From 8c3d609f62034fbb53bebb13ffd03ec232119e7b Mon Sep 17 00:00:00 2001
From: Georges Kunstler <Georges.Kunstler@gmail.com>
Date: Mon, 10 Nov 2014 21:09:33 +0100
Subject: [PATCH] output all with sp.name
---
R/analysis/lmer.all.no.log.output.R | 2 +-
docs/paper/Makefile | 4 +--
docs/paper/paper.md | 44 ++++++++++++++++++++++++++---
3 files changed, 43 insertions(+), 7 deletions(-)
diff --git a/R/analysis/lmer.all.no.log.output.R b/R/analysis/lmer.all.no.log.output.R
index 6efe16e..9d9b948 100644
--- a/R/analysis/lmer.all.no.log.output.R
+++ b/R/analysis/lmer.all.no.log.output.R
@@ -8,7 +8,7 @@ source("R/analysis/lmer.run.R")
format.all.output.lmer(file.name = "biomes.results.nolog.all.rds",
list.file.name = 'list.lmer.out.all.biomes.no.log.rds',
models = c(model.files.lmer.Tf.1
- #, model.files.lmer.Tf.2
+ , model.files.lmer.Tf.2
)
)
diff --git a/docs/paper/Makefile b/docs/paper/Makefile
index 1eb79fd..8b0fa25 100644
--- a/docs/paper/Makefile
+++ b/docs/paper/Makefile
@@ -2,8 +2,8 @@ TARGETS = $(subst md,pdf,$(shell ls *.md))
all: narrative.pdf
-narrative.pdf: narrative.md include.tex
- pandoc $< --template=include.tex --variable mainfont="Times New Roman" --variable sansfont=Arial --variable fontsize=12pt --latex-engine=xelatex -o $@
+narrative.pdf: narrative.md include.tex refs.bib
+ pandoc $< --csl=nature.csl --filter pandoc-citeproc --bibliography=refs.bib --template=include.tex --variable mainfont="Times New Roman" --variable sansfont=Arial --variable fontsize=12pt --latex-engine=xelatex -o $@
clean:
diff --git a/docs/paper/paper.md b/docs/paper/paper.md
index c748e71..cc45f59 100644
--- a/docs/paper/paper.md
+++ b/docs/paper/paper.md
@@ -1,5 +1,5 @@
-% Functional traits have globally consistent effects on plant competition
-% Georges Kunstler
+%Functional traits have globally consistent effects on plant competition
+%Georges Kunstler
# Letters to nature guideline
@@ -12,8 +12,44 @@
- Word counts refer to the text of the paper. References, title, author list and acknowledgements do not have to be included in total word counts.
# Summary paragraph outline (max 200 words)
+
Competition is a very important type of ecological interaction, especially in terrestrial vegetation where plants greatly modify the local environment for each other. Competition has influence on growth of individuals and survival, on how species mixtures will change over time into the future, and on community composition. However firm generalizations have yet to be established about outcomes of competition among tree species.Here we show how key species traits have consistent influences on growth and competition. The data sources are very large, including national forest inventories monitoring growth in sometimes millions of trees, and we here synthesize across a global set of such inventories plus also several large forest-monitoring plots. Some traits have strong effect on the growth rate of the species. Then traits in part determine the tolerance to competition and the impact of the competitor. A notable generalization is that trait values that favour tolerance to competition also render species slow growing in absence of competition. There is also a small but detectable benefit in reducing competition from trait-dissimilarity between focal plant and its competitors. The trait-based picture that emerges is much simpler and more general than a quantification of competition coefficients between each pair of species, which is intractable at the global scale. Our results demonstrate that traits may be used to predict competitive interactions between forest tree species at a large scale. We anticipate that our results can have profound influence on trait model of community assembly.
-# Introduction
+# Main text
+
+Competition is a fundamental type of interaction in ecological communities. Each individual modify their neighbouring environment and thus influences the growth, survival and reproduction of neighbouring individuals. Competition thus connects individuals in a community and influences species composition and its changes over time. Maybe competition is especially important for vegetation on land because most vegetation types have high enough cover that shading and water and nutrient depletion are conspicuous. There have thus been a very large number of studies on competition among plants, but firm generalizations have yet to be established about outcomes of competition among plant species.
+
+When competition is described as interactions between pairs of species (as it traditionally has been), the number of different interactions to be measured grows explosively with the number of species (N^2) interacting, and becomes quickly intractable. Also this species-pair approach does not lead naturally to generalization across forests on different continents with different composition. Here we quantify competition between trees (in the sense of influence of neighbours on growth of a focal tree) within a framework, which is novel in two important ways: (i) competition is modelled as a function of traits rather than of species and (ii) we partition how traits drive the outcome of competition in four different key processes (Fig. 1). Competition can select trait values that are the most competitive. This competitive advantage of trait values can arise because (1) there are correlated with higher potential growth (in absence of competition) [@wright_functional_2010], (2) they are correlated with a higher tolerance to competition [@goldberg_competitive_1996], or (3) they are correlated with higher impact of neighbourhood competitors on the focal individual [@gaudet_comparative_1988]. In contrast, competition can promotes the coexistence of a mixture of traits values. The classical process though to be at play in that case is that (4) competition decrease with increasing dissimilarity of the traits of the competitor and the focal tree [@macarthur_limiting_1967]. However, how key traits defining plant strategies affect these four processes is uncertain.
+Here we dissect how three traits (maximum height, wood density and specific leaf area - SLA) affect these four processes involved in competition between trees using neighbouring modelling approach. We compiled data of growth along side local abundance of their competitor for more than 8 million trees representing more than 2500 species covering all the major biomes of the earth (Fig. 1b). We analysed how the potential growth of each individual tree was reduced by the local abundance of its competitors. Our analysis accounts for the trait of both the focal tree and its competitors estimating the trait effect for each of the processes presented in Fig. 1.
