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      Bathymetric evolution of black corals through deep time

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          Abstract

          Deep-sea lineages are generally thought to arise from shallow-water ancestors, but this hypothesis is based on a relatively small number of taxonomic groups. Anthozoans, which include corals and sea anemones, are significant contributors to the faunal diversity of the deep sea, but the timing and mechanisms of their invasion into this biome remain elusive. Here, we reconstruct a fully resolved, time-calibrated phylogeny of 83 species in the order Antipatharia (black coral) to investigate their bathymetric evolutionary history. Our reconstruction indicates that extant black coral lineages first diversified in continental slope depths (∼250–3000 m) during the early Silurian (∼437 millions of years ago (Ma)) and subsequently radiated into, and diversified within, both continental shelf (less than 250 m) and abyssal (greater than 3000 m) habitats. Ancestral state reconstruction analysis suggests that the appearance of morphological features that enhanced the ability of black corals to acquire nutrients coincided with their invasion of novel depths. Our findings have important conservation implications for anthozoan lineages, as the loss of ‘source’ slope lineages could threaten millions of years of evolutionary history and confound future invasion events, thereby warranting protection.

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          ModelFinder: Fast Model Selection for Accurate Phylogenetic Estimates

          Model-based molecular phylogenetics plays an important role in comparisons of genomic data, and model selection is a key step in all such analyses. We present ModelFinder, a fast model-selection method that greatly improves the accuracy of phylogenetic estimates. The improvement is achieved by incorporating a model of rate-heterogeneity across sites not previously considered in this context, and by allowing concurrent searches of model-space and tree-space.
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            IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

            Abstract IQ-TREE (http://www.iqtree.org, last accessed February 6, 2020) is a user-friendly and widely used software package for phylogenetic inference using maximum likelihood. Since the release of version 1 in 2014, we have continuously expanded IQ-TREE to integrate a plethora of new models of sequence evolution and efficient computational approaches of phylogenetic inference to deal with genomic data. Here, we describe notable features of IQ-TREE version 2 and highlight the key advantages over other software.
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              Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7

              Abstract Bayesian inference of phylogeny using Markov chain Monte Carlo (MCMC) plays a central role in understanding evolutionary history from molecular sequence data. Visualizing and analyzing the MCMC-generated samples from the posterior distribution is a key step in any non-trivial Bayesian inference. We present the software package Tracer (version 1.7) for visualizing and analyzing the MCMC trace files generated through Bayesian phylogenetic inference. Tracer provides kernel density estimation, multivariate visualization, demographic trajectory reconstruction, conditional posterior distribution summary, and more. Tracer is open-source and available at http://beast.community/tracer.
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                Author and article information

                Contributors
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: InvestigationRole: MethodologyRole: Project administrationRole: Writing – original draftRole: Writing – review & editing
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: Project administrationRole: ResourcesRole: SupervisionRole: Writing – original draftRole: Writing – review & editing
                Role: ConceptualizationRole: InvestigationRole: MethodologyRole: Project administrationRole: SupervisionRole: Writing – original draftRole: Writing – review & editing
                Role: MethodologyRole: ResourcesRole: SupervisionRole: Writing – original draftRole: Writing – review & editing
                Role: Data curationRole: MethodologyRole: Project administrationRole: SupervisionRole: Writing – original draftRole: Writing – review & editing
                Role: ConceptualizationRole: Funding acquisitionRole: InvestigationRole: Project administrationRole: SupervisionRole: Writing – original draftRole: Writing – review & editing
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: Project administrationRole: SupervisionRole: Writing – original draftRole: Writing – review & editing
                Journal
                Proc Biol Sci
                Proc Biol Sci
                RSPB
                royprsb
                Proceedings of the Royal Society B: Biological Sciences
                The Royal Society
                0962-8452
                1471-2954
                October 4, 2023
                October 2023
                October 4, 2023
                : 290
                : 2008
                : 20231107
                Affiliations
                [ 1 ] Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, , 101 Angus Smith Drive, Townsville, Queensland 4811, Australia
                [ 2 ] Biodiversity and Geosciences Program, Museum of Tropical Queensland, Queensland Museum, , 70-102 Flinders street, Townsville, Queensland 4810, Australia
                [ 3 ] Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, , 10th street and Constitution avenue North West, Washington, DC 20560, USA
                [ 4 ] Department of Natural Sciences, University of South Carolina Beaufort, , 1100 Boundary Street, Beaufort, SC 29902, USA
                [ 5 ] Division of Invertebrate Zoology, American Museum of Natural History, , Central Park West at 79th Street, New York, NY 10024, USA
                [ 6 ] Centre for Tropical Bioinformatics and Molecular Biology, Molecular and Cell Biology, James Cook University, , 101 Angus Smith Drive, Townsville, Queensland 4811, Australia
                [ 7 ] College of Science and Engineering, James Cook University, , 101 Angus Smith Drive, Townsville, Queensland 4811, Australia
                Author notes

                Electronic supplementary material is available online at https://doi.org/10.6084/m9.figshare.c.6837183.

                Author information
                http://orcid.org/0000-0002-2643-5200
                http://orcid.org/0000-0003-3676-1226
                http://orcid.org/0000-0003-3951-284X
                Article
                rspb20231107
                10.1098/rspb.2023.1107
                10547549
                37788705
                c22fedd3-5fca-4802-b586-184f9772603d
                © 2023 The Authors.

                Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, provided the original author and source are credited.

                History
                : May 17, 2023
                : September 5, 2023
                Funding
                Funded by: ARC DECRA fellowships;
                Award ID: DE170100516
                Award ID: DE180100746
                Funded by: ARC Centre of Excellence Program;
                Award ID: CE140100020
                Funded by: Port Royal Sound Foundation;
                Categories
                1001
                70
                22
                198
                Evolution
                Research Articles

                Life sciences
                ultraconserved elements,antipatharia,shelf,slope,abyss,adaptations
                Life sciences
                ultraconserved elements, antipatharia, shelf, slope, abyss, adaptations

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