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Browse subject: forest genetics
Number of records: 175

Forest Genetic Resources
About this Resource: Forest Genetic Resources is a FAO Forestry publication. Issues from No. 1 (1973) to No. 30 (2003) are available online in English, French and Spanish. Most are in the html format but a few are in pdf form. Users can also request a hard copy of the resource. The site allows users to search through species and authors to find the articles needed.

Arborea : A project in Functional Genomics of Regulation in Forest Trees
About this Resource: Descriptive details on forest genomic topics are available from this home page link. Provided by the Forest Biology Research Centre at Laval University. Research in these areas also involves researchers at the Canadian Forestry Service, Carleton University and the Center for Computational Genomics and Bioinformatics at the University of Minnesota. The website describes this collaborative research, offering a project overview and is a source for research output (which is available in full text).

Dendrome | Institute of Forest Genetics
About this Resource: Based in Davis, California (with the University of California, Davis) this website offers a wealth of genomic information to those involved in forest genetics. Dendrome offers a collection of forest tree genome databases, along with other forest genetic information resources. The Colleague Directory (the Directory of Forest Geneticists) provides contact information and research interests for specialists studing the field. There is a link to David Neale's web page (the websites principal investigator); the site also identifies relevant news, job openings and newsletters. The section on genome resources includes external links, projects, an image database, software and the "populus genome project". The "Tree Genes Database" includes genetic maps, DNA sequence data, germplasm information and related information for numerous species of forest trees.

Finnish Forest Research Institute
About this Resource: Established in 1917, the Finish Forest Research Institute (Metla) is a signifigant resource realtive to Finland's forests. The website accomodates both English and Finish speaking audiences. Metla provides organizational background for site visitors, with staff introductions and descriptions of research, experiments, services and products. The Institute is making its' publications accessible in full-text and there is an explanation of the METINFO services. A sitemap faciliates site navigation and Metla places emphasis on currency by highlighting news items. The Finnish Forest Research Institute reports to Finland's Ministry of Agriculture and Forestry. The journal "Silva Fennica" is full-text accessible - beginning in 1998 (with pdf formatting), abstracts date back to 1994. The "Working Papers of the Finnish Research Institute" was launched in 2004.

New Zealand Forest Research Institute
About this Resource: The New Zealand Forest Research Institute site contains information about biomaterials and other research projects the institute is working on. The site also provides links to products and services, software, and publications, some of which are free online. Also, there is an area entitled "Targeted Knowledge" where the site discusses specific aspects of forest research.

Global Forest Information System
About this Resource: GFIS is an Internet gateway to forest information resources from around the world. Users can locate maps, datasets, web resources, journal articles, books and other resources relevant to their forest information needs.","GFIS is an internet gateway that provides access to various types of information resources through partnerships with information providers. GFIS search facilities (in the style of commonly used Internet search facilities), allows the user to locate forest related information through a single entry point based on the different search options.","* An updated version of a previous GFIS metadata search provides users with the ability to search the catalogues of information resources (a total of 130,000 metadata records) provided by GFIS partners. The metadata search allows users to search all metadata fields for specific terms or phrases.","* Browsing is a way of navigating among categories and their subcategories to pinpoint the resources that you want to search. GFIS offers browsing among selected information sources from its partners, organized by key types of resources.","* A GFIS Online resource search service uses the Google Web APIs, which is an experimental and free program. The Google API currently makes it possible to carry out 1,000 queries per day with a maximum of 10 keywords. Each query is confined to one single domain.","To describe the content of this information GFIS uses a standardized metadata format and provides conversion facilities for metadata submitted in other formats. In addition a universally accepted terminology facilitates the search operations and the respective results.

WWW Virtual Library: Forestry: Forest Genetics & Tree Breeding
About this Resource: This link is a subdirectory to: WWW Virtual Library: Forestry. Maintained by Matti Haapanen (with METLA, the Finnish Forest Research Institute) it places special emphasis on tree improvement research activities and forest genetics. The subdirectory offers several indexes to: mailing lists, journals and books, software, molecular forest genetics.

Canadian Forestry Links
About this Resource: This directory points to links related to Canadian forestry. Organizational links are identified by the following arrangements: government, universities, associations companies and forest publications. The topical indexes relate to: biodiversity, forest genetics, forest products, forest fires, forest management, silviculture, sustainable forestry, soils, insects and disease and geographical information systems.

Pacific Forestry Centre
About this Resource: The Pacific Forestry Centre focuses on research in forest biology and forest resources. This includes research in remote sensing, biological control of weeds and insects, insect and disease management, alternative silvicultural systems, timber production, fire management, and ecosystem dynamics. Their website provides information about their research as well as information about related programs, policies, and publications.

Southern Research Station | USDA Forest Service
About this Resource: The Southern Research Station creates the science and technology needed to sustain and enhance forest ecosystems in southern regions of the U.S. This link, which connects to the Research Station's homepage is a source for identifying publications; work units; employees and background on the Station. The Homepage features: current highlights; scientists' and their research; new additions; the Stations' strategic framework and the ten most recent publications added to the site. A section for "additional information" points to glossaries; educational products and photo galleries. Additional web features include a publications electronic mailing list, employment information, online videos and relevant external links.

Centre for Plant Conservation Genetics | Southern Cross University, Australia
About this Resource: An access point for the Centre for Plant Conservation Genetics. The Centre generates research, and has promoted commercial services into, areas that involve plant gene characterisation, genetic fingerprinting technology and genetic tranformation. The Centre studies: barley quality improvement; forest molecular genetics; grapevine genetics; as well as marker development into: rice, sorghum, sugarcane, tea trees and wheat. The Centre also hosts several databases which link from its' website (these are identified in the "keyword section" of this record). Newsletters are online, available as pdf-formatted publications. As a consequence its' various areas of expertise, commercial links are furnished to these web services: Southern Cross Plant Genomics and the Australian Plant DNA Bank.

