DOI: 10.5281/zenodo.2024581
title: Landuse change and species invasion

description: <b>Description: </b>Small vegetation plots of understory and herbaceous native and exotic plant cover<b>Project: </b>This dataset was collected as part of the following SAFE research project: <b>Land use change and species invasion: synergistic effects of multiple drivers of global change on species interactions</b><b>XML metadata: </b>GEMINI compliant metadata for this dataset is available here<b>Files: </b>This consists of 1 file: template_Doebert.xlsx<b>template_Doebert.xlsx</b>This file contains dataset metadata and 4 data tables:<b>Plot descriptors</b> (described in worksheet DoebertTF_SAFE_PlotData)Description: The full database of characteristics for each of 180 vegetation plots including logging metrics, environmental variables as well as taxonomic, functional and phylogenetic diversity indices.Number of fields: 44Number of data rows: 1485Fields: <b>plot.code</b>: Site code for the plot:  the first letter indicates the block, the first number indicates the fragment, the letter f means fragment, the letter m means matrix, the second number indicates the distance from the edge, and the final letter indicates the type of plot (e.g. r = removal, m = monitor etc). (Field type: Location)<b>block</b>: Nominal SAFE Project Sample block IDs used for sample labelling (Field type: ID)<b>Fragment</b>: SAFE Project sample area (Field type: Location)<b>fragment</b>: Nominal SAFE Project fragment IDs used for field site labellig (Field type: ID)<b>elevation</b>: The elevation of a plot (Field type: Numeric)<b>plot.treatment</b>: Type of plot (Field type: Categorical)<b>forestloss17</b>: The proportion of forest canopy loss at the local scale, i.e. within a 17m radius (Field type: Numeric)<b>forestloss562</b>: The proportion of forest canopy loss at the landscape scale, i.e. within a 562m radius (Field type: Numeric)<b>roaddensprim</b>: Regional-scale density of continuously-maintained primary logging roads (Field type: Numeric)<b>roaddenssec</b>: Regional-scale density of occasionally-used secondary logging roads (Field type: Numeric)<b>roaddistprim</b>: Distance to nearest primary road (Field type: Numeric)<b>roaddistsec</b>: Distance to nearest secondary road (Field type: Numeric)<b>riverdist</b>: Distance to nearest river (&gt; 3m width) (Field type: Numeric)<b>pH</b>: Soil pH (Field type: Numeric)<b>humus</b>: Soil humus depth (Field type: Numeric)<b>soilN</b>: Total soil nitrogen content (Field type: Numeric)<b>soilP</b>: Plant available soil phosphorus content (Field type: Numeric)<b>bulkdens</b>: Soil bulk density (Field type: Numeric)<b>soilmoist</b>: Soil moisture factor (Field type: Numeric)<b>soilPC1.Biotr</b>: Principal component axis 1 scores from a PCA of the six soil-biogeochemical variables  (Field type: Numeric)<b>soilPC2.Biotr</b>: Principal component axis 2 scores from a PCA of the six soil-biogeochemical variables  (Field type: Numeric)<b>ex.richness</b>: The species richness of exotic plants (Field type: Numeric)<b>ex.drywght</b>: The dry above-ground biomass of exotic plants (Field type: Numeric)<b>ex.lai</b>: The leaf area index of exotic plants (Field type: Numeric)<b>native.richness</b>: The