Multiple source pools and dispersal barriers for Galapagos plant species distribution

We reexamined geographic factors explaining the number of plant species on islands in the Galapagos Archipelago. We hypothesized that plant species richness (S) was related to the number of source pools and that plant species dispersal preferentially followed direct, oceanic pathways. To test different dispersal pathways from multiple source pools, the total number of islands within a given dispersal radius (i) was posed as the sum of the number of line-of-sight islands (C-i) and of the number of islands without line-of-sight connection (B-i). In partial regression analyses, controlling for nearest island area (A(2)) and for recipient island elevation (E) and area (InA), C-i and C-i x E were found to be positively correlated with S in the Galapagos for nearly all dispersal ranges from 10 km to 419 km (maximum inter-island separation). In contrast, B-i x E was negatively correlated with S at the longest dispersal ranges. The connectivity index, C-i, multiplied by elevation, E, explained more variation in S in the Galapagos than prior regression models using additive forms of E, InA, A(2), and isolation from the central island. Using the variables C-i x E and InA, multiple-regression models explained \u3e 90% of the variance in both endemic and total plant species richness in the Galapagos Archipelago

Differential Effects of Understory and Overstory Gaps on Tree Regeneration

Gaps in the forest canopy can increase the diversity of tree regeneration. Understory shrubs also compete with tree seedlings for limited resources and may depress tree recruitment. We compared effects of shrub removal and canopy windthrow gaps on seedling recruitment and understory resource levels. Shrub removal, with the canopy left intact, was associated with increased levels of understory light and soil moisture and coincided with increased species richness and diversity of tree regeneration compared to both control plots and canopy gaps. Canopy windthrow gaps, however, resulted in a more than 500 fold increase in soil nitrate concentrations, and seedling growth rates that were twice as high as that observed with shrub removal. Our results suggest that gaps in the understory shrub layer and the overstory canopy may have complementary effects on resource availability with corresponding benefits to seedling establishment and growth

How Well has Land-Use Planning Worked Under Different Governance Regimes? A Case Study in the Portland, OR-Vancouver, WA Metropolitan Area, USA

We examine land use planning outcomes over a 30-year period in the Portland, OR-Vancouver, WA (USA) metropolitan area. The four-county study region enables comparisons between three Oregon counties subject to Oregon’s 1973 Land Use Act (Senate Bill 100) and Clark County, WA which implemented land use planning under Washington’s 1990 Growth Management Act. We describe county-level historical land uses from the mid-1970s to the mid-2000s, including low-density residential and urban development, both outside and inside of current urban growth boundaries. We use difference-in-differences models to test whether differences in the proportions of developed land resulting from implementation of urban growth boundaries are statistically significant and whether they vary between Oregon and Washington. Our results suggest that land use planning and urban growth boundaries now mandated both in Oregon and Washington portions of the study area have had a measurable and statistically significant effect in containing development and conserving forest and agricultural lands in the Portland-Vancouver metropolitan area. Our results also suggest, however, that these effects differ across the four study-area counties, likely owing in part to differences in counties’ initial levels of development, distinctly different land use planning histories, and how restrictive their urban growth boundaries were drawn

Combining and Aggregating Environmental Data for Status and Trend Assessments: Challenges and Approaches

Increasingly, natural resource management agencies and nongovernmental organizations are sharing monitoring data across geographic and jurisdictional boundaries. Doing so improves their abilities to assess local-, regional-, and landscape-level environmental conditions, particularly status and trends, and to improve their ability to make short-and long-term management decisions. Status monitoring assesses the current condition of a population or environmental condition across an area. Monitoring for trends aims at monitoring changes in populations or environmental condition through time. We wrote this paper to inform agency and nongovernmental organization managers, analysts, and consultants regarding the kinds of environmental data that can be combined with suitable techniques and statistically aggregated for new assessments. By doing so, they can increase the (1) use of available data and (2) the validity and reliability of the assessments. Increased awareness of the difficulties inherent in combining and aggregating data for local-and regional-level analyses can increase the likelihood that future monitoring efforts will be modified and/or planned to accommodate data from multiple sources

