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Optimising Regionalisation Techniques: Identifying Centres of Endemism in the Extraordinarily Endemic-Rich Cape Floristic Region.

Bradshaw PL, Colville JF, Linder HP - PLoS ONE (2015)

Bottom Line: We show that weighted data (down-weighting widespread species), similarity calculated using Kulczinsky's second measure, and clustering using UPGMA resulted in the optimal classification.Post-clustering GIS manipulation substantially enhanced the endemic composition and geographic size of candidate CoEs.Although there was broad spatial congruence with previous phytogeographic studies, our techniques allowed for the recovery of additional phytogeographic detail not previously described for the CFR.

View Article: PubMed Central - PubMed

Affiliation: Park Planning and Development Unit, South African National Parks, Port Elizabeth, South Africa; Department of Botany, Nelson Mandela Metropolitan University, Port Elizabeth, South Africa.

ABSTRACT
We used a very large dataset (>40% of all species) from the endemic-rich Cape Floristic Region (CFR) to explore the impact of different weighting techniques, coefficients to calculate similarity among the cells, and clustering approaches on biogeographical regionalisation. The results were used to revise the biogeographical subdivision of the CFR. We show that weighted data (down-weighting widespread species), similarity calculated using Kulczinsky's second measure, and clustering using UPGMA resulted in the optimal classification. This maximized the number of endemic species, the number of centres recognized, and operational geographic units assigned to centres of endemism (CoEs). We developed a dendrogram branch order cut-off (BOC) method to locate the optimal cut-off points on the dendrogram to define candidate clusters. Kulczinsky's second measure dendrograms were combined using consensus, identifying areas of conflict which could be due to biotic element overlap or transitional areas. Post-clustering GIS manipulation substantially enhanced the endemic composition and geographic size of candidate CoEs. Although there was broad spatial congruence with previous phytogeographic studies, our techniques allowed for the recovery of additional phytogeographic detail not previously described for the CFR.

No MeSH data available.


Flow Chart of methods.This flow chart should be read in conjunction with the methods section. [K2 = Kulczinsky2; J = Jaccard; S = Simpson; Clusters delimited using modified branch order cut-off (BOC3m; step 4 and see methods)].
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pone.0132538.g001: Flow Chart of methods.This flow chart should be read in conjunction with the methods section. [K2 = Kulczinsky2; J = Jaccard; S = Simpson; Clusters delimited using modified branch order cut-off (BOC3m; step 4 and see methods)].

Mentions: We developed an analysis flow chart that leads through the combinations of four weighting types, three similarity coefficients and two clustering techniques (Fig 1). The consensus (strict and majority rule) of the three best similarity-clustering techniques on weighted datasets was used to derive the final phytogeographic map and to indicate robustness of patterns.


Optimising Regionalisation Techniques: Identifying Centres of Endemism in the Extraordinarily Endemic-Rich Cape Floristic Region.

Bradshaw PL, Colville JF, Linder HP - PLoS ONE (2015)

Flow Chart of methods.This flow chart should be read in conjunction with the methods section. [K2 = Kulczinsky2; J = Jaccard; S = Simpson; Clusters delimited using modified branch order cut-off (BOC3m; step 4 and see methods)].
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4493007&req=5

pone.0132538.g001: Flow Chart of methods.This flow chart should be read in conjunction with the methods section. [K2 = Kulczinsky2; J = Jaccard; S = Simpson; Clusters delimited using modified branch order cut-off (BOC3m; step 4 and see methods)].
Mentions: We developed an analysis flow chart that leads through the combinations of four weighting types, three similarity coefficients and two clustering techniques (Fig 1). The consensus (strict and majority rule) of the three best similarity-clustering techniques on weighted datasets was used to derive the final phytogeographic map and to indicate robustness of patterns.

Bottom Line: We show that weighted data (down-weighting widespread species), similarity calculated using Kulczinsky's second measure, and clustering using UPGMA resulted in the optimal classification.Post-clustering GIS manipulation substantially enhanced the endemic composition and geographic size of candidate CoEs.Although there was broad spatial congruence with previous phytogeographic studies, our techniques allowed for the recovery of additional phytogeographic detail not previously described for the CFR.

View Article: PubMed Central - PubMed

Affiliation: Park Planning and Development Unit, South African National Parks, Port Elizabeth, South Africa; Department of Botany, Nelson Mandela Metropolitan University, Port Elizabeth, South Africa.

ABSTRACT
We used a very large dataset (>40% of all species) from the endemic-rich Cape Floristic Region (CFR) to explore the impact of different weighting techniques, coefficients to calculate similarity among the cells, and clustering approaches on biogeographical regionalisation. The results were used to revise the biogeographical subdivision of the CFR. We show that weighted data (down-weighting widespread species), similarity calculated using Kulczinsky's second measure, and clustering using UPGMA resulted in the optimal classification. This maximized the number of endemic species, the number of centres recognized, and operational geographic units assigned to centres of endemism (CoEs). We developed a dendrogram branch order cut-off (BOC) method to locate the optimal cut-off points on the dendrogram to define candidate clusters. Kulczinsky's second measure dendrograms were combined using consensus, identifying areas of conflict which could be due to biotic element overlap or transitional areas. Post-clustering GIS manipulation substantially enhanced the endemic composition and geographic size of candidate CoEs. Although there was broad spatial congruence with previous phytogeographic studies, our techniques allowed for the recovery of additional phytogeographic detail not previously described for the CFR.

No MeSH data available.