Modelling growth, recruitment and mortality to describe and simulate dynamics of subtropical rainforests following different levels of disturbance

The capacity of rainforests to recover from logging disturbance is difficult to model due to the compounding interactions between long-term disturbance effects, natural dynamics, site characteristics and tree species regeneration strategies. The aim of this study was to develop a quantitative model using over three decades of data from stands subjected to various levels of disturbance ranging from natural, through increasing intensities of tree removal to intensive logging. Data for trees >10 cm diameter at 1.3 m above the ground (dbh) in subtropical rainforest of north-east New South Wales, Australia were used. Botanical identity of trees at species level, species-specific shade tolerance and size at maturity were used to classify 117 species into five groups. These groups include the emergent and shade tolerant main canopy species, shade tolerant mid canopy species, shade tolerant understorey species, moderate shade tolerant species, and shade intolerant tree species. Multilevel nonlinear regression was used to estimate growth, recruitment and mortality parameters, based on the assumption of variations in tree species performance at both the plot and tree levels. The species group, tree size and competition from larger trees accounted for most variation at the tree level. Significant stand level variables included topography (elevation, slope and aspect), stand basal area, and time since the disturbance. The final model is a classical matrix management-oriented model with an ecological basis and maximum size-dependent parameters of ingrowth and outgrowth. The model provides a tool to simulate stand performance after logging and to assess silvicultural prescriptions before they are applied. Simulations with estimated parameters indicate that moderate harvesting (47% overstorey basal area (BA) removal) in a checkerboard of logged and unlogged patches (group selection) on a 120-year cycle could enable sustainable timber production without compromising the ecological integrity in these rainforests. This is due to reduced logging damage in group selection, which also released retained stems and facilitated recruitment of both shade tolerant and intolerant trees. Single-tree selection (35% BA removal) created small canopy gaps that resulted in low recruitment, a slight increase in the growth of retained stems and recovery time of 150 years. Intensive single-tree selection (50% BA removal) resulted in high logging damage that increased recovery time to 180 years. Intensive logging (65-80% BA removal) decreased the stem density and created larger canopy gaps allowing for high growth rates and recruitment of both shade tolerant and intolerant trees. However, few retained stems and high mortality of recruits, increased the recovery time to 180-220 years. Pre-harvest climber cutting coupled with poisoning of nontimber species followed by logging could allow harvesting on a 300-year cycle. Shorter logging cycles may lead to changes in species composition as well as in the forest structure

Resolving Australian analogs for an Eocene Patagonian paleorainforest using leaf size and floristics

• Premise of the study: The diverse early Eocene flora from Laguna del Hunco (LH) in Patagonia, Argentina has many nearest living relatives (NLRs) in Australasia but few in South America, indicating the differential survival of an ancient, trans‐Antarctic rainforest biome. To better understand this significant biogeographic pattern, we used detailed comparisons of leaf size and floristics to quantify the legacy of LH across a large network of Australian rainforest‐plot assemblages. • Methods: We applied vein scaling, a new method for estimating the original areas of fragmented leaves. We then compared leaf size and floristics at LH with living Australian assemblages and tabulated the climates of those where NLRs occur, along with additional data on climatic ranges of “ex‐Australian” NLRs that survive outside of Australia. • Key results: Vein scaling estimated areas as accurately as leaf‐size classes. Applying vein scaling to fossil fragments increased the grand mean area of LH by 450 mm2, recovering more originally large leaves. The paleoflora has a majority of microphyll leaves, comparable to leaf litter in subtropical Australian forests, which also have the greatest floristic similarity to LH. Tropical Australian assemblages also share many taxa with LH, and ex‐Australian NLRs mostly inhabit cool, wet montane habitats no longer present in Australia. • Conclusions: Vein scaling is valuable for improving the resolution of fossil leaf‐size distributions by including fragmented specimens. The legacy of LH is evident not only in subtropical and tropical Australia but also in tropical montane Australasia and Southeast Asia, reflecting the disparate histories of surviving Gondwanan lineages.Fil: Merkhofer, Lisa. State University of Pennsylvania; Estados UnidosFil: Wilf, Peter. State University of Pennsylvania; Estados UnidosFil: Haas, M. Tyler. State University of Pennsylvania; Estados UnidosFil: Kooyman, Robert M.. Macquarie University; AustraliaFil: Sack, Lawren. University of California at Los Angeles; Estados UnidosFil: Scoffoni, Christine. University of California at Los Angeles; Estados UnidosFil: Cúneo, Néstor Rubén. Museo Paleontológico Egidio Feruglio; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentin

