Irish Vegetation Classification Technical Progress Report No. 5

Prepared by

Philip M. Perrin

BEC Consultants Ltd

29th November 2019

Irish Vegetation Classification Technical Report No. 5

1 Scope

This document reports on progress made during the fifth phase of the development of the Irish Vegetation Classification (IVC). Work was conducted by BEC Consultants Ltd under agreement with the National Biodiversity Data Centre (NBDC) between August and November 2019. The proposal for this phase specified several tasks which are summarised here:

1. Production of web page content (.docx, .jpeg, .png format) for each of the communities defined within the targeted divisions of the classification, including photographs, distribution maps and descriptive text; 2. Production of community synopses (.pdf format) for each of the communities defined within the targeted divisions of the classification, including photographs, distribution maps and data, descriptive text, synoptic tables, proxy environmental values and affinities with other classifications; 3. Production of an updated version of the ERICA application (.zip format) allowing analysis of data from the targeted habitats; 4. Production of an updated version of the ERICA manual (.pdf format within the application); 5. Production of a technical report detailing all work conducted (.pdf format).

Work conducted to complete these tasks is reported in sections 2 to 4 of this report. Section 5 makes recommendations for the subsequent phases of the project. Technical Progress Reports (TPRs) #1-#4 should be consulted for background information on the project and the methods used.

2 Classification process

2.1 Remit and approach The remit of this phase of the project was defined as including vegetation of (i) sand dunes, (ii) strandline and shingle, (iii) coastal rocks, (iv) scrub, (v) herb fringes and (vi) ruderal communities. The analysis was initially split into two subphases: subphase Va tackled (i) and (ii) above, subphase Vb tackled (iii), (iv), (v) and (vi) above. Ultimately, a third subphase, Vc, was required to draw out some of the target communities. No national-scale plot-based classifications have previously been proposed for these habitats.

2.2 Collation of data The National Vegetation Database (NVD) was screened for relevant data with the aid of the habitat type notes in the NVD bibliography dated 2013. Within most of the constituent databases of the NVD, plots have been classified using the Guide to Habitats in Ireland (Fossitt, 2000, hereafter GHI) either by NBDC staff upon entry of the data into the NVD or by the original authors. Within subphase Va, special consideration was thus given to plots labelled as SD (sand dunes), CB (shingle and gravel banks) and LS (littoral sediment) to check if they fell within the remit of this section of work. Within subphase Vb, special consideration was given to CS (sea

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cliffs and islets), WS (scrub), HD (bracken), ED (disturbed ground), BL (built land) and BC (cultivated land).

In addition to using the NVD, data were utilised from a limited number of additional relevant sources: (i) the Sand Dunes Monitoring Project (SDMP) whose dataset contained full plot data from a subset of the sites surveyed by that project; (ii) data from dunes recorded as part of the recent national Vertigo survey; (iii) a national dataset on dune slacks from provided by A. Delaney; (iv) a dataset on the dune slacks of North Bull Island provided by F. Devaney; (v) a recent NPWS survey of Chenopodion stands; (vi) the Irish Juniper Monitoring Survey 2017; (vii) the National Survey of Irish Sea Cliffs.

The full list of databases from which data were selected is presented in Tables 1 and 2. Plots classified as ‘noise’ in subphase Va were reanalysed in subphase Vb.

Table 1. Datasets from which data were extracted for subphase Va, with cover scales and number of remit plots classified by data quality Type. Number Number of plots of each Type of remit Dataset code/source Cover scale plots 1 2 3 4 INDEP 001 Domin 40 36 0 0 4 INDEP 005 Modified Domin 1 36 35 1 0 0 INDEP 009 Modified Domin 2 22 18 4 0 0 INDEP 024 Braun-Blanquet (old) 83 76 0 0 7 NPWS 003 Braun-Blanquet (old) 5 4 1 0 0 NPWS 004 Braun-Blanquet (old)/Domin 5 3 2 0 0 NPWS 005 Braun-Blanquet (old) 7 5 0 2 0 NPWS 006 Domin 640 583 57 0 0 NPWS 008 Braun-Blanquet (old)/Domin 21 20 1 0 0 NPWS 010 Braun-Blanquet (new) 184 169 12 0 3 NPWS 031 Braun-Blanquet (old) 21 21 0 0 0 NPWS 033 Domin 26 24 2 0 0 NPWS 041 Braun-Blanquet (old) 1 1 0 0 0 NPWS 045 Braun-Blanquet (old) 9 8 1 0 0 NPWS 049 Braun-Blanquet (old) 2 2 0 0 0 NPWS 058a* Braun-Blanquet (old)/Tansley 61 26 29 0 6 NPWS 062 Domin 4 4 0 0 0 TCD 001 Domin 43 28 0 15 0 UCD 002 Braun-Blanquet (old) 5 5 0 0 0 UCD 003 Braun-Blanquet (old) 145 134 11 0 0 UCD 004 Braun-Blanquet (old) 17 12 5 0 0 UCD 004a Braun-Blanquet (old) 21 11 7 0 3 UCD 012 Braun-Blanquet (old) 530 525 1 0 4 Delaney Percentage 109 105 4 0 0 Devaney Braun-Blanquet (old) 75 67 8 0 0 SDMP Domin 124 119 5 0 0 Vertigo Percentage 90 86 4 0 0 Total 2,326 2,127 155 17 27 * This composite dataset has been split into its six components for ease of processing.

