Gene flow among populations or species and incomplete lineage sorting (ILS) are two evolutionary processes responsible for generating gene tree discordance and therefore hindering species tree estimation. Numerous studies have evaluated the impacts of ILS on species tree inference, yet the ramifications of gene flow on species trees remain less studied. Here, we simulate and analyse multilocus sequence data generated with ILS and gene flow to quantify their impacts on species tree inference. We characterize species tree estimation errors under various models of gene flow, such as the isolation-migration model, the n-island model, and gene flow between non-sister species or involving ancestral species, and species boundaries crossed by a single gene copy (allelic introgression) or by a single migrant individual. These patterns of gene flow are explored on species trees of different sizes (4 vs. 10 species), at different time scales (shallow vs. deep), and with different migration rates. Species trees are estimated with the multispecies coalescent model using Bayesian methods (BEST and *BEAST) and with a summary statistic approach (MPEST) that facilitates phylogenomic-scale analysis. Even in cases where the topology of the species tree is estimated with high accuracy, we find that gene flow can result in overestimates of population sizes (species tree dilation) and underestimates of species divergence times (species tree compression). Signatures of migration events remain present in the distribution of coalescent times for gene trees, and with sufficient data it is possible to identify those loci that have crossed species boundaries. These results highlight the need for careful sampling design in phylogeographic and species delimitation studies as gene flow, introgression, or incorrect sample assignments can bias the estimation of the species tree topology and of parameter estimates such as population sizes and divergence times.

Students from underrepresented groups start college with the same level of interest in STEM majors as their peers, but leave STEM at higher rates. We tested the hypothesis that low grades in general chemistry contribute to this “weeding,” using records from 25,768 students. In the first course of a general chemistry series, grade gaps based on binary gender, race/ethnicity, socioeconomic status, and family education background ranged from 0.12 to 0.54 on a four-point scale. Gaps persisted when the analysis controlled for academic preparation, indicating that students from underrepresented groups underperformed relative to their capability. Underrepresented students were less likely than well-represented peers to persist in chemistry if they performed below a C−, but more likely to persist if they got a C or better. This “hyperpersistent zone” suggests that reducing achievement gaps could have a disproportionately large impact on efforts to achieve equity in STEM majors and professions.

Since the initial description of the genomic patterns expected under models of positive selection acting on standing genetic variation and on multiple beneficial mutations—so-called soft selective sweeps—researchers have sought to identify these patterns in natural population data. Indeed, over the past two years, large-scale data analyses have argued that soft sweeps are pervasive across organisms of very different effective population size and mutation rate—humans, Drosophila, and HIV. Yet, others have evaluated the relevance of these models to natural populations, as well as the identifiability of the models relative to other known population-level processes, arguing that soft sweeps are likely to be rare. Here, we look to reconcile these opposing results by carefully evaluating three recent studies and their underlying methodologies. Using population genetic theory, as well as extensive simulation, we find that all three examples are prone to extremely high false-positive rates, incorrectly identifying soft sweeps under both hard sweep and neutral models. Furthermore, we demonstrate that well-fit demographic histories combined with rare hard sweeps serve as the more parsimonious explanation. These findings represent a necessary response to the growing tendency of invoking parameter-heavy, assumption-laden models of pervasive positive selection, and neglecting best practices regarding the construction of proper demographic null models.

Aim Unique amongst birds, megapodes (family Megapodiidae) have exchanged the strategy of incubating eggs with the warmth of their bodies for incubation behaviours that rely entirely on environmental heat sources. Typically, mound‐builders capture heat released from the decomposition of organic materials, while burrow‐nesters lay their eggs in geothermal or solar‐heated soils. The evolutionary path towards novel incubation behaviours has led to ecological and physiological adaptations unique to megapodes. Here, we present a species tree for all extant megapodes that settles long‐standing debates about megapode evolution: namely, their biogeographical origins and ancestral nesting behaviour. Location Australasia. Methods A time‐calibrated multilocus species tree for all extant megapodes was constructed using *beast. We estimated and compared divergence dates for megapodes obtained from molecular rates, fossils, and a combination of fossils and rates. Using this tree, Bayesian estimation of ancestral nesting behaviour was conducted in BayesTraits and ancestral ranges were estimated in BioGeoBEARS. Results Recent dispersal has led to the recolonization of mainland Australia and New Guinea by Megapodius. Bayesian estimation of ancestral states indicates that mound building is the most probable ancestral nesting behaviour in megapodes (posterior probability = 0.75). Burrow nesting was acquired early in the diversification of the family (at least 14 Ma), followed by a single switch back to mound building. Main conclusions Divergence dates and biogeographical reconstructions strongly suggest that dispersal, and not vicariance, led to the isolation of megapodes in Australasia. We propose that flight‐mediated dispersal to environmentally variable islands is responsible for the behavioural lability in nesting behaviours observed in some Megapodius species today.