First year results: Question 1
SP
2023-10-02
Characterizing plant assemblies
Identify plant assemblages highlighting dominant and indicator species of the pastoral mountains in Castril, Santiago and Pontones (CSP) pasturelands.
We hypothesise that pastoral commons shape plant diversity in CSP. Second, we hypothesise that livestock mobility, referred here to long- or short-transhumance, shape vegetation in CSP.
Transect repartition
Assessing patterns in the ‘arrangement’ of plant transects by employing ordination methods in order to evaluate the effect of transhumance and commons on plant diversity.
NMDS
nmds_results_csp <- metaMDS(comm = community_data_presence_2,distance = "bray", k=4, trymax=1000) round(nmds_results_csp$stress, digits = 3)## [1] 0.125sites_scores_csp <- as.data.frame(scores(nmds_results_csp$points))
sites_scores_csp = sites_scores_csp %>% mutate(site3)
sites_scores_csp = sites_scores_csp %>% separate(site3,into = c("common","code"),sep=1) %>% separate(code,into = c("code","thr"),sep=2)
sites_scores_csp <- within(sites_scores_csp, {common<-factor(common)})
#sites_scores_csp[11,5] <- "P" # S05 --> P05
species_scores_csp <- as.data.frame(scores(nmds_results_csp, "species"))
species_scores_csp = species_scores_csp%>% filter(if_any(everything(), ~ .x >= 0.6)|if_any(everything(), ~ .x <= -0.6))Dimensions one and two of the NMDS
ggplot(sites_scores_csp, aes(x = MDS1, y = MDS2, label = site3,colour=common)) +
geom_text_repel(alpha = 1, size = 3) + theme_minimal() + theme(legend.position = "bottom") + ylim(-1.0,1.2) + xlim(-1.2,1)
Figure 1: Site ordination
ggplot(data = species_scores_csp, aes(x = NMDS1, y = NMDS2, label = rownames(species_scores_csp))) + theme_minimal() +
geom_text_repel(color ="dodgerblue4",alpha = 0.6, size = 2.5,max.overlaps = 100,force = 1) + ylim(-1.2,1.2) + xlim(-1.2,1.2)
Figure 2: Species ordination
Here I highlighted those species featuring more than 0.5 in one of the axis (I do so because of a matter of overlapping in the graph)
Dimensions one and three of the NMDS
(d1_3_a = ggplot(sites_scores_csp, aes(x = MDS1, y = MDS3, label = site3,color=common)) +
geom_text_repel(alpha = 1, size = 3) + theme_minimal())+ theme(legend.position = "bottom") + ylim(-1.0,1.2) + xlim(-1.2,1)
Figure 3: Site ordination
(d1_3_b = ggplot(species_scores_csp, aes(x = NMDS1, y = NMDS3, label = rownames(species_scores_csp))) + theme_minimal() + geom_text_repel(color ="dodgerblue4",alpha = 0.6, size = 2.5,max.overlaps = 100,force = 1) + ylim(-1.2,1.2) + xlim(-1.2,1.2)) #check_overlap = TRUE) +
Figure 4: Species ordination
Ellipses by commons
par(mfrow=c(1,2))
ade4::s.class(sites_scores_csp[,c(1,2)],factor(sites_scores_csp$common), cellipse=1, cstar=0,
ylim = c(-1.0,1.2),xlim = c(-1.2,1))
text(sites_scores_csp[,c(1,2)],labels=site3,adj=c(-.1,-.8),cex=0.6)
ade4::s.class(sites_scores_csp[,c(1,3)],factor(sites_scores_csp$common), cellipse=1, cstar=0,
ylim = c(-1.0,1.2),xlim = c(-1.2,1))
text(sites_scores_csp[,c(1,3)],labels=site3,adj=c(-.1,-.9),cex=0.6)
left : axes 1-2 NMDS ; right: axes 1-3 NMDS
Ellipses by transhumance modality
par(mfrow=c(1,2))
ade4::s.class(sites_scores_csp[,c(1,2)],factor(sites_scores_csp$thr), cellipse=1, cstar=0,
ylim = c(-1.0,1.2),xlim = c(-1.2,1))
text(sites_scores_csp[,c(1,2)],labels=site3,adj=c(-.1,-.8),cex=0.6)
ade4::s.class(sites_scores_csp[,c(1,3)],factor(sites_scores_csp$thr), cellipse=1, cstar=0,
ylim = c(-1.0,1.2),xlim = c(-1.2,1))
text(sites_scores_csp[,c(1,3)],labels=site3,adj=c(-.1,-.9),cex=0.6)
left : axes 1-2 NMDS ; right: axes 1-3 NMDS
As first view, there is neither an arrangement related to common nor an arrangement related to long- or short-transhumance. In the further analysis we will dissect long- or short-transhumance, i.e., into day of entry in the summer pasture lands or how many days they stay in the mountains considering also the stoking rate, to find the possible signature of livestock mobility in the vegetation.
