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1. Quantifying the effects of exceptional fossil preservation on the global availability of phylogenetic data in deep time

   https://doi.org/10.1371/journal.pone.0297637  

   Woolley, C Henrik; Bottjer, David J; Corsetti, Frank A; Smith, Nathan D (February 2024, PLOS ONE)

   Dececchi, T Alexander (Ed.)

   Fossil deposits with exceptional preservation (“lagerstätten”) provide important details not typically preserved in the fossil record, such that they hold an outsized influence on our understanding of biodiversity and evolution. In particular, the potential bias imparted by this so-called “lagerstätten effect” remains a critical, but underexplored aspect of reconstructing evolutionary relationships. Here, we quantify the amount of phylogenetic information available in the global fossil records of 1,327 species of non-avian theropod dinosaurs, Mesozoic birds, and fossil squamates (e.g., lizards, snakes, mosasaurs), and then compare the influence of lagerstätten deposits on phylogenetic information content and taxon selection in phylogenetic analyses to other fossil-bearing deposits. We find that groups that preserve a high amount of phylogenetic information in their global fossil record (e.g., non-avian theropods) are less vulnerable to a “lagerstätten effect” that leads to disproportionate representation of fossil taxa from one geologic unit in an evolutionary tree. Additionally, for each taxonomic group, we find comparable amounts of phylogenetic information in lagerstätten deposits, even though corresponding morphological character datasets vary greatly. Finally, we unexpectedly find that ancient sand dune deposits of the Late Cretaceous Gobi Desert of Mongolia and China exert an anomalously large influence on the phylogenetic information available in the squamate fossil record, suggesting a “lagerstätten effect” can be present in units not traditionally considered lagerstätten. These results offer a phylogenetics-based lens through which to examine the effects of exceptional fossil preservation on biological patterns through time and space, and invites further quantification of evolutionary information in the rock record. 

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2. An Enigmatic Miniaturized and Attenuate Whole Lizard from the Mid-Cretaceous Amber of Myanmar

   https://doi.org/doi.org/10.3099/MCZ49.1  

   DAZA, JD; BAUER, AM; STANLEY, EL; BOLET, A; DICKSON, B; LOSOS, JB (November 2018, Breviora)

   We report the discovery of a new genus and species of amber-preserved lizard from the mid-Cretaceous of Myanmar. The fossil is one of the smallest and most complete Cretaceous lizards ever found, preserving both the articulated skeleton and remains of the muscular system and other soft tissues. Despite its completeness, its state of preservation obscures important diagnostic features.We determined its taxonomic allocation using two approaches: we used previously identified autapomorphies of squamates that were observable in the fossil; and we included the fossil in a large squamate morphological data set. The apomorphy-based identification of this specimen, including comparative data on trunk elongation in squamates, suggests its allocation to the stem-group Anguimorpha. Results from the phylogenetic analysis places the fossil in one of four positions: as sister taxon of either Shinisaurus crocodilurus or Parasaniwa wyomingensis, at the root of Varanoidea, or in a polytomy with Varanoidea and a fossorial group retrieved in a previous assessment of squamate relationships. It is clear that this fossil has many similarities with anguimorph squamates and, if this taxonomic allocation is correct, this fossil would represent the first amber-preserved member of stem Anguimorpha ever recorded, and the smallest known member of that group. It further emphasizes the role of amber inclusions in expanding our understanding of the diversity of Cretaceous lizard communities. 

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3. The oldest dairoidid crab (Decapoda, Brachyura, Parthenopoidea) from the Eocene of Spain

   https://doi.org/10.1002/spp2.1494  

   Ferratges, Fernando_A; Luque, Javier; Domínguez, José_Luis; Ossó, Àlex; Aurell, Marcos; Zamora, Samuel (June 2023, Papers in Palaeontology)

   Abstract Eubrachyurans, or ‘higher’ true crabs, are the most speciose group of decapod crustaceans and have a rich fossil record extending into the Early Cretaceous. However, most extant families are first found in the fossil record in the Palaeogene, and particularly in the Eocene. Unfortunately, fossils of many early eubrachyuran groups are often fragmentary, and only a few studies have combined extinct and extant taxa in a phylogenetic context using different optimality criteria. Here, we report the dairoidid crabPhrynolambrus sagittalissp. nov., an enigmatic eubrachyuran from the upper Eocene of Huesca (northern Spain), whose completeness and exquisite preservation permit examination of its anatomy in a phylogenetic context. Dairoidids have previously been considered among the oldest stone crabs (Eriphioidea) or elbow crabs (Parthenopoidea), two disparate and distantly related groups of true crabs living today. Mechanical preparation and computed tomography of the fossil material revealed several diagnostic features that allow a detailed comparison with families across the crab tree of life, and test hypotheses about its phylogenetic affinities.Phrynolambrus sagittalisis the first record of the genus in the Iberian Peninsula, and represents one of the oldest crown parthenopoidean crabs worldwide, expanding our knowledge of the biogeographical distribution of elbow crabs during the Palaeogene, as well as their early origins, anatomical diversity and systematic affinities. Understanding the disparity of Eocene eubrachyurans is pivotal to disentangling the systematic relationships among crown families, and interpreting the spatio‐temporal patterns leading to the evolution of modern faunas. 

