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1. The Cretaceous Diatom Database: A tool for investigating early diatom evolution

   https://doi.org/10.1111/jpy.13499  

   Bryłka, Karolina; Ashworth, Matt P; Alverson, Andrew J; Conley, Daniel J (August 2024, Journal of Phycology)

   The Cretaceous period is the time of the first appearance of the diatoms in the fossil record. These fossils give us direct evidence of the age and early evolution of the diatom lineage. The fossil record, however, is incomplete and therefore often extrapolated through time‐calibrated phylogenies. These two approaches offer different perspectives on the early evolution of diatoms, which is still poorly understood. We compiled the first comprehensive Cretaceous Diatom Database, a tool to investigate the taxonomy, diversity, and occurrence of the earliest known diatom lineages. To further aid the integration and use of the oldest diatom fossils in molecular clock analyses, we present a set of well‐documented Cretaceous fossils that can be placed onto molecular phylogenetic trees of extant and extinct species, making them ideal candidates for the calibration of molecular clocks. The analysis of the fossil record and the Cretaceous Diatom Database revealed Cretaceous diversity is substantially greater than previously thought, yet considerable taxonomic work is still needed. The Cretaceous Diatom Database and the list of Cretaceous fossils for calibrating molecular clocks represent valuable resources for future evolutionary and taxonomic studies of modern and fossil diatoms. 

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2. Developmental bias, macroevolution, and the fossil record.

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

   Jablonski, D. (January 2020, Evolution development)

   null (Ed.)

   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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3. Fossil calibrations for molecular analyses and divergence time estimation for true crabs (Decapoda: Brachyura)

   https://doi.org/10.26879/1332  

   Luque, Javier; Bracken-Grissom, Heather; Ortega-Hernández, Javier; Wolfe, Joanna (January 2024, Palaeontologia Electronica)

   True crabs, or Brachyura, comprise over 7,600 known species and are among the most ecologically dominant, economically significant, and popularly recognized groups of extant crustaceans. There are over 3,000 fossil brachyuran species known from mid and upper Jurassic, Cretaceous, and Cenozoic deposits across the globe, many of them preserved in exquisite detail, but their origins and early evolution remain unresolved. This uncertainty hinders the identification of the stratigraphically earliest occurrence of major brachyuran groups in the fossil record, obscuring our understanding of their phylogenetic relationships and thus the ability to estimate divergence times to answer large-scale macroevolutionary questions. We present 36 vetted fossil node calibration points for molecular phylogenetic analysis of crabs (one Anomura and 35 Brachyura) and reassess the earliest occurrences of several key clades based on recent fossil discoveries or re-examination of previous studies. For each calibrated node, we provide minimum and tip maximum ages for the stratigraphically oldest fossil that can be reliably assigned to the group. Disentangling the anatomical disparity of fossil forms and their phylogenetic relationships is crucial to recognizing the earliest branching members among brachyuran groups. This represents a critical first step in understanding the evolution of carcinization and decarcinization, the appearance of key adaptations, and the transition from sea to land and freshwater in brachyurans. The identification and critical examination of reliable fossils for deep time calibrations, both as tips and nodes, is pivotal to ensure not only precise but more accurate divergence time estimations when reconstructing the crab tree of life. 

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4. 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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5. Extinction risk in extant marine species integrating palaeontological and biodistributional data.

   Collins, K.S.; Edie, S.M.; Hunt, G.; Roy, K.; Jablonski, D. (July 2018, Proceedings - Royal Society. Biological sciences)

   Extinction risk assessments of marine invertebrate species remain scarce, which hinders effective management of marine biodiversity in the face of anthropogenic impacts. To help close this information gap, in this paper we provide a metric of relative extinction risk that combines palaeontological data, in the form of extinction rates calculated from the fossil record, with two known correlates of risk in the modern day: geographical range size and realized thermal niche.We test the performance of this metric—Palaeontological Extinction Risk In Lineages (PERIL)—using survivorship analyses of Pliocene bivalve faunas from California and New Zealand, and then use it to identify present-day hotspots of extinction vulnerability for extant shallow-marine Bivalvia. Areas of the ocean where concentrations of bivalve species with higher PERIL scores overlap with high levels of climatic or anthropogenic stressors should be considered of most immediate concern for both conservation and management. 

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