phylogeography across this region: (i) comparing and contrasting the patterns seen in plants and animals; (ii) assessing the extent of pseudocongruence; and (iii) discussing the potential applications of regional phylogeography to issues in ecology, such as response to climatic change. Unglaciated eastern North America is a large, geologically and topographically complex area with the species examined having diverse distributions. Nonetheless, some recurrent patterns emerge: (i) maritime - Atlantic vs. Gulf Coast; (ii) Apalachicola River discontinuity; (iii) Tombigbee River discontinuity; (iv) the Appalachian Mountain discontinuity; (v) the Mississippi River discontinuity; and (vi) the Apalachicola River and Mississippi River discontinuities. Although initially documented in animals, most of these patterns are also apparent in plants, providing support for phylogeographical generalizations. These patterns may generally be attributable to isolation and differentiation during Pleistocene glaciation, but in some cases may be older (Pliocene). Molecular studies sometimes agree with longstanding hypotheses of glacial refugia, but also suggest additional possible refugia, such as the southern Appalachian Mountains and areas close to the Laurentide Ice Sheet. Many species exhibit distinct patterns that reflect the unique, rather than the shared, aspects of species' phylogeographical histories. Furthermore, similar modern phylogeographical patterns can result from different underlying causal factors operating at different times (i.e. pseudocongruence). One underemphasized component of pseudocongruence may result from the efforts of researchers to categorize patterns visually - similar patterns may, in fact, not fully coincide, and inferring agreement may obscure the actual patterns and lead to erroneous conclusions. Our modelling analyses indicate no clear spatial patterning and support the hypothesis that phylogeographical structure in diverse temperate taxa is complex and was not shaped by just a few barriers.

The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families.

Abstract: Metagenomics projects based on shotgun sequencing of populations of micro-organisms yield insight into protein families. We used sequence similarity clustering to explore proteins with a comprehensive dataset consisting of sequences from available databases together with 6.12 million proteins predicted from an assembly of 7.7 million Global Ocean Sampling (GOS) sequences. The GOS dataset covers nearly all known prokaryotic protein families. A total of 3,995 medium- and large-sized clusters consisting of only GOS sequences are identified, out of which 1,700 have no detectable homology to known families. The GOS-only clusters contain a higher than expected proportion of sequences of viral origin, thus reflecting a poor sampling of viral diversity until now. Protein domain distributions in the GOS dataset and current protein databases show distinct biases. Several protein domains that were previously categorized as kingdom specific are shown to have GOS examples in other kingdoms. About 6,000 sequences (ORFans) from the literature that heretofore lacked similarity to known proteins have matches in the GOS data. The GOS dataset is also used to improve remote homology detection. Overall, besides nearly doubling the number of current proteins, the predicted GOS proteins also add a great deal of diversity to known protein families and shed light on their evolution. These observations are illustrated using several protein families, including phosphatases, proteases, ultraviolet-irradiation DNA damage repair enzymes, glutamine synthetase, and RuBisCO. The diversity added by GOS data has implications for choosing targets for experimental structure characterization as part of structural genomics efforts. Our analysis indicates that new families are being discovered at a rate that is linear or almost linear with the addition of new sequences, implying that we are still far from discovering all protein families in nature.

"Some of My Best Friends" Intergroup Contact, Concealable Stigma, and Heterosexuals' Attitudes Toward Gay Men and Lesbians

Abstract: In a two-wave national telephone survey, a probability sample of English-speaking adults indicated their attitudes toward gay men at Wave 1 (1990-91; n = 538) and toward both gay men and lesbians approximately 1 year later (n = 382 at Wave 2). At Wave 1, heterosexuals reporting interpersonal contact (31.3%) manifested more positive attitudes toward gay men than those without contact. Their attitudes were more favorable to the extent that they reported more relationships, closer relationships, and receiving direct disclosure about another's homosexuality. At Wave 2, these findings were generally replicated for attitudes toward lesbians as well as gay men. Cross-wave analyses suggest a reciprocal relationship between contact and attitudes. Theoretical and policy implications of the results are discussed, with special attention to the role of interpersonal disclosure in reducing stigma based on a concealable status.

Genome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landraces and cultivars.

Abstract: Domesticated crops experience strong human-mediated selection aimed at developing high-yielding varieties adapted to local conditions. To detect regions of the wheat genome subject to selection during improvement, we developed a high-throughput array to interrogate 9,000 gene-associated single-nucleotide polymorphisms (SNP) in a worldwide sample of 2,994 accessions of hexaploid wheat including landraces and modern cultivars. Using a SNP-based diversity map we characterized the impact of crop improvement on genomic and geographic patterns of genetic diversity. We found evidence of a small population bottleneck and extensive use of ancestral variation often traceable to founders of cultivars from diverse geographic regions. Analyzing genetic differentiation among populations and the extent of haplotype sharing, we identified allelic variants subjected to selection during improvement. Selective sweeps were found around genes involved in the regulation of flowering time and phenology. An introgression of a wild relative-derived gene conferring resistance to a fungal pathogen was detected by haplotype-based analysis. Comparing selective sweeps identified in different populations, we show that selection likely acts on distinct targets or multiple functionally equivalent alleles in different portions of the geographic range of wheat. The majority of the selected alleles were present at low frequency in local populations, suggesting either weak selection pressure or temporal variation in the targets of directional selection during breeding probably associated with changing agricultural practices or environmental conditions. The developed SNP chip and map of genetic variation provide a resource for advancing wheat breeding and supporting future population genomic and genome-wide association studies in wheat.

The role of highly unsaturated fatty acids in aquatic foodweb processes

Abstract: 1. Polyunsaturated fatty acids (PUFA) are almost exclusively synthesized by plants. Animals can convert from one form of PUFA to another through elongation and desaturation, but very few can synthesize PUFA de novo. PUFA play an important role in regulating cell membrane properties, serve as precursors for important animal hormones and are essential for animals. 2. In aquaculture studies, highly unsaturated fatty acids (HUFA), a subset of PUFA, have been found to be critical for maintaining high growth, survival and reproductive rates and high food conversion efficiencies for a wide variety of marine and freshwater organisms. 3. The plankton literature suggests high food-quality algae species are rich in HUFA and low food-quality algae are poor in HUFA. Adding semi-pure emulsions of HUFA to algae monocultures can markedly increase the growth rates of zooplankton feeding on these mixtures. 4. A study measuring zooplankton biomass accrual when feeding on natural phytoplankton found a strong correlation between phytoplankton HUFA (specifically eicosapentaenoic acid) content and herbivorous zooplankton production. 5. The aquatic ecology literature suggests that planktonic foodwebs with high HUFA content phytoplankton have high zooplankton to phytoplankton biomass ratios, while systems with low HUFA phytoplankton have low zooplankton biomass. Also, the seasonal succession of plankton in many temperate lakes follows patterns tied to phytoplankton HUFA content, with intense zooplankton grazing and ‘clear-water-phases’ characteristic of periods when the phytoplankton is dominated by HUFA-rich species. 6. Herbivorous zooplankton production is constrained by the zooplankton’s ability to ingest and digest phytoplankton. It is becoming increasingly clear, however, that much of the phytoplankton which is assimilated may be nutritionally inadequate. HUFA may be key nutritional constituents of zooplankton diets, and may determine energetic efficiency across the plant–animal interface, secondary production and the strength of trophic coupling in aquatic pelagic foodwebs.