The Genealogical Sorting Index and species delimitation

13 The Genealogical Sorting Index (gsi) has been widely used in species-delimitation studies, where 14 it is usually interpreted as a measure of the degree to which each of several predefined groups of 15 specimens display a pattern of divergent evolution in a phylogenetic tree. Here we show that the gsi 16 value obtained for a given group is highly dependent on the structure of the tree outside of the 17 group of interest. By calculating the gsi from simulated datasets we demonstrate this dependence 18 undermines some of desirable properties of the statistic. We also review the use of the gsi 19 delimitation studies, and show that the gsi has typically been used under scenarios in which it is 20 expected to produce large and statistically significant results for samples that are not divergent from 21 all other populations and thus should not be considered species. Our proposed solution to this 22 problem performs better than the gsi in under these conditions. Nevertheless, we show that our 23 modified approach can produce positive results for populations that are connected by substantial 24 levels of gene flow, and are thus unlikely to represent distinct species. We stress that the properties 25 of gsi made clear in this manuscript must be taken into account if the statistic is used in species26 delimitation studies. More generally, we argue that the results of genetic species-delimitation 27 methods need to be interpreted in the light the biological and ecological setting of a study, and not 28 treated as the final test applied to hypotheses generated by other data. 29