Urban and Rural-residential Land Uses: Their Role in Watershed Health and the Rehabilitation of Oregon’s Wild Salmonids

This technical report by the Independent Multidisciplinary Science Team (IMST) is a comprehensive review of how human activities in urban and rural-residential areas can alter aquatic ecosystems and resulting implications for salmonid recovery, with a geographic focus on the state of Oregon. The following topics are considered in the form of science questions, and comprise the major components of this report: The effects of urban and rural-residential development on Oregon’s watersheds and native wild salmonids. Actions that can be used to avoid or mitigate undesirable changes to aquatic ecosystems near developing urban and rural-residential areas. The benefits and pitfalls of salmonid habitat rehabilitation within established urban or rural-residential areas. Suggested research and monitoring focus areas that will facilitate the recovery of salmonid populations affected by development. The fundamental concepts presented in this report should be applicable to most native salmonid populations across the state. IMST encourages managers and policy-makers with interest in a specific species or geographic region to carefully research local ecological conditions, as well as specific life history characteristics of salmonids in the region. Conserving watershed condition and salmonids in the face of increasing development requires consideration of two distinct sets of processes. First are the human social and economic processes that drive patterns in land use change. Second are the ecological processes, altered by land use, that underlie salmonid habitat changes. This report focuses on the latter and summarizes the effects of rural-residential and urban development on native, wild salmonid populations and the watersheds upon which they depend

Combining and aggregating environmental data for status and trend assessments: challenges and approaches

Increasingly, natural resource management agencies and nongovernmental organizations are sharing monitoring data across geographic and jurisdictional boundaries. Doing so improves their abilities to assess local-, regional-, and landscape-level environmental conditions, particularly status and trends, and to improve their ability to make short-and long-term management decisions. Status monitoring assesses the current condition of a population or environmental condition across an area. Monitoring for trends aims at monitoring changes in populations or environmental condition through time. We wrote this paper to inform agency and nongovernmental organization managers, analysts, and consultants regarding the kinds of environmental data that can be combined with suitable techniques and statistically aggregated for new assessments. By doing so, they can increase the (1) use of available data and (2) the validity and reliability of the assessments. Increased awareness of the difficulties inherent in combining and aggregating data for local-and regional-level analyses can increase the likelihood that future monitoring efforts will be modified and/or planned to accommodate data from multiple sources.Keywords: Lurking variable, Change of support problem, Simpson's paradox, Modifiable areal unit problem, Data aggregation, Environmental monitorin

Water Supply, Demand, and Quality Indicators for Assessing the Spatial Distribution of Water Resource Vulnerability in the Columbia River Basin

We investigated water resource vulnerability in the US portion of the Columbia River basin (CRB) using multiple indicators representing water supply, water demand, and water quality. Based on the US county scale, spatial analysis was conducted using various biophysical and socio-economic indicators that control water vulnerability. Water supply vulnerability and water demand vulnerability exhibited a similar spatial clustering of hotspots in areas where agricultural lands and variability of precipitation were high but dam storage capacity was low. The hotspots of water quality vulnerability were clustered around the main stem of the Columbia River where major population and agricultural centres are located. This multiple equal weight indicator approach confirmed that different drivers were associated with different vulnerability maps in the sub-basins of the CRB. Water quality variables are more important than water supply and water demand variables in the Willamette River basin, whereas water supply and demand variables are more important than water quality variables in the Upper Snake and Upper Columbia River basins. This result suggests that current water resources management and practices drive much of the vulnerability within the study area. The analysis suggests the need for increased coordination of water management across multiple levels of water governance to reduce water resource vulnerability in the CRB and a potentially different weighting scheme that explicitly takes into account the input of various water stakeholders

A Review of Urban Water Body Challenges and Approaches: (1) Rehabilitation and Remediation

