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1. New results on orbital resonances

   https://doi.org/10.48550/arXiv.2111.09289  

   Malhotra, Renu (September 2022, Proceedings of the International Astronomical Union)

   Celletti, Alessandra; Beaugé, Cristian; Galeş, Cătălin; Lemaître, Anne (Ed.)

   Perturbative analyses of planetary resonances commonly predict singularities and/or divergences of resonance widths at very low and very high eccentricities. We have recently re-examined the nature of these divergences using non-perturbative numerical analyses, making use of Poincaré sections but from a different perspective relative to previous implementations of this method. This perspective reveals fine structure of resonances which otherwise remains hidden in conventional approaches, including analytical, semi-analytical and numerical-averaging approaches based on the critical resonant angle. At low eccentricity, first order resonances do not have diverging widths but have two asymmetric branches leading away from the nominal resonance location. A sequence of structures called ``low-eccentricity resonant bridges" connecting neighboring resonances is revealed. At planet-grazing eccentricity, the true resonance width is non-divergent. At higher eccentricities, the new results reveal hitherto unknown resonant structures and show that these parameter regions have a loss of some -- though not necessarily entire -- resonance libration zones to chaos. The chaos at high eccentricities was previously attributed to the overlap of neighboring resonances. The new results reveal the additional role of bifurcations and co-existence of phase-shifted resonance zones at higher eccentricities. By employing a geometric point of view, we relate the high eccentricity phase space structures and their transitions to the shapes of resonant orbits in the rotating frame. We outline some directions for future research to advance understanding of the dynamics of mean motion resonances. 

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2. Deconstructing the Gestalt: New concepts and tests of homology, as exemplified by a re‐conceptualization of “microstomy” in squamates

   https://doi.org/10.1002/ar.24630  

   Strong, Catherine_R_C; Scherz, Mark_D; Caldwell, Michael_W (April 2021, The Anatomical Record)

   Abstract Snakes—a subset of lizards—have traditionally been divided into two major groups based on feeding mechanics: “macrostomy,” involving the ingestion of proportionally large prey items; and “microstomy,” the lack of this ability. “Microstomy”—considered present in scolecophidian and early‐diverging alethinophidian snakes—is generally viewed as a symplesiomorphy shared with non‐snake lizards. However, this perspective of “microstomy” as plesiomorphic and morphologically homogenous fails to recognize the complexity of this condition and its evolution across “microstomatan” squamates. To challenge this problematic paradigm, we formalize a new framework for conceptualizing and testing the homology of overall character complexes, or “morphotypes,” which underlies our re‐assessment of “microstomy.” Using micro‐computed tomography (micro‐CT) scans, we analyze the morphology of the jaws and suspensorium across purported “microstomatan” squamates (scolecophidians, early‐diverging alethinophidians, and non‐snake lizards) and demonstrate that key components of the jaw complex are not homologous at the level of primary character state identity across these taxa. Therefore, rather than treating “microstomy” as a uniform condition, we instead propose that non‐snake lizards, early‐diverging alethinophidians, anomalepidids, leptotyphlopids, and typhlopoids each exhibit a unique and nonhomologous jaw morphotype: “minimal‐kinesis microstomy,” “snout‐shifting,” “axle‐brace maxillary raking,” “mandibular raking,” and “single‐axle maxillary raking,” respectively. The lack of synapomorphy among scolecophidians is inconsistent with the notion of scolecophidians representing an ancestral snake condition, and instead reflects a hypothesis of the independent evolution of fossoriality, miniaturization, and “microstomy” in each scolecophidian lineage. We ultimately emphasize that a rigorous approach to comparative anatomy is necessary in constructing evolutionary hypotheses that accurately reflect biological reality. 

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3. The Evolution of euAPETALA2 Genes in Vascular Plants: From Plesiomorphic Roles in Sporangia to Acquired Functions in Ovules and Fruits

   https://doi.org/10.1093/molbev/msab027  

   Zumajo-Cardona, Cecilia; Pabón-Mora, Natalia; Ambrose, Barbara A (February 2021, Molecular Biology and Evolution)

   Purugganan, Michael (Ed.)