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Table 2. Datasets from which data were extracted for subphase Vb, with cover scales and number of remit plots classified by data quality Type. Number Number of plots of each Type of remit Dataset code/source Cover scale plots 1 2 3 4 INDEP 001 Domin 69 55 0 0 14 INDEP 010 Crushell 5 4 0 0 1 INDEP 017 Braun-Blanquet (old)/Domin 1 1 0 0 0 INDEP 019 Braun-Blanquet (old) 7 7 0 0 0 INDEP 022 Braun-Blanquet (old) 3 0 3 0 0 INDEP 025 Braun-Blanquet (old) 42 37 0 0 5 INDEP 026 Braun-Blanquet (old) 58 49 0 0 9 INDEP 027 Braun-Blanquet (old) 9 9 0 0 0 INDEP 029 Braun-Blanquet (old) 16 16 0 0 0 INDEP 030 Percentage 21 15 0 0 6 INDEP 031 Modified Domin 7 3 3 0 0 0 IPCC 001 Percentage 1 1 0 0 0 IPCC 003 Percentage 4 2 0 0 2 IPCC 004 Percentage 2 0 0 0 2 NPWS 003 Braun-Blanquet (old) 14 10 2 2 0 NPWS 004 Braun-Blanquet (old)/Domin 2 0 0 2 0 NPWS 005 Braun-Blanquet (old) 3 0 0 3 0 NPWS 006 Domin 28 25 3 0 0 NPWS 009 Braun-Blanquet (new) 4 4 0 0 0 NPWS 013 Braun-Blanquet (old) 1 0 1 0 0 NPWS 015 Percentage 16 0 16 0 0 NPWS 019 Braun-Blanquet (old) 6 0 1 3 2 NPWS 020 Braun-Blanquet (old) 6 6 0 0 0 NPWS 024 Braun-Blanquet (old) 2 0 0 0 2 NPWS 027 Domin 1 1 0 0 0 NPWS 031 Braun-Blanquet (old) 1 1 0 0 0 NPWS 032 Braun-Blanquet (old) 124 123 1 0 0 NPWS 039 Braun-Blanquet (old) 6 5 1 0 0 NPWS 045 Braun-Blanquet (old) 9 8 1 0 0 NPWS 047 Domin 2 2 0 0 0 NPWS 048 Domin 2 1 1 0 0 NPWS 049 Braun-Blanquet (old) 6 5 0 0 1 NPWS 050 Braun-Blanquet (old) 1 0 0 1 0 NPWS 057 Braun-Blanquet (old) 10 8 1 0 1 NPWS 058a* Braun-Blanquet (old)/Tansley 90 50 4 0 36 NPWS 058c* Percentage 3 0 0 0 3 NPWS 059 Domin 83 60 23 0 0 NPWS 061 Domin 2 0 2 0 0 NUIG 004 Braun-Blanquet (old) 16 16 0 0 0 NUIG 008 Braun-Blanquet (old) 21 21 0 0 0 NUIG 009 Braun-Blanquet (old) 23 0 0 0 23 NUIG 010 Braun-Blanquet (old) 10 10 0 0 0 NUIG 015 Braun-Blanquet (old) 11 11 0 0 0 NUIG 019 Modified Braun-Blanquet 3 320 320 0 0 0

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Table 2. continued. Number of plots of each Type Number of remit Dataset code/source Cover scale plots 1 2 3 4 TCD 008 Percentage 41 0 31 10 0 UCD 002 Braun-Blanquet (old) 1 0 0 0 1 UCD 017 Percentage 3 0 0 0 3 UCD 021 Braun-Blanquet (old) 226 142 3 81 0 Chenopodion Domin 30 20 10 0 0 Juniper Percentage 21 21 0 0 0 Sea cliffs Domin 49 19 30 0 0 Noise plots Various 54 54 0 0 0 Total 1,489 1,142 134 102 111 * This composite dataset has been split into its six components for ease of processing.

2.3 Preparation and assessment of data Syntrichia ruralis and Syntrichia ruraliformis are treated as two distinct species on the Ireland2008 checklist used by the NVD. However, Syntrichia ruraliformis has often been regarded as only a subspecies (e.g. Atherton et al., 2010; Blockeel et al., 2014) or variety (e.g. Smith, 2004) of Syntrichia ruralis, as evidenced by the list of synonyms in Gallego et al. (2002). Syntrichia ruraliformis is common on sand dunes and rare inland, whereas Syntrichia ruralis sensu stricto is rare on sand dunes but common in inland habitats (Smith, 2004). This difference in ecology was apparently reflected in the combined sand dunes dataset (subphase Va) with a large number of Syntrichia ruraliformis records (n = 345) but only a small number of Syntrichia ruralis records (n = 18). However, 14 of the 18 Syntrichia ruralis records come from a subsection of dataset NPWS 058 which contains no records of Syntrichia ruraliformis within any of its dune plots; the data in this subsection are from Braun-Blanquet and Tüxen (1949). It was therefore speculated that these 14 records may not actually be Syntrichia ruralis senso stricto as indicated by the NVD. Braun-Blanquet and Tüxen (1949) described a Viola curtisii – Syntrichia ruralis association based on their dune data. When comparing their own data to this association, Ivimey-Cook and Proctor (1964, p. 242) mentioned: “Braun-Blanquet and Tüxen described their association from dunes in Kerry and Sligo, where Tortula ruraliformis (Syntrichia ruralis p.p.) occurs regularly and, with other mosses, covers most of the ground.”

These observations all point to the conclusion that the taxa recorded by Braun-Blanquet and Tüxen should actually be regarded as Syntrichia ruraliformis. These data were thus changed accordingly.