+ Across all biomes we found that strongest drivers of individual growth was first-ranked the local abundance (basal area) of competitors; and second ranked the direct influence of the focal plant’s traits on its growth (Fig. 2a Extended data Table 1). We detected only negative effect of the abundance of competitors showing that competition was the predominant process. Among the three traits wood density had the strongest direct effect, followed by maximum height whereas SLA had no detectable effect (Fig. 2a). Then our results show the influence of neighbour traits on their competitive impact, and of focal species traits on tolerance of competition from neighbours (Fig. 2a). The sum of these two effect is in the range of half or quarter as big as the direct trait effect (Extend data Table 2), down to zero influence depending on the trait (Fig 2a). Finally, there is a small but consistent effect whereby the wider is the absolute trait separation between focal and neighbour species, the weaker is competitive suppression of growth (Fig. 2a), this effect represents ????. An analysis allowing for different effect between biomes did no show strong evidence for any particular biome behaving consistently differently from the others (Fig. 2b). The exception are (1) the temperate biomes where SLA showed much stronger effect, probably ought to the dominance of deciduous species in this biome; and ????.
+
+ The direction of the traits effect agree well with the existing literature and the traits effect. High wood density was lined with slow potential growth rate but high tolerance to competition, in agreement with the view that this is a trait value of shade-tolerant species [@wright_functional_2010]. There was also a tendency to a high competitive effect (** DISUCSS WORK OF LOURENS ON ARCHITECTURE**). **TODO** High SLA makes for a small overall positive effect on growth (remember these are not seedlings but reasonably large plants), an decreased competitive effect and no effect or possible weakly decreased competitive tolerance. The lack of effect of SLA on potential growth rate agree well with most previous studies on adult tree [@wright_functional_2010]. Maximum height: Tall eventual height makes for faster growth together with reduced tolerance and possibly reduced competitive effect! **THE RESULTS FOR MAXIMUM HEIGHT IS PROBABLY MORE SURPRISING DISCUSS MORE**.
+
+
+
+# Methods summary
+
+To examine the link between competition and traits we first compiled TREE data. Secondly extracted traits data from global or local data base : mean per species (no intraspecific variability) explain what we did when missing data. Discuss Fig. 1b. Thirdly local basal area in neighbourood. Analyses were restricted to trees with trunk diameter
+$>= 10cm$, and to species having $>=10$ trees. Then to analyse the traits effect on competition for the four processes presented in Fig. 1a, we fitted a mixed model to individual log basal area growth data EXPLAIN IN WORK GIVE EQUATION IN SUPPL MATS.
+
+
+# Outlines
+
+6. Result 2: Influence of neighbour traits on their competitive impact, and of focal species traits on tolerance of competition from neighbours, are in the range of half or quarter as big as the direct trait effect (Result 1), down to zero influence depending on the trait (Fig 2 or Fig 3 in “quick.report.pdfâ€)
+6.1. Digression here to explain that effect size is made up of two components: how wide is the variation in the trait (or in the basal area of competitors), and how large an effect is produced per unit change in the trait or in the amount of competitors. Maybe to quantify briefly? – out of the effect sizes, which of them are big because the trait or BA varies widely in practice, versus which are big because the response is steep per unit change?
+
+7. There is a small but consistent effect whereby the wider is the absolute trait separation between focal and neighbour species, the weaker is competitive suppression of growth (Fig 2 or Fig 3 in “quick.report.pdfâ€)
+7.1. We don’t have evidence what might cause such an effect, but there is much evidence for effects of shared herbivores and pathogens (Janzen-Connell effects), and it’s plausible that separation in SLA or WD or height may be correlated with fewer shared herbivores and pathogens
+
+8. Result 3: The specific effects of particular traits are as might be expected from existing literature
+8.1. High WD makes for slower growth together with higher tolerance of competition
+8.2. High SLA makes for a small overall positive effect on growth (remember these are not seedlings but reasonably large plants), an decreased competitive effect and no effect or possible weakly decreased competitive tolerance .
+8.3. Tall eventual height makes for faster growth together with reduced tolerance and possibly reduced competitive effect
+8.4. Main punchline: there is a fairly consistent tradeoff whereby traits that favour fast growth in absence of competition also make species less tolerant of competition – this obviously can produce some coexistence over successional time in meta-community.
+8.4.1. And the absolute-trait-distance effect can also have some effect in favouring coexistence of more species or wider range of species.
+8.5. In summary effects favouring coexistence are detectable (1. trade-off between growth and competition tolerance, 2. Absolute distance effect), but there is no evidence for them operating more strongly in some vegetation types than others
+8.5.1. (The point being – except that we don’t want this to become the punchline of the whole paper -- that these results don’t show any particular sign of explaining why there are more species in tropical forests, both because the coexistence effects aren’t operating more strongly there, and because anyhow their influence should be on the range of traits, which is not proven to be wider in tropical forests, rather than on the number of species)
+
+9. Despite all the noise at the level of individual trees, overall the influence of specific traits is satisfyingly consistent across many forest types and climate zones. It is not so strong an influence as variation simply in the amount of competitors, but nevertheless has an influence.
-1. Competition is a very important type of ecological interaction. It has influence on growth of individuals and survival, on community composition and its changes over time. Maybe competition is especially important for vegetation on land – compared say to herbivory -- most vegetation types have high enough LAI that shading and water and nutrient depletion are conspicuous.
+10. The trade-off between faster growth in absence of competition and lower tolerance to competition is not in itself a surprise. The achievements of this paper are first to synthesize all that at world scale, and second to express it on a trait basis.
--
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