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1. Calibrating phylogenies assuming bifurcation or budding alters inferred macroevolutionary dynamics in a densely sampled phylogeny of bivalve families

   https://doi.org/10.1098/rspb.2021.2178  

   Crouch, Nicholas M.; Edie, Stewart M.; Collins, Katie S.; Bieler, Rüdiger; Jablonski, David (December 2021, Proceedings of the Royal Society B: Biological Sciences)

   Analyses of evolutionary dynamics depend on how phylogenetic data are time-scaled. Most analyses of extant taxa assume a purely bifurcating model, where nodes are calibrated using the daughter lineage with the older first occurrence in the fossil record. This contrasts with budding, where nodes are calibrated using the younger first occurrence. Here, we use the extensive fossil record of bivalve molluscs for a large-scale evaluation of how branching models affect macroevolutionary analyses. We time-calibrated 91% of nodes, ranging in age from 2.59 to 485 Ma, in a phylogeny of 97 extant bivalve families. Allowing budding-based calibrations minimizes conflict between the tree and observed fossil record, and reduces the summed duration of inferred ‘ghost lineages’ from 6.76 billion years (Gyr; bifurcating model) to 1.00 Gyr (budding). Adding 31 extinct paraphyletic families raises ghost lineage totals to 7.86 Gyr (bifurcating) and 1.92 Gyr (budding), but incorporates more information to date divergences between lineages. Macroevolutionary analyses under a bifurcating model conflict with other palaeontological evidence on the magnitude of the end-Palaeozoic extinction, and strongly reduce Cenozoic diversification. Consideration of different branching models is essential when node-calibrating phylogenies, and for a major clade with a robust fossil record, a budding model appears more appropriate. 

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2. Sorting of persistent morphological polymorphisms links paleobiological pattern to population process

   https://doi.org/10.1017/pab.2023.27  

   Parins-Fukuchi, C. Tomomi (October 2023, Paleobiology)

   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. 

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3. But the Clock, Tick-Tock: An Empirical Case Study Highlights the Preeminence of Relaxed Clock Models in Total-Evidence Dating

   https://doi.org/10.1093/sysbio/syaf055  

   Mongiardino Koch, Nicolás; Thompson, Jeffrey R; Mooi, Rich; Rouse, Greg W (January 2026, Systematic Biology)

   Klopfstein, Seraina (Ed.)

   Abstract Phylogenetic clock models translate inferred amounts of evolutionary change (calculated from either genotypes or phenotypes) into estimates of elapsed time, providing a mechanism for time scaling phylogenetic trees. Relaxed-clock models, which accommodate variation in evolutionary rates across branches, are one of the main components of Bayesian dating, yet their consequences for total-evidence phylogenetics have not been thoroughly explored. Here, we combine morphological, molecular (both transcriptomic and Sanger-sequenced), and stratigraphic data sets for all major lineages of echinoids (sea urchins, heart urchins, sand dollars). We then perform total-evidence dated inference under the fossilized birth–death prior, varying two analytical conditions: the choice between autocorrelated and uncorrelated relaxed clocks, which enforce (or not) evolutionary rate inheritance, and the ability to recover fossil terminals as direct ancestors. Our results highlight a previously unnoticed interaction between tree and clock models, with analyses implementing an autocorrelated clock failing to recover any direct ancestors. Nonetheless, even under conditions conducive to the placement of fossil terminals as ancestors, we find this type of relationship to be accommodated without any impact on either topology or node ages. On the other hand, tree topology, fossil placement, divergence times, and downstream macroevolutionary inferences (e.g., ancestral state reconstructions) were all strongly affected by the type of relaxed clock implemented. In regions of the tree where molecular rate variation is pervasive and morphological signal relatively uninformative, fossil tips seem to play little to no role in informing divergence times, and instead passively move in and out of clades depending on the ages imposed upon surrounding nodes by molecular data. Our results reveal the extent to which the phylogenetic and macroevolutionary conclusions of total-evidence dated analyses are contingent on the choice of relaxed-clock model, highlighting the need for either careful methodological validation or a thorough assessment of sensitivity. Our efforts continue to illuminate the echinoid tree of life, supporting the erection of the order Apatopygoida to include three living species last sharing a common ancestor with other extant lineages around the time of the Jurassic–Cretaceous boundary. Furthermore, they also illustrate how the phylogenetic placement of extinct clades hinges upon the modeling of molecular data, evidencing the extent to which the fossil record remains subservient to phylogenomics. 

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4. Repeated ecological and life cycle transitions make salamanders an ideal model for evolution and development

   https://doi.org/10.1002/dvdy.373  

   Bonett, Ronald M.; Ledbetter, Nicholus M.; Hess, Alexander J.; Herrboldt, Madison A.; Denoël, Mathieu (January 2021, Developmental Dynamics)

   null (Ed.)

   Observations on the ontogeny and diversity of salamanders provided some of the earliest evidence that shifts in developmental trajectories have made a substantial contribution to the evolution of animal forms. Since the dawn of evo-devo there have been major advances in understanding developmental mechanisms, phylogenetic relationships, evolutionary models, and an appreciation for the impact of ecology on patterns of development (eco-evo-devo). Molecular phylogenetic analyses have converged on strong support for the majority of branches in the Salamander Tree of Life, which includes 764 described species. Ancestral reconstructions reveal repeated transitions between life cycle modes and ecologies. The salamander fossil record is scant, but key Mesozoic species support the antiquity of life cycle transitions in some families. Colonization of diverse habitats has promoted phenotypic diversification and sometimes convergence when similar environments have been independently invaded. However, unrelated lineages may follow different developmental pathways to arrive at convergent phenotypes. This article summarizes ecological and endocrine-based causes of life cycle transitions in salamanders, as well as consequences to body size, genome size, and skeletal structure. Salamanders offer a rich source of comparisons for understanding how the evolution of developmental patterns has led to phenotypic diversification following shifts to new adaptive zones. 

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5. ppgm: an R package for integrating neontological, palaeontological, and climate data in a phylogenetic comparative framework

   https://doi.org/10.1111/pala.70034  

   Howard, Alexandra_F C; Hurtado‐Materon, Maria A; Rivera, Julio A; Zúñiga‐Vega, J Jaime; Martins, Emília P; Lawing, A Michelle (November 2025, Palaeontology)

   Abstract Understanding how changes in climate affect habitat availability for species through time is critical for macroevolutionary, ecological, and conservation research. When combined with palaeoclimate reconstructions, the fossil record provides insights into how species' geographic distributions have responded to past climate shifts, including under non‐analogous climate conditions. Palaeophylogeographic models (PPGMs) offer a framework to integrate modern and palaeontological data into phylogenetic comparative analyses of species climate tolerances. TheppgmR package is an implementation of PPGMs, which estimates species climate envelopes, reconstructs ancestral climatic tolerances across phylogenies, and projects these onto palaeoclimatic maps to identify climatically available regions through time. The package also supports direct inclusion of fossil occurrences with associated palaeoclimatic data, allowing a reconstruction of past trends of species climate tolerances projected into palaeoclimatic maps to pinpoint the locations of climate availability through time according to the fossil record. We demonstrate the broad applicability ofppgmthrough detailed case studies, showing its potential for addressing research questions in macroevolutionary and conservation palaeobiology research. Theppgmpackage complements existing R packages by allowing researchers to use analytical techniques on large integrated datasets and facilitates reproducible analyses of species climate niches over deep and shallow time. 

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