Two datasets used in subphase Vb focussed on arable weed communities: NPWS 032 and NUIG 019. Following the approach of Rodwell (2000), records of crop plants were excluded from the plots of dataset NPWS032. These crops comprised Allium cepa (onion), Avena fatua (wild oat), Avena sativa (common oat), Avena strigosa (bristle oat) and Secale cereale (rye). Crop plants were not recorded in dataset NUIG 019 although the NBDC cover page states that these crops included cabbage, turnip, cauliflower, potatoes, kale, beetroot, sugar beet, mangels, sprouts, carrots, beans, French beans, peas, spinach, sprouting broccoli, parsnips, rhubarb, barley, wheat and oats. Bryophyte data were very scanty for dataset NUIG 019 (only three species were recorded) and were absent from NPWS 032. Data presented in Rodwell (2000), suggest that

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bryophyte species (e.g. Bryum rubens) are occasional in these communities but seldom plentiful. These two datasets constitute the vast majority of samples from this habitat and to exclude them on the basis of bryophyte recording would probably have made the definition of any arable weed communities unviable. In a similar vein, all data in dataset NUIG 019 had been recorded from large, 64 m2 plots, which, given the scale of the vegetation, could have warranted exclusion of these plots based on plot size (more reasonably sized 4 m2 plots were used in NPWS 032). Again, however, this would have resulted in the exclusion of the majority of the arable weed plots. Thus, we decided to proceed with the analysis without excluding any data on the basis of these criteria, although an important caveat was manifest: arable weed communities defined by the IVC were likely to significantly underestimate the bryophyte component of the vegetation.

Arctium minus and Arctium nemorosum are treated as two distinct species on the Ireland2008 checklist, but the latter taxa has previously been regarded as subspecies of the former (Webb et al., 1996). Preston et al. (2002) mention that Arctium minus sensu lato is a variable taxon which has received differing taxonomic treatments. Stace (2010) states that there has been much confusion between Arctium nemorosum and Arctium minus and makes no clear distinction with regard to their ecology. Consequently, records for these two taxa have been combined as Arctium minus/nemorosum. The IVC species checklist and model were amended accordingly. Data recorded using non-percentage cover scales were converted to percentages. See tables in Appendix I.

The suitability of the selected data for inclusion in the analysis was assessed. Plots were classified according to the standard of the data as follows (see Tables 1 and 2 for breakdown by dataset):

Type 1. Plots with none of the issues described for Types 2-4.

Type 2. Plots where excluded taxa data (e.g. Festuca sp.) comprised ≥ 5% cover in total.

Type 3. Plots with an apparent significant deficiency in the recording of bryophytes, with the exception of plots categorised as Type 2; whilst recording of lower plants often varies between datasets (and habitats) in terms of both effort and accuracy, it is desirable that at least the main bryophytic components of vegetation should be recorded. However, due to the paucity of records for many habitats, this standard was more leniently applied than in previous phases (for example, see discussion of arable weed communities above).

Type 4. Plots with no recorded size or unusually large or small size, with the exception of plots categorised as Types 2 or 3; this was to ensure that reasonably valid comparisons were made between plots. In subphase Va, plots were classed as Type 4 if they had a recorded size < 1 m2 or > 25 m2; the most common plot size used was 4 m2. In subphase Vb, permitted plot sizes were: 0.1 m2 - 4 m2 for vegetation of crevices, sea cliffs, walls and mine-spoil, 4 m2 - 25 m2 for bracken and tall herb stands, 4 m2 to 64 m2 for weed communities (see reasoning above), 4 m2 - 100 m2 for scrub.

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2.4 Group-level analysis (subphase Va) A group-level version of the IVC classification model produced by Phase IV was created. This used data from 21,511 plots. In subphase Va, function vegclustdist was used to extend this model using the 2,127 Type 1 plots collated above, whilst fixing the existing group centroids. The function was run for k = {2, 3, 4…6} where k is the number of new groups. Standard IVC parameters were used (method = “NC”, m = 1.1, δ = 0.75, number of random starts = 10, maximum number of iterations = 100). The procedure is shown in Fig. 1.

Matrix of Previous Create Create New Type 1 previous reference distance distance data membership data matrix (diss) matrix (dis)

Simplify and Create Comparative New vectorize distance distance distance (defuzzify) matrix (dis) matrix matrix

Vector of Classify to Old distance First group group-level old groups matrix level results membership (vegclass)

Create Create k new Distances to model groups old clusters (as.vegclust) (vegclustdist)

Group level Extended model group level results

Figure 1. Flow chart of the procedure for extending a previous classification using package vegclust. Green shapes are data items. Purple shapes are processes, with the function name in brackets.

Species frequency values were calculated for each of the potential new groups and assessed using expert judgement. With k ≤ 4, a substantial number of plots were assigned to the pre- existing FE3 Agrostis stolonifera – Carex nigra group. This group comprises fen and turlough vegetation together with fen-like dune slacks lacking in coastal indicators such as Carex arenaria and Salix repens. It was, however, deemed desirable to include the more distinctive dune slack types within a new duneland division. With k ≥ 5, a new dune slack and humid machair group was indeed formed, but now Festuca rubra-dominated vegetation was split between two or three groups. Furthermore, Elytrigia juncea stands and Ammophila arenaria stands now formed separate but closely aligned groups which were likely to yield only a single community each. It was therefore decided to use the k = 5 solution, but to merge the two Festuca groups and then to merge the Elytrigia and Ammophila groups, to form a three-group, one- division solution that reflected the major zones of sand dune complexes (Table 3). Strandline and shingle plots failed to form a group, being consistently placed in the noise (outlier) class.

A reasonable number of plots (n = 75) were assigned to grassland (GL) groups, in particular the GL2 and GL3 groups which comprise wet and dry, neutral and calcareous grassland. Fixed dunes and machair chiefly support grassland habitats and it is likely that dune grassland and ‘non- dune’ grassland co-occur at many sites. Far fewer plots were assigned to the FE3 group by this

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solution that others that were examined as just discussed. A reasonable number (n = 88) were still assigned there, however, underlining the close connection between dune slacks and fens. Over 50 plots were assigned to saltmarsh (SM) groups, probably reflecting natural transitions between dune and saltmarsh systems.

