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

   https://doi.org/10.1093/molbev/msae007  

   Stone, Benjamin W; Wessinger, Carolyn A (January 2024, Molecular Biology and Evolution)

   Josephs, Emily (Ed.)

   Abstract 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. 

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2. A vertebrate adaptive radiation is assembled from an ancient and disjunct spatiotemporal landscape

   https://doi.org/10.1073/pnas.2011811118  

   Richards, Emilie J.; McGirr, Joseph A.; Wang, Jeremy R.; St. John, Michelle E.; Poelstra, Jelmer W.; Solano, Maria J.; O’Connell, Delaney C.; Turner, Bruce J.; Martin, Christopher H. (May 2021, Proceedings of the National Academy of Sciences)

   null (Ed.)

   To investigate the origins and stages of vertebrate adaptive radiation, we reconstructed the spatial and temporal histories of adaptive alleles underlying major phenotypic axes of diversification from the genomes of 202 Caribbean pupfishes. On a single Bahamian island, ancient standing variation from disjunct geographic sources was reassembled into new combinations under strong directional selection for adaptation to the novel trophic niches of scale-eating and molluscivory. We found evidence for two longstanding hypotheses of adaptive radiation: hybrid swarm origins and temporal stages of adaptation. Using a combination of population genomics, transcriptomics, and genome-wide association mapping, we demonstrate that this microendemic adaptive radiation of novel trophic specialists on San Salvador Island, Bahamas experienced twice as much adaptive introgression as generalist populations on neighboring islands and that adaptive divergence occurred in stages. First, standing regulatory variation in genes associated with feeding behavior ( prlh , cfap20 , and rmi1 ) were swept to fixation by selection, then standing regulatory variation in genes associated with craniofacial and muscular development ( itga5 , ext1 , cyp26b1 , and galr2 ) and finally the only de novo nonsynonymous substitution in an osteogenic transcription factor and oncogene ( twist1 ) swept to fixation most recently. Our results demonstrate how ancient alleles maintained in distinct environmental refugia can be assembled into new adaptive combinations and provide a framework for reconstructing the spatiotemporal landscape of adaptation and speciation. 

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3. Phenotypic covariation predicts diversification in an adaptive radiation of pupfishes

   https://doi.org/10.1002/ece3.11642  

   Dunker, Julia C; St John, Michelle E; Martin, Christopher H (August 2024, Ecology and Evolution)

   Abstract Phenotypic covariation among suites of traits may constrain or promote diversification both within and between species, yet few studies have empirically tested this relationship. In this study, we investigate whether phenotypic covariation of craniofacial traits is associated with diversification in an adaptive radiation of pupfishes found only on San Salvador Island, Bahamas (SSI). The radiation includes generalist, durophagous, and lepidophagous species. We compared phenotypic variation and covariation (i.e., the P matrix) between (1) allopatric populations of generalist pupfish from neighboring islands and estuaries in the Caribbean, (2) SSI pupfish allopatric lake populations with only generalist pupfish, and (3) SSI lake populations containing the full radiation in sympatry. Additionally, we examine patterns observed in the P matrices of two independent lab‐reared F2 hybrid crosses of the two most morphologically distinct members of the radiation to make inferences about the underlying mechanisms contributing to the variation in craniofacial traits in SSI pupfishes. We found that the P matrix of SSI allopatric generalist populations exhibited higher levels of mean trait correlation, constraints, and integration with simultaneously lower levels of flexibility compared to allopatric generalist populations on other Caribbean islands and sympatric populations of all three species on SSI. We also document that while many craniofacial traits appear to result from additive genetic effects, variation in key traits such as head depth, maxilla length, and lower jaw length may be produced via non‐additive genetic mechanisms. Ultimately, this study suggests that differences in phenotypic covariation significantly contribute to producing and maintaining organismal diversity. 

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4. The unique morphological basis and repeated evolutionary origins of personate flowers in Penstemon

   https://doi.org/10.1002/ajb2.70078  

   Depatie, Trinity H; Wessinger, Carolyn A (August 2025, American Journal of Botany)

   Abstract PremiseAdaptive radiation in ecologically and morphologically diverse plant lineages presents an opportunity to investigate the rapid evolution of novel floral traits. While some types of floral traits, such as flower color, are well characterized, other types of complex morphologies remain understudied. One example is occluded personate flowers, dorsoventrally compressed flowers with obstructed floral passageways, which have evolved in multiple genera, but have only been characterized from snapdragon. MethodsOur study examined the morphological basis and evolutionary history of personate flowers in a clade ofPenstemonspecies that includes three personate‐flowered species. We characterized floral morphology and inferred phylogenetic relationships for 13 species in this group to examine the evolutionary history of personate flowers. We used phylogenomic tests for introgression to examine whether personate‐flowered lineages have a history of introgression. ResultsUnlike the personate flowers of snapdragon, personate flowers inPenstemonare produced by deep pleats in the ventral petal tissue that curve the ventral petal surface upward, obstructing the floral tube opening. Our phylogenetic tree suggests that personate flowers evolved in two separate lineages. Phylogenomic analyses indicate incomplete lineage sorting and introgression between certain taxa have contributed to phylogenomic discordance; however, we found little evidence of recent introgression between the two personate‐flowered lineages. ConclusionsPersonate flowers inPenstemonhave a different morphological basis than those in snapdragon. Personate flowers have evolved multiple times inPenstemonon a rapid evolutionary timescale. The source of genetic variation for repeated shifts may be de novo mutations or pre‐existing variants. 

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5. Adaptive radiation along ecological and morphological lines of least resistance in Cyprinodon pupfishes

   https://doi.org/10.1101/2025.08.13.670168  

   Martin, Christopher H; Zapata, Andrés Alvarez; Paredes, Reyna_Guadalupe Cetz; Cortés, Frida; Hernández, Sonia Gabriela; Kustra, Matthew C; Mar-Silva, Adan Fernando; Mex, Fernando; Palominos, M Fernanda; Tralka, Charles; et al (August 2025, bioRxiv)

   Abstract Adaptive radiation results in part from ecological opportunity in a new environment, but it is unclear how pre-existing constraints in the founding population may limit this process. Genetic lines of least resistance, and by proxy morphological variance, are known to limit adaptive divergence, but ecological variance is rarely investigated. Here we test whether ecological or morphological lines of least resistance in generalist populations may have constrained the directions of species divergence in two independent Caribbean adaptive radiations ofCyprinodonpupfishes. We find almost universal congruence between the major multivariate dimensions of intraspecific craniofacial and dietary variance within generalist populations and the major axes of interspecific divergence within each adaptive radiation. This is surprising given that we document unique trophic specialists within each radiation, including a bivalve-specialist, zooplanktivore, molluscivore/ostracod-specialist, and scale-eating specialist, while nearly all generalist populations were observed to feed rarely on these same resources. We conclude that pre-existing genetic constraints within each founding generalist population, resulting in dimensions of greater ecological and morphological variance, may partially constrain and predict the directions of species divergence and dietary specialization during adaptive radiation. We also provide a new framework for examining ecological lines of least resistance. 

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