Epigenetic variability in the genetically uniform forest tree species Pinus pinea L

There is an increasing interest in understanding the role of epigenetic variability in forest species and how it may contribute to their rapid adaptation to changing environments. In this study we have conducted a genome-wide analysis of cytosine methylation pattern in Pinus pinea, a species characterized by very low levels of genetic variation and a remarkable degree of phenotypic plasticity. DNA methylation profiles of different vegetatively propagated trees from representative natural Spanish populations of P. pinea were analyzed with the Methylation Sensitive Amplified Polymorphism (MSAP) technique. A high degree of cytosine methylation was detected (64.36% of all scored DNA fragments). Furthermore, high levels of epigenetic variation were observed among the studied individuals. This high epigenetic variation found in P. pinea contrasted with the lack of genetic variation based on Amplified Fragment Length Polymorphism (AFLP) data. In this manner, variable epigenetic markers clearly discriminate individuals and differentiates two well represented populations while the lack of genetic variation revealed with the AFLP markers fail to differentiate at both, individual or population levels. In addition, the use of different replicated trees allowed identifying common polymorphic methylation sensitive MSAP markers among replicates of a given propagated tree. This set of MSAPs allowed discrimination of the 70% of the analyzed trees.

Short-term response of the Ca cycle of a montane forest in Ecuador to low experimental CaCl2 additions

The tropical montane forests of the E Andean cordillera in Ecuador receive episodic Sahara- dust inputs particularly increasing Ca deposition. We added CaCl2 to isolate the effect of Ca deposition by Sahara dust to tropical montane forest from the simultaneously occurring pH effect. We examined components of the Ca cycle at four control plots and four plots with added Ca (2 × 5 kg ha?1 Ca annually as CaCl2) in a random arrangement. Between August 2007 and December 2009 (four applications of Ca), we determined Ca concentrations and fluxes in litter leachate, mineral soil solution (0.15 and 0.30 m depths), throughfall, and fine litterfall and Al con- centrations and speciation in soil solutions. After 1 y of Ca addition, we assessed fine-root bio- mass, leaf area, and tree growth. Only < 3% of the applied Ca leached below the acid organic layer (pH 3.5?4.8). The added CaCl2 did not change electrical conductivity in the root zone after 2 y. In the second year of fertilization, Ca retention in the canopy of the Ca treatment tended to decrease relative to the control. After 2 y, 21% of the applied Ca was recycled to soil with throughfall and litterfall. One year after the first Ca addition, fine-root biomass had decreased significantly. Decreasing fine-root biomass might be attributed to a direct or an indirect beneficial effect of Ca on the soil decomposer community. Because of almost complete association of Al with dissolved organic matter and high free Ca2+ : Al3+ activity ratios in solution of all plots, Al toxicity was unlikely. We conclude that the added Ca was retained in the system and had benefi- cial effects on some plants.

A test of alternative models of diversification in tropical rainforests: Ecological gradients vs. rainforest refugia

Comparison of mitochondrial and morphological divergence in eight populations of a widespread leaf-litter skink is used to determine the relative importance of geographic isolation and natural selection in generating phenotypic diversity in the Wet Tropics Rainforest region of Australia. The populations occur in two geographically isolated regions, and within each region, in two different habitats (closed rainforest and tall open forest) that span a well characterized ecological gradient. Morphological differences among ancient geographic isolates (separated for several million years, judging by their mitochondrial DNA sequence divergence) were slight, but morphological and life history differences among habitats were large and occurred despite moderate to high levels of mitochondrial gene flow. A field experiment identified avian predation as one potential agent of natural selection. These results indicate that natural selection operating across ecological gradients can be more important than geographic isolation in similar habitats in generating phenotypic diversity. In addition, our results indicate that selection is sufficiently strong to overcome the homogenizing effects of gene flow, a necessary first step toward speciation in continuously distributed populations. Because ecological gradients may be a source of evolutionary novelty, and perhaps new species, their conservation warrants greater attention. This is particularly true in tropical regions, where most reserves do not include ecological gradients and transitional habitats.

