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The genetic diversity and growth dynamics of fifty-three half-sib families of eleven provenance sources and one bulk seed mixed population of fast growing forest tree species i.e. Melia azedarach were studied at two stand ages viz., fourth year (mid-rotation) and eighth year (end-rotation) to determine the selection stage in northern India. Significant variations were reported between and within seed provenances in all growth characters at both rotational ages. The broad sense heritability was higher at mid-rotational age. This revealed the growth is genetically controlled but with the time environmental effects escort the growth pattern. Growth pattern was different at each stand age. Growth is diameter dependent and the pattern was crown growth type. Families maintained their superiority over the time for tree height, basal diameter and diameter at breast height, which indicated a strong potential to identify good performing families for future plantation program. This study concluded that early stage selection is appropriate that later stage selection for all parameters studied except clear bole height that is much influenced by management practice and environment factors also. Neighbor-joining clustering with similarity index revealed that it is not necessary that the families, originated in one region were distributed in one cluster, indicating that families with same geographic origin could have undergone changes for different characters under selection. [ABSTRACT FROM AUTHOR]

Like many other high elevation alpine tree species, Rocky Mountain bristlecone pine (Pinus aristata Engelm.) may be particularly vulnerable to climate change. To evaluate its potential vulnerability to shifts in climate, we defined the suitable climate space for each of four genetic lineages of bristlecone pine and for other subalpine tree species in close proximity to bristlecone pine forests. Measuring changes in the suitable climate space for lineage groups is an important step beyond models that assume species are genetically homogenous. The suitable climate space for bristlecone pine in the year 2090 is projected to decline by 74% and the proportional distribution of suitable climate space for genetic lineages shifts toward those associated with warmer and wetter conditions. The 2090 climate space for bristlecone pine exhibits a bimodal distribution along an elevation gradient, presumably due to the persistence of the climate space in the Southern Rocky Mountains and exclusion at mid-elevations by conditions that favor the climate space of other species. These shifts have implications for changes in fire regimes, vulnerability to pest and pathogens, and altered carbon dynamics across the southern Rockies, which may reduce the likelihood of bristlecone pine trees achieving exceptional longevity in the future. The persistence and expansion of climate space for southern bristlecone pine genetic lineage groups in 2090 suggests that these sources may be the least vulnerable in the future. While these lineages may be more likely to persist and therefore present opportunities for proactive management (e.g., assisted migration) to maintain subalpine forest ecosystem services in a warmer world, our findings also imply heighted conservation concern for vulnerable northern lineages facing range contractions. [ABSTRACT FROM AUTHOR]

Understanding whether populations can adapt in situ or whether interventions are required is of key importance for biodiversity management under climate change. Landscape genomics is becoming an increasingly important and powerful tool for rapid assessments of climate adaptation, especially in long-lived species such as trees. We investigated climate adaptation in Eucalyptus microcarpa using the DArTseq genomic approach. A combination of FST outlier and environmental association analyses were performed using >4200 genomewide single nucleotide polymorphisms ( SNPs) from 26 populations spanning climate gradients in southeastern Australia. Eighty-one SNPs were identified as putatively adaptive, based on significance in FST outlier tests and significant associations with one or more climate variables related to temperature (70/81), aridity (37/81) or precipitation (35/81). Adaptive SNPs were located on all 11 chromosomes, with no particular region associated with individual climate variables. Climate adaptation appeared to be characterized by subtle shifts in allele frequencies, with no consistent fixed differences identified. Based on these associations, we predict adaptation under projected changes in climate will include a suite of shifts in allele frequencies. Whether this can occur sufficiently rapidly through natural selection within populations, or would benefit from assisted gene migration, requires further evaluation. In some populations, the absence or predicted increases to near fixation of particular adaptive alleles hint at potential limits to adaptive capacity. Together, these results reinforce the importance of standing genetic variation at the geographic level for maintaining species' evolutionary potential. [ABSTRACT FROM AUTHOR]

The umbu-cajá (Spondias sp.) is a fruit specie native of the brazilian semiarid region with high potential for cultivation. The juicy pulp is used in the production of juices and nectars. The aim of this study was to characterize 18 individuals of umbu-cajá tree at three sites located in the Brazilian northeast municipalities of Mossoró/RN and Apodi/RN to identify individuals with superior attributes for fruit processing and/or in natura consumption The morphological, physical and physicochemical characterization of 20 fruits of each individuals were performed. Leaves of trees were used for molecular analyses with Inter Simple Sequence Repeats (ISSR) and Random Amplified Polymorphic DNA (RAPD) markers. It was possible to verify that there are phenotypic variability among the fruits of umbu-cajá trees. The individuals of the same region were grouped in the same group. JZ5, JZ6 and MA6 individuals can be used for pulp processing, while JZ1, JZ2, JZ3 and JZ6 are adequate for in natura consumption. The molecular analyses showed polymorphism for the two molecular markers used. The ISSR marker generated the greatest polymorphism among the individuals. However, the RAPD marker made it possible to achieve a more consistent cluster, which is in agreement with the geographical distribution of these individuals. The use of morphological markers together with molecular markers constitutes an important tool for characterizing umbu-cajá individuals. [ABSTRACT FROM AUTHOR]

