Mapping and sequencing of structural variation from eight human genomes

Genetic variation among individual humans occurs on many different scales, ranging from gross alterations in the human karyotype to single nucleotide changes. Here we explore variation on an intermediate scale--particularly insertions, deletions and inversions affecting from a few thousand to a few million base pairs. We employed a clone-based method to interrogate this intermediate structural variation in eight individuals of diverse geographic ancestry. Our analysis provides a comprehensive overview of the normal pattern of structural variation present in these genomes, refining the location of 1,695 structural variants. We find that 50% were seen in more than one individual and that nearly half lay outside regions of the genome previously described as structurally variant. We discover 525 new insertion sequences that are not present in the human reference genome and show that many of these are variable in copy number between individuals. Complete sequencing of 261 structural variants reveals considerable locus complexity and provides insights into the different mutational processes that have shaped the human genome. These data provide the first high-resolution sequence map of human structural variation--a standard for genotyping platforms and a prelude to future individual genome sequencing projects.     

The Care of Our Hybrid Selves: Ethics in Times of Technical Mediation

What can the art of living after Foucault contribute to ethics in relation to the mediation of human existence by technology? To develop the relation between technical mediation and ethics, firstly the theme of technical mediation is elaborated in line with Foucault’s notion of ethical problematization. Every view of what technology does to us at the same time expresses an ethical concern about technology. The contemporary conception of technical mediation tends towards the acknowledgement of ongoing hybridization, not ultimately good or bad but ambivalent, which means for us the challenge of taking care of ourselves as hybrid beings. Secondly, the work of Foucault provides elements for imagining this care for our hybrid selves, notably his notions of freedom as a practice and of the care of the self. A conclusions about technical mediation and ethics is that whereas the approaches of the delegation of morality to technology by Latour and mediated morality by Verbeek see technical mediation of behavior and moral outlook as an answer in ethics, this should rather be considered the problem that ethics is about.     

Avian use of desert wildlife water developments as determined by remote videography

In the desert Southwest, migrating birds have been documented using upland habitat and xeroriparian washes as well as riparian areas. Yet aside from the river corridors, natural water sources (e.g., natural rock tanks [tinajas], springs, and ephemeral washes) in upland areas are scarce. Because of this scarcity, state and federal resource managers augmented water sources throughout the Southwest by constructing permanent wildlife water developments with the intention of enhancing game populations. However, despite these increases in free-standing water, there is a paucity of information on the use of water by birds during migration. Our objectives were to document use of these wildlife water developments by resident and migratory songbirds and assess the effectiveness of monitoring these species using remote color videography. We placed color video cameras at 2 wildlife water developments in southwestern Arizona during the spring and fall of 2004. Although we observed more use by migrants during spring than fall, overall use by migratory birds was low. However, the wildlife water developments were frequently used by resident birds. Remote videography provided continuous information on daily and seasonal patterns of bird use at wildlife water catchments with negligible disturbance by observers, yet for passerines, we felt that the benefits of remote videography did not justify the high cost of equipment purchase, installation, maintenance, and data processing.     

Influence of experimental habitat manipulations on a desert rodent population in southern Utah

This paper addresses how habitat manipulations in a black sagebrush ( Artemisia nova ) -dominated area, John's Valley of southern Utah, affected resident desert rodent populations. Rodents studied included the deer mouse ( Peromyscus maniculatus ), Great Basin pocket mouse ( Perognathus parvus ), sagebrush vole ( Lagurus curtatus ), Ord's kangaroo rat ( Dipodomys ordii ), and least chipmunk ( Eutamias minimus ). The experimental design involved analyses of treatment and control (nontreatment) plots rather than pre- and posttreatment of all plots. Habitat manipulations emphasized cutting of shrubs (rotobeating), treatment of plants with a herbicide (2,4-D), and reseeding with a mixture of grasses, forbs, and shrubs. Posttreatment trapping indicated the deer mouse was the most abundant rodent in treatment and control plots. Data indicate the prescribed habitat treatments had no significant negative affects on the deer mouse demes on the control or treatment plots. Habitat treatments may have negatively impacted recruitment in pocket mice. Least chipmunks were not captured in plots treated by rotobeating. Our habitat manipulations may have contributed to interspecific competition in this rodent community through the reduction of both food and cover.     

Floristic analysis of the southwestern United States

A study was made of the distributions of native, terrestrial, vascular plants occurring in 50 local floras from throughout the Basin and Range and Colorado Plateau physiographic provinces of the southwestern United States. The objectives of the study were to objectively define and describe the floristic elements-assemblages of species with roughly coincident geographic distribution-occurring in the southwestern United States and to determine what such assemblages reveal about the floristic history of the region. The total flora (native, terrestrial species only) of the Southwest is estimated at 5,458 species, 77% of which were recorded in 1 or more of the local floras. Nearly 22% of these species are endemic to the study region. A majority of the species were found to be relatively rare. The average range of a species included only 4 floras, and 90% of the species were recorded from 11 or fewer floras; only 81 species (1.5%) were recorded from 50% or more of the floras. Trees constitute 2% of the regional flora and have the widest average distribution; perennial herbs constitute 59% of the flora and have the most restricted distributions.  Factor analysis was used to identify seven floristic elements for the region: a Great Basin element, a Mojavean element, a Colorado Plateau element, a Chihuahuan element, an Apachian element, and a Mogollon element. This factor analysis solution was shown to satisfy criteria of interpretability and consistency. The Mojavean, Colorado Plateau, and Apachian elements are believed to be autochthonous. The other four elements show high overlap in species composition with one or more adjacent regions. Each floristic element is mapped to show its geographic form and distribution. Analysis of these maps shows how the existence of objectively defined floristic elements is not contradictory to either the individualistic view of the distribution of a species or local continuity of vegetation and flora. The rarity of the majority of species and the clear association of floristic elements with rather narrowly circumscribed Holocene environments suggests that many Southwestern species have migrated little and are of rather recent, probably postglacial origin. Geographic “principles” derived from the distribution patterns of relatively few, widespread, dominant, usually woody species may not be applicable to entire, regional floras.       

