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1. Rapid macrobenthic diversification and stabilization after the end-Cretaceous mass extinction event

   https://doi.org/10.1130/G47589.1  

   Rodríguez-Tovar, Francisco J.; Lowery, Christopher M.; Bralower, Timothy J.; Gulick, Sean P.S.; Jones, Heather L. (July 2020, Geology)

   Previous ichnological analysis at the Chicxulub impact crater, Yucatán Peninsula, México (International Ocean Discovery Program [IODP]/International Continental Scientific Drilling Program [ICDP] Site M0077), showed a surprisingly rapid initial tracemaker community recovery after the end-Cretaceous (Cretaceous-Paleogene [K-Pg]) mass extinction event. Here, we found that full recovery was also rapid, with the establishment of a well-developed tiered community within ~700 k.y. Several stages of recovery were observed, with distinct phases of stabilization and diversification, ending in the development of a trace fossil assemblage mainly consisting of abundant Zoophycos, Chondrites, and Planolites, assigned to the Zoophycos ichnofacies. The increase in diversity is associated with higher abundance, larger forms, and a deeper and more complex tiering structure. Such rapid recovery suggests that favorable paleoenvironmental conditions were quickly reestablished within the impact basin, enabling colonization of the substrate. Comparison with the end-Permian extinction reveals similarities during recovery, yet postextinction recovery was significantly faster after the K-Pg event. The rapid recovery has significant implications for the evolution of macrobenthic biota after the K-Pg event. Our results have relevance in understanding how communities recovered after the K-Pg impact and how this event differed from other mass extinction events. 

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2. Shifts in trophic architecture and ecospace stability determining survivorship and extinction at the end-Cretaceous

   Chiarenza, Alfio Alessandro; García-Girón, Jorge; Alahuhta, Janne; DeMar, D. G.; Jani, Heino; Mannion, P. D.; Williamson, T. E.; Wilson Mantilla, G. P.; Brusatte, S. L. (November 2022, Journal of Vertebrate Paleontology)

   An explanation for why some species, such as non-avian dinosaurs, became extinct, whereas others, including mammals, survived the Cretaceous/Paleogene (K/Pg) mass extinction, 66 million years ago (Ma) is still debated. What were the mechanisms behind community restructuring and the emergence of new ecological opportunities after the K/Pg event, selectively driving extinction and survivorship patterns? Using Markov networks, ecological niche partitioning and Earth System models, we reconstructed disruptions in continental food web dynamics, simulating long-term trajectories in ecospace occupancy through the latest Cretaceous (83.6–66.0 Ma) and early Paleogene (66.0–61.6 Ma). This method uses partial correlation networks to represent how different trophic groups interact in a food web and builds on empirical spatial co-variations to explore dependencies between trophic groups. Our analyses are based on a spatiotemporally and taxonomically standardized dataset, comprising more than 1,600 fossil occurrences representing more than 470 genera of fish, salamanders, frogs, albanerpetontids, lizards, snakes, champsosaurs, turtles, crocodylians, dinosaurs (including birds), and mammals across the best sampled region for this interval, the Western Interior of North America. We explicitly tested whether: 1) shifts in food web architecture underwent major restructuring before and after the K/Pg transition, including whether some trophic guilds were more prone to these shifts than others; and 2) any of these changes were associated with fluctuations in the realized niche space, helping to explain survivorship and extinction patterns at the boundary. We find a shift in latest Cretaceous dinosaur faunas, as medium-sized species counterbalanced a loss of large herbivores, but that dinosaur niches were otherwise resilient and static until the K/Pg boundary. Smaller terrestrial vertebrates, including mammals, followed a consistent trajectory of increasing trophic impact and relaxation of ecological niche limits that began in the Cretaceous and continued after the extinction. Patterns of mammalian ecological radiation and niche restructuring indicate that these taxa did not simply proliferate after the extinction; rather, their earlier ecological diversification might have helped them survive the K/Pg event, whereas the static niche of dinosaurs might have contributed to their demise. 