Cluster variance (variance in community composition as calculated by function clustvar, package vegclust, using the distance matrix) for the new groups was higher than those calculated for most IVC groups, but less than the values for the fen and freshwater groups in the last phase, and were deemed acceptable. Groups were named after some of the top results from Indicator Species Analysis (function multipatt, package indicspecies, max.order = 1).

Table 3. Assignment of duneland Type 1 plots to groups by noise clustering analysis and cluster variance of the new groups Group Number Cluster of plots variance FE3 Agrostis stolonifera – Carex nigra group 88 - FW2 Ranunculus penicillatus – Fontinalis antipyretica group 1 - FW3 Phragmites australis – Cladium mariscus group 4 - GL1 Juncus acutiflorus – Molinia caerulea group 9 - GL2 Agrostis stolonifera – Ranunculus repens group 16 - GL3 Cynosurus cristatus – Plantago lanceolata group 49 - GL4 Nardus stricta – Galium saxatile group 1 - HE1 Dryas octopetala – Sesleria caerulea group 1 - HE4 Molinia caerulea – Polygala serpyllifolia group 1 - SM1 Salicornia agg. – Spartina agg. group 4 - SM2 Puccinellia maritima – Spergularia media group 1 - SM3 Plantago maritima – Armeria maritima group 2 - SM4 Festuca rubra – Seriphidium maritimum group 26 - SM5 Juncus maritimus – Oenanthe lachenalii group 8 - SM6 Agrostis stolonifera – Juncus gerardii group 25 - WL3 Alnus glutinosa – Filipendula ulmaria group 2 - DU1 Elytrigia juncea – Ammophila arenaria group 469 0.29 DU2 Festuca rubra – Galium verum group 1096 0.26 DU3 Agrostis stolonifera – Carex arenaria group 260 0.29 Noise 64 Total 2127

2.5 Community-level analysis (subphase Va) The same analysis was run on each of the subsets of data delimited by the three DU groups for k = {2, 3, 4…6} to define communities, but with no fixed clusters. Expert judgement examination of constancy (species frequency) tables and results of Indicator Species Analysis was used to identify ecologically meaningful clusters. Eleven communities were identified by this process (Table 4). No sub-community analysis was conducted at this time.

The plots categorised as Assigned by the community-level analysis (n = 1,727) were added to the IVC statistical model (an R object of class vegclust) produced at the end of phase IV, along with the community-level cluster assignments of those plots. The procedure is shown in Fig. 2.

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Table 4. Assignment of plots to duneland communities by noise clustering analysis of group subsets. A = Assigned, T = Transitional. Community A T Total DU1A Elytrigia juncea duneland 231 3 234 DU1B Ammophila arenaria duneland 232 3 235 Noise - 0 0

DU2A Ammophila arenaria – Festuca rubra duneland 251 18 269 DU2B Festuca rubra – Syntrichia ruraliformis duneland 309 24 333 DU2C Festuca rubra – Plantago lanceolata – Carex arenaria duneland 271 21 292 DU2D Festuca rubra – Thymus polytrichus duneland 187 15 202 Noise - 0 0

DU3A Salix repens – Lotus corniculatus duneland 60 2 62 DU3B Agrostis stolonifera – Calliergonella cuspidata – Carex arenaria duneland 64 4 68 DU3C Agrostis stolonifera – Festuca rubra – Carex arenaria duneland 13 0 13 DU3D Festuca rubra – Bellis perennis duneland 64 5 69 DU3E Succisa pratensis – Epipactis palustris duneland 45 3 48 Noise - 0 0

Total 1,727 98 1,825

Ordered, Previous Matrix of Assigned, reference previous Type 1 data data membership

Conform Vectorize matrices (defuzzify) (conformveg)

Vector of old cv$x cv$y community membership

Add new Combine Vector of new, data to old vectors ordered (rbind) (c) community membership New Create new New reference model community matrix (as.vegclust) vector

New classification model

Figure 2. Flowchart of the procedure for updating a classification model using package vegclust following definition of new communities. Green shapes are data items. Purple shapes are processes, with the function name in brackets.

All of the duneland plots (n = 2,326) were then reclassified using this new combined model (Table 5). A large number of plots were classified to communities of other divisions, mostly the grasslands, fen and mires, and saltmarsh (the nature of most of these plots has already been mentioned above).

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Table 5. Final assignment of plots to the IVC duneland classification. A = number of Assigned plots, T = number of Transitional plots. See Table 4 for full category names. Type 1 plots Type 2,3,4 plots Sub- Sub- IVC category A T total A T total Total DU1A Elytrigia juncea 210 17 227 26 2 28 255 DU1B Ammophila arenaria 224 4 228 16 1 17 245 DU2A Ammophila arenaria – Festuca rubra 298 24 322 22 1 23 345 DU2B Festuca rubra – Syntrichia ruraliformis 173 31 204 15 6 21 225 DU2C Festuca rubra – Plantago lanceolata – Carex arenaria 222 44 266 12 2 14 280 DU2D Festuca rubra – Thymus polytrichus 229 30 259 33 7 40 299 DU3A Salix repens – Lotus corniculatus 60 5 65 1 1 2 67 DU3B Agrostis stolonifera – Call. cuspidata – Carex arenaria 71 15 86 3 1 4 90 DU3C Agrostis stolonifera – Festuca rubra – Carex arenaria 55 29 84 7 4 11 95 DU3D Festuca rubra – Bellis perennis 65 12 77 13 0 13 90 DU3E Succisa pratensis – Epipactis palustris 42 5 47 6 1 7 54 FE Fen and mire division 41 17 58 1 0 1 59 FW Freshwater division 4 1 5 0 3 3 8 GL Grassland division 49 39 88 0 7 7 95 HE Heath division 0 0 0 1 0 1 1 SM Saltmarsh division 36 19 55 3 1 4 59 WL Woodland division 2 0 2 0 0 0 2 Noise cluster - 54 54 - 3 3 57 Total 1,781 346 2,127 159 40 199 2,326 2.6 Group-level analysis (subphase Vb) This section of analysis followed the routine outlined in section 2.4, except that the model produced as an output of subphase Va was used as the basis of the group-level model and the 1,142 Type 1 plots collated above were used (Table 2). The function was run for k = {2, 3, 4 … 5}. With k = 2, two ruderal/weed groups were defined but there was no scrub/bracken group. With k = 3, a scrub/bracken group was added. With k = 4 or 5, some groups lacking any constant species were produced. It was decided to proceed with the k = 3 solution, but to merge the two weed groups together as they did not appear to represent majorly different ecological conditions (Table 6). The groups were placed in separate divisions representing scrub and wayside (SC) and weed communities (WE). Other habitat types failed to form a group, being consistently placed in the noise (outlier) class.

