DOI: 10.5061/dryad.fn2z34v7r
title: Lineage-specific phylogenetic structure of boreal habitats suggests different assembly processes across phylogenetic and spatial scales

description: The phylogenetic distance among species in a community (community
 phylogenetic structure) has been used to infer deterministic and
 stochastic assembly processes, albeit with criticisms. The effect of
 phylogenetic scale (old versus young lineages) and spatial scale on
 measures of community phylogenetic structure are rarely tested
 simultaneously especially in the boreal biome, yet are essential to
 unravel different assembly processes that might operate in a community. We
 examined lineage-specific phylogenetic structure for six vascular plant
 communities defined at the habitat scale (arctic-alpine barren, bog, fen,
 kalmia barren, limestone barren, and serpentine barren) on the island of
 Newfoundland, Canada, and the phylogenetic structure of plant communities
 defined at a plot scale (72 plots x 1m2). Contrary to the expectation
 under the stress-dominance hypothesis of phylogenetic clustering in
 challenging boreal environments, the majority of clades across the six
 boreal habitats had random phylogenetic structure. However, we observed a
 shift from phylogenetic clustering at the deepest nodes of the angiosperms
 to no phylogenetic structure at shallower nodes (&lt;110 mya),
 suggesting changes in assembly processes with phylogenetic scale within a
 habitat, and the potential role for deterministic processes at deep nodes.
 The random phylogenetic structure of 1m2 plots and our modeling effort to
 test the effect of an environmental stress gradient on community
 composition suggest that a complex set of stochastic and deterministic
 factors is responsible for species assembly at this fine spatial scale,
 not just abiotic filtering in hostile environments like the serpentine as
 predicted by the stress-dominance hypothesis. The interpretation of
 phylogenetic structure metrics did not change when considering species
 abundances or when polytomies were resolved. Taken together, inference of
 assembly processes must be lineage-, habitat- and spatial scale-specific,
 supplemented with knowledge on trait role and evolution for which we
 outline future research hypotheses.
description: # Lineage-specific phylogenetic structure of boreal habitats suggests
 different assembly processes across phylogenetic and spatial scales This
 repository contains the supplementary data, R scripts, and supporting
 information associated with the manuscript. The materials provide
 additional details on the study system, methods, datasets, and results.
 The study examined lineage-specific community phylogenetic structure of
 vascular plant communities across six boreal habitats in Newfoundland,
 Canada, and at fine-scale vegetation plots. ## 1. Data files ###
 Environmental_variables.xls Environmental variables for 72 permanent 1 m²
 vegetation plots (coordinates, elevation, slope, geology, distances to
 water, wetland/rock/soil percentages, ecosubregion). | Variable |
 Definition | Units/Values | Interpretation Key | | :--------------- |
 :-------------------------------------------------------------------- |
 :------------------ |
 :------------------------------------------------------------ | | stress |
 Environmental stress classification from Marilyn Anions | Categorical |
 Competitive, Intermediate, Harsh | | site\_id | Unique plot identifier |
 Text | Format: P#-# (Peatland), T#-# (Tundra) | | site\_type | Plot type |
 Text | P = Peatland, T = Tundra | | sur\_geo | Surface geology type |
 Categorical | See geological classifications below | | bed\_geo | Bedrock
 geology type | Categorical | See geological classifications below | |
 ecoregion | Broad ecoregion classification | Text | Northern Peninsula,
 Southwestern Newfoundland | | ECO\_NAME | Detailed ecoregion name | Text |
 Forest ecoregion designation | | SUB\_NAME | Ecoregion subdivision | Text
 | Specific subregion within ecoregion | | site\_utm\_east | UTM Easting
 coordinate | Meters | NAD83 coordinate system | | site\_utm\_north | UTM
 Northing coordinate | Meters | NAD83 coordinate system | | elevation |
 Site elevation above sea level | Meters | | | slope | Slope angle category
 | Categorical/Degrees | Level = 0°, Slight = 10°, Steep = 30° | | aspect |
 Slope aspect/direction | Degrees | 0-360° from north | | pond\_m |