Patterns and drivers of plant diversity across Australia

Biodiversity analyses across continental extents are important in providing comprehensive information on patterns and likely drivers of diversity. For vascular plants in Australia, community-level diversity analyses have been restricted by the lack of a consistent plot-based survey dataset across the continent. To overcome these challenges, we collated and harmonised plot-based vegetation survey data from the major data sources across Australia and used them as the basis for modelling species richness (α-diversity) and community compositional dissimilarity (β-diversity), standardised to 400 m2, with the aim of mapping diversity patterns and identifying potential environmental drivers. The harmonised Australian vegetation plot (HAVPlot) dataset includes 219 552 plots, of which we used 115 083 to analyse plant diversity. Models of species richness and compositional dissimilarity both explained approximately one-third of the variation in plant diversity across Australia (D2 = 33.0% and 32.7%, respectively). The strongest environmental predictors for both aspects of diversity were a combination of temperature and precipitation, with soil texture and topographic heterogeneity also important. The fine-resolution (≈ 90 m) spatial predictions of species richness and compositional dissimilarity identify areas expected to be of particular importance for plant diversity, including south-western Australia, rainforests of eastern Australia and the Australian Alps. Arid areas of central and western Australia are predicted to support assemblages that are less speciose or unique; however, these areas are most in need of additional survey data to fill the spatial, environmental and taxonomic gaps in the HAVPlot dataset. The harmonised data and model predictions presented here provide new insight into plant diversity patterns across Australia, enabling a wide variety of future research, such as exploring changes in species abundances, linking compositional patterns to functional traits or undertaking conservation assessments for selected components of the flora

Functional distinctiveness of major plant lineages

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/106060/1/jec12208.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/106060/2/jec12208-sup-0001-Supp_Info.pd

Regeneration Changes in Tree Species Abundance, Diversity and Structure in Logged and Unlogged Subtropical Rainforest over a Thirty-Six-Year Period

The long-term effects of logging treatments on rainforest regeneration are difficult to quantify due to compounding interactions between natural dynamics, site characteristics and tree species. The aim of this study was to compare regeneration differences over a 36 year period in stands subjected to various levels of disturbance ranging from natural, through an increasing intensity of individual tree removal to intensive logging. Data for tree

Plant functional traits have globally consistent effects on competition.

Phenotypic traits and their associated trade-offs have been shown to have globally consistent effects on individual plant physiological functions, but how these effects scale up to influence competition, a key driver of community assembly in terrestrial vegetation, has remained unclear. Here we use growth data from more than 3 million trees in over 140,000 plots across the world to show how three key functional traits--wood density, specific leaf area and maximum height--consistently influence competitive interactions. Fast maximum growth of a species was correlated negatively with its wood density in all biomes, and positively with its specific leaf area in most biomes. Low wood density was also correlated with a low ability to tolerate competition and a low competitive effect on neighbours, while high specific leaf area was correlated with a low competitive effect. Thus, traits generate trade-offs between performance with competition versus performance without competition, a fundamental ingredient in the classical hypothesis that the coexistence of plant species is enabled via differentiation in their successional strategies. Competition within species was stronger than between species, but an increase in trait dissimilarity between species had little influence in weakening competition. No benefit of dissimilarity was detected for specific leaf area or wood density, and only a weak benefit for maximum height. Our trait-based approach to modelling competition makes generalization possible across the forest ecosystems of the world and their highly diverse species composition.We are especially grateful to the researchers whose long-term commitment to establish and maintain forest plots and their associated databases made this study possible, and to those who granted us data access: forest inventories and permanent plots of New Zealand, Spain (MAGRAMA), France, Switzerland, Sweden, US and Canada (for the provinces of Quebec provided by the Ministère des Ressources Naturelles du Québec, Ontario provided by OnTAP’s Growth and Yield Program of the Ontario Ministry of Natural Resources, Saskatchewan, Manitoba, New Brunswick, Newfoundland and Labrador), CTFS (BCI and LTER-Luquillo), Taiwan (Fushan), Cirad (Paracou with funding by CEBA, ANR-10-LABX-25-01), Cirad, MEFCP and ICRA (M’Baïki) and Japan. We thank MPI-BGC Jena, who host TRY, and the international funding networks supporting TRY (IGBP, DIVERSITAS, GLP, NERC, QUEST, FRB and GIS Climate). G.K. was supported by a Marie Curie International Outgoing Fellowship within the 7th European Community Framework Program (Demo-Traits project, no. 299340). The working group that initiated this synthesis was supported by Macquarie University and by Australian Research Council through a fellowship to M.W.This is the author accepted manuscript. The final version is available from Nature Publishing Group via http://dx.doi.org/10.1038/nature1647

