An essential textbook for any student or researcher in biology needing to design experiments, sample programs or analyse the resulting data The text begins with a revision of estimation and hypothesis testing methods, covering both classical and Bayesian philosophies, before advancing to the analysis of linear and generalized linear models Topics covered include linear and logistic regression, simple and complex ANOVA models (for factorial, nested, block, split-plot and repeated measures and covariance designs), and log-linear models Multivariate techniques, including classification and ordination, are then introduced Special emphasis is placed on checking assumptions, exploratory data analysis and presentation of results The main analyses are illustrated with many examples from published papers and there is an extensive reference list to both the statistical and biological literature The book is supported by a website that provides all data sets, questions for each chapter and links to software

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Experimental Design and Data Analysis for Biologists

I. the origin of species by means of natural selection

The Lund-Potsdam-Jena Dynamic Global Vegetation Model (LPJ) combines process-based, large-scale representations of terrestrial vegetation dynamics and land-atmosphere carbon and water exchanges in a modular framework. Features include feedback through canopy conductance between photosynthesis and transpiration and interactive coupling between these 'fast' processes and other ecosystem processes including resource competition, tissue turnover, population dynamics, soil organic matter and litter dynamics and fire disturbance. Ten plants functional types (PFTs) are differentiated by physiological, morphological, phenological, bioclimatic and fire-response attributes. Resource competition and differential responses to fire between PFTs influence their relative fractional cover from year to year. Photosynthesis, evapotranspiration and soil water dynamics are modelled on a daily time step, while vegetation structure and PFT population densities are updated annually. Simulations have been made over the industrial period both for specific sites where field measurements were available for model evaluation, and globally on a 0.5degrees x 0.5degrees grid. Modelled vegetation patterns are consistent with observations, including remotely sensed vegetation structure and phenology. Seasonal cycles of net ecosystem exchange and soil moisture compare well with local measurements. Global carbon exchange fields used as input to an atmospheric tracer transport model (TM2) provided a good fit to observed seasonal cycles of CO2 concentration at all latitudes. Simulated inter-annual variability of the global terrestrial carbon balance is in phase with and comparable in amplitude to observed variability in the growth rate of atmospheric CO2 . Global terrestrial carbon and water cycle parameters (pool sizes and fluxes) lie within their accepted ranges. The model is being used to study past, present and future terrestrial ecosystem dynamics, biochemical and biophysical interactions between ecosystems and the atmosphere, and as a component of coupled Earth system models.

Evaluation of ecosystem dynamics, plant geography and terrestrial carbon cycling in the LPJ dynamic global vegetation model

Publisher Summary In this chapter, the advances that have been made in understanding the ecology of the mineral nutrition of wild plants from terrestrial ecosystems have been reviewed. This chapter is organized along three lines. First, the issues of nutrient-limited plant growth and nutrient uptake, with special emphasis on the importance of the uptake of nutrients in organic form—both by mycorrhizal and by non-mycorrhizal plants—and the importance of symbiotic nitrogen fixation is treated. In addition, the influence of allocation patterns on mineral nutrient uptake is described. Next, a few of the nutritional aspects of leaf functioning and how nutrients are used for biomass production by the plant are explored. That is done by studying the nutrient use efficiency (NUE) of plants and the various components of NUE. Finally, the feedback of plant species to soil nutrient availability by reviewing patterns in litter decomposition and nutrient mineralization is investigated. The chapter concludes with a synthesis of the various aspects of the mineral nutrition of wild plants. The chapter ends with a conceptual description of plant strategies with respect to mineral nutrition.