species richness of native plants (Field type: Numeric)<b>native.drywght</b>: The dry above-ground biomass of native plants (Field type: Numeric)<b>native.lai</b>: The leaf area index of native plants (Field type: Numeric)<b>dissim</b>: dissimilarity of each of the logged forest plots (blocks A–F and LF) to the average dissimilarity of the 33 old-growth (OG) plots as a collective old-growth forest reference point derived from the Gower distance matrix in the NMDS analysis (Field type: Numeric)<b>clihir.pre</b>: The presence (present) or absence (absent) of Clidemia hirta. (Field type: Categorical)<b>dipt.drywght</b>: The dry above-ground biomass of dipterocarp trees (Field type: Numeric)<b>native.drywght.nodipt</b>: The dry above-ground biomass of native plants excluding dipterocarps (Field type: Numeric)<b>SoilPC1.Jecol</b>: Principal component axis 1 scores from a PCA of the six soil-biogeochemical variables  (Field type: Numeric)<b>soilPC2.Jecol</b>: Principal component axis 2 scores from a PCA of the six soil-biogeochemical variables (Field type: Numeric)<b>ntaxa</b>: Species richness  (Field type: Numeric)<b>FDisLOG</b>: Biomass-weighted functional dispersion (standardized effect sizes) (Field type: Numeric)<b>nriLOG</b>: Biomass-weighted net relatedness index (phylogenetic dispersion based on the branch length between each pair of taxa in a plot) (Field type: Numeric)<b>FRicLOG</b>: Biomass-weighted functional richness (standardized effect sizes) (Field type: Numeric)<b>FDisLOGr</b>: Biomass-weighted functional dispersion of response traits (standardized effect sizes) (Field type: Numeric)<b>FDisLOGe</b>: Biomass-weighted functional dispersion of effect traits (standardized effect sizes) (Field type: Numeric)<b>woody</b>: The proportion of woody species in a plot  (Field type: Numeric)<b>treesapling</b>: The proportion of tree saplings out of all species per plot (Field type: Numeric)<b>nriLOGWoody</b>: Biomass-weighted net relatedness index of woody species only (Field type: Numeric)<b>nriLOGSapling</b>: Biomass-weighted net relatedness index of tree saplings only (Field type: Numeric)<b>nriLOGnonWoody</b>: Biomass-weighted net relatedness index of non-woody species only (Field type: Numeric)<b>Plant functional traits</b> (described in worksheet SpeciesTraitDataEcol)Description: Directly measured plant functional traitsNumber of fields: 14Number of data rows: 691Fields: <b>species.code</b>: Species identity (Field type: Taxa)<b>tree</b>: Distinction between tree (yes), no tree (no) (Field type: Categorical Trait)<b>woody</b>: Distinction between woody (yes), non-woody (no) (Field type: Categorical Trait)<b>origin</b>: Distinction between native (n) and exotic (e) plant species (Field type: Categorical Trait)<b>pgf</b>: Plant growth form (Field type: Categorical Trait)<b>height</b>: Maximum plant height (Field type: Numeric Trait)<b>sla</b>: Specific leaf area (Field type: Numeric Trait)<b>wood.dens</b>: Wood density (Field type: Numeric Trait)<b>dispersal</b>: Predominant dispersal mode (Field type: Categorical Trait)<b>fruit</b>: The type of fruit (Field type: Categorical Trait)<b>seed</b>: The number of seeds per fruit (Field type: Categorical Trait)<b>reproduction</b>: The reproduction