Sampling scarab beetles in tropical forests: the effect of light source and night sampling periods

Light traps have been used widely to sample insect abundance and diversity, but their performance for sampling scarab beetles in tropical forests based on light source type and sampling hours throughout the night has not been evaluated. The efficiency of mercury-vapour lamps, cool white light and ultraviolet light sources in attracting Dynastinae, Melolonthinae and Rutelinae scarab beetles, and the most adequate period of the night to carry out the sampling was tested in different forest areas of Costa Rica. Our results showed that light source wavelengths and hours of sampling influenced scarab beetle catches. No significant differences were observed in trap performance between the ultraviolet light and mercury-vapour traps, whereas these two methods caught significantly more species richness and abundance than cool white light traps. Species composition also varied between methods. Large differences appear between catches in the sampling period, with the first five hours of the night being more effective than the last five hours. Because of their high efficiency and logistic advantages, we recommend ultraviolet light traps deployed during the first hours of the night as the best sampling method for biodiversity studies of those scarab beetles in tropical forests.

Tropical climate and vegetation simulations during the Heinrich event 1 using an Earth System Model of Intermediate Complexity (EMIC) - the University of Victoria Earth System-Climate Model (UVic ESCM)

Abrupt climate changes from 18 to 15 thousand years before present (kyr BP) associated with Heinrich Event 1 (HE1) had a strong impact on vegetation patterns not only at high latitudes of the Northern Hemisphere, but also in the tropical regions around the Atlantic Ocean. To gain a better understanding of the linkage between high and low latitudes, we used the University of Victoria (UVic) Earth System-Climate Model (ESCM) with dynamical vegetation and land surface components to simulate four scenarios of climate-vegetation interaction: the pre-industrial era, the Last Glacial Maximum (LGM), and a Heinrich-like event with two different climate backgrounds (interglacial and glacial). We calculated mega-biomes from the plant-functional types (PFTs) generated by the model to allow for a direct comparison between model results and palynological vegetation reconstructions. Our calculated mega-biomes for the pre-industrial period and the LGM corresponded well with biome reconstructions of the modern and LGM time slices, respectively, except that our pre-industrial simulation predicted the dominance of grassland in southern Europe and our LGM simulation resulted in more forest cover in tropical and sub-tropical South America. The HE1-like simulation with a glacial climate background produced sea-surface temperature patterns and enhanced inter-hemispheric thermal gradients in accordance with the "bipolar seesaw" hypothesis. We found that the cooling of the Northern Hemisphere caused a southward shift of those PFTs that are indicative of an increased desertification and a retreat of broadleaf forests in West Africa and northern South America. The mega-biomes from our HE1 simulation agreed well with paleovegetation data from tropical Africa and northern South America. Thus, according to our model-data comparison, the reconstructed vegetation changes for the tropical regions around the Atlantic Ocean were physically consistent with the remote effects of a Heinrich event under a glacial climate background.

U.S.D.A. Forest Service research note ITF.

Mode of access: Internet.

Forest Service research paper ITF.

Mode of access: Internet.

Evolution of tropical forestry : Puerto Rico and beyond : an interview with Frank H. Wadsworth /

"FS-610."

Development of forest structure on cleared rainforest land in eastern Australia under different styles of reforestation

Rainforests in eastern Australia have been extensively cleared over the past two centuries. In recent decades, there have been increasing efforts to reforest some of these cleared lands, using a variety of methods, to meet a range of economic and environmental objectives. However, the extent to which the various styles of reforestation restore structure, composition and ecological function to cleared land is not presently understood. In this study, we develop and apply a method for quantifying the structural attributes of reforestation sites in tropical and subtropical Australia. The types of reforestation studied were plantation monocultures, mixed-species cabinet timber plots, diverse restoration plantings and unmanaged regrowth. Two age classes of reforestation were examined: 'young' (5-22 years), incorporating sites from all categories, and 'old' (30-70 years), in which only monoculture plantations and regrowth were represented. A total of 104 sites were surveyed including reference sites in intact rainforest and pasture. Intact rainforest was characterised by a suite of complex structural features including abundant special life forms (vines, epiphytes, hemi-epiphytes and strangler figs), a dense stand of trees in a range of size classes, a closed canopy, a shrubby understorey and a well-developed ground layer of leaf litter and woody debris. These features were lost on conversion to pasture. While all types of reforestation returned some elements of structural complexity to cleared land, young plantation monocultures, cabinet timber plots and young regrowth had a relatively simple structure. These sites typically had a low density of woody stems, a relatively open canopy and grassy ground cover, and lacked large trees, coarse woody debris and most special life forms. Restoration plantings and old regrowth were more complex, with a high density of woody stems, a relatively closed canopy and shrubby understorey. Old monoculture plantations in the tropics had acquired many of the structural attributes of intact forest, however this was not the case in the subtropics, where plantations were subject to more intensive management. The marked differences in structural complexity between sites suggest that the different types of reforestation practiced in eastern Australia are likely to vary considerably in their value as habitat for rainforest biota. (C) 2003 Elsevier Science B.V. All rights reserved.