Phylogenetic inference is an attractive means to reconstruct transmission histories and epidemics. However, there is not a perfect correspondence between transmission history and virus phylogeny. Both node height and topological differences may occur, depending on the interaction between within-host evolutionary dynamics and between-host transmission patterns. To investigate these interactions, we added a within-host evolutionary model in epidemiological simulations and examined if the resulting phylogeny could recover different types of contact networks. To further improve realism, we also introduced patient-specific differences in infectivity across disease stages, and on the epidemic level we considered incomplete sampling and the age of the epidemic. Second, we implemented an inference method based on approximate Bayesian computation (ABC) to discriminate among three well-studied network models and jointly estimate both network parameters and key epidemiological quantities such as the infection rate. Our ABC framework used both topological and distance-based tree statistics for comparison between simulated and observed trees. Overall, our simulations showed that a virus time-scaled phylogeny (genealogy) may be substantially different from the between-host transmission tree. This has important implications for the interpretation of what a phylogeny reveals about the underlying epidemic contact network. In particular, we found that while the within-host evolutionary process obscures the transmission tree, the diversification process and infectivity dynamics also add discriminatory power to differentiate between different types of contact networks. We also found that the possibility to differentiate contact networks depends on how far an epidemic has progressed, where distance-based tree statistics have more power early in an epidemic. Finally, we applied our ABC inference on two different outbreaks from the Swedish HIV-1 epidemic. [ABSTRACT FROM AUTHOR]

Whitebark pine (WBP, Pinus albicaulis Engelm.) is an endangered conifer species due to heavy mortality from white pine blister rust (WPBR, caused by Cronartium ribicola) and mountain pine beetle (Dendroctonus ponderosae). Information about genetic diversity and population structure is of fundamental importance for its conservation and restoration. However, current knowledge on the genetic constitution and genomic variation is still limited for WBP. In this study, an integrated genomics approach was applied to characterize seed collections from WBP breeding programs in western North America. RNA-seq analysis was used for de novo assembly of the WBP needle transcriptome, which contains 97,447 protein-coding transcripts. Within the transcriptome, single nucleotide polymorphisms (SNPs) were discovered, and more than 22,000 of them were non-synonymous SNPs (ns-SNPs). Following the annotation of genes with ns-SNPs, 216 ns-SNPs within candidate genes with putative functions in disease resistance and plant defense were selected to design SNP arrays for high-throughput genotyping. Among these SNP loci, 71 were highly polymorphic, with sufficient variation to identify a unique genotype for each of the 371 individuals originating from British Columbia (Canada), Oregon and Washington (USA). A clear genetic differentiation was evident among seed families. Analyses of genetic spatial patterns revealed varying degrees of diversity and the existence of several genetic subgroups in the WBP breeding populations. Genetic components were associated with geographic variables and phenotypic rating of WPBR disease severity across landscapes, which may facilitate further identification of WBP genotypes and gene alleles contributing to local adaptation and quantitative resistance to WPBR. The WBP genomic resources developed here provide an invaluable tool for further studies and for exploitation and utilization of the genetic diversity preserved within this endangered conifer and other five-needle pines. [ABSTRACT FROM AUTHOR]

During post glacial colonization, loss of genetic diversity due to leading edge effects may be attenuated in forest trees because of their prolonged juvenile phase, allowing many migrants to reach the colonizing front before populations become reproductive. The northern range margins of temperate tree taxa in Europe are particularly suitable to study the genetic processes that follow colonization because they have been little affected by northern refugia. Here we examined how post glacial range dynamics have shaped the genetic structure of common ash (Fraxinus excelsior L.) in its northern range compared to its central range in Europe. We used four chloroplast and six nuclear microsatellites to screen 42 populations (1099 trees), half of which corresponded to newly sampled populations in the northern range and half of which represented reference populations from the central range obtained from previously studies. We found that northern range populations of common ash have the same chloroplast haplotypes as south-eastern European populations, suggesting that colonization of the northern range took place along a single migration route, a result confirmed by the structure at the nuclear microsatellites. Along this route, diversity strongly decreased only in the northern range, concomitantly with increasing population differentiation and complex population substructures, a pattern consistent with a leading edge colonization model. Our study highlights that while diversity is maintained in the central range of common ash due to broad colonizing fronts and high levels of gene flow, it profoundly decreases in the northern range, where colonization was unidirectional and probably involved repeated founder events and population fluctuations. Currently, common ash is threatened by ash dieback, and our results on northern populations will be valuable for developing gene conservation strategies. [ABSTRACT FROM AUTHOR]