Also from the graphs, we draw that there is a greater dispersion in plant diversity in Castril than Santiago and Pontones. Also this latter shows greater dispersion than Santiago.So, interestingly, the geographical distances do not seem to fully modulate the plant repartition. In further analysis, the geographical distances should be explicitly considered.
Cluster analysis
Non hierarchical clustering; k-means. This procedure
maximize the among-group variability.
The best k-means partition is indicated by the highest Simple
Structure Index (SSI) value. In our case, 6 clusters feature the
highest SSI.
library(vegan) ; library(factoextra)
spe.norm <- decostand(community_data_presence_2, "nor")
spe.KM.cascade = cascadeKM(spe.norm,inf.gr = 2,sup.gr = 8,iter = 100, criterion = "ssi")
plot(spe.KM.cascade, sortg = TRUE)
Figure 5: Different K-means clustering (left) and ssi criterion (right). Objects = Plant transects
Clusters in CSP plant transects
Table 1: Transects and their related transect group
spe.kmeans <- kmeans(spe.norm, centers = 6, nstart = 100) ; spe.kmeans.g <- spe.kmeans$cluster
(cluster_csp = as.data.frame(spe.kmeans.g) %>% mutate(transect=rownames(.)) %>%
group_by(spe.kmeans.g) %>% dplyr::summarise_all(list(~toString(unique(.)))))## # A tibble: 6 × 2
## spe.kmeans.g transect
## <int> <chr>
## 1 1 C01s, C02s, S01s, S04l, S06l
## 2 2 S12s, P02s, P06l
## 3 3 C03s, S07l, S09l, S10l, S11s, P01l, P03s, P04s, P05l
## 4 4 S02s, P05s, P07l
## 5 5 C04l, C05l, C06s
## 6 6 S03l, S08l, P08sfviz_cluster(spe.kmeans, data = spe.norm,geom = c("point","text"), repel = TRUE,ellipse.type = "convex",ggtheme = theme_bw())
Figure 6: Plant transects and their related transect group of k-means clustering
Indicator species
\[A_{ij} = N individuals_{ij} /N individuals_{i}\] \[B_{ij} = N sites_{ij} /N sites_{j}\]
\[IndVal_{ij} = A_{ij} * B_{ij} * 100\]
(Dufrêne and Legendre, 1997)
For each species i in each site group j:
\(A_{ij}\) is the mean abundance of species i in the sites of group j compared to all groups in the study
\(B_{ij}\). is the relative frequency of occurrence of species i in the sites of group j. B is a measure of fidelity.
Indicator species by transect groups
library(indicspecies)
indval = multipatt(community_data_presence_2, spe.kmeans.g,duleg = TRUE,control = how(nperm=1000))
summary(indval, indvalcomp=TRUE)##
## Multilevel pattern analysis
## ---------------------------
##
## Association function: IndVal.g
## Significance level (alpha): 0.05
##
## Total number of species: 200
## Selected number of species: 23
## Number of species associated to 1 group: 23
## Number of species associated to 2 groups: 0
## Number of species associated to 3 groups: 0
## Number of species associated to 4 groups: 0
## Number of species associated to 5 groups: 0
##
## List of species associated to each combination:
##
## Group 1 #sps. 4
## A B stat p.value
## Hippocrepis_bourgaei 0.8045 0.8000 0.802 0.010989 *
## Sedum_album 0.6429 0.8000 0.717 0.030969 *
## Koeleria_vallesiana 0.4373 1.0000 0.661 0.003996 **
## Helianthemum_cinereum 0.3326 1.0000 0.577 0.000999 ***
##
## Group 2 #sps. 6
## A B stat p.value
## Minuartia_hybrida 0.6660 1.0000 0.816 0.003996 **
## Galium_minutulum 0.5732 1.0000 0.757 0.006993 **
## Senecio_minutus 0.8571 0.6667 0.756 0.017982 *
## Veronica_sp 0.5587 1.0000 0.747 0.009990 **
## Velezia_rigida 0.5000 1.0000 0.707 0.035964 *
## Poa_ligulata 0.4331 1.0000 0.658 0.000999 ***
##
## Group 3 #sps. 1
## A B stat p.value
## Thymus_serpylloides 0.4531 1.0000 0.673 0.000999 ***
##
## Group 4 #sps. 5
## A B stat p.value
## Bromus_tectorum 0.7850 1.0000 0.886 0.00799 **
## Festuca_larga/suave 0.7664 1.0000 0.875 0.01299 *
## Galium_verum 1.0000 0.6667 0.816 0.02797 *
## Bromus_hordeaceus 