Inferring Geographic Isolation of Wolverines in California Using Historical DNA
About this Resource: Delineating a species' geographic range using the spatial distribution of museum specimens or even contemporary detection-non-detection data can be difficult. This is particularly true at the periphery of a species range where species' distributions are often disjunct. Wolverines (Gulo gulo) are wide-ranging mammals with discontinuous and potentially isolated populations at the periphery of their range. One potentially disjunct population occurred in the Sierra Nevada Mountains, California, USA, and appears to have been extirpated by the 1930s. Many early 20th century naturalists believed that this population was connected to other populations occurring in the Cascade Range of northern California, Oregon, and Washington, USA, but a recent analysis of historical records suggests that California wolverines were isolated from other populations in North America. We used DNA extracted from museum specimens to examine whether California wolverines were isolated. Both nuclear and mitochondrial DNA data indicate that California wolverines were genetically distinct from extant populations, suggesting long-term isolation. We identified 2 new control region (mitochondrial DNA) haplotypes located only within California. We used these data and referenced sequences from the Rocky Mountains, USA, to make inferences regarding potential wolverine translocations into California. In addition, we used these genetic data to make inferences about wolverine conservation throughout western North America.

Information System on Genetic Resources
About this Resource: The Information System on Genetic Resources (GENRES) is maintained by the Information Centre for Biological Diversity (IBV) at the German Centre for Documentation and Information in Agriculture (ZADI). ZADI is an Information Service Provider operating under the auspices of the German Federal Ministry for Consumer Protection, Food and Agriculture (BMVEL). GENRES provides information about national, european and international activities on conservation and sustainable utilization of genetic resources for food, agriculture and forestry.

An economic analysis of hardwood fiber production on dryland irrigated sites in the US Southeast
About this Resource: Although there is renewed interest in intensively managed, short-rotation plantations as a source of hardwood for pulp mills, few have been established in the Southeast. Understanding all the costs associated with these plantations will help determine their feasibility. Using a model developed to summarize all the costs, a break-even analysis was completed to determine the delivered cost for plantations of eastern cottonwood (Populus deltoides Bartr.) from a hypothetical fiber farm in 2003. Using current yield from an experimental fiber farm, short-rotation cottonwood plantations were not cost effective, as delivered cost to a pulp mill averaged 78$ t-1. If yield can be increased by 40% through improvements in genetics and silvicultural practices, delivered cost is reduced to 60$ t-1. Thus, finding this additional yield is key to the cost feasibility of intensively managed, short-rotation hardwood plantations.

Spatio-Temporal Analysis of Xyleborus glabratus (Coleoptera: Circulionidae: Scolytinae) Invasion in Eastern U.S. Forests
About this Resource: The non-native redbay ambrosia beetle, Xyleborus glabratus Eichhoff (Coleoptera: Curculionidae: Scolytinae), has recently emerged as a significant pest of southeastern U.S. coastal forests. Specifically, a fungal symbiont (Raffaelea sp.) of X. glabratus has caused mortality of redbay (Persea borbonia) and sassafras (Sassafras albidum) trees in the region; several other Lauraceae species also seem susceptible. Although the range of X. glabratus continues to expand rapidly, little is known about the species' biology and behavior. In turn, there has been no broad-scale assessment of the threat it poses to eastern U.S. forests. To provide a basic information framework, we performed analyses exploiting relevant spatio-temporal data available for X. glabratus. First, we mapped the densities of redbay and sassafras from forest inventory data. Second, we used climate matching to delineate potential geographic limits for X. glabratus. Third, we used county infestation data to estimate the rate of spread and modeled spread through time, incorporating host density as a weighting factor. Our results suggest that (1) key areas with high concentrations of redbay have yet to be invaded, but some are immediately threatened; (2) climatic conditions may serve to constrain X. glabratus to the southeastern U.S. coastal region; and (3) if unchecked, X. glabratus may spread throughout the range of redbay in <40 yr. Disruption of anthropogenic, long-distance dispersal could reduce the likelihood of this outcome.

Presettlement and modern disturbance regimes in coast redwood forests: Implications for the conservation of old-growth stands
About this Resource: Coast redwood (Sequoia sempervirens), a western North American conifer of ancient lineage, has a paradoxical combination of late-successional characteristics and strong adaptations to disturbance. Despite its shade tolerance and heavy dominance of the canopy on many sites, redwood saplings are uncommon in upland old-growth stands. Information needed to ensure the conservation of old-growth redwood forests has been limited. In this review paper, we integrate evidence on redwood biology with data on the historic and modern disturbance regimes to help clarify the degree to which key attributes of redwood forests may have been dependent upon periodic disturbance. Available evidence suggests that episodes of fire, flooding, and slope failure prior to European settlement were frequent but predominantly of low to moderate severity and extent, resulting in broadly uneven-aged forests. The majority of fires prior to European settlement were apparently of human origin. Frequency and severity of the major disturbance agents have been radically changed in modern times. Fires have been largely excluded, and flooding has been altered in ways that have often been detrimental to old-growth redwoods on alluvial terraces. However, because of the apparent anthropogenic origin of most presettlement fires, the long-term evolutionary role of fire for coast redwood is ecologically ambiguous. With fire exclusion, redwood possibly could be displaced to some extent on upland sites by increasing abundance of fire-sensitive competitors. Alternatively, redwood may be able to maintain dominance by vegetative sprouting and new seedling establishment on root-wad mounds, fallen logs, and on soil exposed by slope failure. Future research priorities are suggested that will help resolve some of the current ambiguities.

