Biogeographical disparity in the functional diversity and redundancy of corals

Brief description

Data used in the article entitled “Biogeographical disparity in the functional diversity and redundancy of corals” published in PNAS in March 2018. 

https://doi.org/10.1073/pnas.1716643115

traitbiogeography.csv : This file contains functional trait and biogeographical data merged primarily from the Coral Traits Database https://coraltraits.org/ and Keith et al. (2013) https://doi.org/10.1098/rspb.2013.0818. Rows represent 821 zooxanthellate coral species. 

Traits: Columns E to K (starting with “cat_”) indicate numerical categories for seven traits used for the analyses. Infilled trait data for four of these seven traits are in columns L to O (starting with “dat_”). Raw data for the same four traits are presented in columns P to S (starting with “raw_”). Column T represents a modified version of “growth_form_typical” from the Coral Traits Database. Column U to V represent raw and infilled “reproductive mode” values. 

Biogeographic provinces. Species used in Keith et al (2013) are presented in Column W, and species with updated nomenclature used for alignment with the Coral Traits Data are presented in column X. Columns Y through to AR are species presences-absences for 20 biogeographical provinces, 12 of which were analysed in the paper.  

Full description

Data used in the article entitled “Biogeographical disparity in the functional diversity and redundancy of corals” published in PNAS in March 2018: https://doi.org/10.1073/pnas.1716643115

COLLATION OF DATA

Step 1: Download. Raw data was downloaded for five traits (“maximum colony diameter”, “maximum corallite width”, “skeletal density”, “growth rate” and “reproductive mode”), from the coral traits database https://coraltraits.org/. Species means were found for each numerical trait, ensuring that unit-measurements were consistent for each of the values used. Two other attributes (“growth form typical” and “molecular family”) were downloaded for use in data infilling.

Step 2: Infill. A statistical infilling approach was conducted based on evidence that traits such as growth rate and skeletal density can be predicted by a combination of phylogeny (molecular family) and morphology (growth form typical). The infilling procedure is outlined in the article, and described in greater detail in Chao Yang Kuo’s PhD thesis “Adaptive strategies of Scleractinian Corals”. Reproductive modes were infilled based Genus, except for genera that are known to be mixed.

Step 3: Trim. After infilling, we removed azoozanthellate taxa leaving a dataset of 864 species. A further 43 species with unresolved taxonomy or discontinued species-level statuses were removed, leaving 821 species.

Step 4: Categorise. Traits were subsequently placed into numerical categories from 1 (lowest) to 5 (highest). The rationale for using numerical categories was to facilitate further infilling for species-level traits that could not be predicted using the statistical approach (see above). In line with the morphology/phylogeny approach, taxa with the same morphology and genus were given the same trait category. The data was scanned independently by two coral specialists for possible mistakes that were corrected by expert opinion. The trait that required most correction, and therefore relied most heavily on expert opinion, was colony size (i.e., maximum colony diameter), perhaps due to the difficulty in predicting colony size using morphology or phylogeny.

Step 5: Quantify morphology: Using numerical categories also allowed us to quantify morphology. We produced rankings of three simple morphological traits (height, surface area and interstitial spacing) using ‘growth form typical.’ See the article supplement for and the rankings of morphological traits for each growth form.

NOTE: The data for “growth form typical” in the coral traits database does not include a category for solitary or non-attached species (e.g. Fungia) or a category for bifacial species (i.e. frondiferous, e.g. Pavona spp.), and these groups were subsequently amended.  

Step 6: Align: We then aligned biogeographical presence-absence data (from Keith et al. 2013 https://doi.org/10.1098/rspb.2013.0818 ) with trait data produced from the steps above. Biogeographical data includes presence-absences for 732 Indo-Pacific species, and Atlantic species (from the Caribbean, Brazil and East Atlantic) were added manually following the system used by Veron in Corals in Space and Time (1995). The trait data and presence absence data uses different taxonomic nomenclature for certain species, mostly due to old versus new taxonomy. We therefore transfered the species names between old and new taxonomy. Other differences due to spelling (e.g. Montastraea and Monstastrea) were also corrected before merging the two datasets.   

Abstract [Related Publication]: Corals are major contributors to a range of key ecosystem functions on tropical reefs, including calcification, photosynthesis, nutrient cycling, and the provision of habitat structure. The abundance of corals is declining at multiple scales, and the species composition of assemblages is responding to escalating human pressures, including anthropogenic global warming. An urgent challenge is to understand the functional consequences of these shifts in abundance and composition in different biogeographical contexts. While global patterns of coral species richness are well known, the biogeography of coral functions in provinces and domains with high and low redundancy is poorly understood. Here, we quantify the functional traits of all currently recognized zooxanthellate coral species (n = 821) in both the Indo-Pacific and Atlantic domains to examine the relationships between species richness and the diversity and redundancy of functional trait space. We find that trait diversity is remarkably conserved (>75% of the global total) along latitudinal and longitudinal gradients in species richness, falling away only in species-poor provinces (n < 200), such as the Persian Gulf (52% of the global total), Hawaii (37%), the Caribbean (26%), and the East-Pacific (20%), where redundancy is also diminished. In the more species-poor provinces, large and ecologically important areas of trait space are empty, or occupied by just a few, highly distinctive species. These striking biogeographical differences in redundancy could affect the resilience of critical reef functions and highlight the vulnerability of relatively depauperate, peripheral locations, which are often a low priority for targeted conservation efforts.