Novel tools for conservation genomics: comparing two high-throughput approaches for SNP discovery in the transcriptome of the European hake

The growing accessibility to genomic resources using next-generation sequencing (NGS) technologies has revolutionized the application of molecular genetic tools to ecology and evolutionary studies in non-model organisms. Here we present the case study of the European hake (Merluccius merluccius), one of the most important demersal resources of European fisheries. Two sequencing platforms, the Roche 454 FLX (454) and the Illumina Genome Analyzer (GAII), were used for Single Nucleotide Polymorphisms (SNPs) discovery in the hake muscle transcriptome. De novo transcriptome assembly into unique contigs, annotation, and in silico SNP detection were carried out in parallel for 454 and GAII sequence data. High-throughput genotyping using the Illumina GoldenGate assay was performed for validating 1,536 putative SNPs. Validation results were analysed to compare the performances of 454 and GAII methods and to evaluate the role of several variables (e.g. sequencing depth, intron-exon structure, sequence quality and annotation). Despite well-known differences in sequence length and throughput, the two approaches showed similar assay conversion rates (approximately 43%) and percentages of polymorphic loci (67.5% and 63.3% for GAII and 454, respectively). Both NGS platforms therefore demonstrated to be suitable for large scale identification of SNPs in transcribed regions of non-model species, although the lack of a reference genome profoundly affects the genotyping success rate. The overall efficiency, however, can be improved using strict quality and filtering criteria for SNP selection (sequence quality, intron-exon structure, target region score).

Natural Resources in 2025 - Implications for Development : Opportunity of a trunaround: An expert reassessment

In recent years developing countries have faced highly dynamic changes affecting their natural resource base and their potential for development. Taking into account these changes in the development context, InfoResources initiated a critical reassessment of the results of InfoResources Trends 2005 and again invited experts from around the world to assess trends that least developed countries are likely to be facing by 2025. The unanimous signal conveyed by the international experts for this assessment is alarming: The degradation of natural resources is progressing. By 2025 it will reach a point where livelihoods in least developing countries will be significantly threatened and an increasing number of agro-ecosystems will lose their capacity to deliver important services. Expected positive social trends will not suffice as leverage to reverse the degradation of natural resources and thus alleviate poverty and hunger. However, the present reassessment clearly reveals that a change in thinking and a shift in paradigms have begun to take place. However, a turnaround can only succeed if the emerging awareness of the need to reorient policy-making and the economy is followed by concrete action. It will be crucial that policies and institutions regain regulating power over greedy economic forces. This reassessment does not claim to be comprehensive. However, the present publication, which synthesises the experts’ inputs, aims at providing food for thought and initiating discussions.

Dynamics of Traditional Ecological Knowledge, Local Use and Conservation of Native Trees and Shrubs in the Bolivian Andes

Native trees and shrubs are essential components of rural landscapes in the semi-arid inner-Andean valleys of Bolivia. They can be found as hedges and bushes in various agroecosystems such as terrace walls, slopes, field boundaries and fallow land. Their distribution and floristic composition are the result of dynamic spatial and temporal interactions between local farmers and the environment. Local uses of natural resources and biodiversity reflect the constantly evolving Andean culture, which can be generally characterised as an intertwining of the human, natural, and spiritual worlds. The aim of the present ethnobotanical study was to analyse the dynamics of traditional ecological knowledge, to ascertain local farmers’ perceptions and uses of native woody species in Andean communities and to associate the results with local conservation activities for the trees and shrubs concerned. Our case study was carried out within two communities of the Tunari National Park (Dept. Cochabamba) in Bolivia. For data collection, research methods from social science (semi-structured interviews, participative observation, participatory mapping) as well as vegetation surveys were combined. Local actors included women and men of all ages as well as families from different social categories and altitudinal levels of permanent residence. Our study indicates that, due to a multitude of socio-economic pressures (e.g. migration of young people) as well as changes in use of biodiversity (e.g. replacement of native by exotic introduced species), the traditional ecological knowledge base of native trees and shrubs and their respective uses has become diminished over time. In many cases it has led to a decline in people’s awareness of native species and as a consequence their practical, emotional and spiritual relationships with them have been lost. However, results also show that applied traditional ecological knowledge has led to local conservation strategies, which have succeeded in protecting those tree and shrub species which are most widely regarded for their multifunctional, constant and exclusive uses (e.g. Schinus molle, Prosopis laevigata, Baccharis dracunculifolia). The presentation will discuss the question if and how applied traditional ecological knowledge positively contributes to local initiatives of sustainable use and conservation of biodiversity in rural areas.

Annual report of the Conservation Commission.

1914

Conservation reminiscences of Wm. J.P. Aberg.

"Copied 9-64"--P. 22.

Monitoring the condition of our nation's ecological resources.

Mode of access: Internet.

Resource conservation and development [microform] : hearing before the Subcommittee on Environment, Soil Conservation, and Forestry of the Committee on Agriculture, Nutrition, and Forestry, United States Senate, Ninety-sixth Congress, first session, March 20, 1979.

Reuse of record except for individual research requires license from Congressional Information Service, Inc.

The Second RCA appraisal : soil, water, and related resources on nonfederal land in the United States : analysis of condition and trends /

Item 10.

Conservation in the Department of the Interior,

Mode of access: Internet.

Biennial report of the Department of Conservation and Development of the State of North Carolina [serial].

Title from cover.

Conservation C.O.N.G.R.E.S.S. : Department of Conservation analysis of recommendations.

Cover title.

Lower Sangamon River Valley : an inventory of the region's resources /

"March 2003."

Natural capital of Illinois /

"July 1996."

PLAN-IT EARTH : pairing learners and nature with innovative technology for the environmental assessment of resources, trends, and habitats.

"Illinois."

The Cache River Basin : an inventory of the region's resources /

This is a product of the Critical Trends Assessment Program (CTAP) and the Ecosystems Program of the Illinois Dept. of Natural Resources (DNR). Both are funded largely through Conservation 2000, a six-year State of Illinois initiative to enhance nature protection and outdoor recreation by reversing the decline of the state's ecosystems. Conservation 2000 is the culmination of recommendations from CTAP, the Illinois Conservation Congress, and Governor Edgar's Water Resources Land Use Priorities Task Force.--T.p. verso.