Blockage and recovery of nitrification in soils exposed to acetylene

Acetylene gas is very useful in laboratory and in situ assay procedures for nitrogen fixation and denitrification. There is concern, however, that measurements of denitrification may be underestimated because nitrification, a major source of nitrate, is inhibited by C 2 H 2 . The objective of this study was to examine the effects of C 2 H 2 partial pressure and length of exposure time on nitrification in soils. Acetylene partial pressures of 0.1, 1.0, and 10.0 kPa were found to effectively inhibit nitrification in soil samples incubated in the laboratory. Both the partial pressure of C 2 H 2 and the length of exposure time were found to affect the recovery time of nitrification in soil samples. Nitrification recovered within seven days in samples exposed to 0.1 and 1.0 kPa C 2 H 2 for only 24 hours. The recovery of nitrification in samples exposed to 10.0 kPa C 2 H 2 for 24 hours or to 0.1 and 1.0 kPa C 2 H 2 for 216 hours was delayed for an additional seven days, however.     

Influence of substrate size, Cladophora , and caddisfly pupal cases on colonization of macroinvertebrates in Sagehen Creek, California

Colonization of stream macroinvertebrates onto artificial substrates was examined in Sagehen Creek, California, during 1993. Substrate size and presence or absence of pupal cases of the caddisfly Anagapetus (Glossosomatidae) were examined as possible influences on macroinvertebrate colonization. Macroinvertebrates were collected from substrates after 60 d of incubation and identified to the lowest feasible taxonomic unit. Dry weight of the filamentous green alga Cladophora also was determined for each substrate. A general linear model indicated a significant positive relationship between both substrate size and presence of pupal cases on richness ( P Anagapetus cases on Micrasema bactro , Epeorus , and Rhyacophila sp. 1, and of substrate size on Hydropsyche occidentalis and Epeorus . Neither cases nor substrate size had a significant effect on Cladophora density ( P > 0.05). There were significant negative correlations between Cladophora density and both Shannon H′ and J′ indices. There were significant positive relationships between Cladophora density with Baetis , Simulium , and Chironomidae density. Combined main effects of substrate size, Anagapetus pupal cases, and Cladophora have dynamic influences on this macroinvertebrate fauna. This study demonstrates the complex interplay of biotic and abiotic factors that determine macroinvertebrate distribution and abundance in this system.     

Variance and replenishment of nectar in wild and greenhouse populations of Mimulus

We compared nectar production in wild populations and greenhouse-grown populations of the monkey flower species of section Erythranthe of the genus Mimulus . Nectar was sampled from over 1000 flowers. For each flower the volume of nectar was measured with a calibrated micropipette and the percentage of sugar with a hand refractometer. Percentage of sugar varied little from flower to flower in both field and greenhouse studies, but volume varied markedly from flower to flower in field studies and even more in greenhouse studies. This high variance in nectar volumes appears to be intrinsic. The amount of nectar in greenhouse populations tended to increase with time in the absence of pollinators. The amount of nectar in field populations tended to remain the same to pollinator withdrawals. The latter conclusion was corroborated by sampling nectar at 2-h intervals all day and comparing the total volume produced by a flower to the volume of nectar produced in control flowers sampled only at the end of the day.     

Plant species richness at different scales in native and exotic grasslands in southeastern Arizona

Species richness in Madrean mixed-grass prairies dominated by native or exotic species in southeastern Arizona was characterized at the community and point scales using ten 1-m 2 quadrats nested within each of eight 1000-m 2 plots. In the 1000-m 2 plots average richness was significantly higher in oak savanna (OS, 121.0 species) than in exotic grassland on mesa tops (EMT, 52.0 species), whereas native grassland on mesa slopes (NMS, 92.5 species) and native grassland on mesa tops (NMT, 77.0 species) did not differ significantly in richness from OS or EMT. When richness was partitioned by life form, EMT was notably poorer than other community types in species of perennial grasses, perennial herbs, and summer annuals. In the 1-m 2 quadrats, OS (21.2 species), NMS (20.9 species), and NMT (20.7 species) were significantly richer than EMT (5.9 species). Cover in 1-m 2 plots was significantly higher in EMT than in NMT, NMS, or OS. Species richness at the point scale showed a unimodal relation to canopy cover, with cover accounting for 30% of the variation in number of species in 1-m2 quadrats. Competitive exclusion and allelopathy have perhaps limited species richness at the point scale in exotic grassland. There was no evidence of a species-pool effect between point and community scales, but such an effect between community and landscape scales was supported. Madrean mixed-grass prairies are landscapes with high species richness in comparison to other grassland types in North America, providing a large pool of potential colonizing species at the community scale. Beta-diversity (between communities) within the landscape of the Appleton-Whittell Research Ranch was consequently high despite a relative lack of habitat diversity.