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4. Fossil fern rhizomes as a model system for exploring epiphyte community structure across geologic time: evidence from Patagonia

   https://doi.org/10.7717/peerj.8244  

   Bippus, Alexander C.; Escapa, Ignacio H.; Wilf, Peter; Tomescu, Alexandru M. F. (December 2019, PeerJ)

   BackgroundIn extant ecosystems, complex networks of ecological interactions between organisms can be readily studied. In contrast, understanding of such interactions in ecosystems of the geologic past is incomplete. Specifically, in past terrestrial ecosystems we know comparatively little about plant biotic interactions besides saprotrophy, herbivory, mycorrhizal associations, and oviposition. Due to taphonomic biases, epiphyte communities are particularly rare in the plant-fossil record, despite their prominence in modern ecosystems. Accordingly, little is known about how terrestrial epiphyte communities have changed across geologic time. Here, we describe a tinyin situfossil epiphyte community that sheds light on plant-animal and plant-plant interactions more than 50 million years ago. MethodsA single silicifiedTodea(Osmundaceae) rhizome from a new locality of the early Eocene (ca. 52 Ma) Tufolitas Laguna del Hunco (Patagonia, Argentina) was studied in serial thin sections using light microscopy. The community of organisms colonizing the tissues of the rhizome was characterized by identifying the organisms and mapping and quantifying their distribution. A 200 × 200 µm grid was superimposed onto the rhizome cross section, and the colonizers present at each node of the grid were tallied. ResultsPreservedin situ, this community offers a rare window onto aspects of ancient ecosystems usually lost to time and taphonomic processes. The community is surprisingly diverse and includes the first fossilized leafy liverworts in South America, also marking the only fossil record of leafy bryophyte epiphytes outside of amber deposits; as well as several types of fungal hyphae and spores; microsclerotia with possible affinities in several ascomycete families; and evidence for oribatid mites. DiscussionThe community associated with the Patagonian rhizome enriches our understanding of terrestrial epiphyte communities in the distant past and adds to a growing body of literature on osmundaceous rhizomes as important hosts for component communities in ancient ecosystems, just as they are today. Because osmundaceous rhizomes represent an ecological niche that has remained virtually unchanged over time and space and are abundant in the fossil record, they provide a paleoecological model system that could be used to explore epiphyte community structure through time. 

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5. Estimating the Age of Poorly Dated Fossil Specimens and Deposits Using a Total-Evidence Approach and the Fossilized Birth-Death Process

   https://doi.org/10.1093/sysbio/syac073  

   Barido-Sottani, Joëlle; Żyła, Dagmara; Heath, Tracy A.; Matschiner, ed., Michael (November 2022, Systematic Biology)

   Abstract Bayesian total-evidence approaches under the fossilized birth-death model enable biologists to combine fossil and extant data while accounting for uncertainty in the ages of fossil specimens, in an integrative phylogenetic analysis. Fossil age uncertainty is a key feature of the fossil record as many empirical data sets may contain a mix of precisely dated and poorly dated fossil specimens or deposits. In this study, we explore whether reliable age estimates for fossil specimens can be obtained from Bayesian total-evidence phylogenetic analyses under the fossilized birth-death model. Through simulations based on the example of the Baltic amber deposit, we show that estimates of fossil ages obtained through such an analysis are accurate, particularly when the proportion of poorly dated specimens remains low and the majority of fossil specimens have precise dates. We confirm our results using an empirical data set of living and fossil penguins by artificially increasing the age uncertainty around some fossil specimens and showing that the resulting age estimates overlap with the recorded age ranges. Our results are applicable to many empirical data sets where classical methods of establishing fossil ages have failed, such as the Baltic amber and the Gobi Desert deposits. [Bayesian phylogenetic inference; fossil age estimates; fossilized birth-death; Lagerstätte; total-evidence.] 

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