Background: Inferring species trees from gene trees using the coalescent-based summary methods has been the subject of much attention, yet new scalable and accurate methods are needed. Results: We introduce DISTIQUE, a new statistically consistent summary method for inferring species trees from gene trees under the coalescent model. We generalize our results to arbitrary phylogenetic inference problems; we show that two arbitrarily chosen leaves, called anchors, can be used to estimate relative distances between all other pairs of leaves by inferring relevant quartet trees. This results in a family of distance-based tree inference methods, with running times ranging between quadratic to quartic in the number of leaves. Conclusions: We show in simulated studies that DISTIQUE has comparable accuracy to leading coalescent-based summary methods and reduced running times. [ABSTRACT FROM AUTHOR]

Tree mortality is an important component of forest tree and stand growth models, which provide decision support for forest managers. Mortality patterns, however, are highly variable and difficult to describe. Despite numerous investigations aimed at developing tree survival models, there are still important gaps that need to be filled. This paper used a large-scale repeated measure dataset collected from permanent sample plots established in 1980/81 across the natural range of loblolly pine ( Pinus taeda L.) in the Piedmont, Atlantic Coastal Plain and Gulf Coastal Plain physiographic regions of the US. The primary objective of this study was to explain the survival of loblolly pine trees using time-varying covariates such as diameter at breast height, total tree height, crown ratio, stand age, stand basal area, and dominant height. In this paper, individual-tree mortality was described using a semiparametric proportional hazards regression model. Shared frailty models were used to account for unobserved heterogeneity not explained by the observed covariates. Our investigation involved developing a modeling comparison procedure, predicting mortality based on a frailty model, and quantifying the predictive ability for tree mortality. The survival model developed using a large scale database provides further understanding of mortality trends in planted stands of loblolly pine. The survival model will enable forest managers to more accurately specify initial planting density, thinning schedules, and other management interventions. [ABSTRACT FROM AUTHOR]

Uncovering the genes and molecular basis of phenotypic variation and adaptation is a major goal in conservation and evolutionary genetics; it also sets the basis for future operational breeding in commercial species, like forest trees. These taxa are characterized by their large size, growth habit and longevity, which hampers the use of reverse-genetic approaches (i.e. from gene function to phenotype) to pinpoint adaptive molecular variants. In this chapter, we summarize the basis of the forward-genetic approaches (i.e. from phenotype to gene function) currently used in forest trees. For each strategy, we provide a brief overview of the statistical approaches employed to identify candidate genes, and then highlight the main findings of landmark studies that provide evidence for adaptation in forest trees. Adaptive and commercial traits are generally well inherited in trees, although they are mostly affected by the variation of multiple genes, each one accounting for a small part of the phenotypic variance of each character. However, some individual and important genes involved in growth, phenology, drought resistance and cold hardiness have been identified; many of them showing evidence of selection across multiple taxa (sometimes including angiosperms and gymnosperms). Future challenges for detecting the signatures and understanding the molecular basis of adaptation in trees include more adequate and precise phenotype assessment in natural populations, and the inclusion of gene interactions and epigenetic variations in current models. The implications of these findings in conservation and breeding of forest trees are finally discussed. [ABSTRACT FROM AUTHOR]

Trees use environmental cues such as drought, temperature and light to synchronize growth and development with seasonal changes, and to compete for resources with other plants. The ability of trees to effectively sense and respond to these signals requires molecular programs to enable them to track change rapidly and adapt accordingly. Advances in genomics, transcriptomics and metabolomics have improved our understanding, but there are still considerable gaps and for trees in particular. This chapter reviews recent advances in understanding tree responses to episodes of drought, elevated temperature, low temperature and photoperiod, because these cues are amongst the most important environmental factors affecting tree performance over the course of the season and in a changing climate. For example, trees are expected to suffer more from extreme low temperature events during winter or increased frequency of heat waves during summer and, in many regions, from longer periods of drought. In addition, elevated temperature is expected to extend the length of the growing season, while responses to photoperiod might constrain positive responses to warmer spring or autumn. Finally, the interaction of multiple cues is reviewed and emerging areas of research are discussed such as the role of natural variation, adaptation, plasticity and epigenetics. [ABSTRACT FROM AUTHOR]

Trees are important sources of food, fibre, fodder, fuel, and timber. Fruit and forest trees provide habitat for wildlife, sequester carbon, and protect soil and water resources. Despite a very long history of domestication of some fruit tree species, such as apple, domestication and breeding of many tree species is still in their early stages. The domestication of trees can be accelerated by modern tree breeding practices. Advances in genomic technologies are providing valuable tools to tree breeders. Breeders can be more efficient in improving the traits of interest to increase productivity, and develop genetic resources that can adapt to changing environment and have resistance to disease and pests. In this chapter, we first briefly examined the current status of major forest (conifers, eucalypts) and fruit trees (apple, peach, pear) breeding across the world. We then described the breeding strategies employed to improve the populations. A summary of genomic resources available for major tree species is also covered. The challenges and opportunities of genomic selection applications are finally summarized. [ABSTRACT FROM AUTHOR]