strategy (Field type: Categorical Trait)<b>lifehistory</b>: The lifehistory strategy (Field type: Categorical Trait)<b>pollination</b>: The pollination syndrome (Field type: Categorical Trait)<b>Additional plant functional traits</b> (described in worksheet DoebertTF_SAFE_TraitDataAdd)Description: Plant functional traits INFERRED FROM PHYLOGENETIC ANALYSESNumber of fields: 4Number of data rows: 1320Fields: <b>species.code</b>: Species identity (Field type: Taxa)<b>sla.dry</b>: Dry specific leaf area (Field type: Numeric Trait)<b>shrinkage</b>: Proportional change in SLA between fresh and dry leaves (Field type: Numeric Trait)<b>plant_growth_form</b>: Plant growth form (Field type: Categorical Trait)<b>Field measurements</b> (described in worksheet DoebertTF_SAFE_PlotSpeciesMeasu)Description: Field records for all individual plantsNumber of fields: 14Number of data rows: 9324Fields: <b>plot.code</b>: Site sample was collected from (Field type: Location)<b>fragment</b>: Nominal SAFE Project fragment IDs used for field site labellig (Field type: ID)<b>abs.edge.dist</b>: Distance of sample site from fragment edge (Field type: Numeric)<b>habitat</b>: Type of habitat at sample point (Field type: Categorical)<b>species.code</b>: Species identity (Field type: Taxa)<b>braunblanquet</b>: Braun-Blanquet scale (Field type: Categorical)<b>leafdrwgt</b>: Dry weight of the individual's leaves (Field type: Numeric Trait)<b>stemdrywgt</b>: Dry weight of the individual's stem (Field type: Numeric Trait)<b>drywgt</b>: Dry weight of the individual (Field type: Numeric Trait)<b>area.dry</b>: Size of a dry leaf (Field type: Numeric Trait)<b>sla.dry</b>: Dry specific leaf area (Field type: Numeric Trait)<b>shrinkage</b>: Proportional change in SLA between fresh and dry leaves (Field type: Numeric Trait)<b>lai1</b>: Leaf area index - NB: not clear what the difference is between lai1 and lai2 (Field type: Numeric Trait)<b>lai2</b>: Leaf area index - NB: not clear what the difference is between lai1 and lai2 (Field type: Numeric Trait)<b>Date range: </b>2011-12-01 to 2014-03-31<b>Latitudinal extent: </b>4.6395 to 4.7800<b>Longitudinal extent: </b>116.9500 to 117.6901<b>Taxonomic coverage: </b><br> All taxon names are validated against the GBIF backbone taxonomy. If a dataset uses a synonym, the accepted usage is shown followed by the dataset usage in brackets. Taxa that cannot be validated, including new species and other unknown taxa, morphospecies, functional groups and taxonomic levels not used in the GBIF backbone are shown in square brackets.Plantae<br> - Bryophyta<br> -  -  -  -  -  - [<i>Unknown sp.</i>]<br> -  -  -  -  -  - [<i>Semnostachys galeopsis</i>]<br> -  -  -  -  -  - [<i>Sleumenia auriculata</i>]<br> -  -  -  -  -  - [<i>Stemonorus grandiflorus</i>]<br> -  -  -  -  -  - [<i>Stemonorus malaccensis</i>]<br> -  -  -  -  -  - [<i>Syndophyllum excelsum</i>]<br> - Tracheophyta<br> -  - Gnetopsida<br> -  -  - Gnetales<br> -  -  -  - Gnetaceae<br> -  -  -  -  - <i>Gnetum</i><br> -  -  -  -  -  - <i>Gnetum gnemon</i><br> -  -  -  -  -  - <i>Gnetum gnemonoides</i><br> -  -  -  -  -  - [gne076]<br> -  - Liliopsida<br> -  -  - Alismatales<br> -  -  -  - Araceae<br> -  -  -  -  - <i>Aglaonema</i><br> -  -  -  -  -  - [agl251]<br> -  -  -  -  - <i>Alocasia</i><br> -  -  -  -  -  - <i>Alocasia scabriuscula</i><br> -  -  -  -  -  - [alo023]<br> -  -  -  -  -  - [aloden1]<br> -  -  -  -  -  - [aloreg1]<br> -  -  -  -  -  - [alosca1]<br> -  -  -  -  -  - [alowon1]<br> -  -  -  -  - <i>Amydrium</i><br> -  -  -  -  -  - <i>Amydrium medium</i><br> -  -  -  -  - <i>Arisaema</i><br> -  -  -  -  -  - [ari252]<br> -  -  -  -  - <i>Epipremum</i><br> -  -  -  -  -  - [epi024]<br> -  -  -  -  - <i>Homalomena</i><br> -  -  -  -  -  - <i>Homalomena humilis</i><br> -  -  -  -  -  - [hom025]<br> -  -  -  -  - <i>Piptospatha</i><br> -  -  -  -  -  - [pip253]<br> -  -  -  -  - <i>Pothos</i><br> -  -  -  -  -  - <i>Pothos barberianus</i><br> -  -  -  -  -  - <i>Pothos beccarianus</i><br> -  -  -  -  -  - <i>Pothos scandens</i><br> -  -  -  -  -  - [pot026]<br> -  -  -  -  -  - [potbor1]<br> -  -  -  -  - <i>Rhaphidophora</i><br> -  -  -  -  -  - <i>Rhaphidophora latevaginata</i><br> -  -  -  -  -  - <i>Rhaphidophora puberula</i><br> -  -  -  -  -  - [rha254]<br> -  -  -  -  - <i>Schismatoglottis</i><br> -  -  -  -  -  - [sch027]<br> -  -  -  -  -  - [schcle1]<br> -  -  -  -  - <i>Scindapsus</i><br> -  -  -  -  -  - <i>Scindapsus pictus</i><br> -  -  -  -  -  - [sci028]<br> -  -  -  -  -  - [scipic1]<br> -  -  -  -  - [araunk]<br> -  -  - Arecales<br> -  -  -  - Arecaceae<br> -  -  -  -  - <i>Areca</i><br> -  -  -  -  -  - [are260]<br> -  -  -  -  - <i>Calamus</i><br> -  -  -  -  -  - <i>Calamus blumei</i><br> -  -  -  -  -  - <i>Calamus caesius</i><br> -  -  -  -  - <i>Daemonorops</i><br> -  -  -  -  -  - [dae205]<br> -  -  -  -  - <i>Elaeis</i><br> -  -  -  -  -  - <i>Elaeis guineensis</i><br> -  -  -  -  - <i>Korthalsia</i><br> -  -  -  -  -  - [kor030]<br> -  -  -  -  - <i>Licuala</i><br> -  -  -  -  -  - [lic271]<br> -  -  -  -  - [cal029]<br> -  -  -  -  - [palunk]<br> -  -  - Asparagales<br> -  -  -  - Asparagaceae<br> -  -  -  -  - <i>Dracaena</i><br> -  -  -  -  -  - <i>Dracaena angustifolia</i><br> -  -  -  -  -  - [draang1]<br> -  -  -  - Hypoxidaceae<br> -  -  -  -  - <i>Curculigo</i><br> -  -  -  -  -  - <i>Curculigo latifolia</i><br> -  -  -  -  -  - [cur077]<br> -  -  -  -  -  - [curlat1]<br> -  -  -  -  - [hypunk]<br> -  -  -  - Orchidaceae<br> -  -  -  -  - <i>Aplectrum</i><br> -  -  -  -  -  - [<i>Aplectrum divaricatum</i>]<br> -  -  -  -  - <i>Calanthe</i><br> -  -  -  -  -  - [cal128]<br> -  -  -  -  - [orcunk]<br> -  -  - Commelinales<br> -  -  -  - Commelinaceae<br> -  -  -  -  - <i>Amischotolype</i><br> -  -  -  -  -  - <i>Amischotolype glabrata</i><br> -  -  -  -  -  - <i>Amischotolype griffithii</i><br> -  -  -  -  -  - [ami042]<br> -  -  -  -  -  - [amigla1]<br> -  -  - Dioscoreales<br> -  -  -  - Dioscoreaceae<br> -  -  -  -  - <i>Dioscorea</i><br> -  -  -  -  -  - [dio056]<br> -  -  -  -  -  - [diolau1]<br> -  -  -  -  - [diounk]<br> -  -  - Liliales<br> -  -  -  - Smilacaceae<br> -  -  -  -  - <i>Smilax</i><br> -  -  -  -  -  - <i>Smilax borneensis</i><br> -  -  -  -  -  - <i>Smilax corbularia</i><br> -  -  -  -  -  -  - Smilax corbularia woodii<br> -  -  -  -  -  - <i>Smilax laevis</i><br> -  -  -  -  -  - <i>Smilax megacarpa</i><br> -  -  -  -  -  - [smi178]<br> -  -  -  -  -  - [smilae1]<br> -  -  -