Early genetic testing of coastal Douglas-fir for Swiss needle cast tolerance.
About this Resource: The possibility of early testing coastal Douglas-fir (Pseudotsuga menziesii var. menziesii (Mirb.) Franco) for Swiss needle cast (SNC; caused by Phaeocryptopus gaeumannii (Rohde) Petrak) tolerance was investigated using 55 Douglas-fir families from western Oregon. Seedlings were inoculated with P. gaeumannii naturally in the field and were visually scored for a variety of SNC symptom traits (i.e., needle and foliage color, and retention) at the seedling stage (age 2) and in "mature" (ages 10 and 12) trees at two test sites for both the seedling and mature ages. Seedlings were also assessed in the laboratory for SNC symptom traits, for proportion of needle stomata occluded with pseudothecia (PSOP), and for amount of P. gaeumannii DNA in needles. Although families differed significantly at both ages for all SNC symptom traits and for PSOP, they did not differ for amount of fungal DNA. Thus, genetic variation in SNC symptoms appears to be primarily due to differences in tolerance to the disease rather than to resistance to infection per se. Estimated individual-tree heritabilities for SNC symptom traits were low to moderate (mean h(i)2 = 0.19, range 0.06-0.37) at both ages, and within each age-class these traits were moderately to strongly genetically correlated (mean r(A) = 0.69, range 0.42-0.95). Type B genetic correlations between SNC symptom traits in seedlings and mature trees ranged from 0 to 0.83 and were weakest for traits measured in the laboratory. Genetic gain estimates indicated that family selection for SNC tolerance (i.e., greener needles or greater foliage retention) at the seedling stage can be very effective in increasing tolerance in older trees.

The Plant Pathology Internet Guide Book
About this Resource: The Plant Pathology Internet Guide Book (PPIGB) is a subject oriented internet resource guide for plant pathology, applied entomology, and related fields. The Guide Book is designed with an index to fascilitate browsing. A search engine is also a part of the site. The index includes subject terms and other descriptive items (like "societies", "journals", "jobs & positions" so that a records can be accessed by its type). Updated weekly, the records are annotated and descriptive and include links to the referred websites.

AGRICOLA (AGRICultural OnLine Access).
About this Resource: AGRICOLA (AGRICultural OnLine Access) is a bibliographic database of citations to the agricultural literature created by the National Agricultural Library and its cooperators. Production of these records in electronic form began in 1970, but the database covers materials in all formats, including printed works from the 15th century. The records describe publications and resources encompassing all aspects of agriculture and allied disciplines, including animal and veterinary sciences, entomology, plant sciences, forestry, aquaculture and fisheries, farming and farming systems, agricultural economics, extension and education, food and human nutrition, and earth and environmental sciences. Although AGRICOLA does not contain the materials, thousands of AGRICOLA records are linked to online full-text documents, with new links being added every day. AGRICOLA is searchable on the World Wide Web at http://www.nal.usda.gov/ag98. For information on how to obtain library materials from NAL, see NAL's Document Delivery Services Web site: http://www.nal.usda.gov/ddsb/

Harvard Forest , Harvard University
About this Resource: Scientists, students, and collaborators have been actively involved in studying the Harvard Forest since its' establishment in 1907. Both as an education and research facility, staff at Harvard Forest pursue forest biology and conservation; with work that also includes regional studies. Two leading projects involve the National Science Foundation and the Department of Energy. The website is a source for additional detail; included are publications - either online available for purchase.

Gene Flow in Complex Landscapes: Testing Multiple Hypotheses with Causal Modeling
About this Resource: Predicting population-level effects of landscape change depends on identifying factors that influence population connectivity in complex landscapes. However, most putative movement corridors and barriers have not been based on empirical data. In this study, we identify factors that influence connectivity by comparing patterns of genetic similarity among 146 black bears (Ursus americanus), sampled across a 3,000-km2 study area in northern Idaho, with 110 landscape-resistance hypotheses. Genetic similarities were based on the pairwise percentage dissimilarity among all individuals based on nine microsatellite loci (average expected heterozygosity = 0.79). Landscape-resistance hypotheses describe a range of potential relationships between movement cost and land cover, slope, elevation, roads, Euclidean distance, and a putative movement barrier. These hypotheses were divided into seven organizational models in which the influences of barriers, distance, and landscape features were statistically separated using partial Mantel tests. Only one of the competing organizational models was fully supported: patterns of genetic structure are primarily related to landscape gradients of land cover and elevation. The alternative landscape models, isolation by barriers and isolation by distance, are not supported. In this black bear population, gene flow is facilitated by contiguous forest cover at middle elevations.

