Geo-referenced population-specific microsatellite data across American continents, the MacroPopGen Database

Abstract

Population genetic data from nuclear DNA has yet to be synthesized to allow broad scale comparisons of intraspecific diversity versus species diversity. The MacroPopGen database collates and geo-references vertebrate population genetic data across the Americas from 1,308 nuclear microsatellite DNA studies, 897 species, and 9,090 genetically distinct populations where genetic differentiation (F ST ) was measured. Caribbean populations were particularly distinguished from North, Central, and South American populations, in having higher differentiation (F ST = 0.12 vs. 0.07–0.09) and lower mean numbers of alleles (MNA = 4.11 vs. 4.84–5.54). While mammalian populations had lower MNA (4.86) than anadromous fish, reptiles, amphibians, freshwater fish, and birds (5.34–7.81), mean heterozygosity was largely similar across groups (0.57–0.63). Mean F ST was consistently lowest in anadromous fishes (0.06) and birds (0.05) relative to all other groups (0.09–0.11). Significant differences in Family/Genera variance among continental regions or taxonomic groups were also observed. MacroPopGen can be used in many future applications including latitudinal analyses, spatial analyses (e.g. central-margin), taxonomic comparisons, regional assessments of anthropogenic impacts on biodiversity, and conservation of wild populations.

Latitudinal biodiversity gradients at three levels: Linking species richness, population richness and genetic diversity

“…Miraldo et al, ). Although non‐neutrality has been observed in some studies involving nuclear microsatellite loci (Ranathunge et al, ; Selkoe & Toonen, ; Wiehe, ), this does not appear to be widespread in MacroPopGen (Lawrence et al, ; see also Selkoe & Toonen, ).…”

“…We outline and test three novel hypotheses to explain latitudinal trends in intraspecific diversity. Data used to test the hypotheses below were obtained from the MacroPopGen database (Lawrence et al, ), a georeferenced dataset of microsatellite genetic diversity for almost 900 vertebrate species and over 9,000 genetically distinct populations across the Americas (see Supporting Information Appendix S1 for details). Populations were designated as genetically distinct within MacroPopGen using a commonly applied, operational definition of a population (reviewed in Waples & Gaggiotti, ); population richness in the database (PopPerSpp or TotPopR) represented only populations that had been sampled with microsatellite loci.…”

“…(b) Number of genetically distinct populations across vertebrate species in each grid cell. Data obtained from MacroPopGen database (Lawrence et al, ) and projected with the World Behrmann projection [Colour figure can be viewed at wileyonlinelibrary.com]…”

“…HO for MNA, MNA for HO), and other study‐specific metrics (for details see Supporting Information Appendix S1: H3). All population‐specific data can be found in the MacroPopGen database (Lawrence et al, ). After model selection, the mixed model for heterozygosity included the interaction between MNA and the number of microsatellite loci as well as taxonomic class, and the random effects for study, species and family (Supporting Information Table S2):…”

“…To ensure use of standardized terms throughout the review as well as to clarify distinctions among past works, we have broken down population richness and genetic diversity into five categories (see Glossary): (a) total number of populations across species in an area (TotPopR); (b) the number of populations for a given species in an area (PopPerSpp); (c) the average number of populations per species in an area (AvgPopSpp); (d) total genetic diversity in an area, as the sum of genetic diversity across all species at a population level (TotGenDiv); and (e) average genetic diversity across populations for a given species in an area (GenPerSpp). Note that our definition of genetic diversity refers largely to neutral genetic diversity, not adaptive genetic diversity, as it allows us to make usage of a comprehensive population genetics database that we recently compiled from c. 900 vertebrate species spanning the American continents (Lawrence et al, ). While data on adaptive genetic diversity are increasing, to date they are insufficiently rich for similar, standardized collation and would likely have different expectations that should be explored in future works.…”