The two groups comprised only 58% of the plots in the combined dataset, with a substantial proportion being assigned to previous groups (27%) or the large noise cluster (15%). A reasonable number of plots were assigned to the saltmarsh (SM) and grassland (GL) groups; these probably include the coastal rock data.

2.7 Community-level analysis (subphase Vb) This section of analysis followed the routine outlined in section 2.5, except that the function was run for k = {2, 3, 4…7}. Twelve communities were identified by this process (Table 7). No sub- community analysis was conducted at this time. The plots categorised as Assigned by this community-level analysis (n = 630) were added to the IVC statistical model produced at the end of subphase Va, along with the community-level cluster assignments of those plots.

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Table 6. Assignment of scrub, bracken, coastal rock and arable weed Type 1 plots to groups by noise clustering analysis and cluster variance of the new groups Group Number Cluster of plots variance BG2 Erica tetralix – Sphagnum capillifolium group 3 - DU1 Elytrigia juncea – Ammophila arenaria group 6 - DU2 Festuca rubra – Galium verum group 24 - DU3 Agrostis stolonifera – Carex arenaria group 5 - FE1 Schoenus nigricans – Campylium stellatum group 2 - FE2 Menyanthes trifoliata – Potentilla palustris group 4 - FE3 Agrostis stolonifera – Carex nigra group 11 - FW1 Littorella uniflora – Eriocaulon aquaticum group 4 - FW2 Ranunculus penicillatus – Fontinalis antipyretica group 1 - GL1 Juncus acutiflorus – Molinia caerulea group 1 - GL2 Agrostis stolonifera – Ranunculus repens group 19 - GL3 Cynosurus cristatus – Plantago lanceolata group 16 - GL4 Nardus stricta – Galium saxatile group 51 - HE1 Dryas octopetala – Sesleria caerulea group 16 - HE2 Erica cinerea - Calluna vulgaris group 7 - HE3 Vaccinium myrtillus – Racomitrium lanuginosum group 2 - HE4 Molinia caerulea – Polygala serpyllifolia group 10 - RH1 Asplenium ruta-muraria – Geranium robertianum group 17 - RH2 Saxifraga spathularis – Racomitrium lanuginosum group 6 - SM3 Plantago maritima – Armeria maritima group 18 - SM4 Festuca rubra – Seriphidium maritimum group 43 - SM6 Agrostis stolonifera – Juncus gerardii group 5 - WL1 Quercus petraea – Luzula sylvatica group 9 - WL2 Fraxinus excelsior – Hedera helix group 11 - WL3 Alnus glutinosa – Filipendula ulmaria group 10 - WL4 Betula pubescens – Molinia caerulea group 2 - SC1 Rubus fruticosus agg. – Galium aparine group 132 0.35 WE1 Poa annua – Stellaria media group 536 0.28 Noise 171 Total 1,142

Table 7. Assignment of plots to scrub/wayside and weed communities by noise clustering analysis of group subsets. A = Assigned, T = Transitional. Community A T Total WE1A Stellaria media – Senecio vulgaris weed community 52 3 55 WE1B Cerastium fontanum – Ranunculus repens weed community 72 4 76 WE1C Veronica persica – Lamium purpureum weed community 114 10 124 WE1D Lolium perenne – Anagallis arvensis weed community 111 2 113 WE1E Poa annua – Plantago major weed community 63 6 69 WE1F Persicaria maculosa – Polygonum aviculare weed community 89 7 96 Noise - 3 3

SC1A Prunus spinosa – Crataegus monogyna scrub 23 0 23 SC1B Crataegus monogyna – Rubus fruticosus agg. scrub 41 0 41 SC1C Pteridium aquilinum – Rubus fruticosus agg. scrub 26 1 27 SC1D Ulex europaeus – Rubus fruticosus agg. scrub 6 0 6 SC1E Rubus fruticosus agg. – Holcus lanatus wayside community 21 2 23 SC1F Galium aparine – Urtica dioica wayside community 12 0 12

Total 630 38 668

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Following the now familiar procedure, all of the subphase Vb plots (n = 1,489) were then reclassified using this new combined model (Table 8). It should be noted that some of the SC communities are rather weakly defined due to low sample size.

