Multispecies coalescent delimits structure, not species Jeet Sukumarana,1,2 and L. Lacey Knowlesa,1 aDepartment of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor MI 48109-1079 Edited by David M. Hillis, University of Texas at Austin, Austin, TX, and approved December 29, 2016 (received for review May 23, 2016) The multispecies coalescent model underlies many approaches consequence, the increased resolution of genomic data makes it used for species delimitation. In previous work assessing the per- possible to not only detect divergent species lineages, but also formance of species delimitation under this model, speciation was local population structure within them—that is, a fractal hierar- treated as an instantaneous event rather than as an extended chy of divergences. process involving distinct phases of speciation initiation (struc- Misidentification of population structure as putative species turing) and completion. Here, we use data under simulations is therefore emerging as a key issue (8) that has received insuf- that explicitly model speciation as an extended process rather ficient attention, especially with respect to methodologies for than an instantaneous event and carry out species delimitation delimiting taxa based on genetic data alone. Because species inference on these data under the multispecies coalescent. We delimitation is inextricably linked to patterns of species diversity, show that the multispecies coalescent diagnoses genetic struc- the models used to delimit species are not just limited to issues ture, not species, and that it does not statistically distinguish about species boundaries, but are also paramount to understand- structure associated with population isolation vs. species bound- ing the generation and dynamics of biodiversity (9–12). Conse- aries. Because of the misidentification of population structure as quently, when the lines become blurred—delimiting species in putative species, our work raises questions about the practice of some cases, but populations in other cases—species delimita- genome-based species discovery, with cascading consequences in tion becomes a critical issue with ramifications across multiple other fields. Specifically, all fields that rely on species as units fields of study, such as, for example, the estimation of diversity in of analysis, from conservation biology to studies of macroevolu- macroecological studies (13–15), analyses of food webs (16), or tionary dynamics, will be impacted by inflated estimates of the conservation, where oversplitting of small, isolated populations number of species, especially as genomic resources provide based on genetic data could be detrimental (17). More funda- EVOLUTION unprecedented power for detecting increasingly finer-scaled mentally, distinguishing between species- and population-level genetic structure under the multispecies coalescent. As such, lineages is central to understanding the speciation process itself our work also represents a general call for systematic study to (18, 19). reconsider a reliance on genomic data alone. Until new meth- Not all populations become species. Instead, speciation theory ods are developed that can discriminate between structure due points to a continuum for the probability that a population lin- to population-level processes and that due to species boundaries, eage will evolve into a new species (20). Depending on the extent genomic-based results should only be considered a hypothesis and duration of isolation and the form and strength of selection, that requires validation of delimited species with multiple data speciation becomes more or less a protracted process, with new types, such as phenotypic and ecological information. lineages only gradually and stochastically evolving from the ini- tially isolated lineages into true species over time (18, 19, 21). This multispecies coalescent j species delimitation j coalescent theory process is in contrast to commonly applied birth–death models, in which speciation is abstracted as an instantaneous event, such that all divergent lineages are treated as immediately forming true ajor advances in understanding the patterns of biodiver- species (22). Here, we investigate the robustness of species delim- Msity and the processes that generate those patterns are itation under the multispecies coalescent model when speciation being made with increasing rapidity, scope, and scale, as we study species across the tree of life (e.g., refs. 1–3). These advances take the boundaries of the species that constitute their funda- Significance mental units as known. Identification of these boundaries—that is, species delimitation—currently is making increasing use of Despite its widespread application to the species delim- genomic data under statistical model-based approaches, typi- itation problem, our study demonstrates that what the cally using the multispecies coalescent model (4), as opposed multispecies coalescent actually delimits is structure. The to traditional taxonomic work based on phenotypic data. Cou- current implementations of species delimitation under the pled with technological advances for collecting genomic datasets multispecies coalescent do not provide any way for distin- across many individuals per putative species, inference under guishing between structure due to population-level processes the multispecies coalescent model provides us with consider- and that due to species boundaries. The overinflation of able power in identifying recently diverged taxon boundaries. species due to the misidentification of general genetic struc- For example, simulations show that we can delimit lineages with ture for species boundaries has profound implications for our extremely short divergence times, as with the popular program understanding of the generation and dynamics of biodiver- BPP (Bayesian Phylogenetics and Phylogeography) (5). How- sity, because any ecological or evolutionary studies that rely ever, these remarkable gains have also paradoxically given rise to on species as their fundamental units will be impacted, as a new challenge—determining whether what we delimited genet- well as the very existence of this biodiversity, because con- ically represents lineages isolated due to speciation or simply servation planning is undermined due to isolated populations within-species population structure. Population genetic structure incorrectly being treated as distinct species. is ubiquitous among all taxa in which gene flow is reduced by geo- graphic and/or environmental barriers (6). However, the extent Author contributions: J.S. and L.L.K. designed research, performed research, analyzed of population structure varies as the level of gene flow and time data, and wrote the paper. of separation results in more or less evolutionary independence The authors declare no conflict of interest. among populations (7). With more loci, there is the possibility This article is a PNAS Direct Submission. of detecting ever-more-fine population structure and potentially 1J.S. and L.L.K. contributed equally to this work. confounding population structure with species boundaries. As a 2To whom correspondence should be addressed. Email: [email protected]. www.pnas.org/cgi/doi/10.1073/pnas.1607921114 PNAS Early Edition j 1 of 6 Downloaded by guest on September 28, 2021 Splitting events such as this are initiation of speciation through, e.g. population isolation. Color change indicates completion of speciation and development of true species from erred under the multispecies coalescent incipient species Tree inf True speciation history Fig. 1. (Left) The tree represents the true history upon which the gene genealogies (shown by thin purple lines) are conditioned, with the colors repre- senting species. Note that here we show a single representative gene genealogy, with four individuals sampled per lineage, whereas in practice multiple gene genealogies are sampled for delimiting species. This tree shows speciation as a process rather than speciation as an event. That is, the internal nodes of the containing tree do not represent instantaneous complete speciation events, but, rather, initiation of the speciation process due to microevolutionary processes that result in population isolation. Not all of the lineages that arise due to population isolation develop into true species. For example, some may merge back into the other lineages of the same species in the future if whatever barriers led to their isolation were to be removed (i.e., the evolutionary independence will be ephemeral because two populations belonging to the same species do not have an impediment to reproduction). Some of these isolated incipient species lineages, however, do stochastically develop into true species (indicated by shift in color), so that they will remain distinct lineages with independent evolutionary trajectories that do not merge back into their parental species, even if the isolation barriers were to disappear. (Upper Right) The tree shows the results of inference under the multispecies coalescent using BPP, which includes the structuring both due to species boundaries as well as due to lineage splitting as a result of population isolation. As such, the inference corresponds to the full structural history, but not the true speciation history, which is shown by the tree in Lower Right. That is, the multispecies coalescent does not distinguish between structuring due to population isolation vs. structuring due to speciation: It only identifies genetic structure. is considered