0.6034 1.0000 0.777 0.01499 *
## Festuca_sp 0.7742 0.6667 0.718 0.02797 *
##
## Group 5 #sps. 5
## A B stat p.value
## Pilosella_pseudopilosella 0.9066 1.0000 0.952 0.000999 ***
## Aegilops_geniculata 0.8160 1.0000 0.903 0.008991 **
## Crataegus_sp 1.0000 0.6667 0.816 0.048951 *
## Lotus_corniculatus-subsp-carpetanus 1.0000 0.6667 0.816 0.036963 *
## Helianthemum_appenninum 0.5371 1.0000 0.733 0.008991 **
##
## Group 6 #sps. 2
## A B stat p.value
## Arenaria_tetraquetra 0.5743 1.0000 0.758 0.014 *
## Festuca_hystrix 0.3316 1.0000 0.576 0.004 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Dominant species
We calculate the Specific Contribution that is the Specific Frequency of a species divided by the sum of the Specific Frequencies of all the species evaluated in the 100 points of the transect. Those species featuring a Specific Contribution exceeding 10% are considered as dominant (Daget and Poissonet 1971).
test = community_data_presence_2 %>% as.data.frame(.) %>% mutate(total_count = rowSums(.)) ; abundance <- test
for (i in 1:(ncol(test) - 1)) { abundance[i] <- abundance[i] / abundance$total_count }Dominant species by transect groups
In the Table highlighted the species that exceed a Specific
Contribution of 10% in all the transects of a given group.
In the next table you can see all the dominant species by transect.
| spe.kmeans.g | transect | ind_species | d_species |
|---|---|---|---|
| 1 | C01s, C02s, S01s, S04l, S06l | Helianthemum_cinereum, Koeleria_vallesiana, Hippocrepis_bourgaei, Sedum_album | Thymus_serpylloides, Helianthemum_cinereum |
| 2 | S12s, P02s, P06l | Poa_ligulata, Minuartia_hybrida, Veronica_sp, Senecio_minutus, Galium_minutulum, Velezia_rigida | Poa_ligulata |
| 3 | C03s, S07l, S09l, S10l, S11s, P01l, P03s, P04s, P05l | Thymus_serpylloides | Thymus_serpylloides |
| 4 | S02s, P05s, P07l | Bromus_tectorum, Festuca_larga/suave, Bromus_hordeaceus, Festuca_sp, Galium_verum | Festuca_hystrix |
| 5 | C04l, C05l, C06s | Pilosella_pseudopilosella, Helianthemum_appenninum, Aegilops_geniculata, Crataegus_sp, Lotus_corniculatus-subsp-carpetanus | Pilosella_pseudopilosella |
| 6 | S03l, S08l, P08s | Festuca_hystrix, Arenaria_tetraquetra | Festuca_hystrix |
The group featuring only Thymus serpylloides as indicator species and the group highlighting Sedum album may point out stony and xeric slope. Thyme-related plant community (Tomillares) and the dry perennial herbaceous community are usually present on stony limestone and dolomitic places. Similarly, the group characterized by Festuca hystrix and Arenaria tetraquetra may feature reduced topsoil and be in steep and xeric areas.
The group S12s, P02s, P06l highlights therophyte plants as indicator species. These plant species thrive in somewhat nitrogen-rich soils and xeric areas. Also, it is interesting, Poa ligulata as indicador and dominant species as this is a characteristic plant of the dry perennial herbaceous community but it is more present in disturbance-prone dry perennial communities (Mercado 2011; Blanca et al. 2011).
Regarding the group composed of C04l, C05l, C06s, two (Lotus corniculatus, Pilosella pseudopilosella) out of five indicator species are mesophyllous plant mostly associated to herbaceous community with deeper or/and richer soils. Here, we could surmise deep soil and good water retention capacity. Also, Aegilops geniculata as indicator species may indicate nitrogen-rich soils that could be the results of former crops (Mercado 2011). Similarly, the group of S02s, S05s, P07l, Bromus tectorum, Bromus hordeaceus and Galium verum may indicate nitrogen-rich soils areas yet the areas of this group may be stony as Festuca spp, which are indicator species, were usually founded in near rocks and stones.