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3. Small mammals in a large tree: examining the timing of the early therian radiation using a novel phylogenetic metatree; Journal of Vertebrate Paleontology, Program and Abstracts, 2023

   Grossnickle, D; Hellert, S; Ely, R; Slater, G; Lloyd, G; Angielczyk, K_D; Bormet, A; Wilson_Mantilla, G (October 2023, Society of Vertebrate Paleontology)

   Mammals achieved considerably greater ecological diversity in the Cenozoic compared to the Mesozoic. However, there remains uncertainty about the origins of this rise in diversity, such as whether it was triggered by novel ecological opportunities following the Cretaceous-Paleogene (K-Pg) mass extinction event 66 Ma. To test hypotheses on the timing of the mammalian radiation, studies commonly rely on analyses of fossil-only datasets, which often ignore the influence of phylogeny, or analyses of extant- only datasets, which struggle to recreate macroevolutionary patterns in deep time. Thus, an integrative approach is needed that incorporates paleontological data, neontological data, and phylogenetic comparative methods. To this end, we generated a time-calibrated meta-phylogeny(‘metatree’) comprising over 3000 species of trechnotherians (therians and close relatives) from the Mesozoic and Cenozoic, based on 115 published character matrices and a molecular phylogeny of extant mammals. To quantify ecomorphological patterns, we collected jaw lengths (as a proxy for size) and jaw measurements that correlate with diet for 430 extinct and extant species. We then fit a suite of evolutionary models to the data to test various hypotheses on the i) timing of the start of the therian radiation and ii) potential shift in mode of evolution. Although results are sensitive to time-calibration methods and phylogenetic uncertainty, they generally show evidence for a shift in mode of evolution prior to the K-Pg boundary. For both the jaw correlates of diet and body size analyses, results suggest a shift from a constrained (Ornstein-Uhlenbeck) or stochastic (Brownian motion) mode of evolution to an ‘early burst’ mode of evolution, with the best-fitting models being those that model this shift occurring between 76 and 66 Ma. These results suggest that the ecological diversification of therians began in the latest Cretaceous, prior to the K-Pg extinction event. However, our results are also congruent with the hypothesis that the therian radiation was a multiple-step process that involved bursts in diversification at multiple points in time, such as following both the Cretaceous Terrestrial Revolution (ca. 80 Ma) and the K-Pg extinction event. Further, we emphasize the importance of continued efforts to collect early mammal fossils and resolve relevant stratigraphic information, which will allow for more robust tests on the timing of the mammalian radiation. 

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4. A genomic timescale for placental mammal evolution

   https://doi.org/10.1126/science.abl8189  

   Foley, Nicole M.; Mason, Victor C.; Harris, Andrew J.; Bredemeyer, Kevin R.; Damas, Joana; Lewin, Harris A.; Eizirik, Eduardo; Gatesy, John; Karlsson, Elinor K.; Lindblad-Toh, Kerstin; et al (April 2023, Science)

