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1. 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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2. Developmental and Functional Interactions Structure Patterns of Variational Modularity in the Lunar Wrasse Skull

   https://doi.org/10.1093/icb/icaf099  

   Hugi, April L; Chan, Howan; Rummel, Andrea; Motomura, Hiroyuki; Dewa, Yuna; Matsuoka, Midori; Sato, Masayuki C; Larouche, Olivier; Evans, Kory M (June 2025, Integrative And Comparative Biology)

   Synopsis Trait modularity is a defining feature of complex life. However, the drivers of modularity across different scales of biological organization remain opaque. Studies have shown that a combination of developmental and functional interactions can structure patterns of trait covariation at the developmental, population, and even macroevolutionary level. However, it remains unclear how developmental and functional interactions may translate or influence macroevolutionary patterns of trait covariance and diversification. Pharyngognathy is a striking evolutionary innovation that has evolved multiple times in acanthomorph fishes and has resulted in the evolution of robust pharyngeal jaws that are used to process hard prey. Recent studies have found strong patterns of evolutionary integration among the jaw systems in pharyngognathous fishes suggesting that this innovation was brought about by the evolutionary coupling of two otherwise distinct trait complexes. Furthermore, the pharyngeal jaws have been hypothesized to act as a constraining force on the evolution of the oral jaws potentially due to their developmental origins in the more conserved hox-positive region of the skull. While multiple studies have recovered strong evolutionary integration between the jaw systems, patterns of modularity at the population (variational) level appear to differ, where a high degree of modularity has been found between the oral and pharyngeal jaws suggesting a disconnect between patterns of evolutionary modularity and patterns of variational modularity. Here, we are using three-dimensional geometric morphometrics to test for modularity between the oral and pharyngeal jaws at the variational level in a population of Lunar wrasse collected from Kagoshima, Japan and additionally test for differences in morphological disparity between the oral and pharyngeal jaws. We find strong support for a developmental hypothesis of modularity that separates the jaw systems into distinct modules. We additionally find mixed support for the constraint hypothesis of the pharyngeal jaws, where some elements of the pharyngeal jaws were found to exhibit less morphological disparity than the oral jaws while others exhibited more morphological disparity. Our findings suggest that developmental and functional interactions at the variational level may impart patterns of covariation that are distinct from evolutionary patterns of modularity that are found between species. 

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3. Cranial modularity drives phenotypic diversification and adaptive radiation of Antarctic icefishes

   https://doi.org/10.1073/pnas.2503283122  

   Neves, Mayara P; Chan, HoWan; M_Santos, Elizabeth C; Evans, Kory M (October 2025, Proceedings of the National Academy of Sciences)

   Modularity among traits is thought to drive morphological evolution and diversification, with more modular species often showing greater morphological disparity and faster evolutionary rates. However, recent studies suggest this pattern is not universal, as higher integration can sometimes be linked to faster rates of evolution. In adaptive radiation, modularity likely facilitates morphological divergence, but its specific role in trait diversification within these events remains uncertain. Antarctic icefishes (Perciformes: Notothenioidei) have undergone adaptive radiation in the frigid Southern Ocean, yet the role of modularity in their craniofacial evolution remains poorly understood. Emerging from a common ancestor 22 Mya, these fishes developed unique morpho-physiological adaptations, such as antifreeze glycoproteins, that contributed to their evolutionary success, but the contribution of cranial modularity to their diversification is still unexplored. Here, we analyze skull shape across 172 perciform species using micro-CT scanning and geometric morphometrics to investigate the tempo and mode of skull evolution in 80 notothenioids versus 92 perciform relatives. Notothenioids exhibit considerable cranial shape diversity, with skull shapes ranging from short to long faces. Fast rates of skull shape evolution occurred in smaller subclades following the emergence of cranial elongation, a derived trait within notothenioids. They also exhibit elevated evolutionary modularity relative to their perciform relatives, with reduced covariation among skeletal elements over time, likely corresponding with Miocene cooling events and the formation of the Antarctic Circumpolar Current. We propose that greater phenotypic modularity in notothenioid skulls represents a pivotal innovation, facilitating their evolutionary response to new ecological opportunities in the Antarctic. 

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4. We get by with a little help from our friends: shared adaptive variation provides a bridge to novel ecological specialists during adaptive radiation

   https://doi.org/10.1098/rspb.2022.0613  

   Richards, Emilie J.; Martin, Christopher H. (May 2022, Proceedings of the Royal Society B: Biological Sciences)

   Adaptive radiations involve astounding bursts of phenotypic, ecological and species diversity. However, the microevolutionary processes that underlie the origins of these bursts are still poorly understood. We report the discovery of an intermediate C. sp. ‘wide-mouth’ scale-eating ecomorph in a sympatric radiation of Cyprinodon pupfishes, illuminating the transition from a widespread algae-eating generalist to a novel microendemic scale-eating specialist. We first show that this ecomorph occurs in sympatry with generalist C. variegatus and scale-eating specialist C. desquamator on San Salvador Island, Bahamas, but is genetically differentiated, morphologically distinct and often consumes scales. We then compared the timing of selective sweeps on shared and unique adaptive variants in trophic specialists to characterize their adaptive walk. Shared adaptive regions swept first in both the specialist desquamator and the intermediate ‘wide-mouth’ ecomorph, followed by unique sweeps of introgressed variation in ‘wide-mouth’ and de novo variation in desquamator . The two scale-eating populations additionally shared 9% of their hard selective sweeps with the molluscivore C. brontotheroides , despite no single common ancestor among specialists. Our work provides a new microevolutionary framework for investigating how major ecological transitions occur and illustrates how both shared and unique genetic variation can provide a bridge for multiple species to access novel ecological niches. 

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5. PRJNA833158 Characterizing a new 'wide-mouth' scale-eating ecomorph in San Salvador Island Cyprinodon pupfish radiation

   Richards, EJ; Martin, CH (April 2022, NCBI)

   Adaptive radiations involve astounding bursts of phenotypic, ecological, and species diversity. However, the microevolutionary processes that underlie the origins of these bursts are still poorly understood. We report the discovery of an intermediate wide-mouth scale-eating ecomorph in a sympatric radiation of Cyprinodon pupfishes, illuminating the transition from a widespread algae-eating generalist to a novel microendemic scale-eating specialist. We first show that this ecomorph occurs in sympatry with generalist C. variegatus and scale-eating specialist C. desquamator on San Salvador Island, Bahamas, but is genetically differentiated, morphologically distinct, and often consumes scales. We then compared the timing of selective sweeps on shared and unique adaptive variants in trophic specialists to characterize their adaptive walk. Shared adaptive regions swept first in both the specialist desquamator and the intermediate wide-mouth ecomorph, followed by unique sweeps of introgressed variation in wide-mouth and de novo variation in desquamator. The two scale-eating populations additionally shared 9% of their hard selective sweeps with molluscivores C. brontotheroides, despite no single common ancestor among specialists. Our work provides a new microevolutionary framework for investigating how major ecological transitions occur and illustrates how both shared and unique genetic variation can provide a bridge for multiple species to access novel ecological niches. 

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