Genetic effects of chronic habitat fragmentation on tree species: the case of Sorbus aucuparia in a deforested Scottish landscape

Sustainable forest restoration and management practices require a thorough understanding of the influence that habitat fragmentation has on the processes shaping genetic variation and its distribution in tree populations. We quantified genetic variation at isozyme markers and chloroplast DNA (cpDNA), analysed by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) in severely fragmented populations of Sorbus aucuparia (Rosaceae) in a single catchment (Moffat) in southern Scotland. Remnants maintain surprisingly high levels of gene diversity (H-E) for isozymes (H-E = 0.195) and cpDNA markers (H-E = 0.490). Estimates are very similar to those from non-fragmented populations in continental Europe, even though the latter were sampled over a much larger spatial scale. Overall, no genetic bottleneck or departures from random mating were detected in the Moffat fragments. However, genetic differentiation among remnants was detected for both types of marker (isozymes Theta(n) = 0.043, cpDNA Theta(c) = 0.131; G-test, P-value < 0.001). In this self-incompatible, insect-pollinated, bird-dispersed tree species, the estimated ratio of pollen flow to seed flow between fragments is close to 1 (r = 1.36). Reduced pollen-mediated gene flow is a likely consequence of habitat fragmentation, but effective seed dispersal by birds is probably helping to maintain high levels of genetic diversity within remnants and reduce genetic differentiation between them.

Monitoring genetic diversity in tropical trees with multilocus dominant markers

Since no universal codominant markers are currently available, dominant genetic markers, such as amplified fragment length polymorphism (AFLP), are valuable tools for assessing genetic diversity in tropical trees. However, the measurement of genetic diversity (H) with dominant markers depends on the frequency of null homozygotes (Q) and the fixation index (F) of populations. While Q can be estimated for AFLP loci, F is less accessible. Through a modelling approach, we show that the monolocus estimation of genetic diversity is strongly dependent on the value of F, but that the multilocus diversity estimate is surprisingly robust to variations in F. The robustness of the estimate is due to a mechanistic effect of compensation between negative and positive biases of H by different AFLP loci exhibiting contrasting frequency profiles of Q. The robustness was tested across contrasting theoretical frequency profiles of Q and verified for 10 neotropical species. Practical recommendations for the implementation of this analytical method are given for genetic surveys in tropical trees, where such markers are widely applied.

Links between tree species, symbiotic fungal diversity and ecosystem functioning in simplified tropical ecosystems

We studied the relationships among plant and arbuscular mycorrhizal (AM) fungal diversity, and their effects on ecosystem function, in a series of replicate tropical forestry plots in the La Selva Biological Station, Costa Rica. Forestry plots were 12 yr old and were either monocultures of three tree species, or polycultures of the tree species with two additional understory species. Relationships among the AM fungal spore community, host species, plant community diversity and ecosystem phosphorus-use efficiency (PUE) and net primary productivity (NPP) were assessed. Analysis of the relative abundance of AM fungal spores found that host tree species had a significant effect on the AM fungal community, as did host plant community diversity (monocultures vs polycultures). The Shannon diversity index of the AM fungal spore community differed significantly among the three host tree species, but was not significantly different between monoculture and polyculture plots. Over all the plots, significant positive relationships were found between AM fungal diversity and ecosystem NPP, and between AM fungal community evenness and PUE. Relative abundance of two of the dominant AM fungal species also showed significant correlations with NPP and PUE. We conclude that the AM fungal community composition in tropical forests is sensitive to host species, and provide evidence supporting the hypothesis that the diversity of AM fungi in tropical forests and ecosystem NPP covaries.

Chloroplast and total genomic diversity in the endemic Costa Rican tree Lonchocarpus costaricensis (J.D. Smith) Pittier (Papilionaceae).