 Distance to nearest pond | Meters | | | river\_m | Distance to nearest
 river | Meters | | | p100\_wet | Wetland percentage in vicinity |
 Percentage (0-100) | Percentage of area within 20m radius that is wetland
 | | rock/soil cover | Rock and soil cover index | Scale 0-5 | 0 = minimum
 cover, 5 = maximum cover | | PA\_SESMPD | Standardized Effect Size of Mean
 Pairwise Distance (Presence-Absence) | Standardized units | Phylogenetic
 community structure metric | | AW\_SESMPD | Abundance-Weighted
 Standardized Effect Size of Mean Pairwise Distance | Standardized units |
 Phylogenetic community structure metric weighted by abundance | |
 speciesRichness | Number of species per plot | Count | Total vascular
 plant species count | ### Plot_species_list.xlsx Species identity and
 cover (%) per plot across two habitat types. **Sheet 1: "Rawdata
 Arctic-Alpine"** Contains two data tables: * **Table 1**:
 Species-plot matrix with environmental data (79 species) * **Table 2**:
 Binary presence-absence matrix for Tundra plots (T#-#) **Sheet 2:
 "Rawdata Peatland"** Contains two data tables: * **Table 1**:
 Species-plot matrix with environmental data (76 species) * **Table 2**:
 Binary presence-absence matrix for Peatland plots (P#-#) **Sheet 3:
 "Species status"**  * Provides species conservation information
 for taxa recorded in both habitat types. * Columns
 include: *Species*, *Status* (IUCN global listing), and *Source* (URL to
 the IUCN Red List entry). Example entries: * *Agrostis mertensii* — Not
 listed (IUCN, global). * *Alnus crispa* — Not listed (IUCN, global). *
 *Arethusa bulbosa* — LC (Least Concern). | Variable | Definition |
 Units/Values | Notes | | :---------------------- | :----------------------
 | :----------- | :------------------------------------- | | # | Record
 number | Count | Sequential identifier (Table 1 only) | | Plot | Plot
 identifier | Text | T#-# (Tundra) or P#-# (Peatland) | | Species | Species
 name | Text | Binomial nomenclature with underscores | | Cover\_Adjusted |
 Adjusted species cover | Percentage | Vegetation cover percentage | |
 UTM\_East\_Rounded10km | UTM Easting coordinate | Meters | NAD83
 coordinate system | | UTM\_North\_Rounded10km | UTM Northing coordinate |
 Meters | NAD83 coordinate system | | Elevation (m) | Plot elevation |
 Meters | Above sea level | | Slope | Slope category | Text | Level,
 Slight, Steep | | Aspect | Slope direction | Degrees | 0-360° from north |
 **Binary matrices**: Rows = plots, Columns = species names, Values = 1
 (present) or 0 (absent) ### Vascan.list881-and-habitat-list.xlsx Full list
 of 881 native vascular plant species compiled from VASCAN. **Sheet 1:
 "habitat-list"** Binary presence-absence matrix across six
 boreal habitats. | Variable | Definition | Values | Notes | |
 :------------------- | :-------------------------------------------------
 | :----- | :------------------------------------------ | | Species names
 (rows) | Full species names with family and higher taxonomy | Text |
 Format: Genus\_species\_Family\_HigherTaxon | | Kalmia heathland | Species
 presence in Kalmia heath habitat | Binary | 1 = present, 0 = absent | |
 Limestone Barren | Species presence in limestone barren habitat | Binary |
 1 = present, 0 = absent | | Serpentine Barren | Species presence in
 serpentine barren habitat | Binary | 1 = present, 0 = absent | |
 Arctic-Alpine | Species presence in arctic-alpine habitat | Binary | 1 =
 present, 0 = absent | | Bog | Species presence in bog habitat | Binary | 1
 = present, 0 = absent | | Fen | Species presence in fen habitat | Binary |
 1 = present, 0 = absent | **Sheet 2:
 "Vascan.list881sp-regionaltree"** Master checklist with complete
 taxonomic information for all 881 native vascular plant species of
 Newfoundland. | Variable | Definition | Values | Notes | | :------- |
 :--------------------------- | :----- |
 :--------------------------------------------------------- | | Species |
 Species scientific name | Text | Binomial nomenclature | | Taxonomy |
 Complete taxonomic hierarchy | Text | Format:
 Genus\_species\_Family\_HigherTaxonomy\_MAJORGROUP | ###
 rare_species_gros_morne_1998.xlsx List of rare species found in Peatland
 and Tundra plots with rarity status and location information. | Variable |
 Definition | Values | Notes | | :----------------------------------- |
 :-------------------------------- | :---------- |
