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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 noveltymore »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.« less
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;more »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.« less
3. 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— Anomodontiamore »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.« less
4. Incongruence of morphological disparity and evolutionary rate in the forelimbs of Paleozoic synapsids

   Lungmus, Jacqueline K. ; Angielczyk, Kenneth D. ( October 2022 , Journal of vertebrate paleontology)

   Previous work has shown increased morphological variance within the forelimbs of the Permian synapsid group known as Therapsida over that of their Carboniferous and early Permian forerunners (“pelycosaurs”). Considering that disparity trends have been known to point to underlying macroevolutionary transitions, here we analyzed morphological variance alongside several additional macroevolutionary metrics to better isolate possible evolutionary mechanisms. Shape data was collected on a sample of 119 humeri and 99 ulnae comprising three major synapsid radiations with a temporal range from the Carboniferous into the Triassic. Taxonomic sample included all major groups of pelycosaur-grade synapsids, all five recognized non-cynodontian therapsid clades, and a sample of pre-prozostrodontian cynodonts. Procrustes variance - a multivariate quantification of morphospace occupation - was the chosen disparity metric for the study. Rate of phenotypic change, which considers the amount of shape change that would be necessary to achieve observed morphologies given the shape of the closely related taxa, was analyzed as the metric for evolutionary rate. Both metrics were considered through-time upon genera present in sequential 5 million year time bins. Our results expand upon previous findings that disparity increases throughout the earliest stages of the Permian, coincident with the diversification of pelycosaurs and the emergence ofmore »Therapsida. This expanded dataset further shows that disparity approaches an asymptote around 270 million years ago and only increases marginally through the late Permian, remaining between 0.018–0.021 from 275-245 mya. In contrast, evolutionary rate does not appear to asymptote during this same interval, starting at a low of 6.17e-6 (300 mya) and increasing to a peak of 1.78e-5 right before the End Permian Mass Extinction Event (252 mya). The continuing increase of evolutionary rate shows that morphological change continues across taxa, but the plateauing of morphological disparity suggests that morphospace is not expanding concurrent with this. The incongruence between these two metrics suggests a critical change in evolutionary mode, wherein morphological change continues rapidly but does not result in the evolution of novel morphologies. These results provide some of the strongest quantitative data yet of an evolutionary constraint acting upon the morphology of the synapsid forelimb through deep time.« less
5. Using GIS to examine biogeographic and macroevolutionary patterns in some late Paleozoic cephalopods from the North American Midcontinent Sea

   https://doi.org/10.7717/peerj.6910  

   Kolis, Kayla M. ; Lieberman, Bruce S. ( May 2019 , PeerJ)

   Geographic range is an important macroevolutionary parameter frequently considered in paleontological studies as species’ distributions and range sizes are determined by a variety of biotic and abiotic factors well known to affect the differential birth and death of species. Thus, considering how distributions and range sizes fluctuate over time can provide important insight into evolutionary dynamics. This study uses Geographic Information Systems (GIS) and analyses of evolutionary rates to examine how in some species within the Cephalopoda, an important pelagic clade, geographic range size and rates of speciation and extinction changed throughout the Pennsylvanian and early Permian in the North American Midcontinent Sea. This period is particularly interesting for biogeographic and evolutionary studies because it is characterized by repetitive interglacial-glacial cycles, a global transition from an icehouse to a greenhouse climate during the Late Paleozoic Ice Age, and decelerated macroevolutionary dynamics, i.e. low speciation and extinction rates. The analyses presented herein indicate that cephalopod species diversity was not completely static and actually fluctuated throughout the Pennsylvanian and early Permian, matching findings from other studies. However, contrary to some other studies, the mean geographic ranges of cephalopod species did not change significantly through time, despite numerous climate oscillations; further, geographic rangemore »size did not correlate with rates of speciation and extinction. These results suggest that pelagic organisms may have responded differently to late Paleozoic climate changes than benthic organisms, although additional consideration of this issue is needed. Finally, these results indicate that, at least in the case of cephalopods, macroevolution during the late Paleozoic was more dynamic than previously characterized, and patterns may have varied across different clades during this interval.

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