DOI: 10.5061/dryad.w0vt4b8zk
title: Impact of Phytophthora cinnamomi on the taxonomic and functional diversity of forest plants in a mediterranean-type biodiversity hotspot

description: Aim Diversity-rich mediterranean-type sclerophyllous forests are home to
 20% of described species on Earth. In the Eucalyptus marginata (jarrah)
 forest of southwest of Western Australia diversity is being reduced by
 extensive human use and the introduction of the plant pathogen
 Phytophthora cinnamomi. This study investigated the influence of P.
 cinnamomi infestation on the structure, taxonomic and functional
 diversity, and species composition of the forest. Location: Jarrah forest
 of southwestern Australia Methods Species abundance, understorey cover and
 canopy cover were assessed along 22, 30-m long transects which crossed
 infested and non-infested zones in five reserves in the jarrah forest. A
 trait database was assembled for 137 plants using 13 traits related to
 nutrient- and carbon acquisition, disturbance tolerance and reproduction.
 The responses of canopy cover, understorey cover, species richness,
 Shannon diversity, evenness, abundance, and functional diversity for trait
 groups, and all groups combined were modelled against reserve and zone as
 fixed effects and transect and transect section as random effects. To
 assess the species composition, NMDS ordination based on Bray Curtis
 resemblance and indicator species analyses were used. Results
 Significantly higher understorey cover, species richness, Shannon
 diversity and evenness were recorded in non-infested compared to infested
 zones, but there were no changes in the canopy cover and overall
 abundance. In non-infested zones, the functional diversity of nutrient
 acquisition and reproductive traits was higher, but the functional
 diversity of carbon acquisition traits was lower. No difference in
 functional diversity was recorded in disturbance tolerance and overall
 traits between the two zones. NMDS ordination and ANOSIM revealed a
 significant difference in the species composition between the two zones,
 and 11 indicator species significantly associated with infested and
 non-infested zones were identified.  Conclusion Phytophthora
 cinnamomi has significantly affected the forest structure, taxonomic and
 functional diversity, and species composition. Contrasting responses of
 functional trait groups obscured overall trait responses to P. cinnamomi.
description: This dataset was collected between October and November in 22
 transects set up in five reserves (Alps Street, Black Cockatoo, Falls
 Road, Quail Street and Super Block) of the jarrah (<em>Eucalyptus
 marginata</em>) forest using the line transect method. These
 reserves were impacted by the plant pathogen <em>Phytophthora
 cinnamomi</em> and transects were set up at the right angles across
 the dieback front. A 45-m transect was marked from the active disease edge
 in both infested and non-infested zones and the first 15 m of the transect
 in both directions was excluded as it was considered a transitional area.
 The data was collected along the 30-m transect from both infested and
 non-infested zones. Each 30-m transect was further divided into 4 equal
 sections (7.5 m) to improve the statistical power of the data analyses.
 The abundance and cover (as cm long) of each species ≤ 2 m height
 occurring in the understorey and percentage canopy cover averaged from
 four readings using a spherical densitometer oriented North, South, East,
 and West were recorded along four 7.5-m sections of each 30 m transect.
 Abundance data includes counts and cover data includes cover of each
 understorey species recorded. Species richness, abundance, Shannon
 diversity, evenness and understory cover were calculated for each 7.5-m
 transect section based on the preliminary data using R
 software.  Plant functional trait data (Trait data)
 were collected for ten categorical and three qualitative traits, grouped
 according to nutrient acquisition, carbon acquisition, disturbance
 tolerance and reproduction. The trial data sheet was prepared based on the
 trait data collected from the field observations or literature for all
 recorded species.
