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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. Lacustrine speciation associated with chromosomal inversion in a lineage of riverine fishes

   https://doi.org/10.1093/evolut/qpad067  

   MacGuigan, Daniel J; Krabbenhoft, Trevor J; Harrington, Richard C; Wainwright, Dylan K; Backenstose, Nathan J; Near, Thomas J (April 2023, Evolution)

   Abstract Geographic isolation is the primary driver of speciation in many vertebrate lineages. This trend is exemplified by North American darters, a clade of freshwater fishes where nearly all sister species pairs are allopatric and separated by millions of years of divergence. One of the only exceptions is the Lake Waccamaw endemic Etheostoma perlongum and its riverine sister species Etheostoma maculaticeps, which have no physical barriers to gene flow. Here we show that lacustrine speciation of E. perlongum is characterized by morphological and ecological divergence likely facilitated by a large chromosomal inversion. While E. perlongum is phylogenetically nested within the geographically widespread E. maculaticeps, there is a sharp genetic and morphological break coinciding with the lake–river boundary in the Waccamaw River system. Despite recent divergence, an active hybrid zone, and ongoing gene flow, analyses using a de novo reference genome reveal a 9 Mb chromosomal inversion with elevated divergence between E. perlongum and E. maculaticeps. This region exhibits striking synteny with known inversion supergenes in two distantly related fish lineages, suggesting deep evolutionary convergence of genomic architecture. Our results illustrate that rapid, ecological speciation with gene flow is possible even in lineages where geographic isolation is the dominant mechanism of speciation. 

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3. Radiation with reticulation marks the origin of a major malaria vector

   https://doi.org/10.1073/pnas.2018142117  

   Small, Scott T.; Labbé, Frédéric; Lobo, Neil F.; Koekemoer, Lizette L.; Sikaala, Chadwick H.; Neafsey, Daniel E.; Hahn, Matthew W.; Fontaine, Michael C.; Besansky, Nora J. (December 2020, Proceedings of the National Academy of Sciences)

   null (Ed.)

   Advances in genomics have led to an appreciation that introgression is common, but its evolutionary consequences are poorly understood. In recent species radiations the sharing of genetic variation across porous species boundaries can facilitate adaptation to new environments and generate novel phenotypes, which may contribute to further diversification. Most Anopheles mosquito species that are of major importance as human malaria vectors have evolved within recent and rapid radiations of largely nonvector species. Here, we focus on one of the most medically important yet understudied anopheline radiations, the Afrotropical Anopheles funestus complex (AFC), to investigate the role of introgression in its diversification and the possible link between introgression and vector potential. The AFC comprises at least seven morphologically similar species, yet only An. funestus sensu stricto is a highly efficient malaria vector with a pan-African distribution. Based on de novo genome assemblies and additional whole-genome resequencing, we use phylogenomic and population genomic analyses to establish species relationships. We show that extensive interspecific gene flow involving multiple species pairs has shaped the evolutionary history of the AFC since its diversification. The most recent introgression event involved a massive and asymmetrical movement of genes from a distantly related AFC lineage into An. funestus , an event that predated and plausibly facilitated its subsequent dramatic geographic range expansion across most of tropical Africa. We propose that introgression may be a common mechanism facilitating adaptation to new environments and enhancing vectorial capacity in Anopheles mosquitoes. 

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4. Power of Bayesian and Heuristic Tests to Detect Cross-Species Introgression with Reference to Gene Flow in the Tamias quadrivittatus Group of North American Chipmunks

   https://doi.org/10.1093/sysbio/syac077  

   Ji, Jiayi; Jackson, Donavan J; Leaché, Adam D; Yang, Ziheng (December 2022, Systematic Biology)

   Thompson, Dr Robert (Ed.)

   Abstract In the past two decades, genomic data have been widely used to detect historical gene flow between species in a variety of plants and animals. The Tamias quadrivittatus group of North America chipmunks, which originated through a series of rapid speciation events, are known to undergo massive amounts of mitochondrial introgression. Yet in a recent analysis of targeted nuclear loci from the group, no evidence for cross-species introgression was detected, indicating widespread cytonuclear discordance. The study used the heuristic method HYDE to detect gene flow, which may suffer from low power. Here we use the Bayesian method implemented in the program BPP to re-analyze these data. We develop a Bayesian test of introgression, calculating the Bayes factor via the Savage-Dickey density ratio using the Markov chain Monte Carlo (MCMC) sample under the model of introgression. We take a stepwise approach to constructing an introgression model by adding introgression events onto a well-supported binary species tree. The analysis detected robust evidence for multiple ancient introgression events affecting the nuclear genome, with introgression probabilities reaching 63%. We estimate population parameters and highlight the fact that species divergence times may be seriously underestimated if ancient cross-species gene flow is ignored in the analysis. We examine the assumptions and performance of HYDE and demonstrate that it lacks power if gene flow occurs between sister lineages or if the mode of gene flow does not match the assumed hybrid-speciation model with symmetrical population sizes. Our analyses highlight the power of likelihood-based inference of cross-species gene flow using genomic sequence data. [Bayesian test; BPP; chipmunks; introgression; MSci; multispecies coalescent; Savage-Dickey density ratio.] 

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5. Parallel and non-parallel features of adaptive radiation in Yucatán pupfishes

   https://doi.org/10.1101/2025.11.17.688971  

   Kustra, Matthew C; Tian, David; Palominos, M Fernanda; Guo, Feifei; Chau, Dylan; Golwala, Oskar; Chan, HoWan; Zapata, Andrés Alvarez; Paredes, Reyna_Guadalupe Cetz; Sánchez, Frida_Ximena Cortés; et al (November 2025, bioRxiv)

   Abstract Understanding the extent of parallelism across adaptive radiations remains a central problem in evolutionary biology. We used whole-genome resequencing of 123 individuals to compare an adaptive radiation ofCyprinodonpupfishes in Laguna Chichancanab, Mexico, to an independent radiation of San Salvador Island (SSI) pupfishes in the Bahamas, and assess the repeatability of adaptive genetic architecture, sources of adaptive variation, and stages of selection. Despite rapid craniofacial divergence of trophic specialists within 8-15 kya, only two candidate genes (3.6%) were shared between Caribbean radiations. Although adaptive introgression played a major role on SSI, we found minimal evidence of adaptive introgression in Chichancanab, likely due to geographic isolation of this inland lake. Instead, de novo mutations provided a substantial source of adaptive variation (30.6%) for the endemic zooplanktivore, 15.3 times higher than the endemic scale-eater on SSI. We found strong evidence that selection occurred in stages, first on regulatory and standing genetic variation, then on de novo and nonsynonymous mutations, parallel to SSI. We then verified that adaptive variants near vision-development and spermatogenesis genes, uniquely within Chichancanab, are consistent with greater visual acuity and divergent sperm morphology in the zoooplanktivore. Consistent with extensive adaptive de novo mutations inWNT10Aand rapid diversification of tooth size in the zooplanktivore, we found that experimental inhibition of this pathway in generalists results in narrower teeth. We conclude that de novo mutations, not introgression, can drive rapid adaptive radiations in isolated environments. 

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