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Reduced representation sequencing for symbiotic anthozoans: are reference genomes necessary to eliminate endosymbiont contamination and make robust phylogeographic inference?

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Specialist and generalist symbionts show counterintuitive levels of genetic diversity and discordant demographic histories along the Florida Reef Tract

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Population connectivity of the plating coral Agaricia lamarcki from southwest Puerto Rico

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Draft Assembly of the Symbiodinium minutum Nuclear Genome Reveals Dinoflagellate Gene Structure

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Empty Niches after Extinctions Increase Population Sizes of Modern Corals

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Systematic Revision of Symbiodiniaceae Highlights the Antiquity and Diversity of Coral Endosymbionts

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Reef fishes use sea anemones as visual cues for cleaning interactions with shrimp

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Giant ephemeral anemones? Rapid growth and high mortality of corkscrew sea anemones Bartholomea annulata (Le Sueur, 1817) under variable conditions

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Adaptation from standing genetic variation

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The origins of tropical marine biodiversity

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Applications of next-generation sequencing to phylogeography and phylogenetics

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Trans-Pacific RAD-Seq population genomics confirms introgressive hybridization in Eastern Pacific Pocillopora corals

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Elucidating the evolutionary relationships of the Aiptasiidae, a widespread cnidarian–dinoflagellate model system (Cnidaria: Anthozoa: Actiniaria: Metridioidea)

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Coral hybridization or phenotypic variation? Genomic data reveal gene flow between Porites lobata and P. Compressa

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Patterns of cleaning behaviour on coral reef fish by the anemoneshrimpAncylomenes pedersoni

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Global warming and recurrent mass bleaching of corals

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Gene expression plasticity as a mechanism of coral adaptation to a variable environment

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A genomic glance through the fog of plasticity and diversification in Pocillopora

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Comparative analysis of the genomes of Stylophora pistillata and Acropora digitifera provides evidence for extensive differences between species of corals

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Symbiodinium genomes reveal adaptive evolution of functions related to coral-dinoflagellate symbiosis

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Genome-wide SNP analysis explains coral diversity and recovery in the Ryukyu Archipelago

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Genomes of coral dinoflagellate symbionts highlight evolutionary adaptations conducive to a symbiotic lifestyle

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Slow mitochondrial DNA sequence evolution in the Anthozoa (Cnidaria)

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The genome of Aiptasia , a sea anemone model for coral symbiosis

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Comparative phylogeography of the ocean planet

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In the light of evolution X: Comparative phylogeography

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Ribosomal RNA sequences and the diversity of symbiotic dinoflagellates (zooxanthellae).

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PyRAD: assembly of de novo RADseq loci for phylogenetic analyses

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Endemic diversification in an isolated archipelago with few endemics: an example from a cleaner shrimp species complex in the Tropical Western Atlantic

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A genetic discontinuity in a continuously distributed species: mitochondrial DNA in the American oyster, Crassostrea virginica.

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Inference of Population Structure Using Multilocus Genotype Data

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The Physiological Mechanisms of Acclimatization in Tropical Reef Corals

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Phylogeography: The History and Formation of Species

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Phylogenetic Signal in Mitochondrial and Nuclear Markers in Sea Anemones (Cnidaria, Actiniaria)

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Large Variation in the Ratio of Mitochondrial to Nuclear Mutation Rate across Animals: Implications for Genetic Diversity and the Use of Mitochondrial DNA as a Molecular Marker

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The Promises and Pitfalls of Next-Generation Sequencing Data in Phylogeography

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Unforeseen Consequences of Excluding Missing Data from Next-Generation Sequences: Simulation Study of RAD Sequences

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Comparative behavioural observations demonstrate the ‘cleaner’ shrimp Periclimenes yucatanicus engages in true symbiotic cleaning interactions

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Specificity is rarely absolute in coral–algal symbiosis: implications for coral response to climate change

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Phylogenomics provides new insight into evolutionary relationships and genealogical discordance in the reef-building coral genusAcropora

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Draft genomes of the corallimorpharians Amplexidiscus fenestrafer and Discosoma sp.

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Restricted gene flow and local adaptation highlight the vulnerability of high‐latitude reefs to rapid environmental change

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Functional genomic analysis of corals from natural CO 2 ‐seeps reveals core molecular responses involved in acclimatization to ocean acidification

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Contrasting abundance and contribution of clonal proliferation to the population structure of the corkscrew sea anemone Bartholomea annulata in the tropical Western Atlantic

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Phylogeography: retrospect and prospect

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Regionally isolated populations of an imperiled Caribbean coral, Acropora palmata

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Detecting the number of clusters of individuals using the software structure : a simulation study

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Connectivity of Caribbean coral populations: complementary insights from empirical and modelled gene flow

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genalex 6: genetic analysis in Excel. Population genetic software for teaching and research

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GLOBAL POPULATION STRUCTURE AND NATURAL HISTORY OF THE GREEN TURTLE ( CHELONIA MYDAS ) IN TERMS OF MATRIARCHAL PHYLOGENY

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GLOBAL PHYLOGEOGRAPHY OF THE LOGGERHEAD TURTLE ( CARETTA CARETTA ) AS INDICATED BY MITOCHONDRIAL DNA HAPLOTYPES

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Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows

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Shifting seas: the impacts of Pleistocene sea‐level fluctuations on the evolution of tropical marine taxa

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Shared phylogeographical breaks in a Caribbean coral reef sponge and its invertebrate commensals

