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Genomic Analyses Implicate the Amazon–Orinoco Plume as the Driver of Cryptic Speciation in a Swimming Crab

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What this work says

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

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Endemism and dispersal: comparative phylogeography of three surgeonfishes across the Hawaiian Archipelago

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Cryptic species within the commercially most important lobster in the tropical Atlantic, the spiny lobster Panulirus argus

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Contrasting patterns of connectivity among endemic and widespread fire coral species (Millepora spp.) in the tropical Southwestern Atlantic

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Salinity tolerance explains the contrasting phylogeographic patterns of two swimming crabs species along the tropical western Atlantic

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STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method

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Marine speciation on a small planet

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Physical observations in the plume region of the Amazon River during peak discharge—II. Water masses

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K+ and NH4+ modulate gill (Na+, K+)-ATPase activity in the blue crab, Callinectes ornatus: Fine tuning of ammonia excretion

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Genetic differentiation in populations of lane snapper (Lutjanus synagris – Lutjanidae) from Western Atlantic as revealed by multilocus analysis

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Evidence for a prolonged retroflection of the North Brazil Current during glacial stages

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Influence of the Amazon River development and constriction of the Central American Seaway on Middle/Late Miocene oceanic conditions at the Ceara Rise

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Millennial-scale sea-level control on avulsion events on the Amazon Fan

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The genomics of speciation-with-gene-flow

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The Syllis gracilis species complex: A molecular approach to a difficult taxonomic problem (Annelida, Syllidae)

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Phylogenetic comparative methods and the geography of speciation

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The barrier layer in the western tropical Atlantic Ocean

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Genomics and the origin of species

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The Amazon River plume, a barrier to animal dispersal in the Western Tropical Atlantic

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Biogeography of tropical reef fishes: the South Atlantic puzzle

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Patterns of distribution and processes of speciation in Brazilian reef fishes

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TCS: a computer program to estimate gene genealogies

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GENETIC COMPARISONS OF GERMAN POPULATIONS OF THE STONE CRAYFISH, AUSTROPOTAMOBIUS TORRENTIUM (CRUSTACEA: ASTACIDAE)

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Reticulation, divergence, and the phylogeography–phylogenetics continuum

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Species Concepts and Species Delimitation

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Pelagic Larval Duration and Dispersal Distance Revisited

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Fast and accurate short read alignment with Burrows–Wheeler transform

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The Sequence Alignment/Map format and SAMtools

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Fast and accurate long-read alignment with Burrows–Wheeler transform

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The variant call format and VCFtools

inferredcites →https://doi.org/10.1093/g3journal/jkab212openalex-snapshot

Chromosome-level genome assembly of the blue crab,Callinectes sapidus

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Inference of Population Structure Using Multilocus Genotype Data

inferredcites →https://doi.org/10.1093/gigascience/giaa005openalex-snapshot

GADMA: Genetic algorithm for inferring demographic history of multiple populations from allele frequency spectrum data

inferredcites →https://doi.org/10.1093/icb/icr024openalex-snapshot

Speciation in the Sea: Overview of the Symposium and Discussion of Future Directions

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MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

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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

inferredcites →https://doi.org/10.1093/molbev/msx248openalex-snapshot

DnaSP 6: DNA Sequence Polymorphism Analysis of Large Data Sets

inferredcites →https://doi.org/10.1093/nar/16.3.1215openalex-snapshot

A simple salting out procedure for extracting DNA from human nucleated cells

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inferredcites →https://doi.org/10.1098/rspb.2018.2924openalex-snapshot

Genomics overrules mitochondrial DNA, siding with morphology on a controversial case of species delimitation

inferredcites →https://doi.org/10.1098/rstb.2011.0263openalex-snapshot

Genomic divergence during speciation: causes and consequences

inferredcites →https://doi.org/10.1098/rstb.2019.0528openalex-snapshot

Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers

inferredcites →https://doi.org/10.1101/gr.159426.113openalex-snapshot

Genome-wide evidence for speciation with gene flow in Heliconius butterflies

inferredcites →https://doi.org/10.1101/gr.191338.115openalex-snapshot

High mutational rates of large-scale duplication and deletion in Daphnia pulex

inferredcites →https://doi.org/10.1111/1755-0998.12592openalex-snapshot

pcadapt : an R package to perform genome scans for selection based on principal component analysis

inferredcites →https://doi.org/10.1111/1755-0998.12995openalex-snapshot

Minor allele frequency thresholds strongly affect population structure inference with genomic data sets

inferredcites →https://doi.org/10.1111/1755-0998.13145openalex-snapshot

genodive version 3.0: Easy‐to‐use software for the analysis of genetic data of diploids and polyploids

inferredcites →https://doi.org/10.1111/2041-210x.12410openalex-snapshot

popart : full‐feature software for haplotype network construction

inferredcites →https://doi.org/10.1111/ddi.13072openalex-snapshot

Cryptic speciation in gentoo penguins is driven by geographic isolation and regional marine conditions: Unforeseen vulnerabilities to global change