description: # Impact of Phytophthora cinnamomi on the taxonomic and functional
 diversity of forest plants in a mediterranean-type biodiversity hotspot
 [https://doi.org/10.5061/dryad.w0vt4b8zk](https://doi.org/10.5061/dryad.w0vt4b8zk) GENERAL INFORMATION 1\. Title of Dataset: Impact of *Phytophthora cinnamomi* on the taxonomic and functional diversity of forest plants in a mediterranean-type biodiversity hotspot 2\. Author information i) Himbutugoda Shanika Harshani <sup> </sup>Harry Butler Institute, Murdoch University, 90 South Street, Murdoch, WA, 6150, Perth, Australia ii) James L. Tsakalos School of Biosciences and Veterinary Medicine, Plant Diversity and Ecosystems Management Unit, University of Camerino, Via Pontoni 5, I-62032 Camerino MC, Italy Harry Butler Institute, Murdoch University, 90 South Street, Murdoch, WA, 6150, Perth, Australia iii) Thomas M. Mansfield <sup> </sup>Harry Butler Institute, Murdoch University, 90 South Street, Murdoch, WA, 6150, Perth, Australia iv) Jen McComb <sup> </sup>Harry Butler Institute, Murdoch University, 90 South Street, Murdoch, WA, 6150, Perth, Australia v) Treena I. Burgess <sup> </sup>Harry Butler Institute, Murdoch University, 90 South Street, Murdoch, WA, 6150, Perth, Australia vi) Giles E. St. J. Hardy <sup> </sup>Harry Butler Institute, Murdoch University, 90 South Street, Murdoch, WA, 6150, Perth, Australia <sup> </sup>ArborCarbon, ROTA Compound, Murdoch University, Murdoch 6150, WA Australia 3\. Data collected from October to November 2020\. 4\. Geographic location of data collection: Jarrah \(*Eucalyptus marginata*) forest, Western Australia 5\. Information about funding sources that supported the collection of the data: Murdoch University\, Shire of Mundaring\, Holsworth Wildlife Research Endowment FILE LIST 1\. Files included A) Abundance.csv B) Cover.csv C) Abundance\_two\_sections.csv D) Trait\_data.csv E) Structural\_and\_taxonomic\_data.csv F) NMDS\_scores.csv 2\. Relationship between files\, if important: No 3\. Additional related data collected that was not included in the current data package: None 4\. Are there multiple versions of the dataset? No A. If yes, name of file(s) that was updated: NA i. Why was the file updated? NA ii. When was the file updated? NA #### DATA-SPECIFIC INFORMATION FOR: Abundance.csv Includes the species counts (abundance) of each species recorded in the 7.5 m section of each transect in both infested and non-infested zones of five reserves. 1\. Number of variables: 141 2\. Number of cases/rows: 177 3\. Variable List: * Reserve: Reserves of the Jarrah forest where data was collected. * Transect: Line transect number * Zone: Whether the area is infested by *Phytophthora cinnamomi* or not * Section: The transect section (Each 30m long transect was divided into four equal sections). * Variable from 5 - 141: The plant species recorded 4\. Missing data codes: None 5\. Specialized formats or other abbreviations used: None ##### DATA-SPECIFIC INFORMATION FOR: Cover.csv Includes the species cover recorded for each species in the 7.5 m section of each transect in both infested and non-infested zones of five reserves. 1\. Number of variables: 141 2\. Number of cases/rows: 177 3\. Variable List: * Reserve: Reserves of the Jarrah forest where data was collected. * Transect: Line transect number * Zone: Whether the area is infested by *Phytophthora cinnamomi* or not * Section: The transect section (Each 30m long transect was divided into four equal sections). * Variable from 5 - 141: The plant species recorded 4\. Missing data codes: None 5\. Specialized formats or other abbreviations used: None ##### DATA-SPECIFIC INFORMATION FOR: Abundance\_two\_sections.csv Includes the species counts (abundance) recorded for each species in the 15 m section of each transect in both infested and non-infested zones of five reserves. 