The Mineral Nutrition of Wild Plants Revisited: A Re-evaluation of Processes and Patterns

Couplings Between Changes in the Climate System and Biogeochemistry Coordinating Lead Authors: Kenneth L. Denman (Canada), Guy Brasseur (USA, Germany) Lead Authors: Amnat Chidthaisong (Thailand), Philippe Ciais (France), Peter M. Cox (UK), Robert E. Dickinson (USA), Didier Hauglustaine (France), Christoph Heinze (Norway, Germany), Elisabeth Holland (USA), Daniel Jacob (USA, France), Ulrike Lohmann (Switzerland), Srikanthan Ramachandran (India), Pedro Leite da Silva Dias (Brazil), Steven C. Wofsy (USA), Xiaoye Zhang (China) Contributing Authors: D. Archer (USA), V. Arora (Canada), J. Austin (USA), D. Baker (USA), J.A. Berry (USA), R. Betts (UK), G. Bonan (USA), P. Bousquet (France), J. Canadell (Australia), J. Christian (Canada), D.A. Clark (USA), M. Dameris (Germany), F. Dentener (EU), D. Easterling (USA), V. Eyring (Germany), J. Feichter (Germany), P. Friedlingstein (France, Belgium), I. Fung (USA), S. Fuzzi (Italy), S. Gong (Canada), N. Gruber (USA, Switzerland), A. Guenther (USA), K. Gurney (USA), A. Henderson-Sellers (Switzerland), J. House (UK), A. Jones (UK), C. Jones (UK), B. Karcher (Germany), M. Kawamiya (Japan), K. Lassey (New Zealand), C. Le Quere (UK, France, Canada), C. Leck (Sweden), J. Lee-Taylor (USA, UK), Y. Malhi (UK), K. Masarie (USA), G. McFiggans (UK), S. Menon (USA), J.B. Miller (USA), P. Peylin (France), A. Pitman (Australia), J. Quaas (Germany), M. Raupach (Australia), P. Rayner (France), G. Rehder (Germany), U. Riebesell (Germany), C. Rodenbeck (Germany), L. Rotstayn (Australia), N. Roulet (Canada), C. Sabine (USA), M.G. Schultz (Germany), M. Schulz (France, Germany), S.E. Schwartz (USA), W. Steffen (Australia), D. Stevenson (UK), Y. Tian (USA, China), K.E. Trenberth (USA), T. Van Noije (Netherlands), O. Wild (Japan, UK), T. Zhang (USA, China), L. Zhou (USA, China) Review Editors: Kansri Boonpragob (Thailand), Martin Heimann (Germany, Switzerland), Mario Molina (USA, Mexico) This chapter should be cited as: Denman, K.L., G. Brasseur, A. Chidthaisong, P. Ciais, P.M. Cox, R.E. Dickinson, D. Hauglustaine, C. Heinze, E. Holland, D. Jacob, U. Lohmann, S Ramachandran, P.L. da Silva Dias, S.C. Wofsy and X. Zhang, 2007: Couplings Between Changes in the Climate System and Biogeochemistry. In: Climate Change 2007: The Physical Science Basis. Contribution of Working Group I to the Fourth Assessment Report of the Intergovernmental Panel on Climate Change [Solomon, S., D. Qin, M. Manning, Z. Chen, M. Marquis, K.B. Averyt, M.Tignor and H.L. Miller (eds.)]. Cambridge University Press, Cambridge, United Kingdom and New York, NY, USA.

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Couplings between changes in the climate system and biogeochemistry

Publisher Summary This chapter reviews the evidence for the pattern of growth decline with age and discusses the evidence for the mechanisms that may be responsible. It begins with an overview of the proposed mechanisms. The chapter also presents a framework for understanding the changes in stand productivity with age, because many of the proposed mechanisms are linked and affect carbon allocation. The available information on the importance of various mechanisms behind growth decline, in the context of the stand carbon cycle is presented. The common patterns of a decline in stand leaf area and leaf photosynthetic capacity suggest a new model of carbon balance with stand development. In this model, photosynthesis and above-ground dry-matter production increase with canopy development. After the forest reaches a maximum leaf area, photosynthesis and dry-matter production decline as leaf area, photosynthetic capacity, and photosynthesis also decline. The model assumes that allocation to respiration and below ground to roots and symbionts is a constant fraction of assimilation over the life of a forest stand.