Table 8. Final assignment of plots to the IVC scrub/wayside/weed classification. A = number of Assigned plots, T = number of Transitional plots. See Table 7 for full category names. Type 1 plots Type 2,3,4 plots Sub- Sub- IVC category A T total A T total Total WE1A Stellaria media – Senecio vulgaris 53 2 55 0 1 1 56 WE1B Cerastium fontanum – Ranunculus repens 73 12 85 0 3 3 88 WE1C Veronica persica – Lamium purpureum 115 8 123 1 2 3 126 WE1D Lolium perenne – Anagallis arvensis 103 6 109 0 0 0 109 WE1E Poa annua – Plantago major 52 17 69 21 7 28 97 WE1F Persicaria maculosa – Polygonum aviculare 83 18 101 14 2 16 117 SC1A Prunus spinosa – Crataegus monogyna 23 0 23 11 3 14 37 SC1B Crataegus monogyna – Rubus fruticosus agg. 41 0 41 22 6 28 69 SC1C Pteridium aquilinum – Rubus fruticosus agg. 30 10 40 12 2 14 54 SC1D Ulex europaeus – Rubus fruticosus agg. 6 0 6 2 0 2 8 SC1E Rubus fruticosus agg. – Holcus lanatus 19 11 30 4 5 9 39 SC1F Galium aparine – Urtica dioica 16 5 21 4 5 9 30 BG Bog division 2 1 3 0 6 6 9 DU Duneland division 6 12 18 2 7 9 27 FE Fen and mire division 4 10 14 4 6 10 24 FW Freshwater division 2 2 4 1 7 8 12 GL Grassland division 48 64 112 31 43 74 186 HE Heath division 15 13 28 2 6 8 36 RH Rocky habitats 7 13 20 2 5 7 27 SM Saltmarsh division 27 27 54 4 22 26 80 WL Woodland division 6 23 29 16 10 26 55 Noise cluster - 157 157 - 46 46 203 Total 731 411 1,142 153 194 347 1,489

2.8 Subphase Vc After the first two subphases, there still remained 157 plots in the Type 1 noise cluster, representing a variety of habitats including strandline and shingle. Therefore, a third subphase of analysis was conducted to try to define some additional communities, bearing in mind that sample sizes for each were likely to be low.

At this point it was noticed that the plots #17713-#17715 in dataset INDEP 027, that were included in subphase Vb, were direct duplicates of plots #28737-#28739 in dataset NPWS 058, also used in that subphase. Plot #17715 had been assigned to a GL community and the other two plots had been assigned to the noise cluster. Exclusion of these plots meant subsequent analysis was based a dataset of 155 plots.

A new group-level model was created and the noise clustering function was run with the 155 plots for k = {2, 3, 4…16}. Many of these solutions produced a large cluster with no constant species that was a de facto noise class. Seeking a solution with a smaller, genuine noise class, higher values than normal of k had to be tested. Given these large numbers of clusters and the resultant small cluster sizes, the clusters were regarded as potential new communities rather than potential new groups.

The solution for k = 14 was deemed the best; it had a relatively small noise cluster (n = 37), and yielded clusters representing communities of strandline and shingle, Leymus arenaria stands, walls, mine-spoil, sea cliff crevices and Rhododendron thickets. Larger values of k did not

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produce additional meaningful clusters. One cluster produced by the k = 14 solution was trivial, however, comprising a single plot, so was excluded. Furthermore, there were three bryophyte communities from mine-spoil that did not seem to differ in terms of ecological interpretation; these three clusters were therefore combined. More significantly, preliminary testing found a problem with the Leymus cluster which created an error in the classification model apparently related to the within-cluster sum of squares for this cluster. This error may be connected to the relationship between this cluster and the DU1A Elytrigia juncea duneland community, which also contains plots with Leymus. To prevent this error, the Leymus plots were excluded for now, but the optimal solution is probably to split DU1A to create a new Leymus arenaria duneland community (DU1C) and this should be investigated in phase VI.

After these amendments had been made, the remaining clusters were named based on top indicators (Table 9). Three communities were brought together as a new group (ST1) within a new strandline and shingle division (ST). Two mine spoil communities were put in a new group (RH3) within the existing rocky habitat division (RH). One sea cliff community was placed in in a new group (RH4) within the existing rocky habitat division (RH). Two base-rich wall communities were added the existing RH1 group and one base-poor wall community was added to the existing RH2 group. The Rhododendron thicket community was placed in a new group (IN1) within a new invasive plants division (IN).

Table 9. Assignment of subphase Vc plots to groups/communities by noise clustering analysis. A = number of Assigned plots, T = number of Transitional plots. Group A T Total DU1 Elytrigia juncea – Ammophila arenaria group - - 1 FE1 Schoenus nigricans – Campylium stellatum group - - 1 FW3 Phragmites australis – Cladium mariscus group - - 1 GL2 Agrostis stolonifera – Ranunculus repens group - - 1 WL2 Fraxinus excelsior – Hedera helix group - - 1 WE1 Poa annua – Stellaria media group - - 4 ST1 Atriplex prostrata – Honckenya peploides group ST1A Atriplex prostrata – Tripleurospermum maritimum strandline community 6 3 9 ST1B Cakile maritima – Atriplex prostrata strandline community 6 3 9 ST1C Honckenya peploides – Beta vulgaris strandline community 10 3 13 RH1 Asplenium ruta-muraria – Geranium robertianum group RH1C Asplenium ruta-muraria – Cymbalaria muralis wall community 5 7 12 RH1D Parietaria judaica – Tortula muralis wall community 3 2 5 RH2 Saxifraga spathularis – Racomitrium lanuginosum group RH2E Aira caryophyllea – Polytrichum juniperum wall community 6 2 8 RH3 Cephaloziella nicholsonii – Silene uniflora group RH3A Cephaloziella nicholsonii – Cephaloziella stellulifera mine-spoil community 16 5 21 RH3B Silene uniflora – Euphrasia officinalis agg. mine-spoil community 5 2 7 RH4 Asplenium marinum group RH4A Asplenium marinum crevice community 4 4 8 IN1 Invasive plants group IN1A Rhododendron ponticum invasive community 6 5 11 Excluded - - 6 Noise - 37 37 Total 67 36 155

The plots categorised as Assigned by this analysis (n = 67) were added to the IVC statistical model produced at the end of subphase Vb, along with the community-level cluster assignments of those plots. All of the subphase Vc plots (n = 155) were then reclassified using this new combined model (Table 10).