   INTRODUCTION Resolving the role that different environmental forces may have played in the apparent explosive diversification of modern placental mammals is crucial to understanding the evolutionary context of their living and extinct morphological and genomic diversity. RATIONALE Limited access to whole-genome sequence alignments that sample living mammalian biodiversity has hampered phylogenomic inference, which until now has been limited to relatively small, highly constrained sequence matrices often representing <2% of a typical mammalian genome. To eliminate this sampling bias, we used an alignment of 241 whole genomes to comprehensively identify and rigorously analyze noncoding, neutrally evolving sequence variation in coalescent and concatenation-based phylogenetic frameworks. These analyses were followed by validation with multiple classes of phylogenetically informative structural variation. This approach enabled the generation of a robust time tree for placental mammals that evaluated age variation across hundreds of genomic loci that are not restricted by protein coding annotations. RESULTS Coalescent and concatenation phylogenies inferred from multiple treatments of the data were highly congruent, including support for higher-level taxonomic groupings that unite primates+colugos with treeshrews (Euarchonta), bats+cetartiodactyls+perissodactyls+carnivorans+pangolins (Scrotifera), all scrotiferans excluding bats (Fereuungulata), and carnivorans+pangolins with perissodactyls (Zooamata). However, because these approaches infer a single best tree, they mask signatures of phylogenetic conflict that result from incomplete lineage sorting and historical hybridization. Accordingly, we also inferred phylogenies from thousands of noncoding loci distributed across chromosomes with historically contrasting recombination rates. Throughout the radiation of modern orders (such as rodents, primates, bats, and carnivores), we observed notable differences between locus trees inferred from the autosomes and the X chromosome, a pattern typical of speciation with gene flow. We show that in many cases, previously controversial phylogenetic relationships can be reconciled by examining the distribution of conflicting phylogenetic signals along chromosomes with variable historical recombination rates. Lineage divergence time estimates were notably uniform across genomic loci and robust to extensive sensitivity analyses in which the underlying data, fossil constraints, and clock models were varied. The earliest branching events in the placental phylogeny coincide with the breakup of continental landmasses and rising sea levels in the Late Cretaceous. This signature of allopatric speciation is congruent with the low genomic conflict inferred for most superordinal relationships. By contrast, we observed a second pulse of diversification immediately after the Cretaceous-Paleogene (K-Pg) extinction event superimposed on an episode of rapid land emergence. Greater geographic continuity coupled with tumultuous climatic changes and increased ecological landscape at this time provided enhanced opportunities for mammalian diversification, as depicted in the fossil record. These observations dovetail with increased phylogenetic conflict observed within clades that diversified in the Cenozoic. CONCLUSION Our genome-wide analysis of multiple classes of sequence variation provides the most comprehensive assessment of placental mammal phylogeny, resolves controversial relationships, and clarifies the timing of mammalian diversification. We propose that the combination of Cretaceous continental fragmentation and lineage isolation, followed by the direct and indirect effects of the K-Pg extinction at a time of rapid land emergence, synergistically contributed to the accelerated diversification rate of placental mammals during the early Cenozoic. The timing of placental mammal evolution. Superordinal mammalian diversification took place in the Cretaceous during periods of continental fragmentation and sea level rise with little phylogenomic discordance (pie charts: left, autosomes; right, X chromosome), which is consistent with allopatric speciation. By contrast, the Paleogene hosted intraordinal diversification in the aftermath of the K-Pg mass extinction event, when clades exhibited higher phylogenomic discordance consistent with speciation with gene flow and incomplete lineage sorting. 

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5. The end-Cretaceous plant extinction: Heterogeneity, ecosystem transformation, and insights for the future

   https://doi.org/10.1017/ext.2023.13  

   Wilf, Peter; Carvalho, Mónica R; Stiles, Elena (January 2023, Cambridge Prisms: Extinction)

   Abstract The Cretaceous–Paleogene (K–Pg) mass extinction was geologically instantaneous, causing the most drastic extinction rates in Earth’s History. The rapid species losses and environmental destruction from the Chicxulub impact at 66.02 Ma made the K–Pg the most comparable past event to today’s projected “sixth” mass extinction. The extinction famously eliminated major clades of animals and plankton. However, for land plants, losses primarily occurred among species observed in regional studies but left no global trace at the family or major-clade level, leading to questions about whether there was a significant K–Pg plant extinction. We review emerging paleobotanical data from the Americas and argue that the evidence strongly favors profound (generally >50%), geographically heterogeneous species losses and recovery consistent with mass extinction. The heterogeneity appears to reflect several factors, including distance from the impact site and marine and latitudinal buffering of the impact winter. The ensuing transformations have affected all land life, including true angiosperm dominance in the world’s forests, the birth of the hyperdiverse Neotropical rainforest biome, and evolutionary radiations leading to many crown angiosperm clades. Although the worst outcomes are still preventable, the sixth mass extinction could mirror the K–Pg event by eliminating comparable numbers of plant species in a geologic instant, impoverishing and eventually transforming terrestrial ecosystems while having little effect on global plant-family diversity. 

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