 :------------------------------------------------------------- | | Rare
 Species | Scientific name of rare species | Text | Binomial nomenclature |
 | P2 | Presence in Peatland site 2 | Binary | X = present, blank = absent
 | | T1, T2, T3, T4, T5, T7, T8, T11, T12 | Presence in specific Tundra
 sites | Binary | X = present, blank = absent | | Rarity National |
 National rarity status | Categorical | N1 = critically rare nationally | |
 Rarity Province | Provincial rarity status | Categorical | S1 = critically
 rare, S2 = threatened, SH = historically known | | Notes | Additional
 information | Text | Location notes, specimen details | **Rarity Status
 Codes:** * **S1**: Critically endangered (5 or fewer locations or very few
 individuals) * **S2**: Threatened (6 to 20 locations or a few individuals)
 * **SH**: Historically known, but presence unverified in the past 20 years
 * **N1**: Critically rare at the national level ### Phylogenetic trees *
 **Newfoundland_species_tree.tre**: Mega-tree reconstructed with
 V.PhyloMaker2 * **Habitat_phylogenies/**: Six pruned phylogenies, one per
 habitat * **Trees_nwk.zip**: Archive containing the full and habitat-level
 trees in .nwk format * **No_polytomies(500_tress_per_habitat).zip**: 500
 randomly resolved trees per habitat, used to evaluate sensitivity to
 polytomies ## 2. R Scripts * **mpd.by.clade.R**: Automates calculation of
 standardized effect size of mean pairwise distance (SES-MPD) for all
 clades * **GAMM_analysis.R**: Fits generalized additive mixed models
 (GAMMs) relating SES-MPD to clade divergence time *
 **Plot_scale_analysis.R**: Runs dbRDA, GLMs, and MEMs to test
 environmental and spatial effects on 1 m² plots ## 3. Software
 requirements All analyses were performed using **R v4.3.0** (R Core Team,
 2023). ### Core Software * **RStudio** (optional IDE) * Spreadsheet
 software (LibreOffice, Excel, or Google Sheets) for .xls/.xlsx files *
 Phylogenetic tree viewers (optional): FigTree, iTOL, or R packages (ape,
 ggtree) ### R Packages * **Phylogenetic analysis**: V.PhyloMaker2 v0.1.0,
 ape v5.8-1, RRphylo v2.8.0, PhyloMeasures v2.1, picante v1.8.2 *
 **Statistical modeling**: mgcv v1.9-0, spdep v1.3-10, adespatial v0.3-28,
 vegan v2.7-0, cluster v2.1.8 * **Data handling & visualization**:
 dplyr v1.1+, tibble v3.2+, ggplot2 v3.4+, stringr v1.5+, readr v2.1+ ## 4.
 Workflow 1. Load phylogenetic trees (Trees_nwk.zip or No_polytomies...zip)
 2. Run mpd.by.clade.R with PhyloMeasures to compute SES-MPD 3. Use
 GAMM_analysis.R with mgcv to model SES-MPD vs divergence time (using the
 extracted variables NODE, AGE, AND SES-MPD) 4. Generate figures
 (phylogenies, GAMM fits, dbRDA) using ggplot2 5. Analyze plot-scale
 structure with Plot_scale_analysis.R using vegan, cluster, spdep,
 adespatial (USING THE Environmental_variables.txt file) ## 5. Data
 standards and missing values ### Missing value codes * Environmental and
 species data: `NA` * Species absence in habitat lists: `0` * Species
 absence in plot data: blank cell * Missing cover data: `NA` ### Plot
 identifier codes * **P = Peatland plots** * **T = Tundra plots** ###
 Geological classifications **Surface Geology (sur_geo):** * TILL VENEER:
 Thin glacial till deposits * MARINE GRAVEL: Marine-deposited gravel *
 BEDROCK: Exposed bedrock * PEAT AND MUCK: Organic deposits * TILL WITH
 FLATTENED SLOPES: Glacial till on flattened terrain * TILL WITH SMOOTHED
 SLOPES: Glacial till on smoothed terrain * TILL BLANKET: Thick glacial
 till cover * BLOCKY RUBBLE (TALUS): Angular rock fragments **Bedrock
 Geology (bed_geo):** * BROKEN SEDIMENT (MELANGE): Mixed sedimentary rocks
 * LIMESTONE: Carbonate rock * GABBRO: Mafic igneous rock * PERIDOTITE:
 Ultramafic igneous rock * DEFORMED PERIDOTITE: Tectonically altered
 ultramafic rock * GNEISS: Metamorphic rock * SANDSTONE: Sedimentary rock *
 GRANITE: Felsic igneous rock ### Technical standards * **Coordinate
 System**: NAD83 UTM * **Taxonomic Authority**: VASCAN (Vascular Plants of
 Canada database) * **Phylogenetic Reconstruction**: V.PhyloMaker2 * **Plot
 Size**: 1 m² permanent vegetation plots (n=72) ### Coordinate
 Generalization All geographic coordinates in this dataset were generalized
 to reduce spatial precision, following GBIF sensitive species best
 practices while maintaining scientific utility. * **Fields
 included:** `UTM_East_Rounded10km`, `UTM_North_Rounded10km` * **Formula
 applied:** =ROUND(VALUE(coordinate)/10000, 0)*10000