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Table 10. Final assignment of subphase Vc plots to the IVC strandline/invasive/rocky habitats classification. A = number of Assigned plots, T = number of Transitional plots. Type 1 plots Sub- IVC category A T total ST1A Atriplex prostrata – Tripleurospermum maritimum strandline community 9 0 9 ST1B Cakile maritima – Atriplex prostrata strandline community 9 1 10 ST1C Honckenya peploides – Beta vulgaris strandline community 13 0 13 RH1C Asplenium ruta-muraria – Cymbalaria muralis wall community 12 0 12 RH1D Parietaria judaica – Tortula muralis wall community 5 0 5 RH2E Aira caryophyllea – Polytrichum juniperum wall community 8 0 8 RH3A Cephaloziella nicholsonii – Cephaloziella stellulifera mine-spoil community 16 6 22 RH3B Silene uniflora – Euphrasia officinalis agg. mine-spoil community 7 0 7 RH4A Asplenium marinum crevice community 8 0 8 IN1A Rhododendron ponticum invasive community 11 0 11 Noise cluster - 50 50 Total

3 Production of community synopses

To produce the hectad maps, a grid reference identifying the 10 km × 10 km square was needed for each of the plots. These were available for all of the plots from the additional datasets and the majority of the NVD plots. Indeed, they were available for all plots used in subphases Va and Vc. For a proportion of NVD plots used in subphase Vb, however, there was either no grid reference available or the grid reference data did not identify the specific hectad (Table 11). For example, the grid reference information for most of the plots in NPWS 032 is simply “L70, L71, L80, L81, L90”, referring to five hectads, as it is not noted where in the Aran Islands these plots were recorded. Unfortunately, grid references are also missing from the other main weed community dataset, NUIG 019, meaning that the maps for the WE1 community are rather uninformative. However, the NVD cover page for this dataset states that a map does exist in the original Ph.D. thesis. Grid references in Irish Transverse Mercator format (e.g. in the Chenopodion dataset) were converted to Irish National Grid using the Grid Inquest II freeware available from Ordnance Survey Ireland.

Table 11. Phase V plots from the NVD for which hectads could not be determined. Plots without adequate grid references

NVD code Type 1 Types 2-4 Total NUIG 004 1 0 1 NUIG 015 11 0 11 NUIG 019 320 0 320 NPWS 032 116 0 116 NPWS 057 5 1 6 NPWS 058a 2 3 5 Total 455 5 459

The synopses for the new communities were produced in broadly the same manner as in the previous phases (see TPR#1-#4). One difference was that previously affinities with the Zürich- Montpellier school of phytosociology had been made subjectively, most recently using the new

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list and codes for European vegetation alliances of Mucina (2016). In this phase, affinities to this same list were calculated statistically using the European Expert System (EES) available in the JUICE software application. This involved two compromises. Firstly, affinities are now with orders rather than alliances. Secondly, the EES requires identification to subspecies for a large proportion of its indicator species and our data do not meet this requirement. To work around this problem, EES indicator species were only considered at the species level; this will have had the effect of reducing the power of the analysis.

The distribution of all mappable plots used in the analyses are shown in Figs. 3-5. These maps include plots that were ultimately assigned to the noise class or to previously defined IVC communities. Overall coverage was reasonable for dunelands but poor for all other communities.

Figure 3. Distribution and frequency of subphase Va plots mapped at the hectad level.

Photographs of plots were available from the SDMP monitoring project for most of the duneland and strandline communities. Others were kindly provided by Rory Hodd. Some new photos were taken specifically for this project by the author and Fionnuala O’Neill. However, many communities, including all the weeds assemblages, lack photographs. This deficiency will need to be rectified during a later phase.

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Figure 4. Distribution and frequency of subphase Vb plots mapped at the hectad level.

Figure 5. Distribution and frequency of subphase Vc plots mapped at the hectad level.

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4 Updating of the ERICA application

The ERICA web application was updated with the expanded classification hierarchy and selected plot data from the habitats covered in this phase. For any species within these data that were not already part of the IVC classification model, Ellenberg values, native status and hectad distribution data were added to the reference files. Changes in nomenclature were also made to the species list as reported in section 2.3. Some new code was added to remove blank columns or blank rows from uploaded data. The new release version of ERICA is flagged as V5.0.

5 Recommendations

Some brief notes are made here to highlight issues which arose during this phase. The reader is also referred to the same section in TPR#1-#4 as many of the points made there remain valid.

1. The sample sizes for several of the communities defined in this phase are small and this largely reflects under-recording rather than any real rarity of the habitats. Indeed, several of these communities appear very commonplace and are probably regarded as being beneath the interest of many botanists (e.g. WE1A, SC1E, RH1C). Some communities are uninviting to survey with low chances of unusual species (e.g. SC1D, SC1F, IN1A). Some are not so common and indeed are of recognised conservation value but nevertheless have been poorly covered (e.g. ST1A-C, RH4A). Surveying of these communities across the country should be encouraged (or funded) so that at least a critical mass of data can be acquired. 2. Grid references are missing from the two key weed community datasets. Efforts should be made to locate this information if it still exists. 3. A potential DU1C Leymus arenaria duneland community should be investigated.

6 Acknowledgements

Many thanks are due to my colleagues at BEC Consultants for their input on this project, in particular Orla Daly and Fionnuala O’Neill. Aoife Delaney and Fiona Devaney kindly provided data from dune slacks.