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Range‐wide population genetic structure of the C aribbean sea fan coral, G orgonia ventalina

inferredcites →https://doi.org/10.1111/mec.12276openalex-snapshot

RAD seq underestimates diversity and introduces genealogical biases due to nonrandom haplotype sampling

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How to fail at species delimitation

inferredcites →https://doi.org/10.1111/mec.12722openalex-snapshot

Model choice for phylogeographic inference using a large set of models

inferredcites →https://doi.org/10.1111/mec.13048openalex-snapshot

Species are hypotheses: avoid connectivity assessments based on pillars of sand

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Do ecological communities disperse across biogeographic barriers as a unit?

inferredcites →https://doi.org/10.1111/mec.14223openalex-snapshot

Demographic model selection using random forests and the site frequency spectrum

inferredcites →https://doi.org/10.1111/mec.14702openalex-snapshot

Host‐targeted RAD ‐Seq reveals genetic changes in the coral Oculina patagonica associated with range expansion along the Spanish Mediterranean coast

inferredcites →https://doi.org/10.1111/mec.15157openalex-snapshot

Genomic signatures of sympatric speciation with historical and contemporary gene flow in a tropical anthozoan (Hexacorallia: Actiniaria)

inferredcites →https://doi.org/10.1126/sciadv.1602373openalex-snapshot

Deep reefs are not universal refuges: Reseeding potential varies among coral species

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Sea Anemone Genome Reveals Ancestral Eumetazoan Gene Repertoire and Genomic Organization

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Mechanisms of reef coral resistance to future climate change

inferredcites →https://doi.org/10.1126/science.251.4999.1348openalex-snapshot

A Molecular Genetic Classification of Zooxanthellae and the Evolution of Animal-Algal Symbioses

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The genomic landscape of rapid repeated evolutionary adaptation to toxic pollution in wild fish

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Cell Biology of Cnidarian-Dinoflagellate Symbiosis

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Reproduction in three species of sea anemones from Key West, Florida

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Flexibility and Specificity in Coral-Algal Symbiosis: Diversity, Ecology, and Biogeography of Symbiodinium

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Statistical Phylogeography

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Morphological revision of the genus Aiptasia and the family Aiptasiidae (Cnidaria, Actiniaria, Metridioidea)

inferredcites →https://doi.org/10.1186/1471-2105-10-421openalex-snapshot

BLAST+: architecture and applications

inferredcites →https://doi.org/10.1371/journal.pgen.1003905openalex-snapshot

Robust Demographic Inference from Genomic and SNP Data

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Do Reef Fish Habituate to Diver Presence? Evidence from Two Reef Sites with Contrasting Historical Levels of SCUBA Intensity in the Bay Islands, Honduras

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THE SIGNATURE OF POSITIVE SELECTION ON STANDING GENETIC VARIATION

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Phylogeography: The History and Formation of Species

inferredcites →https://doi.org/10.2307/2409742openalex-snapshot

Global Population Structure and Natural History of the Green Turtle (Chelonia mydas) in Terms of Matriarchal Phylogeny

inferredcites →https://doi.org/10.2307/2410511openalex-snapshot

Global Phylogeography of the Loggerhead Turtle (Caretta caretta) as Indicated by Mitochondrial DNA Haplotypes

inferredcites →https://doi.org/10.2307/3802723openalex-snapshot

Model Selection and Multimodel Inference: A Practical Information-Theoretic Approach

inferredcites →https://doi.org/10.3354/meps10030openalex-snapshot

Ecological traits of Caribbean sea anemones and symbiotic crustaceans

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Population dynamics of corkscrew sea anemones Bartholomea annulata in the Florida Keys

inferredcites →https://doi.org/10.3389/fmars.2016.00112openalex-snapshot

Thermal and pCO2 Stress Elicit Divergent Transcriptomic Responses in a Resilient Coral

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Estimating the daily contribution of carbon from zooxanthellae to coral animal respiration1

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Phylogeography unplugged: comparative surveys in the genomic era

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Genome-wide survey of single-nucleotide polymorphisms reveals fine-scale population structure and signs of selection in the threatened Caribbean elkhorn coral, Acropora palmata

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1016/j.ympev.2021.107233openalex-snapshot

Comparison of sequence-capture and ddRAD approaches in resolving species and populations in hexacorallian anthozoans

inferred← citeshttps://doi.org/10.1038/s41437-019-0266-3openalex-snapshot

The many faced symbiotic snakelocks anemone (Anemonia viridis, Anthozoa): host and symbiont genetic differentiation among colour morphs

inferred← citeshttps://doi.org/10.1101/2020.09.04.282673openalex-snapshot

Microbiomes and host genetics provide evidence for ecological diversification among Caribbean members of the sponge genus Ircinia Nardo, 1833

inferred← citeshttps://doi.org/10.1101/523936openalex-snapshot

A next generation approach to species delimitation reveals the role of hybridization in a cryptic species complex of corals

inferred← citeshttps://doi.org/10.1186/s12862-019-1427-yopenalex-snapshot

A next generation approach to species delimitation reveals the role of hybridization in a cryptic species complex of corals

inferred← citeshttps://doi.org/10.3390/d17030173openalex-snapshot

Uncovering the Evolutionary History in Lineage of Caribbean Octocorals: Phylogenomics Reveals Unrecognized Diversity in Eunicea

inferred← citeshttps://doi.org/10.70675/f3111967z3a61z40b0z9bb2z880e97578bbbopenalex-snapshot

Diversités génétiques chez l’holobiote Anemonia viridis : des morphotypes de l’hôte à la différenciation symbiotique

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