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1. Approaches to macroevolution: 1. General concepts and origin of variation.

   Jablonski, D. ( July 2017 , Evolutionary biology)

   Abstract Approaches to macroevolution require integration of its two fundamental components, i.e. the origin and the sorting of variation, in a hierarchical framework. Macroevolution occurs in multiple currencies that are only loosely correlated, notably taxonomic diversity, morphological disparity, and functional variety. The origin of variation within this conceptual framework is increasingly understood in developmental terms, with the semi-hierarchical structure of gene regulatory networks (GRNs, used here in a broad sense incorporating not just the genetic circuitry per se but the factors controlling the timing and location of gene expression and repression), the non-linear relation between magnitude of genetic change and the phenotypic results, the evolutionary potential of co-opting existing GRNs, and developmental responsiveness to nongenetic signals (i.e. epigenetics and plasticity), all requiring modification of standard microevolutionary models, and rendering difficult any simple definition of evolutionary novelty. The developmental factors underlying macroevolution create anisotropic probabilities—i.e., an uneven density distribution—of evolutionary change around any given phenotypic starting point, and the potential for coordinated changes among traits that can accommodate change via epigenetic mechanisms. From this standpoint, “punctuated equilibrium” and “phyletic gradualism” simply represent two cells in a matrix of evolutionary models of phenotypic change, and the origin of trends and evolutionary novelty are not simply functions of ecological opportunity. Over long timescales, contingency becomes especiallyimportant, and can be viewed in terms of macroevolutionary lags (the temporal separation between the origin of a trait or clade and subsequent diversification); such lags can arise by several mechanisms: as geological or phylogenetic artifacts, or when diversifications require synergistic interactions among traits, or between traits and external events. The temporal and spatial patterns of the origins of evolutionary novelties are a challenge to macroevolutionary theory; individual events can be described retrospectively, but a general model relating development, genetics, and ecology is needed. An accompanying paper (Jablonski in Evol Biol 2017) reviews diversity dynamics and the sorting of variation, with some general conclusions. 

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2. Evolvability and Macroevolution: Overview and Synthesis

   https://doi.org/10.1007/s11692-022-09570-4  

   Jablonski, David ( September 2022 , Evolutionary Biology)

   Abstract Evolvability is best addressed from a multi-level, macroevolutionary perspective through a comparative approach that tests for among-clade differences in phenotypic diversification in response to an opportunity, such as encountered after a mass extinction, entering a new adaptive zone, or entering a new geographic area. Analyzing the dynamics of clades under similar environmental conditions can (partially) factor out shared external drivers to recognize intrinsic differences in evolvability, aiming for a macroevolutionary analog of a common-garden experiment. Analyses will be most powerful when integrating neontological and paleontological data: determining differences among extant populations that can be hypothesized to generate large-scale, long-term contrasts in evolvability among clades; or observing large-scale differences among clade histories that can by hypothesized to reflect contrasts in genetics and development observed directly in extant populations. However, many comparative analyses can be informative on their own, as explored in this overview. Differences in clade-level evolvability can be visualized in diversity-disparity plots, which can quantify positive and negative departures of phenotypic productivity from stochastic expectations scaled to taxonomic diversification. Factors that evidently can promote evolvability include modularity—when selection aligns with modular structure or with morphological integration patterns; pronounced ontogenetic changes in morphology, as in allometry or multiphase life cycles; genome size; and a variety of evolutionary novelties, which can also be evaluated using macroevolutionary lags between the acquisition of a trait and phenotypic diversification, and dead-clade-walking patterns that may signal a loss of evolvability when extrinsic factors can be excluded. High speciation rates may indirectly foster phenotypic evolvability, and vice versa. Mechanisms are controversial, but clade evolvability may be higher in the Cambrian, and possibly early in the history of clades at other times; in the tropics; and, for marine organisms, in shallow-water disturbed habitats. 

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3. Why are red flowers so rare? Testing the macroevolutionary causes of tippiness

   https://doi.org/10.1111/jeb.13381  

   Ng, Julienne ; Smith, Stacey D. ( October 2018 , Journal of Evolutionary Biology)

