A mechanistic understanding of the causes of naturalization in terrestrial plant communities, and the consequences for associated ecosystems, relies on understanding whether and how native and non‐native plant traits differ. Traits of non‐native plants may either help them compete or avoid competition with natives, and depending on their interaction with the native community, the non‐native may act as more or less of an active driver vs. a passive passenger of change in the native ecosystem. Trait comparisons between native and non‐native plants are often laboratory‐based, providing insights that can be difficult to apply to natural communities. Studies of the impacts of non‐native plants, by contrast, are generally performed in natural communities, but usually do not compare observed impacts of the non‐natives with those exerted by dominant natives on each other and the community. Thus, the likely relative disruption of the non‐native to the community is unclear. In a four‐year observational study conducted at the microhabitat scale in the herbaceous layer of a Midwestern oak forest, we compared the non‐native herb Alliaria petiolata (garlic mustard) with dominant native herbaceous species in terms of correlational patterns related to three broad categories of traits: (1) environmental correlates (light, topography, soil nutrients) with presence and cover, (2) inter‐annual regeneration and phenology, and (3) associations with other species (competition and herbivory). We found that Alliaria differed strongly from dominant native herbs in all three categories. Compared with native herbs, Alliaria was more strongly associated with south‐facing slopes and high nutrient levels, displayed earlier phenology and enhanced dispersal ability, and was strongly avoided by the generalist native herbivore, Odocoileus virginianus (white‐tailed deer). Despite well‐described allelopathic effects of Alliaria on mycorrhizae and mycorrhizal plants, we found little evidence to suggest that Alliaria had negative interactions with native plants that were stronger than those of native community members. Overall, our data suggest that naturalization of Alliaria in this site is primarily due to differences from native plants in phenology, dispersal capability, and avoidance of herbivory, and that Alliaria is therefore more likely to be acting as a passenger than as a driver of change in our site.

Molecular phylogenies are a cornerstone of modern comparative biology and are commonly employed to investigate a range of biological phenomena, such as diversification rates, patterns in trait evolution, biogeography, and community assembly. Recent work has demonstrated that significant biases may be introduced into downstream phylogenetic analyses from processing genomic data; however, it remains unclear whether there are interactions among bioinformatic parameters or biases introduced through the choice of reference genome for sequence alignment and variant-calling. We address these knowledge gaps by employing a combination of simulated and empirical data sets to investigate to what extent the choice of reference genome in upstream bioinformatic processing of genomic data influences phylogenetic inference, as well as the way that reference genome choice interacts with bioinformatic filtering choices. We demonstrate that more stringent minor allele filters bias inferred trees away from the true species tree topology, and that these biased trees tend to be more imbalanced and have a higher center of gravity than the true trees. We find greatest topological accuracy when filtering sites for minor allele count > 3--4 in our 51-taxa data sets, while tree center of gravity was closest to the true value when filtering for sites with minor allele count > 1-2. In contrast, filtering for missing data increased accuracy in the inferred topologies; however, this effect was small in comparison to the effect of minor allele filters and may be undesirable due to a subsequent mutation spectrum distortion. The bias introduced by these filters differs based on the reference genome used in short read alignment, indicating that choosing a reference genome for alignment is an important bioinformatic decision with implications for downstream analyses. These results demonstrate that care needs to be taken when choosing parameters for assembling and filtering large genomic data sets from short read data.

Closely related taxa frequently exist in sympatry before the evolution of robust reproductive barriers, which can lead to substantial gene flow. Post‐divergence gene flow can promote several disparate trajectories of divergence ranging from the erosion of distinctiveness and eventual collapse of the taxa to the strengthening of reproductive isolation. Among many relevant factors, understanding the demographic history of divergence (e.g. divergence time and extent of historical gene flow) can be particularly informative when examining contemporary gene flow between closely related taxa because this history can influence gene flow's prevalence and consequences. Here, we used genotyping‐by‐sequencing data to investigate speciation and contemporary hybridization in two closely related and sympatrically distributed Lake Tanganyikan cichlid species in the genus Petrochromis. Demographic modelling supported a speciation scenario involving divergence in isolation followed by secondary contact with bidirectional gene flow. Further investigation of this recent gene flow found evidence of ongoing hybridization between the species that varied in extent between different co‐occurring populations. Relationships between abundance and the degree of admixture across populations suggest that the availability of conspecific mates may influence patterns of hybridization. These results, together with the observation that sets of recently diverged cichlid taxa are generally geographically separated in the lake, suggest that ongoing speciation in Lake Tanganyikan cichlids relies on initial spatial isolation. Additionally, the spatial heterogeneity of admixture between the Petrochromis species illustrates the complexities of hybridization when species are in recent secondary contact.

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