There is a general assumption that intraspecific populations originating from relatively arid climates will be better adapted to cope with the expected increase in drought from climate change. For ecologically and economically important species, more comprehensive, genecological studies that utilize large distributions of populations and direct measures of traits associated with drought-resistance are needed to empirically support this assumption because of the implications for the natural or assisted regeneration of species. We conducted a space-for-time substitution, common garden experiment with 35 populations of coast Douglas-fir ( Pseudotsuga menziesii var. menziesii) growing at three test sites with distinct summer temperature and precipitation (referred to as 'cool/moist', 'moderate', or 'warm/dry') to test the hypotheses that (i) there is large genetic variation among populations and regions in traits associated with drought-resistance, (ii) the patterns of genetic variation are related to the native source-climate of each population, in particular with summer temperature and precipitation, (iii) the differences among populations and relationships with climate are stronger at the warm/dry test site owing to greater expression of drought-resistance traits (i.e., a genotype × environment interaction). During midsummer 2012, we measured the rate of water loss after stomatal closure (transpirationmin), water deficit (% below turgid saturation), and specific leaf area ( SLA, cm2 g−1) on new growth of sapling branches. There was significant genetic variation in all plant traits, with populations originating from warmer and drier climates having greater drought-resistance (i.e., lower transpirationmin, water deficit and SLA), but these trends were most clearly expressed only at the warm/dry test site. Contrary to expectations, populations from cooler climates also had greater drought-resistance across all test sites. Multiple regression analysis indicated that Douglas-fir populations from regions with relatively cool winters and arid summers may be most adapted to cope with drought conditions that are expected in the future. [ABSTRACT FROM AUTHOR]

Today, researchers spend a tremendous amount of time gathering, formatting, filtering and visualizing data collected from disparate sources. Under the umbrella of forest tree biology, we seek to provide a platform and leverage modern technologies to connect biotic and abiotic data. Our goal is to provide an integrated web-based workspace that connects environmental, genomic and phenotypic data via geo-referenced coordinates. Here, we connect the genomic query web-based workspace, DiversiTree and a novel geographical interface called CartograTree to data housed on the TreeGenes database. To accomplish this goal, we implemented Simple Semantic Web Architecture and Protocol to enable the primary genomics database, TreeGenes, to communicate with semantic web services regardless of platform or back-end technologies. The novelty of CartograTree lies in the interactive workspace that allows for geographical visualization and engagement of high performance computing (HPC) resources. The application provides a unique tool set to facilitate research on the ecology, physiology and evolution of forest tree species. CartograTree can be accessed at: http://dendrome.ucdavis.edu/cartogratree. [ABSTRACT FROM AUTHOR]

Background: Due to the rapid progress of next-generation sequencing (NGS) facilities, an explosion of human whole genome data will become available in the coming years. These data can be used to optimize and to increase the resolution of the phylogenetic Y chromosomal tree. Moreover, the exponential growth of known Y chromosomal lineages will require an automatic determination of the phylogenetic position of an individual based on whole genome SNP calling data and an up to date Y chromosomal tree. Results: We present an automated approach, 'AMY-tree', which is able to determine the phylogenetic position of a Y chromosome using a whole genome SNP profile, independently from the NGS platform and SNP calling program, whereby mistakes in the SNP calling or phylogenetic Y chromosomal tree are taken into account. Moreover, AMYtree indicates ambiguities within the present phylogenetic tree and points out new Y-SNPs which may be phylogenetically relevant. The AMY-tree software package was validated successfully on 118 whole genome SNP profiles of 109 males with different origins. Moreover, support was found for an unknown recurrent mutation, wrong reported mutation conversions and a large amount of new interesting Y-SNPs. Conclusions: Therefore, AMY-tree is a useful tool to determine the Y lineage of a sample based on SNP calling, to identify Y-SNPs with yet unknown phylogenetic position and to optimize the Y chromosomal phylogenetic tree in the future. AMY-tree will not add lineages to the existing phylogenetic tree of the Y-chromosome but it is the first step to analyse whole genome SNP profiles in a phylogenetic framework. [ABSTRACT FROM AUTHOR]

The investigation of genetically modified trees requires rapid and reliable techniques to measure the mechanical properties at an early age in order to give timely feedback to forest geneticists. In this study, transmittance near-infrared (NIR) spectroscopy was used to predict the green mechanical properties of 1- and 2-year-old transgenic and wild-type aspen. Green modulus of elasticity (MOE) in three-point bending and green ultimate compression strength (UCS) parallel to the grain were predicted from the NIR spectra of dry wood meal pellets. Green UCS had strong correlation ( R = 0.91) and green MOE had good correlation ( R = 0.78) with the spectra. The latter could be explained by the moderate correlation of MOE with the lignin content of the transgenic samples, suggesting that besides chemical composition MOE also depends on anatomical properties. The ratio of performance to deviation value suggested that the calibration model of both UCS (2.94) and MOE (1.91) could be used for screening. [ABSTRACT FROM AUTHOR]