Inheritance of Fruit, Foliar, and Plant Habit Attributes in Capsicum
About this Resource: Considerable diversity exists in Capsicum L. germplasm for fruit and leaf shape, size, and color as well as plant habit. Using F1, F2, and backcross generations developed from diverse parental stocks, this report describes the inheritance patterns and relationships between unique foliar characters and diverse fruit and plant habit attributes. Our results demonstrate that pepper fruit color, shape, and fruit per cluster were simply inherited with modifying gene action. Broad-sense heritability for fruit color and shape and fruit per cluster was high, whereas narrow-sense heritability for these characters was moderate to low. Although fruit clustering was simply inherited, the number of fruit per cluster exhibited a quantitative mode of inheritance. High fruit counts per cluster were linked with red fruit color and anthocyanin pigmented foliage. Fruit shape was linked with immature fruit color and inherited independently of mature fruit color. Leaf color, length, and plant height were quantitatively inherited. Leaf shape did not vary, but leaf length varied and was positively correlated with leaf width. Broad-sense heritability for leaf characters, including leaf length, leaf width, and leaf color, was high. With the exception of leaf width, which exhibited low narrow-sense heritability, high narrow-sense heritability for leaf characters denoted additive gene action. Plant height displayed high broad-sense heritability. Moderate narrow-sense heritability suggested that additive effects also influence plant height. Analysis of segregating populations demonstrated that red and orange fruit color can be combined with all possible leaf colors from green to black. These results provide new data to clarify and extend available information on the inheritance of Capsicum fruit attributes and provide new information on the genetic control of leaf characters and plant habit.

Population, quantitative and comparative genomics of adaptation in forest trees
About this Resource: High-throughput DNA sequencing and genotyping technologies have enabled a new generation of research in plant genetics where combined quantitative and population genetic approaches can be used to better understand the relationship between naturally occurring genotypic and phenotypic diversity. Forest trees are highly amenable to such studies because of their combined undomesticated and partially domesticated state. Forest geneticists are using association genetics to dissect complex adaptive traits and discover the underlying genes. In parallel, they are using resequencing of candidate genes and modern population genetics methods to discover genes under natural selection. This combined approach is identifying the most important genes that determine patterns of complex trait adaptation observed in many tree populations.

Standardizing the Nomenclature for Clonal Lineages of the Sudden Oak Death Pathogen, Phytophthora ramorum
About this Resource: Phytophthora ramorum, the causal agent of sudden oak death and ramorum blight, is known to exist as three distinct clonal lineages which can only be distinguished by performing molecular marker-based analyses. However, in the recent literature there exists no consensus on naming of these lineages. Here we propose a system for naming clonal lineages of P. ramorum based on a consensus established by the P. ramorum research community. Clonal lineages are named with a two letter identifier for the continent on which they were first found (e.g., NA = North America; EU = Europe) followed by a number indicating order of appearance. Clonal lineages known to date are designated NA1 (mating type: A2; distribution: North America; environment: forest and nurseries), NA2 (A2; North America; nurseries), and EU1 (predominantly A1, rarely A2; Europe and North America; nurseries and gardens). It is expected that novel lineages or new variants within the existing three clonal lineages could in time emerge.

Genetic variation and population structure in Fraser fir (Abies fraseri): a microsatellite assessment of young trees
About this Resource: The island-like populations of Fraser fir (Abies fraseri (Pursh) Poir.) have been isolated since the end of the late-Wisconsinian glaciation on the highest peaks of the Southern Appalachian Mountains and therefore offer an opportunity to investigate the genetic dynamics of a long-fragmented forest tree species. An analysis of eight microsatellite markers isolated from Fraser fir found that the species was out of Hardy-Weinberg equilibrium, with a significant deficiency of heterozygosity and a high degree of inbreeding (F(IS) = 0.223) relative to other conifers, perhaps associated in part with the young life stage of the trees included in the analysis. The analysis detected a significant but small amount of genetic differentiation among Fraser fir populations (F(ST) = 0.004) and revealed that the geographical and latitudinal distances between populations, but not population area, were significantly correlated with their pairwise genetic differences. Both gene flow and postglacial migration history may have influenced the genetic architecture of the species. The results will be useful in the genetic conservation of Fraser fir, a species experiencing severe mortality following infestation by an exotic insect.

Simulation of shoot emergence pattern of cogongrass (Imperata cylindrica) in the humid tropics
About this Resource: Cogongrass is a noxious perennial grass that has invaded many countries in the tropical and subtropical regions of the world. Its management has been a significant challenge because of large rhizome and bud reserves in the soil. The emergence pattern of this weed under field conditions has received little attention. Field trials were conducted in 2002 and 2003 in the humid forest zone of southeastern Nigeria to model shoot emergence. The experiment had four treatments: (1) count and tag crop-free cogongrass shoots, (2) count and suppress crop-free cogongrass shoots with paraquat, (3) count and cut crop-free cogongrass shoots, and (4) count and cut cogongrass shoots in cultivated corn. The rationale for these treatments was to determine the effect of different monitoring techniques on shoot emergence of cogongrass. The development of the model was based on hydrothermal time, which was calculated from soil moisture and soil temperature at a 2-cm depth. A Weibull function was fitted to cumulative percent shoot emergence values of Treatment 4 and hydrothermal time. The model closely fit the observed pattern of cogongrass shoot emergence (r2 = 0.95, n = 36). It also predicted shoot emergence satisfactorily in six treatments (r2 > 0.85, P < 0.001, n = 7 in each treatment) that simulated farmers' practices in southwestern Nigeria. This is the first model developed for cogongrass shoot emergence based on hydrothermal time under field observations. The model should facilitate further analyses of cogongrass emergence patterns and the timing of its management.

Association genetics of complex traits in conifers
About this Resource: Association studies are becoming the experimental approach of choice to dissect complex traits in many organisms from humans to model plant systems. The candidate gene based-association approach has several important advantages for complex trait dissection in many coniferous forest tree species, including random mating and unstructured populations, adequate levels of nucleotide diversity, rapid decay of linkage disequilibrium, and precise evaluation of phenotype from clonal or progeny testing. Allele discovery using association approaches should lead to more-efficient methods of marker-assisted breeding and a deeper understanding of genetic adaptation in forest trees.