We review how urbanization alters aquatic ecosystems, as well as actions that managers can take to remediate urban waters. Urbanization affects streams by fundamentally altering longitudinal and lateral processes that in turn alter hydrology, habitat, and water chemistry; these effects create physical and chemical stressors that in turn affect the biota. Urban streams often suffer from multiple stressor effects that have collectively been termed an “urban stream syndrome,” in which no single factor dominates degraded conditions. Resource managers have multiple ways of combating the urban stream syndrome. These approaches range from whole-watershed protection to reach-scale habitat rehabilitation, but the prescription must be matched to the scale of the factors that are causing the problem, and results will likely not be immediate because of lengthy recovery times. Although pristine or reference conditions are far from attainable, urban stream rehabilitation is a worthy goal because appropriate actions can provide ecosystem improvements as well as increased ecosystem service benefits for human society

A Global View of Cancer-Specific Transcript Variants by Subtractive Transcriptome-Wide Analysis

BACKGROUND: Alternative pre-mRNA splicing (AS) plays a central role in generating complex proteomes and influences development and disease. However, the regulation and etiology of AS in human tumorigenesis is not well understood. METHODOLOGY/PRINCIPAL FINDINGS: A Basic Local Alignment Search Tool database was constructed for the expressed sequence tags (ESTs) from all available databases of human cancer and normal tissues. An insertion or deletion in the alignment of EST/EST was used to identify alternatively spliced transcripts. Alignment of the ESTs with the genomic sequence was further used to confirm AS. Alternatively spliced transcripts in each tissue were then subtractively cross-screened to obtain tissue-specific variants. We systematically identified and characterized cancer/tissue-specific and alternatively spliced variants in the human genome based on a global view. We identified 15,093 cancer-specific variants of 9,989 genes from 27 types of human cancers and 14,376 normal tissue-specific variants of 7,240 genes from 35 normal tissues, which cover the main types of human tumors and normal tissues. Approximately 70% of these transcripts are novel. These data were integrated into a database HCSAS (http://202.114.72.39/database/human.html, pass:68756253). Moreover, we observed that the cancer-specific AS of both oncogenes and tumor suppressor genes are associated with specific cancer types. Cancer shows a preference in the selection of alternative splice-sites and utilization of alternative splicing types. CONCLUSIONS/SIGNIFICANCE: These features of human cancer, together with the discovery of huge numbers of novel splice forms for cancer-associated genes, suggest an important and global role of cancer-specific AS during human tumorigenesis. We advise the use of cancer-specific alternative splicing as a potential source of new diagnostic, prognostic, predictive, and therapeutic tools for human cancer. The global view of cancer-specific AS is not only useful for exploring the complexity of the cancer transcriptome but also widens the eyeshot of clinical research

Wood Microsites at Timberline-Alpine Meadow Borders: Implications for Conifer Seedling Regeneration and Alpine Meadow Conifer Invasion

The importance of climate warming on forests is recognized worldwide and has increased attention on the significance of both timberline advance and alpine meadow invasion by forests. Successful seedling regeneration in alpine meadows depends on availability of suitable substrates, or microsites, for seedling establishment. We sought to determine whether wood microsites (i.e., nurse logs), which are regeneration sites in Pacific Northwest subalpine forests, promoted regeneration at timberline-alpine meadow borders. To determine the ecological role of wood microsites, we examined mechanisms forming wood microsites; compared density, survival, and percent nitrogen content of seedlings growing on wood microsites to adjacent soil substrates; and compared substrate moisture, temperature, and percent nitrogen content. Wood microsites, at 13 of 14 randomly selected sites, were characterized by highly decayed downed wood (\u3e 75% decay class five) originating from tree fall (66%), snow avalanches (17%), forest fires (15%), and by human cutting (2%). Although no differences in percent nitrogen content were detected, greater seedling densities, greater seedling survival, higher temperatures, and higher moisture contents were found on wood microsites compared to adjacent soil. We suggest that greater seedling density and seedling survival on wood microsites was associated with factors including heightened moisture and increased temperature. Assuming sustained downed wood input from timberline trees and continued viable seed input, we expect wood microsites will facilitate accelerated alpine meadow conifer invasion via wood microsites associated with climate warming