Over the past two decades, research in forest tree genomics has lagged behind that of model and agricultural systems. However, genomic research in forest trees is poised to enter into an important and productive phase owing to the advent of next-generation sequencing technologies, the enormous genetic diversity in forest trees and the need to mitigate the effects of climate change. Research on long-lived woody perennials is extending our molecular knowledge of complex life histories and adaptations to the environment - enriching a field that has traditionally drawn biological inference from a few short-lived herbaceous species. [ABSTRACT FROM AUTHOR]

Background: Strong patterns of habitat association are frequent among tropical forest trees and contribute to the maintenance of biodiversity. The relation of edaphic differentiation to tradeoffs among leaf functional traits is less clear, but may provide insights into mechanisms of habitat partitioning in these species rich assemblages. Methodology/Principal Findings: We quantify the leaf economics spectrum (LES) for 16 tree species within a Bornean forest characterized by highly pronounced habitat specialization. Our findings suggest that the primary axis of trait variation in light-limited, lowland tropical forests was identical to the LES and corresponds with the shade tolerance continuum. There was no separation with respect to edaphic variation along this primary axis of trait variation. However, a second orthogonal axis determined largely by foliar P concentrations resulted in a near-perfect separation of species occupying distinct soil types within the forest. Conclusions/Significance: We suggest that this second axis of leaf trait variation represents a ''leaf edaphic habitat spectrum'' related to foliar P and potentially other nutrients closely linked to geological substrate, and may generally occur in plant communities characterized by strong edaphic resource gradients. [ABSTRACT FROM AUTHOR]

Genetic analysis of forest longitudinal height data using random regression (RR) has the potential to be attractive to tree breeders because of its advantages for selection at early ages. Our study provides an example of implementation of RR to forest tree height growth data. The data set comes from the Swedish Scots pine (Pinus sylvestris L.) breeding program with a pedigree over three generations and consists of 899 trees with reconstructed phenotypic height records for 16 years. Legendre polynomials and B-splines were used as base functions in RR models. The restricted maximum likelihood method was employed to estimate (co)variance parameters. Results show that heritability increased with age, except for early ages (years 1 to 4). In general, slightly higher heritabilities were found for the RR model than for the single-trait and paired-trait analyses for most ages. Moreover, the heritabilities obtained with B-splines as the base function tended to be somewhat higher than those obtained with Legendre polynomials. The RR method provides a promising approach for estimating genetic parameters of longitudinal data that can be used in early selection. However, application to real data from other species and to simulated data is needed before general breeding recommendations can be established. [ABSTRACT FROM AUTHOR]

The developing field of community genetics has the potential to broaden the contribution of genetics to conservation biology by demonstrating that genetic variation within foundation plant species can act to structure associated communities of microorganisms, invertebrates, and vertebrates. We assessed the biodiversity consequences of natural patterns of intraspecific genetic variation within the widely distributed Australian forest tree, Eucalyptus globulus. We assessed genetic variation among geographic races of E. globulus (i.e., provenances, seed zones) in the characteristics of tree-trunk bark in a 17-year-old common garden and the associated response of a dependent macroarthropod community. In total, 180 macroarthropod taxa were identified following a collection from 100 trees of five races. We found substantial genetically based variation within E. globulus in the quantity and type of decorticating bark. In the community of organisms associated with this bark, significant variation existed among trees of different races in composition, and there was a two-fold difference in species richness (7–14 species) and abundance (22–55 individuals) among races. This community variation was tightly linked with genetically based variation in bark, with 60% of variation in community composition driven by bark characteristics. No detectable correlation was found, however, with neutral molecular markers. These community-level effects of tree genetics are expected to extend to higher trophic levels because of the extensive use of tree trunks as foraging zones by birds and marsupials. Our results demonstrate the potential biodiversity benefits that may be gained through conservation of intraspecific genetic variation within broadly distributed foundation species. The opportunities for enhancing biodiversity values of forestry and restoration plantings are also highlighted because such planted forests are increasingly becoming the dominant forest type in many areas of the world. [ABSTRACT FROM AUTHOR]

Acquiring nuclear DNA sequences in forest tree species is becoming easier as molecular tools are developing rapidly and we now have at our disposal an array of theoretical methods to carry out statistical inferences from multilocus sequence variation. In the present article we use results from two recent studies of nuclear DNA sequence polymorphism in Norway spruce (Picea abies) and Scots pine (Pinus sylvestris) to illustrate what additional insights to each species' history can be gained compared with classical phylogeographic studies based on chloroplast or mitochondrial DNA. The sampling schemes and statistical analyses used in these two studies were similar facilitating a comparison between them. In both cases we inferred the presence of a rather severe bottleneck predating the Last Glacial Maximum (∼18,000 years ago). This result is discussed in relation to recent reassessments of the fossil pollen record and to its implication for our understanding of adaptation. Finally we briefly outline some suggestions for future research. [ABSTRACT FROM AUTHOR]

