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1. 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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2. 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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3. Understanding the genomics responses of freshwater zooplanktons to salinization: a research hotspot in a saltier world

   https://doi.org/10.1139/gen-2024-0129  

   Bi, Ran; Xiao, Leyao; Zhao, Lei; Coggins, Bret L; Xu, Sen; Pfrender, Michael E; Yin, Mingbo (January 2025, Genome)

   The worldwide salinization of freshwater ecosystems poses a major threat to the biodiversity, functioning and services that these essential ecosystems provide. We are far from fully understanding the ecological and evolutionary consequences of salinization for freshwater organisms. Here we review current research on the genomic responses to salinity in freshwater zooplankton. Surveying transcriptomic studies, we identify many key ion transport genes critical for osmoregulation of ions in multiple zooplankton species in response to salinity stress. Laboratory investigations of natural zooplankton populations inhabiting gradients of salinity often reveal additional candidate genes that are not identified in gene expression experiments (e.g., trehalose). We suggest that future studies should focus on genomic approaches to explore the molecular mechanisms of adaptation to freshwater salinization in zooplanktons, and to predict the eco-evolutionary consequences of freshwater salinization. 

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4. The Legs Have It: In Situ Expression of Ion Transporters V-Type H ⁺ -ATPase and Na ⁺ /K ⁺ -ATPase in the Osmoregulatory Leg Organs of the Invading Copepod Eurytemora affinis

   https://doi.org/10.1086/686323  

   Gerber, Lucie; Lee, Carol Eunmi; Grousset, Evelyse; Blondeau-Bidet, Eva; Boucheker, Nesrine Boudour; Lorin-Nebel, Catherine; Charmantier-Daures, Mireille; Charmantier, Guy (May 2016, Physiological and Biochemical Zoology)

   null (Ed.)

   The copepod Eurytemora affinis has an unusually broad salinity range, as some populations have recently invaded freshwater habitats independently from their ancestral saline habitats. Prior studies have shown evolutionary shifts in ion transporter activity during freshwater invasions and localization of ion transporters in newly discovered "Crusalis organs" in the swimming legs. The goals of this study were to localize and quantify expression of ion transport enzymes V-type H(+)-ATPase (VHA) and Na(+)/K(+)-ATPase (NKA) in the swimming legs of E. affinis and determine the degree of involvement of each leg in ionic regulation. We confirmed the presence of two distinct types of ionocytes in the Crusalis organs. Both cell types expressed VHA and NKA, and in the freshwater population the location of VHA and NKA in ionocytes was, respectively, apical and basal. Quantification of in situ expression of NKA and VHA established the predominance of swimming leg pairs 3 and 4 in ion transport in both saline and freshwater populations. Increases in VHA expression in swimming legs 3 and 4 of the freshwater population (in fresh water) relative to the saline population (at 15 PSU) arose from an increase in the abundance of VHA per cell rather than an increase in the number of ionocytes. This result suggests a simple mechanism for increasing ion uptake in fresh water. In contrast, the decline in NKA expression in the freshwater population arose from a decrease in ionocyte area in legs 4, likely resulting from decreases in number or size of ionocytes containing NKA. Such results provide insights into mechanisms of ionic regulation for this species, with added insights into evolutionary mechanisms underlying physiological adaptation during habitat invasions. 

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5. Local Adaptation Despite Gene Flow in Copepod Populations Across Salinity and Temperature Gradients in the Baltic Sea and North Sea Region

   https://doi.org/10.1111/ddi.70176  

   Diaz, Juanita A; Stern, David B; Lee, Carol Eunmi (May 2026, Diversity and Distributions)

   Climate change is threatening aquatic populations with rapid changes in habitat salinity and temperature. Locally adapted alleles along environmental gradients, along with low but sufficient gene flow, could provide crucial genetic variation to adapt to future climate change and rescue populations from extinction. Thus, we explored whether planktonic populations exhibit genomic signatures of selection and gene flow across salinity and temperature gradients in the Baltic Sea and North Sea region. LocationBaltic Sea, North Sea region. MethodsWe performed whole‐genome sequencing of 11 populations of the copepodEurytemora affinisproper along salinity and temperature gradients. We determined signatures of population structure, admixture, and natural selection by analysing single nucleotide polymorphism (SNP) frequencies across populations using TreeMix, PoPoolation2, poolfstat, and BayPass. ResultsWe found significant population genomic signatures of selection associated with salinity and temperature gradients using BayPass X^TX and environmental association tests, consistent with local adaptation. Several ion transport functional categories (GO terms) were significantly associated with the salinity gradient across all populations, whereas only one GO term, ‘prostaglandin biosynthetic process’, was significantly associated with the temperature gradient in the North Sea region. We found clear population structure with PoPoolation2 and TreeMix. We also found signals of admixture between populations with poolfstat and TreeMix, consistent with the presence of gene flow. Site‐frequency spectra (SFS) of candidate SNPs tested against simulated SFS distributions revealed an excess of intermediate frequency alleles within a few populations. Main ConclusionsThe interplay between local adaptation and gene flow had not been fully explored in passive holoplankton dispersers. Many of the same ion transporter genes showed signatures of selection as in our prior studies, but in this case across a metapopulation ofE. affinisspanning a broad geographic range. The presence of locally adapted alleles along with gene flow across environmental gradients could provide genetic substrate for natural selection, enabling populations to adapt to future climate change. 

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