Inheritance and chromosomal assignment of powdery mildew resistance genes in two winter wheat germplasm lines.
About this Resource: Powdery mildew of wheat (Triticum aestivum L.), caused by Blumeria graminis DC f. sp. tritici Em. Marchal, occurs annually in eastern North America resulting in reduced grain yield and end-use quality in susceptible cultivars. The objectives of this study were to determine the inheritance, chromosomal location, and linkage with molecular markers of powdery mildew resistance genes in the two recently released germplasm lines NC96BGTA4 and NC99BGTAG11. Between 99 and 194 F(2:3) progenies plus parents in two populations, 'Saluda' x NC96BGTA4 and Saluda x NC99BGTAG11, were evaluated in greenhouse and field nurseries for reaction to powdery mildew infection. Results indicated that the germplasm lines each contained a different, partially dominant, major resistance gene. The two segregating populations were subjected to amplified fragment length polymorphism (AFLP) and simple sequence repeat, or microsatellite (SSR) analyses. Both resistance genes were located on the long arm of chromosome 7A. The most likely locus order indicated that the resistance gene in NC96BGTA4 was flanked by the SSR loci Xbarc292 and Xwmc525. The resistance gene in NC99BGTAG11 was most likely flanked by the AFLP markers XE38M54-196 and XE36M55-126, and the SSR loci Xgwm332 and Xwmc525. Both genes mapped to a chromosome arm that contains the powdery mildew resistance loci Pm1 and Pm9. The resistance genes in the two germplasms are different from the Pm1a allele. Our mapping results suggested that the resistance genes were not alleles at the Pm1 or Pm9 loci, but further allelism tests are necessary to determine the relationships both between the two genes themselves and between the two genes and named Pm loci on chromosome 7AL.

Population genetic structure of an edaphic beetle (Ptiliidae) among late successional reserves within the Klamath-Siskiyou ecoregion, California. [Erratum: 2006 Jan., v. 99, no. 1, p. iii.]
About this Resource: The Klamath-Siskiyou ecoregion of northern California is one of the most diverse temperate coniferous forests. A network of "late successional reserves" (LSRs) has been established to maintain characteristics of late successional forest and to promote late successional characteristics in younger stands. Also, an important goal of conservation management is the maintenance of genetic diversity of ecologically important species. However, this management strategy has not yet been implemented among the LSRs. This study examined the level of genetic diversity among populations of a soil-inhabiting beetle, Acrotrichis xanthocera (Matthews) (Ptiliidae), within the LSR network. Using a partial DNA sequence of the mitochondrial cytochrome oxidase I gene, a total of 31 haplotypes were identified for 117 individuals. Genetic fixation indices and phylogenetic and nested clade analyses all suggest moderate gene flow among five LSR and five non-LSR populations. In addition, haplotype diversity was high and the occurrence of unique haplotypes was common for most populations, which suggests current or past isolation of some populations. These results suggest the LSR network maintains considerable genetic variation for this beetle. However, the genetic variation was not equally distributed among the LSRs. Thus, to facilitate gene flow throughout the ecoregion, it is suggested that future LSRs should reduce gaps among the current LSRs.

Migration Patterns of the Emerging Plant Pathogen Phytophthora ramorum on the West Coast of the United States of America
About this Resource: Phytophthora ramorum (oomycetes) is the causal agent of sudden oak death and ramorum blight on trees, shrubs, and woody ornamentals in the forests of coastal California and southwestern Oregon and in nurseries of California, Oregon, and Washington. In this study, we investigated the genetic structure of P. ramorum on the West Coast of the United States, focusing particularly on population differentiation potentially indicative of gene flow. In total, 576 isolates recovered from 2001 to 2005 were genotyped at 10 microsatellite loci. Our analyses of genetic diversity and inferences of reproductive mode confirm previous results for the Oregon and California populations, with the strong majority of the genotypes belonging to the NA1 clonal lineage and showing no evidence for sexual reproduction. The high incidence of genotypes shared among populations and the lack of genetic structure among populations show that important large-scale, interpopulation genetic exchanges have occurred. This emphasizes the importance of human activity in shaping the current structure of the P. ramorum population on the West Coast of the United States.

Population biology of the Florida manatee [electronic resource] / edited by Thomas J. O'Shea, Bruce B. Ackerman, and H. Franklin Percival.
About this Resource: Proceedings of a workshop held at the Austin Cary Forest of the University of Florida, Feb. 4-6, 1992.

Quantitative trait loci conditioning resistance to Phaeospharia leaf spot of maize caused by Phaeospaeria maydis.
About this Resource: Phaeosphaeria leaf spot (PLS) is a potentially important disease of maize (Zea mays) that has appeared in winter breeding nurseries in southern Florida. Inbred lines related to B73 are particularly susceptible to Phaeosphaeria leaf spot, whereas inbreds related to Mo17 are highly resistant. A previous study of the inheritance of resistance to Phaeosphaeria leaf spot in the cross B73 x Mo17 found that resistance is highly heritable and controlled by mostly additive gene action at three or four loci. In this study, we used 158 recombinant inbred (RI) lines derived from the cross B73 x Mo17 to map quantitative trait loci (QTL) governing resistance. The RI lines along with the parent inbred lines and the F1 were evaluated for PLS resistance in replicated trials over two winter growing seasons in southern Florida. Using the composite interval mapping (CIM) function of PLABQTL software, five QTL on four different chromosomes were found to control PLS resistance in Mo17. In addition, the additive x additive interaction between two of these QTL was found to be significant. Our results are in close agreement with the previous study, where generation mean analysis was used to study the inheritance of resistance to PLS.