A model for a balanced tree breeding program that considers genetic gain and cost was used to assess the benefits of increasing the breeding population to allow for a component of among-parent selection while maintaining an equal contribution among grandparents, rather than relaying on within-family selection with an equal parental representation. The scenario used in this study had characteristics similar to those of the phenotypic selection strategy for Scots pine (Pinus sylvestris L.) in Sweden. The results showed that investments in a greater number of parents and families to allow for among-parent selection resulted in a markedly higher genetic gain. The among-parent selection component increased the genetic gain by as much as 70% in a scenario with a high budget and no family creation costs and by as much as 20% in a scenario with a low budget and high family creation costs. [ABSTRACT FROM AUTHOR]

This paper discusses concepts, strategies and priority setting in the conservation of forest biological diversity. It focuses on the management of forest tree and shrub genetic resources, and reviews information on values derived from their sustainable use in support of local and national development. This paper highlights the need to address gaps in information on status and trends in forest biological diversity and genetic resources using relevant indicators, and to improve available knowledge on genetic variation, phenology and breeding systems as a basis for the conservation, improvement and sustainable use of target species. It supports the notion that forest genetic resources action plans, based on country-derived information on status, trends and national priorities, should be seen in a larger regional and global perspective to help strengthen the impact of efforts in individual countries and make full use of comparative institutional strengths among countries. In order to be sustainable over time, conservation and genetic management should be incorporated in wider planning frameworks, such as national forest programmes and rural development plans. To promote and support such integration, there is an urgent need to systematically review, generate and widely publicize studies that quantify the economic, social and environmental gains obtained or obtainable from maintaining biological diversity and wisely using tree and shrub genetic resources, seen in relation to alternative land use options. [ABSTRACT FROM AUTHOR]

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 (FIS = 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 (FST = 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. [ABSTRACT FROM AUTHOR]

This study contributes to the Pinus pinaster Ait. breeding programme, which is reaching the third generation by adding information on wood quality of 46 open-pollinated families from a progeny trial located in Leiria, Portugal, that originated from seed collected in a clonal seed orchard. A total of 552 seventeen-year-old trees were sampled at 2 m height. Trends were studied from the pith outward in variance components and narrow-sense heritability (h2) of wood density components and ring-width characteristics as well as genetic correlations between cambial ages. Mean ring density (RD), minimum density (MND), maximum density (MXD), earlywood density (EWD), latewood density (LWD), earlywood width, latewood width, ring width, latewood percentage, and heterogeneity index were determined using X-ray densitometry procedures. RD had higher genetic control (h2 = 0.63), and heritability values of earlywood components (h2MND = 0.54, h2EWD = 0.60) exceeded those of latewood components (h2MXD = 0.34, h2LWD = 0.26). Heritabilities increased with ring number from pith for almost all wood density components, and there were high age–age genetic correlations for wood density traits (rg > 0.98). [ABSTRACT FROM AUTHOR]

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. [Copyright &y& Elsevier]

Our understanding of leaf acclimation in relation to irradiance of fully grown or juvenile trees is mainly based on research involving tropical wet forest species. We studied sun-shade plasticity of 24 leaf traits of 43 tree species in a Bolivian dry deciduous forest. Sampling was confined to small trees. For each species, leaves were taken from five of the most and five of the least illuminated crowns. Trees were selected based on the percentage of the hemisphere uncovered by other crowns. We examined leaf trait variation and the relation between trait plasticity and light demand, maximum adult stature, and ontogenetic changes in crown exposure of the species. Leaf trait variation was mainly related to differences among species and to a minor extent to differences in light availability. Traits related to the palisade layer, thickness of the outer cell wall, and Narea and Parea had the greatest plasticity, suggesting their importance for leaf function in different light environments. Short-lived pioneers had the highest trait plasticity. Overall plasticity was modest and rarely associated with juvenile light requirements, adult stature, or ontogenetic changes in crown exposure. Dry forest tree species had a lower light-related plasticity than wet forest species, probably because wet forests cast deeper shade. In dry forests light availability may be less limiting, and low water availability may constrain leaf trait plasticity in response to irradiance. [ABSTRACT FROM AUTHOR]

The two most important components of biodiversity, species diversity and genetic diversity, have generally been treated as separate topics, although a coordination between both components is believed to be critical for ecosystem stability and resilience. Based on a new trait concept that allows for the assessment of genetic diversity across species, the relationship between species diversity and genetic diversity was examined in eight forest tree communities composed of different tree genera including both climax and pioneer species. It was intended to check whether a trade-off exists between the two diversity components as was found in a few studies on animal species. Using several isozyme-gene systems as genetic markers, the genetic diversity across species within each of the tree communities was determined by two measures, the commonly used intraspecific genetic diversity averaged over species and the recently developed transspecific genetic diversity per species. Both data sets were compared with the corresponding community-specific species diversity resulting in a positive relationship between the two diversity components. A statistically significant positive correlation was established between the transspecific genetic diversity per species and the species diversity for three isozyme-gene systems. Beyond that, consistent results were obtained using different parameters of the diversity measure which characterize the total, the effective and the number of prevalent variants. The number of prevalent variants reflected most significantly the non-randomness of the observed diversity patterns. These findings can be explained by the observation that the pioneer tree species reveal a by far higher genetic diversity than the climax tree species, which means that an increase in species diversity, due to the addition of several pioneer species at the expense of one or two climax species, goes along with an increase in the level of genetic diversity. Forest tree communities with the highest degree of species diversity exhibit therefore the highest transspecific genetic diversity per species. This result was discussed with regard to the particular composition and stability of forest tree communities. [ABSTRACT FROM AUTHOR]