Thanks also go the staff of the NBDC for their technical support, in particular Úna FitzPatrick. The IVC project makes extensive use of the vegclust R package written by Miquel De Cáceres; without this tool the IVC would not have been possible in its current guise. I would also like to thank Oliver Pescott, who provided unpublished data on bryophyte distributions. This phase of the IVC was funded by National Parks and Wildlife Service, and I thank Deirdre Lynn, the NPWS project officer, for her support.

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7 References

Atherton, I., Bosanquet, S., Lawley, M., 2010. Mosses and liverworts of Britain and Ireland. British Bryological Society. Blockeel, T.L., Bosanquet, S.D.S., Hill, M.O., Preston, C.D., Society, B.B., 2014. Atlas of British & Irish bryophytes: The distribution and habitat of mosses and liverworts in Britain and Ireland. Pisces Publications, Newbury. Braun-Blanquet, J., Tüxen, R., 1949. Irische Pflanzengesellschaften. Die Pflanzenwelt Irlands. Ergebnisse der 9. Internationalen Pflanzengeographischen Exkursion durch Irland 1949. Veröffentlichungen des Geobotanischen Institutes Rübel in Zürich 25, 24–415. Fossitt, J.A., 2000. A guide to habitats in Ireland. The Heritage Council, Kilkenny. Gallego, M.T., Cano, M.J., Ros, R.M., Guerra, J., 2002. An overview of Syntrichia ruralis complex (Pottiaceae: Musci) in the Mediterranean region and neighbouring areas. Botanical Journal of the Linnean Society 138, 209–224. https://doi.org/10.1046/j.1095- 8339.2002.138002209.x Ivimey-Cook, R.B., Proctor, M.C.F., 1964. The plant communities of the Burren, Co. Clare. Proceedings of the Royal Irish Academy. Section B: Biological, Geological, and Chemical Science 64, 211–302. Mucina, L., Bültmann, H., Dierßen, K., Theurillat, J.-P., Raus, T., Čarni, A., Šumberová, K., Willner, W., Dengler, J., García, R.G., Chytrý, M., Hájek, M., Di Pietro, R., Iakushenko, D., Pallas, J., Daniëls, F.J.A., Bergmeier, E., Santos Guerra, A., Ermakov, N., Valachovič, M., Schaminée, J.H.J., Lysenko, T., Didukh, Y.P., Pignatti, S., Rodwell, J.S., Capelo, J., Weber, H.E., Solomeshch, A., Dimopoulos, P., Aguiar, C., Hennekens, S.M., Tichý, L., 2016. Vegetation of Europe: hierarchical floristic classification system of vascular plant, bryophyte, lichen, and algal communities. Applied Vegetation Science 19, 3–264. https://doi.org/10.1111/avsc.12257 Preston, C.D., Pearman, D.A., Dines, D.T., 2002. New atlas of the British and Irish flora. Oxford University Press, Oxford. Rodwell, J.S. (Ed.), 2000. British Plant Communities Volume 5 - Maritime communities and vegetation of open habitats. Cambridge University Press, Cambridge. Smith, A.J.E., 2004. The moss flora of Britain and Ireland, 2nd ed. Cambridge University Press, Cambridge. Stace, C., 2010. New flora of the British Isles, 3rd ed. Cambridge University Press. Webb, D.A., Parnell, J., Doogue, D., 1996. An Irish Flora, 7th ed. Dundalgan Press, Dundalk.

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8 Appendix I

Table A1. Conversion of cover data on (a) the old Braun-Blanquet scale, (b) the new Braun-Blanquet scale and (c) the Domin scale to percentage cover using mid-range values.

(a) Braun-Blanquet (old) Cover range (%) Converted cover (%) 5 76-100 88 4 51-75 63 3 26-50 38 2 5-25 15 1 1-5 3 + <1 0.5 r <1 0.1

(b) Braun-Blanquet (new) Cover range (%) Converted cover (%) 5 76-100 88 4 51-75 63 3 26-50 38 2b 12.6-25 19 2a 5-12.5 9 2m <5 4 1 1-5 3 + <1 0.5 r <1 0.1

(c) Domin Cover range (%) Converted cover (%) 10 91-100 96 9 76-90 83 8 51-75 63 7 34-50 42 6 26-33 30 5 11-25 18 4 5-10 8 3 1-4 3 2 <1 0.5 1 <1 0.3 + <1 0.1

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Table A2. Conversion of cover data to percentage cover for (a) the Modified Domin 1 scale, (b) the Modified Domin 2 scale, (c) the Modified Domin 7 scale, (d) the Tansley scale, (e) the Crushell scale and (f) Modified Braun-Blanquet 3 scale. For the Tansley scales, only the codes present in the IVC datasets are shown.

(a) (b) Modified Domin 1 Converted cover (%) Modified Domin 2* Converted cover (%) 10 95 10 96 9 80 9 86 8 60 8 76 7 43 7 66 6 28 6 56 5 15 5 46 4 8 4 36 3 4 3 26 2 1 2 16 1 0.1 1 5

(c) (d) Modified Domin 7 Converted cover (%) Tansley** Converted cover (%) 10 96 c 30 9 83 a 15 8 63 r 1 7 42 6 30 5 18 4 7 3 3 2 0.5 1 0.1

(e) (f) Crushell Converted cover (%) Modified Braun-Blanq. 3 Converted cover (%) 8 88 8 75 7 63 7 42 6 38 6 29 5 19 5 13 4 9 4 4 3 3 3 3 2 0.5 2 2 1 0.1 1 1 + 0.5

*incorrectly used and reported in TPR #2 and #4.

**incorrectly applied to a single t234 plot in subphase Vb.