Population genetics provides an efficient tool to quantify fragmentation impact in forest ecosystems
About this Resource: A method in population genetics (Dutech et al., Am. J. Bot. 92 (2), 252-261, February 2005) is described and discussed as an interesting tool for investigating the effects of fragmentation in forest ecosystems.

Microsatellite DNA markers and uses thereof
About this Resource: Microsatellite, simple sequence repeat (SSR), markers have much potential for enhancing genome mapping and genotype identification research in forest genetics and tree breeding, SSR markers were developed by isolating and sequencing 1539 loblolly pine SSR clones for 11 SSR motifs. After screening out redundancy among the sequences, 566 oligonucleotide PCR primer pairs flanking the SSRs were synthesized and evaluated for their ability to amplify genomic DNA from loblolly pine. The three SSR motifs that yielded the highest proportion of informative markers from sequenced clones were (AC)n, (AAAT)n, and (AAAC)n. Eighteen polymorphic tri- and tetranucleotide SSR loci were genotyped in 20 loblolly pine trees using automated fluorescent marker analysis. The average number of alleles per locus observed was 6.4, and the average polymorphism information content (PIC) was 0.547. Subsets of the 566 primer pairs were evaluated for their ability to amplify DNA from six other pine species, and 54 primer pairs amplified markers that were polymorphic among the species. The present invention also concerns the methods of using the identified SSR loci as genetic markers.

Rice Germplasm Evaluation and Enhancement at Warda
About this Resource: For more than three decades, breeding research programs have targeted constraints limiting yields to improve the performance of rice varieties. While the products of this research out perform farmer’s traditional varieties under relatively high input systems; their performance under low inputs that dominate rice farming in West Africa has been poor. Rice scientists at WARDA systematically evaluate germplasm from both within and outside Africa. The strategy has been to combine specific adapted attributes of local rice varieties with the yield potential of introduced varieties. During the period of 1994-97, the Germplasm Exchange unit at WARDA distributed to NARS breeders in West Africa, 207 nurseries for a total number of 17,872 varietal requests. WARDA launched an innovative interspecific crossing program between Asian rice, O. sativa and African rice, O. glaberrima in 1991 to develop weed competitive and highly input responsive, but not input-dependent, rice types for various water limited ecosystems. Research characterizing the traits of the indigenous O. glaberrima and its wild relatives has shown a reservoir of useful genes for resistance to various stresses. With the identification of suitable parental varieties, WARDA has covered another milestone in widening the genetic base of the West African rice germplasm by successfully introgressing useful genes from indigenous O. glaberrima into O. sativa. Evaluation of the new progenies showed considerable promise as progenies with high yield potential, high levels of resistance/tolerance to stresses such as weeds, drought, acidity and blast have been identified for further evaluation by NARS, development agents and farmers in participatory research. The interspecific progenies might provide solutions at two levels, the improvement of labor productivity through reduced need for weeding and other management interventions; and the improved sustainability of intensified systems through durable crop resistance to pests and diseases, particularly in lowland systems that so far depends on introduced materials. Working in close partnership with national scientists, development agents, farmers and policy makers, significant impact is expected on farmer’s fields before the end of this decade with increasing momentum in the next century.

Rice Germplasm Enhancement in Japan
About this Resource: Plant genetic resources play an important role in crop improvement programs. Landraces are adapted to local environments and can furnish useful traits to broaden the genetic base of crops. Wild relatives of crop species also have a potential for plant breeding as genetic resources, particularly for pest and disease resistance and tolerance to environmental stresses. These plant genetic resources, however, are now gradually disappearing, a process known as genetic erosion. The reasons for this include the widespread use of improved varieties, socio-economic changes in agriculture and rapid urbanization. The loss of genetic diversity implies that diverse genes are being lost. Due to genetic erosion worldwide and increasing genetic uniformity, there are increasing concerns to conserve genetic diversity for future use. The Ministry of Agriculture, Forestry and Fisheries (MAFF) in Japan has conducted a nationwide project, which is called the ‘MAFF Gene bank Project,’ to conserve genetic diversity since 1983. Development of the genebank system has been accelerated to solve urgent problems in the overall management of genetic resources. The first 10-year plan of the MAFF Gene bank Project included not only plants but also microorganisms, animals, forest trees, and aquatic organisms. The National Institute of Agrobiological Resources (NIAR) is the central organization in Japan for plant, microorganism and animal conservation. The Genetic Resources Center at NIAR is in this way playing a uniting role in close cooperation with co-working national and international research organizations. In 1993, 10 years after the beginning of the project, the project was reconstructed and entered into a second stage for all the areas of genetic resources. In 1994, DNA and molecular genetic information was added as a new category of the MAFF gene bank system, in association with the Rice Genome Research Program (RGP) which has been organized by NIAR.

TreeGenes: A Forest Tree Genome Database
About this Resource: The Dendrome Project and associated TreeGenes database serve the forest genetics research community through a curated and integrated web-based relational database. The research community is composed of approximately 2 000 members representing over 730 organizations worldwide. The database itself is composed of a wide range of genetic data from many forest trees with focused efforts on commercially important members of the Pinaceae family. The primary data types curated include species, publications, tree and DNA extraction information, genetic maps, molecular markers, ESTs, genotypic, and phenotypic data. There are currently ten main search modules or user access points within this PostgreSQL database. These access points allow users to navigate logically through the related data types. The goals of the Dendrome Project are to (1) provide a comprehensive resource for forest tree genomics data to facilitate gene discovery in related species, (2) develop interfaces that encourage the submission and integration of all genomic data, and to (3) centralize and distribute existing and novel online tools for the research community that both support and ease analysis. Recent developments have focused on increasing data content, functional annotations, data retrieval, and visualization tools. TreeGenes was developed to provide a centralized web resource with analysis and visualization tools to support data storage and exchange.