In forest genetics, restricted maximum likelihood (REML) estimation of (co)variance components from normal multiple-trait individual-tree models is affected by the absence of observations in any trait and individual. Missing records affect the form of the distribution of REML estimates of genetics parameters, or of functions of them, and the estimating equations are computationally involved when several traits are analysed. An alternative to REML estimation is a fully Bayesian approach through Markov chain Monte Carlo. The present research describes the use of the full conjugate Gibbs algorithm proposed by Cantet et al. (R.J.C. Cantet, A.N. Birchmeier, and J.P. Steibel. 2004. Genet. Sel. Evol. 36: 49–64) to estimate (co)variance components in multiple-trait individual-tree models. This algorithm converges faster to the marginal posterior densities of the parameters than regular data augmentation from multivariate normal data with missing records. An expression to calculate the deviance information criterion for the selection of linear parameters in normal multiple-trait models is also given. The developments are illustrated by means of data from different crosses of two species of Pinus. [ABSTRACT FROM AUTHOR]

The article presents a study on resistance breeding against nonnative pathogens in forest trees in North America. Genetic resistance potentially provides an invaluable management tool for restoring these disease-resistant species. Western white pine, American chestnut and American elm are among the species in which there are successful breeding programs for disease resistance.

The effects of five different tree species common in the temperate zone, i.e. beech (Fagus sylvatica L.), pedunculate oak (Quercus robur L.), Norway spruce (Picea abies [L.] Karst), Japanese larch (Larix leptolepis [Sichold and Zucc.] Gordon) and mountain pine (Pinus mugo Turra), on soil respiration, gross N mineralization and gross nitrification rates were investigated. Soils were sampled in spring and summer 2002 at a forest trial in Western Jutland, Denmark, where pure stands of the five tree species of the same age were growing on the same soil. Soil respiration, gross rates of N mineralization and nitrification were significantly higher in the organic layers than in the Ah horizons for all tree species and both sampling dates. In summer (July), the highest rates of soil respiration, gross N mineralization and gross nitrification were found in the organic layer under spruce, followed by beech > larch > oak > pine. In spring (April), these rates were also higher under spruce compared to the other tree species, but were significantly lower than in summer. For the Ah horizons no clear seasonal trend was observed for any of the processes examined. A linear relationship between soil respiration and gross N mineralization (r²=0.77), gross N mineralization and gross nitrification rates (r²=0.72), and between soil respiration and gross nitrification (r²=0.81) was found. The results obtained underline the importance of considering the effect of forest type on soil C and N transformations. [ABSTRACT FROM AUTHOR]

This article traces the emergence of industrial tree improvement along the Pacific Slope of western Oregon and Washington. Anxieties about timber famine in the United States prompted research on forest genetics and Douglas-fir provenance as far back as 1913, while diminishing supplies of old-growth timber resources in this region led to tree improvement—systematic tree breeding to enhance commercially attractive characteristics—on an industrial scale beginning in the 1950s and 1960s. Throughout, tree improvement has been characterized by a preponderance of co-operation among private, otherwise competitive capitalist firms, with considerable support from state agencies and from science in both research and applied settings. Pacific Slope tree improvement is explored as a case study of the social production of nature by capital and science, particularly the ways in which, in response to natural-resource constraints, the reproductive biology of forest trees has been increasingly targeted, appropriated, and subsumed as a source of industrial productivity. The general absence of exclusively private, proprietary approaches to tree improvement is discussed as a reflection of a set of particular biophysical challenges, including the “problem” of biological time. Thus, while biophysical nature is increasingly socially produced through tree improvement, the social organization of tree improvement bears the inscription of biophysical nature. The article closes with an examination of one of the main avenues by which biotechnology—including genetic engineering—is being incorporated into tree improvement. The new technological possibilities and opportunities for establishing exclusive property rights over plant varieties that biotechnology entails may lead to a more complete model of commodification in tree improvement. Some evidence of such change is already apparent. Though forestry biotechnology is subject to regulatory and wider social sanction, its advent reinforces a main theme in the article: that social and environmental change are interlocking, dialectical processes. [ABSTRACT FROM AUTHOR]

