Ecological Diversification in an Adaptive Radiation of Plants: The Role of De Novo Mutation and Introgression

Adaptive radiations are characterized by rapid ecological diversification and speciation events, leading to fuzzy species boundaries between ecologically differentiated species. Adaptive radiations are therefore key systems for understanding how species are formed and maintained, including the role of de novo mutations versus preexisting variation in ecological adaptation and the genome-wide consequences of hybridization events. For example, adaptive introgression, where beneficial alleles are transferred between lineages through hybridization, may fuel diversification in adaptive radiations and facilitate adaptation to new environments. In this study, we employed whole-genome resequencing data to investigate the evolutionary origin of hummingbird-pollinated flowers and to characterize genome-wide patterns of phylogenetic discordance and introgression in Penstemon subgenus Dasanthera, a small and diverse adaptive radiation of plants. We found that magenta hummingbird-adapted flowers have apparently evolved twice from ancestral blue-violet bee-pollinated flowers within this radiation. These shifts in flower color are accompanied by a variety of inactivating mutations to a key anthocyanin pathway enzyme, suggesting that independent de novo loss-of-function mutations underlie the parallel evolution of this trait. Although patterns of introgression and phylogenetic discordance were heterogenous across the genome, a strong effect of gene density suggests that, in general, natural selection opposes introgression and maintains genetic differentiation in gene-rich genomic regions. Our results highlight the importance of both de novo mutation and introgression as sources of evolutionary change and indicate a role for de novo mutation in driving parallel evolution in adaptive radiations.

Ecological diversification in an adaptive radiation of plants: the role of de novo mutation and introgression

Adaptive radiations are characterized by rapid ecological diversification and speciation events, leading to fuzzy species boundaries between ecologically differentiated species. Adaptive radiations are therefore key systems for understanding how species are formed and maintained, including the role of de novo mutations vs. pre-existing variation in ecological adaptation and the genome-wide consequences of hybridization events. For example, adaptive introgression, where beneficial alleles are transferred between lineages through hybridization, may fuel diversification in adaptive radiations and facilitate adaptation to new environments. In this study, we employed whole-genome resequencing data to investigate the evolutionary origin of hummingbird-pollinated flowers and to characterize genome-wide patterns of phylogenetic discordance and introgression in Penstemon subgenus Dasanthera, a small and diverse adaptive radiation of plants. We found that magenta hummingbird-adapted flowers have apparently evolved twice from ancestral blue-violet bee-pollinated flowers within this radiation. These shifts in flower color are accompanied by a variety of inactivating mutations to a key anthocyanin pathway enzyme, suggesting that independent de novo loss-of-function mutations underlie parallel evolution of this trait. Although patterns of introgression and phylogenetic discordance were heterogenous across the genome, a strong effect of gene density suggests that, in general, natural selection opposes introgression and maintains genetic differentiation in gene-rich genomic regions. Our results highlight the importance of both de novo mutation and introgression as sources of evolutionary change and indicate a role for de novo mutation in driving parallel evolution in adaptive radiations.

Testing hypotheses of hybrid taxon formation in the shrubby beardtongues (Penstemon subgenus Dasanthera)

PREMISE

Hybridization is increasingly being identified in the genomes of species across the tree of life, leading to a general recognition that hybridization plays an important role in the generation of species diversity. While hybridization may increase species diversity directly via the formation of new taxa through hybrid speciation, it may also act indirectly via the exchange of phenotypic and genetic variance between species, which may in turn stimulate future speciation events.

METHODS

Using high-throughput sequence data, we resolved phylogenetic relationships and investigated the role of hybridization as a diversification mechanism in the shrubby beardtongues (Penstemon subgenus Dasanthera), a group of North American wildflowers that has undergone a recent and rapid adaptive radiation. Specifically, we tested four hypotheses of hybrid taxon formation resulting from hybridization between P. davidsonii and P. fruticosus.

RESULTS

Species tree inference supports the monophyly of subgenus Dasanthera and elucidates relationships between taxa distributed in the Cascades and Sierra Nevada Mountains. Results also provide evidence of gene flow between P. davidsonii and P. fruticosus and support at least one hybrid origin hypothesis (P. davidsonii var. menziesii) in a region of contemporary distributional overlap. Hybridization may have also been facilitated by historical overlap in geographic distribution caused by species' responses to climatic changes during the Pleistocene.

CONCLUSIONS

Our results support a history of hybridization between focal taxa in a rapidly radiating clade of plants and more broadly contribute to our growing understanding of the role of hybridization as a diversification mechanism in plants.

Phylogeographic analysis of shrubby beardtongues reveals range expansions during the Last Glacial Maximum and implicates the Klamath Mountains as a hotspot for hybridization

Quaternary glacial cycles often altered species' geographic distributions, which in turn altered the geographic structure of species' genetic diversity. In many cases, glacial expansion forced species in temperate climates to contract their ranges and reside in small pockets of suitable habitat (refugia), where they were likely to interact closely with other species, setting the stage for potential gene exchange. These introgression events, in turn, would have degraded species boundaries, making the inference of phylogenetic relationships challenging. Using high-throughput sequence data, we employed a combination of species distribution models and hybridization tests to assess the effect of glaciation on the geographic distributions, phylogenetic relationships, and patterns of gene flow of five species of Penstemon subgenus Dasanthera, long-lived shrubby angiosperms distributed throughout the Pacific Northwest of North America. Surprisingly, we found that rather than reducing their ranges to small refugia, most Penstemon subgenus Dasanthera species experienced increased suitable habitat during the Last Glacial Maximum relative to the present day. We also found substantial evidence for gene exchange between species, with the bulk of introgression events occurring in or near the Klamath Mountains of southwestern Oregon and northwestern California. Subsequently, our phylogenetic inference reveals blurred taxonomic boundaries in the Klamath Mountains, where introgression is most prevalent. Our results question the classical paradigm of temperate species' responses to glaciation and highlight the importance of contextualizing phylogenetic inference with species' histories of introgression.

What limits tool use in nonhuman primates? Insights from tufted capuchin monkeys (Sapajus spp.) and chimpanzees (Pan troglodytes) aligning three-dimensional objects to a surface

Perceptuomotor functions that support using hand tools can be examined in other manipulation tasks, such as alignment of objects to surfaces. We examined tufted capuchin monkeys' and chimpanzees' performance at aligning objects to surfaces while managing one or two spatial relations to do so. We presented six subjects of each species with a single stick to place into a groove, two sticks of equal length to place into two grooves, or two sticks joined as a T to place into a T-shaped groove. Tufted capuchins and chimpanzees performed equivalently on these tasks, aligning the straight stick to within 22.5° of parallel to the groove in approximately half of their attempts to place it, and taking more attempts to place the T stick than two straight sticks. The findings provide strong evidence that tufted capuchins and chimpanzees do not reliably align even one prominent axial feature of an object to a surface, and that managing two concurrent allocentric spatial relations in an alignment problem is significantly more challenging to them than managing two sequential relations. In contrast, humans from 2 years of age display very different perceptuomotor abilities in a similar task: they align sticks to a groove reliably on each attempt, and they readily manage two allocentric spatial relations concurrently. Limitations in aligning objects and in managing two or more relations at a time significantly constrain how nonhuman primates can use hand tools.

How FDA safeguards the blood supply

AIDS focused public concern on the safety of the blood supply. New donor screening methods and testing, as well as FDA monitoring and inspection of blood banks, make the blood products in this country safer than ever.