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Species delimitation in the presence of strong incomplete lineage sorting and hybridization: lessons from Ophioderma (Ophiuroidea: Echinodermata)

https://doi.org/10.1101/240218
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Outgoing claims: the papers this work cites, builds on, or argues with.

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DNA barcoding of reef brittle stars (Ophiuroidea, Echinodermata) from the southwestern Indian Ocean evolutionary hot spot of biodiversity
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Seasonal Variations in the Gonads ofOphioderma longicauda(RETZIUS), Ophiuroidea
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Ecological Parallelism and Cryptic Species in the GenusOphiothrixDerived from Mitochondrial DNA Sequences
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A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences
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Conservation implications of significant population differentiation in an endangered estuarine seahorse
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Thermotolerance and regeneration in the brittle star species complex Ophioderma longicauda: A preliminary study comparing lineages and Mediterranean basins
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Genetic data, reproduction season and reproductive strategy data support the existence of biological species in Ophioderma longicauda
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Phylogenomic Resolution of the Class Ophiuroidea Unlocks a Global Microfossil Record
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PCR survey of 50 introns in animals: Cross-amplification of homologous EPIC loci in eight non-bilaterian, protostome and deuterostome phyla
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ABC: A useful Bayesian tool for the analysis of population data
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Cryptic species as a window on diversity and conservation
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Approximate Bayesian Computation (ABC) in practice
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Coalescent-based species delimitation in an integrative taxonomy
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Finding Evolutionary Processes Hidden in Cryptic Species
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Antitropical distributions and species delimitation in a group of ophiocomid brittle stars (Echinodermata: Ophiuroidea: Ophiocomidae)
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Do genes lie? Mitochondrial capture masks the Red Sea collector urchin’s true identity (Echinodermata: Echinoidea: Tripneustes)
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Restructuring higher taxonomy using broad-scale phylogenomics: The living Ophiuroidea
inferredcites →https://doi.org/10.1017/s0025315409990749openalex-snapshot
Morphological diagnosis of the two genetic lineages ofAcrocnida brachiata(Echinodermata: Ophiuroidea), with description of a new species
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Brittle stars from the Saint Peter and Saint Paul Archipelago: morphological and molecular data
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Extensive mitochondrial introgression in North American Great Black-backed Gulls (Larus marinus) from the American Herring Gull (Larus smithsonianus) with little nuclear DNA impact
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Use of RAD sequencing for delimiting species
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Ancient hybridization fuels rapid cichlid fish adaptive radiations
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Genome-wide genetic marker discovery and genotyping using next-generation sequencing
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Contrasted phylogeographic patterns on mitochondrial DNA of shallow and deep brittle stars across the Atlantic-Mediterranean area
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Bayesian species delimitation using multilocus sequence data
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Multispecies coalescent delimits structure, not species
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Estimating Species Phylogeny from Gene-Tree Probabilities Despite Incomplete Lineage Sorting: An Example from Melanoplus Grasshoppers
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Species Concepts and Species Delimitation
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The Impact of Species Concept on Biodiversity Studies
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PGDSpider: an automated data conversion tool for connecting population genetics and genomics programs
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DIYABC v2.0: a software to make approximate Bayesian computation inferences about population history using single nucleotide polymorphism, DNA sequence and microsatellite data
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The art and science of species delimitation
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The BPP program for species tree estimation and species delimitation
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The Elusive Nature of Adaptive Mitochondrial DNA Evolution of an Arctic Lineage Prone to Frequent Introgression
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Inference of Population Structure Using Multilocus Genotype Data: Linked Loci and Correlated Allele Frequencies
inferredcites →https://doi.org/10.1093/jhered/esm119openalex-snapshot
Evaluating Connectivity in the Brooding Brittle Star Astrotoma agassizii across the Drake Passage in the Southern Ocean
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Molecular Species Identification of Astrotoma agassizii from Planktonic Embryos: Further Evidence for a Cryptic Species Complex
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Crossing the Species Barrier: Genomic Hotspots of Introgression between Two Highly Divergent Ciona intestinalis Species
inferredcites →https://doi.org/10.1093/molbev/msu279openalex-snapshot
Unguided Species Delimitation Using DNA Sequence Data from Multiple Loci