Diameter Growth Performance Varies with Species Functional-Group and Habitat Characteristics in Subtropical Rainforests

We examined tree diameter growth in 20 plots subjected to various disturbance intensities (natural, low, moderate and intensive logging) in a bid to understand the general tree growth responses in relation to habitat characteristics in subtropical rainforests of north-eastern New South Wales, Australia. Species-specific regeneration strategy, maximum size and level of shade tolerance were used to classify species into 5 groups; emergent and shade tolerant main canopy (group 1), shade tolerant mid canopy (2), shade tolerant understoreys (3), moderate shade tolerant (4), and shade intolerant (5) tree species. Data series for trees >10 cm diameter at 1.3 m above the ground level (dbh) providing observations spanning over 36 years were used in multilevel regression analyses. The results showed that spatial and temporal effects in tree growth at the stand-level are a combination of the differences between species functional group compositions and environmental gradients. High growth responses were observed in the shade intolerant species while increasing level of shade tolerance and decreasing maximum size decreased trees growth rates. Tree growth increased with altitude on a large scale across regions, and with disturbance intensity on a small scale at the plot (stand) level. Increase in northness (south through flat to north facing sites) increased growth in species group 1 for trees < 67 cm dbh, but beyond this dbh threshold the opposite was true. These showed that saplings of species group 1 may require increased illumination to reach the forest canopy, but once in the canopy, low soil water availability may be limiting to tree growth in the north facing sites. Decrease in northness was associated with increased growth in species group 2 indicating that reduced illumination and improved soil moisture in the south facing sites were conducive for maximum growth in this species group. Maximum growth potential in species group 4 and 5 increased with decrease in eastness, suggesting that the increased afternoon solar radiation and temperature were conducive for high growth rates in these species. Although topographic gradient may determine the spatial and temporal variations in tree growth where growth appeared to increase from the crest down the slope into the creek, its effects on soil fertility and water availability, and interactions between these and other factors may make it difficult to discern clear growth patterns

The retrospective analysis of Antarctic tracking data project

The Retrospective Analysis of Antarctic Tracking Data (RAATD) is a Scientific Committee for Antarctic Research project led jointly by the Expert Groups on Birds and Marine Mammals and Antarctic Biodiversity Informatics, and endorsed by the Commission for the Conservation of Antarctic Marine Living Resources. RAATD consolidated tracking data for multiple species of Antarctic meso- and top-predators to identify Areas of Ecological Significance. These datasets and accompanying syntheses provide a greater understanding of fundamental ecosystem processes in the Southern Ocean, support modelling of predator distributions under future climate scenarios and create inputs that can be incorporated into decision making processes by management authorities. In this data paper, we present the compiled tracking data from research groups that have worked in the Antarctic since the 1990s. The data are publicly available through biodiversity.aq and the Ocean Biogeographic Information System. The archive includes tracking data from over 70 contributors across 12 national Antarctic programs, and includes data from 17 predator species, 4060 individual animals, and over 2.9 million observed locations

Common and rare variant association analyses in amyotrophic lateral sclerosis identify 15 risk loci with distinct genetic architectures and neuron-specific biology

Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease with a lifetime risk of one in 350 people and an unmet need for disease-modifying therapies. We conducted a cross-ancestry genome-wide association study (GWAS) including 29,612 patients with ALS and 122,656 controls, which identified 15 risk loci. When combined with 8,953 individuals with whole-genome sequencing (6,538 patients, 2,415 controls) and a large cortex-derived expression quantitative trait locus (eQTL) dataset (MetaBrain), analyses revealed locus-specific genetic architectures in which we prioritized genes either through rare variants, short tandem repeats or regulatory effects. ALS-associated risk loci were shared with multiple traits within the neurodegenerative spectrum but with distinct enrichment patterns across brain regions and cell types. Of the environmental and lifestyle risk factors obtained from the literature, Mendelian randomization analyses indicated a causal role for high cholesterol levels. The combination of all ALS-associated signals reveals a role for perturbations in vesicle-mediated transport and autophagy and provides evidence for cell-autonomous disease initiation in glutamatergic neurons. A cross-ancestry genome-wide association meta-analysis of amyotrophic lateral sclerosis (ALS) including 29,612 patients with ALS and 122,656 controls identifies 15 risk loci with distinct genetic architectures and neuron-specific biology