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ABSTRACT Understanding how the intrinsic ability of populations and species to meet shifting selective demands shapes evolutionary patterns over both short and long timescales is a major question in biology. One major axis of evolutionary flexibility can be measured by phenotypic integration and modularity. The strength, scale, and structure of integration may constrain or catalyze evolution in the face of new selective pressures. We analyze a dataset of seven leaf measurements across Vitaceae to examine how correlations in trait divergence are linked to transitions between freezing and nonfreezing habitats. We assess this by applying a custom algorithm to compare the timing of habitat shifts to changes in the structure of evolutionary trait correlation at discrete points along a phylogeny. We also explore these patterns in relation to lineage diversification rates to understand how and whether patterns in the evolvability of complex multivariate phenotypes are linked to higher‐level macroevolutionary dynamics. We found that shifts in the structure, but not the overall strength, of phylogenetic integration of leaves precipitate colonization of freezing climates. Lineages that underwent associated shifts in leaf trait integration and subsequent movement into freezing habitats also displayed lower turnover and higher net diversification, suggesting a link among shifting vectors of selection, internal constraint, and lineage persistence in the face of changing environments. 

Gene duplication is an important process of molecular evolutionary change, though identifying these events and their functional implications remains challenging. Studies on gene duplication more often focus on the presence of paralogous genes within the genomes and less frequently explore shifts in expression. We investigated the evolutionary history of calsequestrin (CASQ), a crucial calcium-binding protein in the junctional sarcoplasmic reticulum of muscle tissues. CASQ exists in jawed vertebrates as subfunctionalized paralogs CASQ1 and CASQ2 expressed primarily in skeletal and cardiac muscles, respectively. We used an enhanced sequence dataset to support initial duplication of CASQl in a jawed fish ancestor prior to the divergence of cartilaginous fishes. Surprisingly, we find CASQ2 is the predominant skeletal muscle paralog in birds, while CASQ1 is either absent or effectively nonfunctional. Changes in the amino acid composition and electronegativity of avian CASQ2 suggest enhancement to calcium-binding properties that preceded the loss of CASQ1. We identify this phenomenon as CASQ2 “synfunctionalization,” where one paralog functionally replaces another. While additional studies are needed to fully understand the dynamics of CASQ1 and CASQ2 in bird muscles, the long and consistent history of CASQ subfunctions outside of birds indicate a substantial evolutionary pressure on calcium-cycling processes in muscle tissues, likely connected to increased avian cardiovascular and metabolic demands. Our study provides an important insight into the molecular evolution of birds and shows how gene expression patterns can be comparatively studied across phylum-scale deep time to reveal key evolutionary events 

Biological variation fuels evolutionary change. Across longer timescales, however, polymorphisms at both the genomic and phenotypic levels often persist longer than would be expected under standard population genetic models such as positive selection or genetic drift. Explaining the maintenance of this variation within populations across long time spans via balancing selection has been a major triumph of theoretical population genetics and ecology. Although persistent polymorphisms can often be traced in fossil lineages over long periods through the rock record, paleobiology has had little to say about either the long-term maintenance of phenotypic variation or its macroevolutionary consequences. I explore the dynamics that occur when persistent polymorphisms maintained over long lineage durations are filtered into descendant lineages during periods of demographic upheaval that occur at speciation. I evaluate these patterns in two lineages:Ectocion, a genus of Eocene mammals, and botryocrinids, a Mississippian cladid crinoid family. Following origination, descendants are less variable than their ancestors. The patterns by which ancestral variation is sorted cannot be distinguished from drift. Maintained and accumulated polymorphisms in highly variable ancestral lineages such asBarycrinus rhombiferusOwen and Shumard, 1852 may fuel radiations as character states are sorted into multiple descendant lineages. Interrogating the conditions under which trans-specific polymorphism is either maintained or lost during periods of demographic and ecological upheaval can explain how population-level processes contribute to the emergent macroevolutionary dynamics that shape the history of life as preserved in the fossil record.