inferredcites →https://doi.org/10.1093/molbev/msv216openalex-snapshot
An Exon-Capture System for the Entire Class Ophiuroidea
inferredcites →https://doi.org/10.1093/molbev/msw054openalex-snapshot
MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a026036openalex-snapshot
Median-joining networks for inferring intraspecific phylogenies
inferredcites →https://doi.org/10.1093/sysbio/syr071openalex-snapshot
Evaluation of a Bayesian Coalescent Method of Species Delimitation
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Efficient Bayesian Species Tree Inference under the Multispecies Coalescent
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Bayesian Divergence-Time Estimation with Genome-Wide Single-Nucleotide Polymorphism Data of Sea Catfishes (Ariidae) Supports Miocene Closure of the Panamanian Isthmus
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Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species
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Targeted multiplex next‐generation sequencing: advances in techniques of mitochondrial and nuclear DNA sequencing for population genomics
inferredcites →https://doi.org/10.1111/ivb.12081openalex-snapshot
Brooding behavior in the shallow‐water brittle star Ophioderma wahlbergii
inferredcites →https://doi.org/10.1111/j.0014-3820.2002.tb00121.xopenalex-snapshot
PHYLOGEOGRAPHIC ANALYSIS OF THE BROODING BRITTLE STAR AMPHIPHOLIS SQUAMATA (ECHINODERMATA) ALONG THE COAST OF NEW ZEALAND REVEALS HIGH CRYPTIC GENETIC VARIATION AND CRYPTIC DISPERSAL POTENTIAL
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Incomplete cryptic speciation between intertidal and subtidal morphs of Acrocnida brachiata (Echinodermata: Ophiuroidea) in the Northeast Atlantic
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Defining reproductively isolated units in a cryptic and syntopic species complex using mitochondrial and nuclear markers: the brooding brittle star, Amphipholis squamata (Ophiuroidea)
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ABGD, Automatic Barcode Gap Discovery for primary species delimitation
inferredcites →https://doi.org/10.1111/j.1365-294x.2011.05309.xopenalex-snapshot
Did vicariance and adaptation drive cryptic speciation and evolution of brooding in Ophioderma longicauda (Echinodermata: Ophiuroidea), a common Atlanto-Mediterranean ophiuroid?
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The biogeography of mitochondrial and nuclear discordance in animals
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Hybridization and speciation
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Cryptic speciation and genetic structure of widely distributed brittle stars (Ophiuroidea) in Europe
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THE HIDDEN SIDE OF INVASIONS: MASSIVE INTROGRESSION BY LOCAL GENES
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SPECIES DELIMITATION WITH ABC AND OTHER COALESCENT-BASED METHODS: A TEST OF ACCURACY WITH SIMULATIONS AND AN EMPIRICAL EXAMPLE WITH LIZARDS OF THE LIOLAEMUS DARWINII COMPLEX (SQUAMATA: LIOLAEMIDAE)
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SpedeSTEM: a rapid and accurate method for species delimitation
inferredcites →https://doi.org/10.1111/j.2041-210x.2011.00179.xopenalex-snapshot
abc: an R package for approximate Bayesian computation (ABC)
inferredcites →https://doi.org/10.1111/jbi.12155openalex-snapshot
The Southwestern Indian Ocean as a potential marine evolutionary hotspot: perspectives from comparative phylogeography of reef brittle‐stars
inferredcites →https://doi.org/10.1111/mec.12413openalex-snapshot
How to fail at species delimitation
inferredcites →https://doi.org/10.1111/mec.13456openalex-snapshot
Influence of the larval phase on connectivity: strong differences in the genetic structure of brooders and broadcasters in the Ophioderma longicauda species complex
inferredcites →https://doi.org/10.1111/mec.13685openalex-snapshot
Genomics of hybridization and its evolutionary consequences
inferredcites →https://doi.org/10.1111/mec.14024openalex-snapshot
Positive selection on sperm ion channels in a brooding brittle star: consequence of life‐history traits evolution
inferredcites →https://doi.org/10.1126/science.aao4593openalex-snapshot
Rapid hybrid speciation in Darwin’s finches
inferredcites →https://doi.org/10.1128/aem.01541-09openalex-snapshot
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The Great American Schism: Divergence of Marine Organisms After the Rise of the Central American Isthmus
inferredcites →https://doi.org/10.1146/annurev.es.24.110193.001201openalex-snapshot
Sibling Species in the Sea
inferredcites →https://doi.org/10.11646/zootaxa.2071.1.1openalex-snapshot
Potential cryptic speciation in Mediterranean populations of Ophioderma (Echinodermata: Ophiuroidea)
inferredcites →https://doi.org/10.1186/1471-2148-10-276openalex-snapshot
An efficient method to find potentially universal population genetic markers, applied to metazoans
inferredcites →https://doi.org/10.1186/1471-2148-7-121openalex-snapshot
Cryptic animal species are homogeneously distributed among taxa and biogeographical regions
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Discriminant analysis of principal components: a new method for the analysis of genetically structured populations
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Improved Reversible Jump Algorithms for Bayesian Species Delimitation
inferredcites →https://doi.org/10.3354/ab00138openalex-snapshot
Large-scale genetic patchiness among NE Atlantic populations of the brittle star Ophiothrix fragilis
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Planktonic larvae do not ensure gene flow in the edible sea urchin Paracentrotus lividus
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Caroli Linnaei...Systema naturae per regna tria naturae :secundum classes, ordines, genera, species, cum characteribus, differentiis, synonymis, locis

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Incomplete lineage sorting and ancient admixture, and speciation without morphological change in ghost-worm cryptic species
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