Calycophyllum spruceanum Benth. is an important tree for timber, charcoal and firewood in the Peruvian Amazon. The first provenance trial was established on farms in three zones located in one watershed in the Peruvian Amazon. The three zones differ in soil fertility and rainfall. Seven provenances from the Peruvian Amazon were tested in all three zones. Variation in four stem-growth traits (height, diameter, number of nodes and branches) and two branch-wood traits (basic density, heat content) was analyzed 18 months after establishment. There were significant differences in stem height and number of stem nodes among provenances in the analysis across zones. Provenance-related variation in stem-growth traits was most significant in the zone with the most fertile soils and highest rainfall. Branch-wood traits did not vary significantly among provenances in the analysis across zones or within zones. Branch-wood heat content was correlated with latitude, increasing from north to south, but this was only observed in a zone with low soil fertility and intermediate rainfall. Branch-wood density was correlated positively with stem diameter in the driest zone, but negatively with stem nodes in the intermediate zone and with stem height in the wettest zone. Results illustrate the potential for selection of fast-growing provenances, and the importance of replicating trials on different test environments to detect variation among provenances. [ABSTRACT FROM AUTHOR]

In the moist tropics, studies have demonstrated poor seedling establishment of late-successional trees on lands cleared of forest. Our study examined the potential for establishing late-successional tree species that dominate the canopy of rainforest by plating within and adjacent to experimental openings that were created within a Pinus caribaea plantation. We tested five canopy tree species (Dipterocarpus zeylanicus, Mesua ferrea, Shorea disticha, S. megistophylla and S. trapezifolia) of tropical forest in south-western Sri Lanka. Seedlings were monitored for 2 years within treatments that removed either three rows or one row of Pinus canopy, a canopy edge treatment and a control that left the canopy intact. The greatest growth and dry mass for all species were in the canopy removal treatments. In particular, S. trapezifolia and S. disticha exhibited the greatest height growth in these treatments. In the three-row canopy removal treatment, M. ferrea had a significantly lower dry mass than the other species. Differences were shown in the number and area of leaves among species. Shorea trapezifolia and, to a lesser degree, S. disticha increased area by increasing leaf production. Dipterocarpus zeylanicus and, to a lesser degree. M. ferrea increased area by increasing the size of individual leaves. Guidelines based on results from this study recommend that species grow best when seedling are planted within openings created by the removal of three rows of Pinus canopy. Where planting without canopy removal is required. S. disticha or S. megistophylla should be selected because of greater shade and drought tolerance. This experiment demonstrated that Pinus can be used as a nurse for facilitating the establishment of site-sensitive tropical forest tree species that are late-successional. In particular, results have application for similar mixed dipterocarp forest types in south-east Asia. [ABSTRACT FROM AUTHOR]

We developed genetic markers for three microsatellite loci in the tropical tree Symphonia globulifera and used them to examine the demographic genetic consequences of forest fragmentation. High levels of genetic variation were revealed in samples of adults, saplings, and seedlings. The more-variable loci exhibited less stability in allelic composition across sites and stages. The number of alleles per hectare (ha) of forest was similar when continuous forest plots were compared to plots from fragmented forest for all three stages. This pattern also held for the number of unique multilocus adult and sapling genotypes, but the number of unique seedling genotypes per ha of fragmented forest greatly exceeded expectations based on continuous forest data, probably due to the concentration of seeds into remnant forest patches by foraging bats. Significant inbreeding and genetic differentiation were most often associated with the fragmented forest and the seedlings. Finally, principal component analysis reaffirmed that a bottleneck, acting in concert with pre-existing genetic structure in the adults, had led to enhanced and rapid divergence in the seedlings following deforestation, a result that is of central interest for landscape management. [ABSTRACT FROM AUTHOR]

A mathematical model for a forest consisting of a single species of trees with a steady state distribution of age is suggested. The forest is self-sustained in the sense that trees put out seeds from which new trees will grow. Therefore, there will be trees of different year classes. The rules for tree cutting are obtained to maximize the physical yield from the forest. The rule of cutting is given by function u(τ) of the age τ of the tree which tells which fraction of all trees of age τ of the forest must be felled during unit time. Function u(τ) is obtained by using a slightly generalized optimal control theory which reduces the problem to a fairly simple nonlinear programming problem. The cost of harvesting may be included in the objective functional. All biological characteristics of a forest are contained in two functions of the age of a tree. These functions would be obtained through a process of identification. The model is intended to be a part of a large forest-economy system, therefore mathematical simplicity has been a goal. [ABSTRACT FROM AUTHOR]

In this paper, we demonstrate that the RAPD technique, and variations thereof, can be used in conjunction with high-resolution agarose gel electrophoresis to detect genetic variation among individuals within and between seed sources in a genetically uniform species such as red pine (Pinus resinosa Ait). A total of 57 primers that gave consistent, strongly amplified fragments were selected for further screening with DNA from four mutant trees and a rangewide sample of 21 normal trees. Only three of these primers generated amplification fragment patterns that were polymorphic. Restriction endonuclease digestion of RAPD reaction products (RAPD-RFLP analysis), using enzymes with four base pair recognition sequences, was used to determine if fragments of identical electrophoretic mobility were the result of priming at either single or multiple genomic locations. Out of 64 primer/enzyme combinations tested, one primer/enzyme combination created reproducible polymorphic banding patterns in rangewide red pine DNA samples. Therefore, digestion of RAPD reaction products can be used as a method to increase the probability of detecting genetic variation between highly conserved genomes. [ABSTRACT FROM AUTHOR]