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1. Mechanisms of Parallel Polygenic Adaptation During Habitat Invasions

   https://doi.org/10.1079/9781800626263.0010  

   Lee, Carol Eunmi (December 2025, CABI)

   Bock, Dan G; Ruis, Marc (Ed.)

   Rates of biological invasions are accelerating throughout the world. However, our understanding of the evolutionary mechanisms that promote invasive success remains incomplete. Genome architecture can affect mechanisms of rapid and parallel evolution during invasions. In aquatic habitats, many invaders are crossing biogeographical boundaries from saline to freshwater habitats. The copepod Eurytemora affinis species complex provides a valuable model system for analyzing evolutionary mechanisms underlying these invasions, with populations that have recently invaded freshwater habitats multiple times independently from saline sources. Surprisingly, parallel selection favors the same alleles repeatedly during these invasions, even across clades with differing chromosome number, indicating that salinity adaptation proceeds in a predictable manner. Genome architecture appears to have profound impacts on the response to selection in these populations, with chromosome number likely impacting the relative importance of standing genetic variation versus positive epistasis in promoting parallel evolution. More research is needed to fully explore the role of genome architecture in impacting population responses to selection, especially during habitat invasions. 

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2. Genome architecture underlying salinity adaptation in the invasive copepod Eurytemora affinis species complex: A review

   https://doi.org/10.1016/j.isci.2023.107851  

   Lee, Carol Eunmi (October 2023, iScience)

   With climate change, habitat salinity is shifting rapidly throughout the globe. In addition, many destructive freshwater invaders are recent immigrants from saline habitats. Recently, populations of the copepod Eurytemora affinis species complex have invaded freshwater habitats multiple times independently from saline estuaries on three continents. This review discusses features of this species complex that could enhance their evolutionary potential during rapid environmental change. Remarkably, across independent freshwater invasions, natural selection has repeatedly favored the same alleles far more than expected. This high degree of parallelism is surprising, given the expectation of nonparallel evolution for polygenic adaptation. Factors such as population structure and the genome architecture underlying critical traits under selection might help drive rapid adaptation and parallel evolution. Given the preponderance of saline-to-freshwater invasions and climate-induced salinity change, the principles found here could provide invaluable insights into mechanisms operating in other systems and the potential for adaptation in a changing planet. 

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3. Ion Transporter Gene Families as Physiological Targets of Natural Selection During Salinity Transitions in a Copepod

   https://doi.org/10.1152/physiol.00009.2021  

   Lee, Carol Eunmi (November 2021, Physiology)

   Salinity is a key factor that structures biodiversity on the planet. With anthropogenic change, such as climate change and species invasions, many populations are facing rapid and dramatic changes in salinity throughout the globe. Studies on the copepod Eurytemora affinis species complex have implicated ion transporter gene families as major loci contributing to salinity adaptation during freshwater invasions. Laboratory experiments and population genomic surveys of wild populations have revealed evolutionary shifts in genome-wide gene expression and parallel genomic signatures of natural selection during independent salinity transitions. Our results suggest that balancing selection in the native range and epistatic interactions among specific ion transporter paralogs could contribute to parallel freshwater adaptation. Overall, these studies provide unprecedented insights into evolutionary mechanisms underlying physiological adaptation during rapid salinity change. 

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4. Genome-wide parallelism underlies contemporary adaptation in urban lizards

   https://doi.org/10.1073/pnas.2216789120  

   Winchell, Kristin M.; Campbell-Staton, Shane C.; Losos, Jonathan B.; Revell, Liam J.; Verrelli, Brian C.; Geneva, Anthony J. (January 2023, Proceedings of the National Academy of Sciences)

   Urbanization drastically transforms landscapes, resulting in fragmentation, degradation, and the loss of local biodiversity. Yet, urban environments also offer opportunities to observe rapid evolutionary change in wild populations that survive and even thrive in these novel habitats. In many ways, cities represent replicated “natural experiments” in which geographically separated populations adaptively respond to similar selection pressures over rapid evolutionary timescales. Little is known, however, about the genetic basis of adaptive phenotypic differentiation in urban populations nor the extent to which phenotypic parallelism is reflected at the genomic level with signatures of parallel selection. Here, we analyzed the genomic underpinnings of parallel urban-associated phenotypic change in Anolis cristatellus , a small-bodied neotropical lizard found abundantly in both urbanized and forested environments. We show that phenotypic parallelism in response to parallel urban environmental change is underlain by genomic parallelism and identify candidate loci across the Anolis genome associated with this adaptive morphological divergence. Our findings point to polygenic selection on standing genetic variation as a key process to effectuate rapid morphological adaptation. Identified candidate loci represent several functions associated with skeletomuscular development, morphology, and human disease. Taken together, these results shed light on the genomic basis of complex morphological adaptations, provide insight into the role of contingency and determinism in adaptation to novel environments, and underscore the value of urban environments to address fundamental evolutionary questions. 

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5. Polygenic and monogenic adaptation drive evolutionary rescue at different magnitudes of environmental change

   https://doi.org/10.1101/2025.06.13.659553  

   Bellagio, Tatiana; Exposito-Alonso, Moises (June 2025, bioRxiv)

   Understanding the genetic basis of rapid adaptation is key to predicting species’ evolutionary responses to environmental change. However, it is still debatable whether many small-effect mutations or a few large-effect mutations underlie rapid adaptation, and how this knowledge can predict population survival or extinction. To address this question, we performed a series of ecologically grounded forward-in-time genetic simulations to study rapid adaptation and extinction with increasing magnitudes of environmental change. These simulations were seeded with genomic variation of the plantArabidopsis thalianato have a realistic genomic structure, with one (monogenic) to 1,000 (polygenic) variants with varying heritabilities contributing to an environmental adaptive trait. Our results revealed two distinct scenarios of rapid adaptation and population rescue. Under small to moderate environmental shifts, high polygenic traits increased evolutionary rescue probability. Under extreme environmental shifts, high polygenic traits lead predictably to extinction, yet monogenic traits sometimes produce one-off winning adaptive genotypes. We interpret our rapid evolutionary rescue findings in terms of the fundamental theorem of natural selection, where monogenic and polygenic traits differ in how they create stable versus skewed fitness variance (V_w) and how they respond to environmental shifts. These results highlight the insights genomics gives us into the (un)predictability of species’ evolutionary responses to global change, with management implications for assisted adaptation conservation. 

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