In Mesoamerica, tropical dry forest is a highly threatened habitat, and species endemic to this environment are under extreme pressure. The tree species, Lonchocarpus costaricensis is endemic to the dry northwest of Costa Rica and southwest Nicaragua. It is a locally important species but, as land has been cleared for agriculture, populations have experienced considerable reduction and fragmentation. To assess current levels and distribution of genetic diversity in the species, a combination of chloroplast-specific (cpDNA) and whole genome DNA markers (amplified fragment length polymorphism, AFLP) were used to fingerprint 121 individual trees in 6 populations. Two cpDNA haplotypes were identified, distributed among populations such that populations at the extremes of the distribution showed lowest diversity. A large number (487) of AFLP markers were obtained and indicated that diversity levels were highest in the two coastal populations (Cobano, Matapalo, H = 0.23, 0.28 respectively). Population differentiation was low overall, F-ST = 0.12, although Matapalo was strongly differentiated from all other populations (F-ST = 0.16-0.22), apart from Cobano (F., = 0.11). Spatial genetic structure was present in both datasets at different scales: cpDNA was structured at a range-wide distribution scale, whilst AFLP data revealed genetic neighbourhoods on a population scale. In general, the habitat degradation of recent times appears not to have yet impacted diversity levels in mature populations. However, although no data on seed or saplings were collected, it seems likely that reproductive mechanisms in the species will have been affected by land clearance. It is recommended that efforts should be made to conserve the extant genetic resource base and further research undertaken to investigate diversity levels in the progeny generation.

Integrating JERS-1 imaging radar and elevation models for mapping tropical rainforest communities in far North Queensland, Australia

The Wet Tropics World Heritage Area in Far North Queens- land, Australia consists predominantly of tropical rainforest and wet sclerophyll forest in areas of variable relief. Previous maps of vegetation communities in the area were produced by a labor-intensive combination of field survey and air-photo interpretation. Thus,. the aim of this work was to develop a new vegetation mapping method based on imaging radar that incorporates topographical corrections, which could be repeated frequently, and which would reduce the need for detailed field assessments and associated costs. The method employed G topographic correction and mapping procedure that was developed to enable vegetation structural classes to be mapped from satellite imaging radar. Eight JERS-1 scenes covering the Wet Tropics area for 1996 were acquired from NASDA under the auspices of the Global Rainforest Mapping Project. JERS scenes were geometrically corrected for topographic distortion using an 80 m DEM and a combination of polynomial warping and radar viewing geometry modeling. An image mosaic was created to cover the Wet Tropics region, and a new technique for image smoothing was applied to the JERS texture bonds and DEM before a Maximum Likelihood classification was applied to identify major land-cover and vegetation communities. Despite these efforts, dominant vegetation community classes could only be classified to low levels of accuracy (57.5 percent) which were partly explained by the significantly larger pixel size of the DEM in comparison to the JERS image (12.5 m). In addition, the spatial and floristic detail contained in the classes of the original validation maps were much finer than the JERS classification product was able to distinguish. In comparison to field and aerial photo-based approaches for mapping the vegetation of the Wet Tropics, appropriately corrected SAR data provides a more regional scale, all-weather mapping technique for broader vegetation classes. Further work is required to establish an appropriate combination of imaging radar with elevation data and other environmental surrogates to accurately map vegetation communities across the entire Wet Tropics.

Regional and population-scale influences on genetic diversity partitioning within costa rican populations of the pioneer tree Vochysia ferruginea mart.

The neotropical pioneer species Vochysia ferruginea is locally important for timber and is being increasingly exploited. The sustainable utilisation of this species would benefit from an understanding of the level and partitioning of genetic diversity within remnant and secondary regrowth populations. We used data from total genome (amplified fragment length polymorphism, AFLP) and chloroplast genome markers to assay diversity levels within seven Costa Rican populations. Significant chloroplast differentiation between Atlantic and Pacific watersheds was observed, suggesting divergent historical origins for these populations. Contemporary gene flow, though extensive, is geographically constrained and a clear pattern of isolation by distance was detectable when an inter-population distance representing gene flow around the central Costa Rican mountain range was used. Overall population differentiation was low (F-ST = 0.15) and within-population diversity high, though variable (H-s=0.16-0.32), which fits with the overall pattern of population genetic structure expected for a widespread, outcrossed tropical tree. However genetic diversity was significantly lower and differentiation higher for recently colonised and disturbed populations compared to that at more established sites. Such a pattern seems indicative of a pioneer species undergoing repeated cycles of colonisation and succession.