Indicator species by transhumance modality and common
## groups_thr
## 1 2
## 13 13##
## Multilevel pattern analysis
## ---------------------------
##
## Association function: IndVal.g
## Significance level (alpha): 0.05
##
## Total number of species: 200
## Selected number of species: 2
## Number of species associated to 1 group: 2
##
## List of species associated to each combination:
##
## Group 2 #sps. 2
## A B stat p.value
## Petrorhagia_nanteuilii 0.7368 0.7692 0.753 0.032 *
## Trifolium_campestre 1.0000 0.3846 0.620 0.045 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## groups_csp
## 1 2 3
## 6 11 9##
## Multilevel pattern analysis
## ---------------------------
##
## Association function: IndVal.g
## Significance level (alpha): 0.05
##
## Total number of species: 200
## Selected number of species: 12
## Number of species associated to 1 group: 11
## Number of species associated to 2 groups: 1
##
## List of species associated to each combination:
##
## Group 1 #sps. 9
## A B stat p.value
## Pilosella_pseudopilosella 0.9526 0.8333 0.891 0.00500 **
## Aegilops_geniculata 0.8586 0.8333 0.846 0.00400 **
## Bufonia_tenuifolia 0.8366 0.6667 0.747 0.00599 **
## Ononis_spinosa 0.7857 0.6667 0.724 0.01499 *
## Acinos_alpinus 0.8462 0.5000 0.650 0.02298 *
## Crataegus_sp 1.0000 0.3333 0.577 0.04496 *
## Lotus_corniculatus-subsp-carpetanus 1.0000 0.3333 0.577 0.04496 *
## Medicago_lupulina 1.0000 0.3333 0.577 0.04795 *
## Galium_sp 1.0000 0.3333 0.577 0.04496 *
##
## Group 2 #sps. 1
## A B stat p.value
## Scabiosa_andryaefolia 1.0000 0.4545 0.674 0.016 *
##
## Group 3 #sps. 1
## A B stat p.value
## Anthemis_arvensis 0.9072 0.4444 0.635 0.039 *
##
## Group 1+2 #sps. 1
## A B stat p.value
## Helianthemum_appenninum 0.9126 0.8235 0.867 0.049 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Dominant species by transect
Plant species featuring Specific Contribution greater than 10% by transect.
| transect | d_species |
|---|---|
| C01s | Thymus_serpylloides, Festuca_hystrix, Helianthemum_cinereum |
| C02s | Thymus_serpylloides, Festuca_hystrix, Helianthemum_cinereum, Koeleria_vallesiana |
| C03s | Thymus_serpylloides, Festuca_hystrix, Bromus_tectorum |
| C04l | Festuca_hystrix, Pilosella_pseudopilosella |
| C05l | Festuca_hystrix, Pilosella_pseudopilosella, Ononis_spinosa |
| C06s | Pilosella_pseudopilosella, Aegilops_geniculata, Xeranthemum_inapertum |
| P01l | Thymus_serpylloides |
| P02s | Thymus_serpylloides, Poa_ligulata, Sedum_amplexicaule |
| P03s | Thymus_serpylloides, Festuca_hystrix, Helianthemum_cinereum |
| P04s | Thymus_serpylloides, Festuca_hystrix, Helianthemum_cinereum |
| P05l | Thymus_serpylloides, Festuca_hystrix, Helianthemum_cinereum, Arenaria_tetraquetra |
| P05s | Festuca_hystrix, Poa_bulbosa, Bromus_tectorum |
| P06l | Poa_ligulata, Minuartia_hybrida |
| P07l | Festuca_hystrix, Poa_bulbosa, Festuca_larga/suave |
| P08s | Thymus_serpylloides, Festuca_hystrix, Helianthemum_cinereum |
| S01s | Thymus_serpylloides, Helianthemum_cinereum, Koeleria_vallesiana |
| S02s | Festuca_hystrix, Bromus_tectorum, Sedum_acre |
| S03l | Festuca_hystrix |
| S04l | Thymus_serpylloides, Festuca_hystrix, Helianthemum_cinereum |
| S06l | Thymus_serpylloides, Helianthemum_cinereum |
| S07l | Thymus_serpylloides, Helianthemum_cinereum |
| S08l | Thymus_serpylloides, Festuca_hystrix, Helianthemum_cinereum |
| S09l | Thymus_serpylloides, Helianthemum_cinereum, Cerastium_brachypetalum-subsp-brachypetalum |
| S10l | Thymus_serpylloides, Helianthemum_cinereum |
| S11s | Thymus_serpylloides, Erinacea_anthyllis |
| S12s | Thymus_serpylloides, Festuca_hystrix, Poa_ligulata, Minuartia_hybrida |