   Traits that have arisen multiple times yet still remain rare present a curious paradox. A number of these rare traits show a distinct tippy pattern, where they appear widely dispersed across a phylogeny, are associated with short branches and differ between recently diverged sister species. This phylogenetic pattern has classically been attributed to the trait being an evolutionary dead end, where the trait arises due to some short‐term evolutionary advantage, but it ultimately leads species to extinction. While the higher extinction rate associated with a dead end trait could produce such a tippy pattern, a similar pattern could appear if lineages with the trait speciated slower than other lineages, or if the trait was lost more often that it was gained. In this study, we quantify the degree of tippiness of red flowers in the tomato family, Solanaceae, and investigate the macroevolutionary processes that could explain the sparse phylogenetic distribution of this trait. Using a suite of metrics, we confirm that red‐flowered lineages are significantly overdispersed across the tree and form smaller clades than expected under a null model. Next, we fit 22 alternative models using HiSSE(Hidden State Speciation and Extinction), which accommodates asymmetries in speciation, extinction and transition rates that depend on observed and unobserved (hidden) character states. Results of the model fitting indicated significant variation in diversification rates across the family, which is best explained by the inclusion of hidden states. Our best fitting model differs between the maximum clade credibility tree and when incorporating phylogenetic uncertainty, suggesting that the extreme tippiness and rarity of red Solanaceae flowers makes it difficult to distinguish among different underlying processes. However, both of the best models strongly support a bias towards the loss of red flowers. The best fitting HiSSEmodel when incorporating phylogenetic uncertainty lends some support to the hypothesis that lineages with red flowers exhibit reduced diversification rates due to elevated extinction rates. Future studies employing simulations or targeting population‐level processes may allow us to determine whether red flowers in Solanaceae or other angiosperms clades are rare and tippy due to a combination of processes, or asymmetrical transitions alone.

    

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4. Morphological disparity across the synapsid forelimb: sub-order-level patterns across 80 million years of synapsid evolution

   Lungmus, Jacqueline A. Angielczyk ( October 2018 , Society of Vertebrate Paleontology 2018 Meeting Program and Abstracts)

   Synapsid evolution can be characterized by three successive radiations: the Permo– Carboniferous pelycosaurs, the Permo–Triassic Therapsida, and the Triassic Eucynodontia. Previous geometric morphometric research at the clade level revealed a continuous increase in humeral morphological disparity in Therapsida, in contrast to their pelycosaur forebearers. Here we present associated data on ulnar morphological disparity, as well an an overall taxonomic expansion of the analyses. This increase in sample size brings the dataset to 765 specimens from which functional units across the forelimb were analyzed. Further, it allows for a more detailed discussion of variance within nearly every major group of early Synapsida, as well as across 80 million years of geologic history. Groups were analyzed for Procrustes variance in 5 million year time bins from 305–225 Mya (Carboniferous–Triassic). In all analyzed functional units—the proximal humerus, distal humerus, and proximal elbow—within group disparity is higher in therapsid families than in pelycosaur families. In addition, therapsid family level disparity is much more variable between groups and across time. Ulnar variance values are higher than humeral values for the entire study period. Procrustes variance for the forelimb decreases across the End Permian Mass Extinction Event in the major therapsid groups that survived it— Anomodontia and Cynodontia. Macroevolutionary changes observed in Synapsida have historically been associated with ecological diversification. Cynodontia and Anomodontia have the highest variance in Therapsida, while Gorgonopsia has the lowest. The high values in Anomodontia, as one of the most taxonomically and ecological diverse clades of Therapsida, suggests that forelimb variance is linked to aspects of ecological diversification. Further, within pelycosaurs Sphenacodontidae has the lowest variance through time, while Ophiacodontidae has the highest. The finding of uniquely high variance levels in Ophiacodontidae, hypothesized by some to be semi-acquatic, is suggestive of a potentially unique forelimb ecomorphology. This research provides evidence that along with major shifts in forelimb morphology, within-family disparity dynamics may have been critical to the evolutionary success of individual synapsid sub-orders. 

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5. Developmental bias, macroevolution, and the fossil record

   https://doi.org/10.1111/ede.12313  

   Jablonski, David ( September 2019 , Evolution & Development)

   A fuller understanding of the role of developmental bias in shaping large‐scale evolutionary patterns requires integrating bias (the probability distribution of variation accessible to an ancestral phenotype) with clade dynamics (the differential survival and production of species and evolutionary lineages). This synthesis could proceed as a two‐way exchange between the developmental data available to neontologists and the strictly phenotypic but richly historical and dynamic data available to paleontologists. Analyses starting in extant populations could aim to predict macroevolution in the fossil record from observed developmental bias, while analyses starting in the fossil record, particularly the record of extant species and lineages, could aim to predict developmental bias from macroevolutionary patterns, including the broad range of extinct phenotypes. Analyses in multivariate morphospaces are especially effective when coupled with phylogeny, theoretical and developmental models, and diversity–disparity plots. This research program will also require assessing the “heritability” of an ancestral bias across phylogeny, and the tendency for bias change in strength and orientation over evolutionary time. Such analyses will help find a set of general rules for the macroevolutionary effects of developmental bias, including its impact on and interactions with the other intrinsic and extrinsic factors governing the movement, expansion, and contraction of clades in morphospace.

    

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