Les ressources génétiques forestières
About this Resource: Forest genetic resources.A short synthesis on the subject of forest genetic resources is presented. Their specificity and the threats weighing on them are briefly reviewed. The management of forest genetic resources from the viewpoint of in situ and ex situ conservation, and their valorization through breeding programmes are described. Co-operations at the world, European and Belgian levels are cited, with special reference to the EUFORGEN Network.

Mapping of Forest Biodiversity Values: A Plural Perspective
About this Resource: The Millennium Ecosystem Assessment is built on a conceptual framework that links biodiversity to the services ecosystems provide to society. Based on this framework, we first compile market and non-market forest valuation studies and, secondly, explore the potential of an econometric modeling exercise by conducting a world wide meta-analysis. This exercise aims to highlight the mapping of biodiversity indicators and assesses their respective role on the valuation exercise. Our results show that biodiversity loss is having an effect on forest ecosystem values. In addition, these effects reveal to be dependent on the type of services and global geo-climatic regions.

Evaluation of roe deer effects upon forest structure in Nogueira Mountain (NE of Portugal)
About this Resource: Analytical methodologies that describe ecological functionalities in the landscape are decisive to quantify the effects of their apparent modifications. When dealing with game resource management it is necessary to understand how landscape variables respond to changes in the abundance of particular species.The main goal of the present work is to evaluate how a forest ecosystem reacts to an increment of roe deer (Capreolus capreolus L.) abundance in a reproduction enclosure.This experience has been developed in the Nogueira Mountains (Trás-os-Montes, NE of Portugal), where a relict nucleus of roe deer persists. In order to promote a roe deer increment, a 15 ha enclosure was installed eight years ago in a natural forest of Quercus pyrenaica.The methodology presently proposed is based on a phytostructural approach, where structural basic matrices of vegetation diversity, abundance and cover, obtained from 10 x 10 m sampling areas along two transepts (inside and outside the enclosure) are resumed in a contingency structural matrix. This contingency matrix is characterised according to a set of multivariate statistical analysis (Principal Component Analysis, Discriminant Canonical Analysis, ANOVAs) and results are correlated with roe deer food preferences (previously typified in four classes according to selectivity). The present results emphasised the roe deer’s capacity to transform the structural organization of the vegetation and therefore, the methodology used is a functional tool to describe landscape changes processes promoted by ungulates.

Butterflies from the Uberlândia region, Central Brazil: species list and biological comments
About this Resource: A total of 251 butterfly species were recorded in Uberlândia region, with collecting concentrated mainly in forest areas. Aspects of geographic distribution of some Ithomiinae, as well as interactions of both adults and immatures with plants, and reproduction periods for the more abundant species are discussed. Collections in open, riverside, and wetland areas, as well as the use of bait, should substantially increase the number of species.

Current State and projection of the probable original vegetation of the São Carlos region of São Paulo State, Brazil
About this Resource: A map of the native vegetation remaining in São Carlos County was built based on aerial images, satellite images, and field observations, and a projection of the probable original vegetation was made by checking it against soil and relief surveys. The existing vegetation is very fragmented and impoverished, consisting predominantly of cerrados (savanna vegetation of various physiognomies), semideciduous and riparian forest, and regeneration areas. Araucaria angustifolia (Bertol.) Kuntze, found in patches inside the semideciduous forest beginning at a minimum altitude of 850 m, has practically disappeared. By evaluating areas on the map for different forms of vegetation, we obtained the following results for original coverage: 27% cerrado (sparsely arboreal and short-shrub savanna, and wet meadows); 16% cerradão (arboreal savanna); 55% semideciduous and riparian forests; and 2% forest with A. angustifolia. There are now 2% cerrados; 2.5% cerradão; 1% semideciduous forest and riparian forests; 1.5% regeneration areas; and 0% forest with A. angustifolia.

Bias in random forest variable importance measures: Illustrations, sources and a solution
About this Resource: Abstract Background Variable importance measures for random forests have been receiving increased attention as a means of variable selection in many classification tasks in bioinformatics and related scientific fields, for instance to select a subset of genetic markers relevant for the prediction of a certain disease. We show that random forest variable importance measures are a sensible means for variable selection in many applications, but are not reliable in situations where potential predictor variables vary in their scale of measurement or their number of categories. This is particularly important in genomics and computational biology, where predictors often include variables of different types, for example when predictors include both sequence data and continuous variables such as folding energy, or when amino acid sequence data show different numbers of categories. Results Simulation studies are presented illustrating that, when random forest variable importance measures are used with data of varying types, the results are misleading because suboptimal predictor variables may be artificially preferred in variable selection. The two mechanisms underlying this deficiency are biased variable selection in the individual classification trees used to build the random forest on one hand, and effects induced by bootstrap sampling with replacement on the other hand. Conclusion We propose to employ an alternative implementation of random forests, that provides unbiased variable selection in the individual classification trees. When this method is applied using subsampling without replacement, the resulting variable importance measures can be used reliably for variable selection even in situations where the potential predictor variables vary in their scale of measurement or their number of categories. The usage of both random forest algorithms and their variable importance measures in the R system for statistical computing is illustrated and documented thoroughly in an application re-analyzing data from a study on RNA editing. Therefore the suggested method can be applied straightforwardly by scientists in bioinformatics research.

