Dissecting Biodiversity in a Global Hotspot: Uneven Dynamics of Immigration and Diversification Within the Cape Floristic Region of South Africa
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Wüest, Rafael O et al. ... doi:10.5061/dryad.1cs77qn Data from: Dissecting biodiversity in a global hotspot: uneven dynamics of immigration and diversification within the Cape Floristic Region of South Africa Wüest, Rafael O Boucher, Florian C Bouchenak-Khelladi, Yanis Karger, Dirk N Linder, H Peter Publication date: July 16, 2019 Publisher: Dryad https://doi.org/10.5061/dryad.1cs77qn Citation Wüest, Rafael O et al. (2019), Data from: Dissecting biodiversity in a global hotspot: uneven dynamics of immigration and diversification within the Cape Floristic Region of South Africa, v2, Dataset, https://doi.org/10.5061/dryad.1cs77qn Abstract Aim: Fragmented distributions should show immigration and diversification dynamics consistent with the predictions of island biogeography theory. We test whether this applies to the fragmented Cape fynbos vegetation. Location: Southern Africa, Cape Floristic Region (CFR) Taxon: Angiosperms, Restionaceae (restios) Methods: We used a large occurrence dataset and environmental layers to characterize an existing regionalization and the intervals between the regions ecologically and spatially. We extended the available phylogeny for restios and inferred their historical biogeography using models implemented in BioGeoBEARS. We then measured the relative contribution of immigration and in situ speciation to the species richness of each region within the CFR. We used standard statistical methods to test Dryad Page 1 of 6 Wüest, Rafael O et al. ... doi:10.5061/dryad.1cs77qn the predictions of the island biogeography theory. Results: The area and environmental heterogeneity of the seven regions of the CFR are positively correlated with in situ speciation rate. Furthermore, more isolated areas, and areas colonized more recently, have proportionally higher immigration rates, and more central and older areas proportionally higher in situ speciation rates. Main Conclusions: The variation in immigration and diversification dynamics among the regions within the CFR is extensive and consistent with the archipelago model of island biography theory. This dynamic may contribute significantly to the diversity of the Cape flora. Such a model could be generally useful for understanding the generation and maintenance of diversity in biodiversity hotspots, and may even scale up to explain continental biodiversity. Usage Notes Restionaceae georeferenced occurrence data for the Cape Floristic Region The tab-delimited data contain 12903 georeferenced occurrence records of the Restionaceae occurring in the South African Cape Flora. The columns give the species names (column "GenusSpecies"; with the binary scientific names separated by underscore), the date of collection (column "Date"), the coordinates in WGS84 geographic projection (EPSG:4326; columns "Longitude" and "Latitude"), the locality (column "Locality"). Further, we indicate whether the data represents a single occurrence ("specimen") or is part of a plot-releve ("plot"; indicated in column "RecordType"). In the latter case, we indicate the plot-id in the column "PlotID". In case of specimen-data, we indicate the collector (column "Collector") and collection number ("CollectorNumber"). Where available, we also indicate simple site- characteristics in terms of rockiness (column "Rockyness"; three levels "none", "pebblesboulders", "bedrock"), soil-type (column "SoilType"; three levels "organic", "fine", "coarse"), drainage (column "Drainage"; three levels "dry", "damp", "wet"), and aspect (column "Aspect"; with "level" for flat sites and all possible combinations of "n" for North, "e" for East, "s" for South, "w" for West). restio_georef_data.txt Geology of the Cape Floristic Region The zip-archive contains a shapefile in WGS84 geographic projection (EPSG:4326) that holds (in the column "geology") spatially explicit information on six major geological classes ("calcrete", "granite", "recent sand", "silcrete", "sandstones", "shale", and "others" including water-bodies). The column "UQ_GEOL" contains the original geological class according to the South African Council for Geoscience, and "geol_num" is a numerical representation of the classes coded in column "geology". cape_geology.zip Dryad Page 2 of 6 Wüest, Rafael O et al. ... doi:10.5061/dryad.1cs77qn Environment of the Cape Floristic Region The environmental data used in this study, provided as geo-tiffs. Details are given in Appendix S1 and Table S2 of the associated publication (DOI: 10.1111/jbi.13625). cape_environment.zip Phylogenetic trees of the Restionaceae of the Cape Floristic Region The zip-archive contains the MCC tree of the Restionaceae (in the file "mcc_tree.nex") and a random sample of 