   Abstract The field of evolutionary developmental biology can help address how morphological novelties evolve, a key question in evolutionary biology. In Arabidopsis thaliana, APETALA2 (AP2) plays a role in the development of key plant innovations including seeds, flowers, and fruits. AP2 belongs to the AP2/ETHYLENE RESPONSIVE ELEMENT BINDING FACTOR family which has members in all viridiplantae, making it one of the oldest and most diverse gene lineages. One key subclade, present across vascular plants is the euAPETALA2 (euAP2) clade, whose founding member is AP2. We reconstructed the evolution of the euAP2 gene lineage in vascular plants to better understand its impact on the morphological evolution of plants, identifying seven major duplication events. We also performed spatiotemporal expression analyses of euAP2/TOE3 genes focusing on less explored vascular plant lineages, including ferns, gymnosperms, early diverging angiosperms and early diverging eudicots. Altogether, our data suggest that euAP2 genes originally contributed to spore and sporangium development, and were subsequently recruited to ovule, fruit and floral organ development. Finally, euAP2 protein sequences are highly conserved; therefore, changes in the role of euAP2 homologs during development are most likely due to changes in regulatory regions. 

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4. Stress-Free Evolution: The Nrf-Coordinated Oxidative Stress Response in Early Diverging Metazoans

   https://doi.org/10.1093/icb/icz055  

   Doonan, Liam B; Hartigan, Ashlie; Okamura, Beth; Long, Paul F (May 2019, Integrative and Comparative Biology)

   Abstract Environmental stress from ultraviolet radiation, elevated temperatures or metal toxicity can lead to reactive oxygen species in cells, leading to oxidative DNA damage, premature aging, neurodegenerative diseases, and cancer. The transcription factor nuclear factor (erythroid-derived 2)-like 2 (Nrf2) activates many cytoprotective proteins within the nucleus to maintain homeostasis during oxidative stress. In vertebrates, Nrf2 levels are regulated by the Kelch-family protein Keap1 (Kelch-like ECH-associated protein 1) in the absence of stress according to a canonical redox control pathway. Little, however, is known about the redox control pathway used in early diverging metazoans. Our study examines the presence of known oxidative stress regulatory elements within non-bilaterian metazoans including free living and parasitic cnidarians, ctenophores, placozoans, and sponges. Cnidarians, with their pivotal position as the sister phylum to bilaterians, play an important role in understanding the evolutionary history of response to oxidative stress. Through comparative genomic and transcriptomic analysis our results show that Nrf homologs evolved early in metazoans, whereas Keap1 appeared later in the last common ancestor of cnidarians and bilaterians. However, key Nrf–Keap1 interacting domains are not conserved within the cnidarian lineage, suggesting this important pathway evolved with the radiation of bilaterians. Several known downstream Nrf targets are present in cnidarians suggesting that cnidarian Nrf plays an important role in oxidative stress response even in the absence of Keap1. Comparative analyses of key oxidative stress sensing and response proteins in early diverging metazoans thus provide important insights into the molecular basis of how these lineages interact with their environment and suggest a shared evolutionary history of regulatory pathways. Exploration of these pathways may prove important for the study of cancer therapeutics and broader research in oxidative stress, senescence, and the functional responses of early diverging metazoans to environmental change. 

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5. Early-diverging fungal phyla: taxonomy, species concept, ecology, distribution, anthropogenic impact, and novel phylogenetic proposals

   https://doi.org/10.1007/s13225-021-00480-y  

   Voigt, Kerstin; James, Timothy Y.; Kirk, Paul M.; Santiago, André L.; Waldman, Bruce; Griffith, Gareth W.; Fu, Minjie; Radek, Renate; Strassert, Jürgen F.; Wurzbacher, Christian; et al (July 2021, Fungal Diversity)

   Abstract The increasing number of new fungal species described from all over the world along with the use of genetics to define taxa, has dramatically changed the classification system of early-diverging fungi over the past several decades. The number of phyla established for non-Dikarya fungi has increased from 2 to 17. However, to date, both the classification and phylogeny of the basal fungi are still unresolved. In this article, we review the recent taxonomy of the basal fungi and re-evaluate the relationships among early-diverging lineages of fungal phyla. We also provide information on the ecology and distribution in  Mucoromycota and highlight the impact of chytrids on amphibian populations. Species concepts in Chytridiomycota , Aphelidiomycota , Rozellomycota , Neocallimastigomycota are discussed in this paper. To preserve the current application of the genus Nephridiophaga ( Chytridiomycota : Nephridiophagales ) , a new type species, Nephridiophaga blattellae , is proposed. 

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