Impact of Phytophthora cinnamomi on the taxonomic and functional diversity of forest plants in a mediterranean-type biodiversity hotspot
Data files
Nov 13, 2023 version files 207.34 KB
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Abundance_two_sections.csv
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Abundance.csv
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Cover.csv
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NMDS_scores.csv
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README.md
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Structural_and_taxonomic_data.csv
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Trait_data.csv
Abstract
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.
README: 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
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
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
Harry Butler Institute, Murdoch University, 90 South Street, Murdoch, WA, 6150, Perth, Australia
iv) Jen McComb
Harry Butler Institute, Murdoch University, 90 South Street, Murdoch, WA, 6150, Perth, Australia
v) Treena I. Burgess
Harry Butler Institute, Murdoch University, 90 South Street, Murdoch, WA, 6150, Perth, Australia
vi) Giles E. St. J. Hardy
Harry Butler Institute, Murdoch University, 90 South Street, Murdoch, WA, 6150, Perth, Australia
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– < 50 = 3
- more than 50 – < 160 = 4
- more than 160 –< 600 = 5
- ≥ 600 = 6
- hw = height:width
- h:w >1 = Skinny
- h:w =1 = Normal
- h:w <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
- < 1 = 1
- 1–2 = 2
- 2 - < 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 [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
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
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
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
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
I) Western Australian Herbarium (1998–) Florabase - the Western Australian Flora. Department of Biodiversity, Conservation and Attractions. Available at 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.
Methods
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 (Eucalyptus marginata) forest using the line transect method. These reserves were impacted by the plant pathogen Phytophthora cinnamomi 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.