The importance of hybridization in generating biological diversity has been historically controversial. Previously, inference about hybridization was limited by dependence on morphological data; with the advent of the next-generation sequencing tools for nonmodel organisms, the evolutionary significance of hybridization is more evident. Here, we test classic hypotheses of hybrid origins of two species in the Phlox pilosa complex. Morphological intermediacy motivated the hypotheses that Phlox amoena lighthipei and Phlox pilosa deamii were independent homoploid hybrid lineages derived from P. amoena amoena and P. pilosa pilosa. We use double-digest restriction site-associated DNA sequencing of individuals from throughout the range of these taxa to conduct the most thorough analysis of evolutionary history in this system to date. Surprisingly, we find no support for the hybrid origin of P. pilosa deamii or P. amoena lighthipei. Our data do identify a history of admixture in individuals collected at a contemporary hybrid zone between the putative parent lineages. We show that three very different evolutionary histories, only one of which involves hybrid origin, have produced intermediate or recombinant morphological traits between P. amoena amoena and P. pilosa pilosa. Although morphological data are still an efficient means of generating hypotheses about past gene flow, genomic data are now the standard of evidence for elucidating evolutionary history.

It is becoming increasingly clear that the evolutionary histories of many groups of organisms are riddled with reticulation. Some clades of organisms appear to be hotspots of speciation by hybridization and gene flow. For example, there are two cases of reinforcement and up to nine cases of hypothesized hybrid speciation in the eastern standing Phlox (Polemoniaceae) wildflowers. However, the relationships of these taxa and the hypotheses about their evolution have received limited attention with genomic data. We performed a comprehensive phylogenomic study of the eastern standing Phlox to resolve their evolutionary relationships and test long-standing hypotheses about if and how hybridization and gene flow acted as creative forces in their diversification. Our phylogenomic analyses on genome-wide markers provides resolution into the evolutionary relationships of thirty-two eastern standing Phlox taxa, including well-supported non-monophyletic relationships across species complexes. Explicit tests for introgression support gene flow occurring alongside the evolution of one of the two cases of reinforcement, and patterns of divergence and gene flow support one of the five hypothesized homoploid hybrid speciation events. Additionally, comparative read mapping allowed assignment of putative subgenome ancestries for four allotetraploids hybrid species. Our findings demonstrate the utility and importance of phylogenomics in confirming hypothesized evolutionary histories of non-model systems and add to the growing evidence that gene flow across species boundaries can play a role in the generation of novel biodiversity.

Sustainable cities depend on urban forests. City trees-pillars of urban forests - improve our health, clean the air, store CO2, and cool local temperatures. Comparatively less is known about city tree communities as ecosystems, particularly regarding spatial composition, species diversity, tree health, and the abundance of introduced species. Here, we assembled and standardized a new dataset of N=5,660,237 trees from 63 of the largest US cities with detailed information on location, health, species, and whether a species is introduced or naturally occurring (i.e., 'native'). We further designed new tools to analyze spatial clustering and the abundance of introduced species. We show that trees significantly cluster by species in 98% of cities, potentially increasing pest vulnerability (even in species-diverse cities). Further, introduced species significantly homogenize tree communities across cities, while naturally occurring trees (i.e., 'native' trees) comprise 0.51%-87.3% (median=45.6%) of city tree populations. Introduced species are more common in drier cities, and climate also shapes tree species diversity across urban forests. Parks have greater tree species diversity than urban settings. Compared to past work which focused on canopy cover and species richness, we show the importance of analyzing spatial composition and introduced species in urban ecosystems (and we develop new tools and datasets to do so). Future work could analyze city trees and socio-demographic variables or bird, insect, and plant diversity (e.g., from citizen-science initiatives). With these tools, we may evaluate existing city trees in new, nuanced ways and design future plantings to maximize resistance to pests and climate change. We depend on city trees.

Natural selection shapes diversity across micro and macro-evolutionary scales. Selection causes local adaptation across populations within species and is simultaneously responsible for much of the divergence between species. However, it is unclear if either the force of or the response to selection is the same or different across these scales. Here we show that natural selection drives adaptive divergence between closely related species in a pattern that is distinct from local adaptation within a species. We use reciprocal common-garden transplant experiments across three species of Phlox wildflowers to show widespread adaptive divergence causing species to have highest fitness in their native habitats. Using provenance trials, we also find that one of these Phlox species has strong local adaptation between populations. We compare the axes of divergence and selection between these two scales of diversity and discover that one suite of traits predicts fitness differences between species and that an independent suite of traits predicts fitness variation within species across individuals. Our work reveals how forces of selection can both drive key divergence between species, allowing for and causing speciation, while simultaneously causing extensive diversity that is maintained across populations within a species. The selection landscape is complex and multidimensional.