Age-Related Decline in Forest Productivity: Pattern and Process

We tested the Walker and Syers (1976) conceptual model of soil development and its ecological implications by analyzing changes in soil P, vegetation, and other ecosystem properties on a soil chronosequence with six sites ranging in age from 300 yr to 4.1 x 10 6 yr. Climate, dominant vegetation, slope, and parent material of all of the sites were similar. As fractions of total P, the various pools of soil phosphorus behaved very much as predicted by Walker and Syers. HCl-extractable P (presumably primary mineral phosphates) comprised 82% of total P at the 300-yr-old site, and then decreased to 1% at the 20,000-yr-old site. Organic phosphorus increased from the youngest site to a maximum at the 150000 yr site, and then declined to the 4.1 x 10 6 yr site. Occluded (residual) P increased steadily with soil age. In contrast to the Walker and Syers model, we found the highest total P at the 150000-yr-old site, rather than at the onset of soil development, and we found that the non-occluded, inorganic P fraction persisted through to the oldest chronosequence site. Total soil N and C increased substantially from early to middle soil development in parallel with organic P, and then declined through to the oldest site. Readily available soil P, NH 4 + , and NO 3 - were measured using anion and cation exchange resin bags. P availability increased and decreased unimodally across the chronosequence. NH 4 + and NO 3 - pools increased through early soil development, but did not systematically decline late in soil development. In situ decomposition rates of Metrosideros polymorpha litter were highest at two intermediate-aged sites with high soil fertility (20000 yr and 150000 yr), and lowest at the less-fertile beginning (300 yr) and endpoint (4.1 x 10 6 yr) of the chronosequence. M. polymorpha leaves collected from these same four sites, and decomposed in a common site, suggested that leaves from intermediate-aged sites were inherently more decomposable than those from the youngest and oldest sites. Both litter tissue quality and the soil environment appeared to influence rates of decomposition directly. The highest mean soil N 2 O emissions (809 μg.m -2 .d -1 ) were measured at the 20 000-yr-old site, which also had the highest soil nitrogen fertility status. Plant communities at all six chronosequence sites were dominated primarily by M. polymorpha, and to a lesser extent by several other genera of trees and shrubs. There were, however, differences in overall vegetation community composition among the sites. Using a detrended correspondence analysis (DECORANA), we found that a high proportion of species variance among the sites (eigenvalue = 0.71) can be explained by site age and thus soil developmental stage. Overall, long-term soil development across the chronosequence largely coincides with the conceptual model of Walker and Syers (1976). How P is distributed among different organic and inorganic fractions at a given stage of soil development provides a useful context for evaluating contemporary cycling of P and other nutrients, and for determining how changes in P availability might affect diverse ecosystem processes.

Changes in soil phosphorus fractions and ecosystem dynamics across a long chronosequence in Hawaii.

Rates and patterns of nitrogen mineralization from decomposing plant materials are known to be affected by initial concentrations of N, lignin and soluble polyphenols, but published results show differences in which properties correlated best with N release. We incubated soil with fresh leaves and litter from 12 species commonly used in tropical agroforestry systems, including both legumes and non-legumes, to estimate how release of mineral N was affected by chemical composition. After 16 weeks, net accumulation of mineral N in incubations ranged from 81% of initial N in fresh Sesbania sesban to net depletion equivalent to 70% of initial N in Casuarina equisetifolia litter. Fresh legume leaves generally had net N accumulation, whereas legume litter and non-legume fresh leaves and litter had net depletion. At all sampling dates, the percent of leaf N accumulated was most highly correlated with initial N concentration. Phosphorus and the ratios lignin:N and (lignin + polyphenol):N also strongly correlated with N accumulation, although these indices themselves were correlated with N. We conclude that differences among previous studies in best chemical predictors of mineralization rates arose from relatively small ranges in chemical composition of materials used. Over our wide range of materials, initial soluble polyphenols were secondary to initial N, which explained most of the variation in N accumulation or depletion.