100 trees from the posterior of our phylogenetic analysis (in the file "tree_samples_100.nex"). restio_trees.zip References This dataset is supplement to https://doi.org/10.1111/jbi.13625 Location 17.42 - 26.83E Cape flora 28.90 - 35.00S Cape Floristic Region 30.08 - 34.83S South Africa 16.90 - 28.10E Keywords Thamnochortus stokoei, Thamnochortus paniculatus, Paleocene, Restio bifarius, Restio sporadicus, Thamnochortus gracilis, Askidiosperma insigne, Anthochortus ecklonii, Soroveta ambigua, Thamnochortus obtusus aff, Restio paludicola, Restio decipiens, Restio obscurus, Restio blinkbergensis, Cannomois arenicola, Willdenowia teres, Elegia fistulosa, Restio eleocharis, Thamnochortus serpens, Askidiosperma longiflorum, Elegia coleura, Elegia extensa, Cannomois virgata, Ceratocaryum xerophilum, Holocene, Elegia cernua, Restio calcicola, Willdenowia glomerata, Thamnochortus lucens, Ceratocaryum decipiens, Elegia thyrsoidea, Restio gossypinus var, Rhodocoma fruticosa, Restio bifidus, Restio virgeus, Elegia spathacea, Restio nanus, Restio constipatus aff, Restio venustulus, Restio corneolus, Restio Dryad Page 3 of 6 Wüest, Rafael O et al. ... doi:10.5061/dryad.1cs77qn brachiatus aff, Elegia hutchinsonii, Nevillea singularis, Elegia ebracteata, Ceratocaryum argenteum, Restio durus, Thamnochortus pellucidus, Restio arcuatus, Restio rivulus, Restio dodii var purpureus, Restio verrucosus, Elegia decipiens var, Elegia stokoei, immigration – diversification dynamics, Restio miser, Hypodiscus montanus, Restio rudolfii, Askidiosperma rugosum, Elegia microcarpa var, Restio distichus, Restio zwartbergensis, Thamnochortus pluristachyus, Elegia prominens, Restio saroclados, Thamnochortus insignis, metapopulation, Restio secundus, Restio echinatus, Willdenowia affinis, Restio capensis, Restio pulvinatus, Ceratocaryum pulchrum, Restio triticeus aff, Restio pulcher, island biogeography theory, Hypodiscus albo-aristatus, Hypodiscus sp nov, Cannomois aristata, Restio singularis, Thamnochortus punctatus, Elegia aggregata, Ceratocaryum fimbriatum, Restio degenerans, Restio burchellii, Restio capillaris, Thamnochortus pulcher, Anthochortus insignis, Elegia marlothii, Restio sejunctus, Thamnochortus obtusus, Restio coactilis, Restio wittebergensis, Restio colliculospermus, Restio stokoei, Restio tenuispicatus, Staberoha multispicula, Willdenowia rugosa, Miocene, Askidiosperma delicatulum, Rhodocoma capensis, Elegia dregeana, Platycaulos subcompressus, Restio implicatus, Willdenowia pilleata, Willdenowia bolusii, Hypodiscus procurrens, Cannomois sp, Restio egregius, Elegia acockii, Thamnochortus karooica, Restio cedarbergensis, Restio inconspicuus, Restio versatilis, Mastersiella digitata, Restio sp, Staberoha cernua, Restio nuwebergensis, Elegia microcarpa, Restio triticeus, Restio rupicola, Restio distylus, Rhodocoma gracilis, Staberoha banksii, Elegia thyrsifera, Elegia intermedia, Restio paludosus, Restionaceae, Hypodiscus willdenowia, Restio laniger, Cannomois anfracta, Restio longiaristatus, Restio affinis, Restio barbatus, Restio perplexus, Staberoha remota, Eocene, Restio asperus, Restio taylori, Restio adpressus, Staberoha ornata, Cannomois spicata, Restio paniculatus, Nevillea vlokii, Restio leptoclados, Elegia fenestrata, Restio bifurcus, Restio constipatus, Elegia fastigiata, Restio gossypinus aff, Restio quinquefarius, Willdenowia humilis, Thamnochortus fraternus, Restio sabulosus, Elegia squamosa, Elegia sp, Elegia grandispicata, Thamnochortus nutans, Restio pillansii, Restio pygmaeus, Elegia neesii, Hypodiscus rugosus, Restio pumilus, Restio saxatilis, Restio alticola, Hypodiscus squamosus, Restio anomalus, Restio villosus, Restio dodii var purpurascens, Elegia decipiens, Dispersal, Restio albotuberculatus, Restio scaber, Platycaulos compressus, Elegia persistens, Restio festuciformis, Platycaulos callistachyus, Elegia muirii, Restio confusus, Cannomois grandis, Restio debilis, Elegia namaquense, Restio brachiatus, Restio marlothii, Restio dodii var dodii, Restio aridus, Willdenowia sulcata, Staberoha stokoei, Thamnochortus fruticosus, Hypodiscus laevigatus, Thamnochortus rigidus, Restio luxurians, Restio subverticellatus, Restio nudiflorus, Restio diffusus, Restio acockii, Restio wallichii, Thamnochortus levynsiae, Restio papillosus, Hypodiscus rigidus, Restio elsieae, Restio occultus, Thamnochortus arenarius, Elegia hookeriana, Restio femineus, Staberoha distachyos, Hypodiscus alternans, Restio gossypinus, Platycaulos major, Restio rigoratus, Restio Dryad Page 4 of 6 Wüest, Rafael O et al. ... doi:10.5061/dryad.1cs77qn unispicatus, Restio fragilis, Thamnochortus platypteris, Anthochortus capensis, Rhodocoma vleibergensis, Rhodocoma gigantea, Restio aureolus, Thamnochortus kammanassie, Askidiosperma andreaeanum, Elegia asperiflora, Staberoha vaginata, Restio rottboellioides, Platycaulos depauperatus, Ceratocaryum fistulosum,