Fly pollination and pollinator sharing in two synchronopatric species: Cordia multispicata (Boraginaceae) and Borreria alata (Rubiaceae)
About this Resource: The floral biology of Cordia multispicata (Boraginaceae) and Borreria alata (Rubiaceae) was studied in natural populations in a fragment of the Atlantic forest in Pernambuco, northeastern Brazil. Both species flower during almost the whole year. Cordia multispicata is a shrubby species with white, distylous and tubular flowers. Borreria alata is a herbaceous species. Its flowers are whitish, tubular and have a polymorphism in relation to the size of their style. Floral anthesis in both species begins at 6:00 a.m. Sugar concentration in the nectar was about 16% in C. multispicata and 30% in B. alata. Nine species of flies, mainly of the genus Palpada (Syrphidae), were observed visiting flowers of the two species. Seven of them were observed visiting and pollinating flowers of both C. multispicata and B. alata. Two species visited only flowers of C. multispicata, whereas no fly was exclusive to B. alata flowers. Both species have similar flower morphology, flowering time, habitats in the forest and establish populations very close to each other. These facts can favour the pollinators? sharing and increase pollinator attraction.

Kerala Forest Research Institute
About this Resource: The Kerala Forest Research Institute deals with research in all areas of tropical forestry including biodiversity, wood science & technology, wildlife biology and socio-economics. This resource covers the background of the organization including a list of achievements, the different divisions of the institute, a conference schedule, and a publication listing. The site has listings of ongoing projects and also contains links to full research reports for members. Information about the Teak Museum and Forest Seed Center are also available.

Birds of a central São Paulo woodlot: 1. Censuses 1982-2000
About this Resource: Some 263 birds were recorded near and in a 230-ha patch of semideciduous forest in cane fields of central São Paulo, Brazil. Subtracting 67 open-area species, 22 of marshes or creeks, 10 vagrants and 12 recorded later, 152 forest and border species were recorded in 1982-86, much like what was observed in a similar woodlot near Campinas. Both woodlots lost species gradually over the years. Some birds avoided hard cane-field edges, preferring soft bushy edges. Of open-area species, 22 seemed to have disappeared by 1997 due to earlier high El Niño rains or rare permanently open habitats in the sugar cane; 17 new species were mostly nocturnal ones not noted earlier, or occasional visitors. Forest and borders lost 31 species, gaining five of dry regions and one winter visitor. Several migrants from the south appeared only in wet years before recent greenhouse effects, some resident birds were hunted, and canopy hummingbirds were perhaps still present. Dry-forest travel-prone or "metapopulational" species moved their centers of distribution, partly concealing loss of moist-forest diversity.

Mapping complex traits using Random Forests
About this Resource: Abstract Random Forest is a prediction technique based on growing trees on bootstrap samples of data, in conjunction with a random selection of explanatory variables to define the best split at each node. In the case of a quantitative outcome, the tree predictor takes on a numerical value. We applied Random Forest to the first replicate of the Genetic Analysis Workshop 13 simulated data set, with the sibling pairs as our units of analysis and identity by descent (IBD) at selected loci as our explanatory variables. With the knowledge of the true model, we performed two sets of analyses on three phenotypes: HDL, triglycerides, and glucose. The goal was to approach the mapping of complex traits from a multivariate perspective. The first set of analyses mimics a candidate gene approach with a high proportion of true genes among the predictors while the second set represents a genome scan analysis using microsatellite markers. Random Forest was able to identify a few of the major genes influencing the phenotypes, such as baseline HDL and triglycerides, but failed to identify the major genes regulating baseline glucose levels.

Androlaelaps marmosops (Acari: Laelapidae), a new species associated with the mouse opossum, Marmosops incanus (Lund, 1840) in the Atlantic Forest of Rio de Janeiro State, Brazil
About this Resource: Androlaelaps marmosops, a new species of laelapid mite, is described from the pelage of the mouse opossum, Marmosops incanus (Lund, 1840) (Mammalia: Didelphidae), in two areas of Atlantic Forest of Rio de Janeiro State. Measurements and illustrations are included for females only.

Arboreous vegetation of an alluvial riparian forest and their soil relations: Porto Rico island, Paraná river, Brazil
About this Resource: The dynamics of alluvial deposits in floodplains forms islands and sandbanks. Deposits frequently accumulate at the river margins and on islands with consequent side growths. One of these sandbanks which started to form in 1952 annexed an area of 12.4ha to the Porto Rico island (53masculine15?W and 22masculine45?S). At present a forest fragment of approximately 2.0 ha exists in this place. The structural analysis of arboreous vegetation of this fragment showed a floristic gradient related to the physical and chemical variations of the substratum. High density of pioneer species associated to the absence of recruitment of new individuals of these and other successional categories indicated that the forest was impaired in its succession process. This fact could be associated with constant disturbances caused by cattle in the area.

Landscape genetics of fragmented forests: anticipating climate change by facilitating migration
About this Resource: Habitat fragmentation is a threat to the survival of species and causes population decline, as isolated populations are more susceptible to demographic and genetic stochasticity. This can be compensated for by sufficient spatial connectivity between habitat patches to allow dispersal of individuals among populations. In that case such a network of populations may effectively form a metapopulation. In this paper we discuss some aspects of metapopulation theory, notably with respect to maintaining genetic diversity in fragmented forest patches. In addition we will discuss recent studies that explore ways for forest management to anticipate and mitigate the expected climate change, in relation to range shifts and colonisation opportunities.