Ecology

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To the Editor — In an insightful Comment Bliege Bird and Codding1 highlight a number of important issues to consider in the analysis of cross-cultural anthropological data. However, a casual reader of the Comment could be forgiven for taking away the message that cross-cultural data in anthropology is inherently flawed, and so is of limited use. We want to emphasize that comparative analysis plays an essential role in all non-experimental sciences, including anthropology and archaeology. This is because when systems cannot be manipulated due to scales of time and space, or issues of logistics or ethics, the only way to evaluate alternative outcomes is by analysing the results of natural experiments. More

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Quantification of changes in floristic similarityTo quantify changes in floristic similarity by naturalized flowering plant species, we extracted regional lists of alien species from the Global Naturalized Alien Flora (GloNAF) database45 and regional lists of native species from the Global Inventory of Floras and Traits (GIFT) database46. The GloNAF database contains lists of naturalized vascular plant taxa for 861 regions (countries or subnational administrative units), ranging in size from 0.03 to 6,864,961 km2 (median size is 15,152 km2) and covering >80% of the terrestrial ice-free surface globally47. GloNAF includes 13,803 plant taxa that, according to the original data sources, are alien plants and have established self-sustaining wild populations in the respective regions (i.e., are naturalized5). The GIFT database is a compilation of floras and checklists of predominantly native vascular plant species with an indication of their floristic status for more than 300,000 species across nearly 3000 regions with near global coverage46. We first selected regions that matched perfectly between GloNAF and GIFT. Additionally, we merged some GloNAF regions to match a larger GIFT region, and vice versa, by comparing the overlapping area of nested regions using the R package ‘sf’ (version 0.8-0)48.To ensure the highest data quality, and to be on the conservative side, we restricted our analysis to regions with complete or nearly complete checklists of both native and naturalized alien species. For GloNAF, we only included regions for which there was at least one species list judged to include more than 50% of the naturalized taxa for that region45. Although the judgment of species-list completeness is coarse and for most lists made by the GloNAF curators, it allows the exclusion of regions for which the data are obviously poor. For GIFT, we included a region only if at least one species list aimed to represent its entire native angiosperm flora. Our strict selection criteria resulted in a dataset including native and naturalized species for 658 non-overlapping regions, including 154 island regions, 503 mainland regions and one region including both islands and mainland areas (Chile). These regions covered all continents, except Antarctica, but there was low coverage for parts of Africa and Asia (Fig. 4).We restricted our analyses to flowering plants (angiosperms), which had the most complete species lists, and to species with accepted names in The Plant List24 (http://www.theplantlist.org/). We excluded species with an uncertain native/alien status or with a conflicting status, i.e., being native to a region according to GIFT but being alien to the same region according to GloNAF. Furthermore, since the native/alien status of many infraspecific taxa and hybrid taxa are less clear, we restricted our analyses to the species level (i.e., infraspecific taxa were assigned to the binomial species name), and we excluded hybrids. Our final dataset included 1,139,254 native species-by-region records for 189,110 species and 141,762 naturalized species-by-region records for 10,130 species.For all 216,153 possible pairwise combinations of the 658 regions, we quantified the taxonomic and phylogenetic similarities between their native floras (SimTaxnative, SimPhylnative), and between their floras including both native and naturalized alien species (SimTaxnative+naturalized, SimPhylnative+naturalized). As the regions vary largely in species richness (ranging from 11 to 13,720 species with a median of 1704), we used the Simpson similarity index for taxonomic similarity (Eq. 1)49, which is largely insensitive to species richness:50$${SimTax}=1-frac{{{min }}left(b,cright)}{a+{{min }}left(b,cright)}$$
(1)
Here a is the number of species common to both regions, b is the number of species that occur in the first region but not in the second and c is the number of species that occur in the second region but not in the first51. Likewise, we calculated the Simpson phylogenetic similarity index as phylogenetic similarity (Eq. 2) as implemented in the R package ‘betapart’ (version 1.5.1)52:$${SimPhyl}=1-frac{{{min }}left(B,Cright)}{A+{{min }}left(B,Cright)}$$
(2)
Here A is the total length of the phylogenetic branches in the phylogenetic tree that are shared by the species of both regions, B is the total length of the phylogenetic branches that are shared only by the first region and C is the total length of the phylogenetic branches that are shared only by the second region51. To quantify changes in similarity due to naturalization of alien species, we calculated the degree of homogenization H (or differentiation, see below) for each pair of regions as$$H={ln}frac{{{Sim}}_{{native}+{naturalized}}+0.001}{{{Sim}}_{{native}}+0.001}$$
(3)
A small value of 0.001 was added to both similarities to avoid infinite values. A positive log-response ratio indicates homogenization (i.e., increased floristic similarity between two regions), and a negative one indicates differentiation (i.e., decreased floristic similarity). As an alternative to the Simpson similarity index, we also calculate the Sørensen similarity index, which additionally takes into consideration the nestedness of the floras in the paired regions51. As the results were not sensitive to the choice of similarity indices (Supplementary Fig. 14), we focused our analyses on the Simpson similarity index.To quantify phylogenetic similarity, we used a phylogenetic tree including all angiosperms with accepted names in The Plant List (Supplementary Fig. 2). The tree was developed based on the mega phylogeny of Smith and Brown53. We added missing species (n = 71,124, of which 733 are naturalized in other regions) with their accepted names in The Plant List to the root of their genus or families. For details on the development of the phylogenetic tree, see ref. 47.Quantification of geographic distances and climatic distancesWe calculated the pairwise geographic distance between regions as the distance between their geographic centroids using the R package ‘geosphere’ (version 1.5-10)54. We also calculated the nearest distance between the geographic borders of regions. However, since the distances between geographic centroids are highly correlated with distances between region borders (n = 216,153, r = 0.996, P  More

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AffiliationsDepartment of Integrative Biology, Oregon State University, Corvallis, OR, USABenjamin D. Dalziel & Mark NovakDepartment of Mathematics, Oregon State University, Corvallis, OR, USABenjamin D. DalzielCollege of Earth, Ocean and Atmospheric Sciences, Oregon State University, Corvallis, OR, USAJames R. WatsonDepartment of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USAStephen P. EllnerAuthorsBenjamin D. DalzielMark NovakJames R. WatsonStephen P. EllnerCorresponding authorCorrespondence to
Benjamin D. Dalziel. More

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