Nitrogen mineralization from leaves and litter of tropical plants: Relationship to nitrogen, lignin and soluble polyphenol concentrations

The decline in aboveground wood production after canopy closure in even-aged forest stands is a common pattern in forests, but clear evidence for the mechanism causing the decline is lacking. The problem is fundamental to forest biology, commercial forestry (the decline sets the rotation age), and to carbon storage in forests. We tested three hypotheses about mechanisms causing the decline in wood growth by quantifying the complete carbon budget of developing stands for over six years (a full rotation) in replicated plantations of Eucalyptus saligna near Pepeekeo, Hawaii. Our first hypothesis was that gross primary production (GPP) does not decline with stand age, and that the decline in wood growth results from a shifft in partitioning from wood production to respiration (as tree biomass accumulates), total belowground carbon allocation (as a result of declining soil nutrient supply), or some combination of these or other sinks. An alternative hypothesis was that GPP declines with stand age and that the decline in aboveground wood production is proportional to the decline in GPP. A decline in GPP could be driven be reduced canopy leaf area and photosynthetic capacity resulting from increasing nutrient limitation, increased abrasion between tree canopies, lower turgor pressure to drive foliar expansion, or hydraulic limitation of water flux as tree height increases. A final hypothesis was a combination of the first two: GPP declines, but the decline in wood production is disproportionately larger because partitioning shifts as well. We measured the entire annual carbon budget (aboveground production and respiration, total belowground carbon allocation [TBCA], and GPP) from 0.5 years after seedling planting through 6 1/2 years (when trees were ~25m tall). The replicated plots included two densities of trees (1111 trees/ha and 10 000 trees/ha) to vary the ratio of canopy leaf mass to wood mass in the individual trees, and three fertilization regimes (minimal, intensive, and minimal followed by intensive after three years) to assess the role of nutrition in shaping the decline in GPP and aboveground wood production. The forest closed its canopy in 1-2 years, with peak aboveground wood production, coinciding with canopy closure, of 1.2-1.8 kg C.m-2yr-1. Aboveground wood production declined from 1.4 kg C.m-2yr-1 at age 2 to 0.60 kg C.m-2yr-1 at age 6. Hypothesis 1 failed: GPP declined from 5.0 kg C.m-2yr-1 at age 2 to 3.2 kg C.m-2yr-1 at age 6. Aboveground woody respiration declined from 0.66 kg C.m-2yr-1 at age 2 to 0.22 kg C.m-2yr-1 at age 6 and TBCA declined from 1.9 kg C.m-2yr-1 at age 2 to 1.4 kg C.m-2yr-1 at age 6. Our data supported hypothesis 3: the decline in aboveground wood production (42% of peak) was proportionally greater than the decline in canopy photosynthesis (64% of peak). The fraction of GPP partitioned to belowground allocation and foliar respiration increased with stand age and contributed to the decline in aboveground wood production. The decline in GPP was not caused by nutrient limitation, a decline in leaf area or in photsynthetic capacity, or (from a related study on the same site) by hydraulic limitation. Nutrition did interact with the decline in GPP and aboveground wood production, because treatments with high nutritient availablity declined more slowly than did our control treatment, which was fertilized only during stand establishment.

https://www.nrs.fs.fed.us/pubs/jrnl/2004/rm_2004_ryan_001.pdf

An experimental test of the causes of forest growth decline with stand age

We tested the hypothesis that P was the nutrient limiting net primary production of a nativeMetrosideros polymorpha forest on a highly weathered montane tropical soil in Hawaii. A factorial experiment used all combinations of three fertilizer treatments: nitrogen (N), phosphorus (P) and a mix of other essential nutrients (OE), consisting primarily of mineral derived cations and excluding N and P. P addition, but not N or OE, increased leaf area index within 12 months, foliar P concentration measured at 18 months, and stem diameter increment within 18 months. Stem growth at 18 months was even greater when trees fertilized with P also received the OE treatment. N and P additions increased leaf litterfall and N and P in combination further increased litterfall. The sequence of responses suggests that increased available P promoted an increase in photosynthetic area which led to increased wood production. P was the essential element most limiting to primary production on old volcanic soil in contrast to the N limitation found on young volcanic soils.

James H. Fownes

Papers

Age-Related Decline in Forest Productivity: Pattern and Process

Changes in soil phosphorus fractions and ecosystem dynamics across a long chronosequence in Hawaii.

Nitrogen mineralization from leaves and litter of tropical plants: Relationship to nitrogen, lignin and soluble polyphenol concentrations

An experimental test of the causes of forest growth decline with stand age

Phosphorus limitation of forest leaf area and net primary production on a highly weathered soil.