1\. Number of variables: 141 2\. Number of cases/rows: 89 3\. Variable List: * Reserve: Reserves of the Jarrah forest where data was collected. * Transect: Line transect number * Zone: Whether the area is infested by *Phytophthora cinnamomi* or not * Section: The transect section (Each 30m long transect was divided into two equal sections). * Variable from 5 - 141: The plant species recorded 4\. Missing data codes: None 5\. Specialized formats or other abbreviations used: None ##### DATA-SPECIFIC INFORMATION FOR: Trait\_data.csv Includes 13 plant trait data collected for 137 species recorded during the survey. 1\. Number of variables: 18 2\. Number of cases/rows: 138 3\. Variable List: * Species: The plant species recorded * Family: Family of each species * la = leaf area * aphyllous = 0 * 0–0.2 cm2 = 1 * 0.2–2 = 2 * 2–9 = 3 * 9 = 4 * ls = leaf sclerophylly * aphyllous = 0 * herbaceous = 1 * semi-sclerophylous = 2 * sclerophlyous = 3 * size = plant height * ≤10 cm = 1 * 10–25 = 2 * more than 25– &lt; 50 = 3 * more than 50 – &lt; 160 = 4 * more than 160 –&lt; 600 = 5 * ≥ 600 = 6 * hw = height:width * h:w &gt;1 = Skinny * h:w =1 = Normal * h:w &lt;1 = Fat * life.span * annual * perennial * cs = carbon storage * no specialised storage organs * organs (lignotuber, tuber, rhizomes) * cim = carbon immobilization, * herbaceous monocots * herbaceous dicots * semi-woody dicots * woody dicots * woody dicots with trunk and bark * pseudo-woody monocots * woody gymnosperm pseudo-woody palm * vs = vegetative spread * no clonal expansion (excl. lignotuber, tuber) = 0 * capacity to quickly form clonal patches = 1 * capacity to slowly form clonal patches = 2 * rp = reproductive phenology * no peak * winterish * springish * summerish * seed size * &lt; 1 = 1 * 1–2 = 2 * 2 - &lt; 4 = 3 * 4 - 10 = 4 * more than 10 = 5 * n2 - N fixing * Yes/No * n-mine = nutrient mining * Yes/No * mycorrhizal fungi association * nm = non mycorrhizal * om = orchid mycorrhizal * em = ecto mycorrhizal * am = arbuscular mycorrhizal 4\. Missing data codes: None 5\. Specialized formats or other abbreviations used: None 6\. List of sources used to prepare Trait\.csv data sheet A) Jstor plant digital herbaria catalogue B) Brundrett M. C. (2008) Mycorrhizal Associations: The Web Resource. Available at [https://mycorrhizas.info](https://mycorrhizas.info/) [Accessed 24 November 2022] C) Brundrett, M. C. (2021) One biodiversity hotspot to rule them all: southwestern Australia—an extraordinary evolutionary centre for plant functional and taxonomic diversity. *Journal of Royal Society of Western Australia,* 103, 91–122. D) Falster, D., Gallagher, R., Wenk, E. H., Wright, I. J., Indiarto, D., Andrew, S. C. et al. (2021) AusTraits, a curated plant trait database for the Australian flora. *Scientific Data*, 8, 254. [https://doi.org/10.1038/s41597-021-01006-6](https://doi.org/10.1038/s41597-021-01006-6) E) Tedersoo, L., Laanisto, L., Rahimlou, S., Toussaint, A., Hallikma, T. & Pärtel, M. (2018) Global database of plants with root‐symbiotic nitrogen fixation: Nod DB. *Journal of Vegetation Science,* 29,560-568. [https://doi.org/10.1111/jvs.12627](https://doi.org/10.1111/jvs.12627) F) Tsakalos, J. L., Ottaviani, G., Chelli, S., Rea, A. J., Elder, S., Dobrowolski, M. P. et al. (2022) Plant clonality in a soil-impoverished open ecosystem: insights from southwest Australian shrublands. Annals of Botany, 130, 981–990. [https://doi.org/10.1093/aob/mcac131](https://doi.org/10.1093/aob/mcac131) G) Tsakalos, J. L., Renton, M., Riviera, F., Veneklaas, E. J., Dobrowolski, M. P., & Mucina, L. (2019) Trait-based formal definition of plant functional types and functional communities in the multi-species and multi-traits context. *Ecological Complexity*, 40, 100787. [https://doi.org/10.1016/j.ecocom.2019.100787](https://doi.org/10.1016/j.ecocom.2019.100787) H) Tsakalos, J. L., Renton, M., Riviera, F., Veneklaas, E. J., Dobrowolski, M. P., & Mucina, L.  (2020) Data from: Trait-based formal definition of plant functional types and functional communities in the multi-species and multi-traits context, Dryad, Dataset, [https://doi.org/10.5061/dryad.9kd51c5cb](https://doi.org/10.5061/dryad.9kd51c5cb) I) Western Australian Herbarium (1998–) Florabase - the Western Australian Flora. Department of Biodiversity, Conservation and Attractions. Available at [https://florabase.dpaw.wa.gov.au/](https://florabase.dpaw.wa.gov.au/) [Accessed 24 November 2022]. ##### DATA-SPECIFIC INFORMATION FOR: Structural\_and\_taxonomic\_data.csv Summarised data sheet 1\. Number of variables: 13 2\. Number of cases/rows: 177 3\. Variable List: * Reserve: Reserves of the Jarrah forest where data was collected. * Transect: Line transect number * Zone: Whether the area is infested by *Phytophthora cinnamomi* or not * Section: The transect section data was collected (Each 30m long transect was divided into two equal sections). * Fire year: Fire year of the area transect was located * Vegetation complex: Vegetation type of the area transect was located * Soil Type: Soil Type of the area transect was located * Canopy cover: The projected percentage cover of the canopy trees at each 7.5 m section along the transect was averaged from four readings North, South, East, and West. * Abundance: Summarised the species counts (abundance) recorded in the 7.5 m section of each transect * Species richness: Calculated using base R functions * Diversity: Calculated using base R functions * Evenness: Calculated using base R functions * Total cover: Summarised the total cover recorded in the 7.5 m section of each transect 4\. Missing data codes: None 5\. Specialized formats or other abbreviations used: None DATA-SPECIFIC INFORMATION FOR: NMDS\_scores.csv Includes NMDS scores used to visualise the species composition. This is the updated version of the NMDS scores data sheet saved in NMDS\_for\_species\_composition script. 1\. Number of variables: 6 2\. Number of cases/rows: 177 3\. Variable List: * Reserve: Reserves of the Jarrah forest where data was collected. * Transect: Line transect number * Zone: Whether the area infested by *Phytophthora cinnamomi* or not * Section: The transect section data was collected (Each 30m long transect was divided into four equal sections). * NMDS 1 and NMDS 2: Non-metric multidimentional scaling coordinates to visualise the species composition. 4\. Missing data codes: None 5\. Specialized formats or other abbreviations used: None The R scripts folder contains three scripts. 1\. LMM\_structural\_and\_taxonomic\_diversity \- Includes the script for linear mixed model analysis to evaluate the impact of *Phytophthora cinnamomi* on forest structure (Canopy cover and Understorey Cover) and taxonomic diversity (Abundance, Species Richness, Shannon Diversity and Pilou Evenness). Structural\_and\_taxonomic\_data.csv data sheet is used in this script. 3\. LMM\_functional\_traits \- Includes the script for linear mixed model analysis to evaluate the impact of *Phytophthora cinnamomi* on four functional trait groups. Trait\_data.csv file and Abundance\_two\_sections.csv data sheets are used in this script. 4\. NMDS\_for\_species\_composition\- Includes the script for non\-centric multidimensional scaling \(NMDS\) analysis to evaluate the impact of *Phytophthora cinnamomi* on species composition using Abundance.csv file.