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Ten years of demographic modelling of divergence and speciation in the sea

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Geographical patterns of genetic structure in marine species with contrasting life histories

inferredcites →https://doi.org/10.1111/j.1365-2699.2009.02188.xopenalex-snapshot

Genetic evaluation of marine biogeographical barriers: perspectives from two widespread Indo‐Pacific snappers ( Lutjanus kasmira and Lutjanus fulvus )

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

inferredcites →https://doi.org/10.1111/j.1365-294x.2012.05664.xopenalex-snapshot

The biogeography of mitochondrial and nuclear discordance in animals

inferredcites →https://doi.org/10.1111/j.1420-9101.2012.02599.xopenalex-snapshot

Hybridization and speciation

inferredcites →https://doi.org/10.1111/j.1755-0998.2011.02987.xopenalex-snapshot

Comparison of FST outlier tests for SNP loci under selection

inferredcites →https://doi.org/10.1111/jbi.12082openalex-snapshot

Marine shelf habitat: biogeography and evolution

inferredcites →https://doi.org/10.1111/jbi.12416openalex-snapshot

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

inferredcites →https://doi.org/10.1111/jbi.12938openalex-snapshot

Phylogeography of the reef‐building polychaetes of the genus Phragmatopoma in the western Atlantic Region

inferredcites →https://doi.org/10.1111/jbi.14398openalex-snapshot

The Amazon‐Orinoco Barrier as a driver of reef‐fish speciation in the Western Atlantic through time

inferredcites →https://doi.org/10.1111/mec.12705openalex-snapshot

Genome scan methods against more complex models: when and how much should we trust them?

inferredcites →https://doi.org/10.1111/mec.13513openalex-snapshot

Controlling false discoveries in genome scans for selection

inferredcites →https://doi.org/10.1111/mec.13568openalex-snapshot

At least some meiofaunal species are not everywhere. Indication of geographic, ecological and geological barriers affecting the dispersion of species of Ototyphlonemertes (Nemertea, Hoplonemertea)

inferredcites →https://doi.org/10.1111/mec.14792openalex-snapshot

These aren’t the loci you’e looking for: Principles of effective SNP filtering for molecular ecologists

inferredcites →https://doi.org/10.1111/mec.15153openalex-snapshot

A mirage of cryptic species: Genomics uncover striking mitonuclear discordance in the butterfly Thymelicus sylvestris

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/10.1111/mec.15253openalex-snapshot

Stacks 2: Analytical methods for paired‐end sequencing improve RADseq‐based population genomics

inferredcites →https://doi.org/10.1111/mec.15350openalex-snapshot

Biogeography, habitat transitions and hybridization in a radiation of South American silverside fishes revealed by mitochondrial and genomic RAD data

inferredcites →https://doi.org/10.1126/science.1194585openalex-snapshot

Amazonia Through Time: Andean Uplift, Climate Change, Landscape Evolution, and Biodiversity

inferredcites →https://doi.org/10.1130/0016-7606(1975)86<610:qsotac>2.0.co;2openalex-snapshot

Quaternary Sedimentation on the Amazon Continental Margin: A Model

inferredcites →https://doi.org/10.1130/g25567a.1openalex-snapshot

Late Miocene onset of the Amazon River and the Amazon deep-sea fan: Evidence from the Foz do Amazonas Basin

inferredcites →https://doi.org/10.1146/annurev.es.24.110193.001201openalex-snapshot

Sibling Species in the Sea

inferredcites →https://doi.org/10.1163/156854099502871openalex-snapshot

REPRODUCTIVE BIOLOGY AND MOULTING CYCLE OF THE CRAB CALLINECTES ORNATUS (DECAPODA, PORTUNIDAE) FROM THE UBATUBA REGION, SAO PAULO, BRAZIL

inferredcites →https://doi.org/10.1163/18759866-20191344openalex-snapshot

Speciation with gene flow in marine systems

inferredcites →https://doi.org/10.11646/zootaxa.4872.1.1openalex-snapshot

Checklist of decapod crustaceans from the coast of the São Paulo state (Brazil) supported by integrative molecular and morphological data: III. Infraorder Brachyura Latreille, 1802

inferredcites →https://doi.org/10.1371/journal.pone.0008594openalex-snapshot

Genetic Structure Among 50 Species of the Northeastern Pacific Rocky Intertidal Community

inferredcites →https://doi.org/10.1371/journal.pone.0037135openalex-snapshot

Double Digest RADseq: An Inexpensive Method for De Novo SNP Discovery and Genotyping in Model and Non-Model Species

inferredcites →https://doi.org/10.1534/genetics.108.092221openalex-snapshot

A Genome-Scan Method to Identify Selected Loci Appropriate for Both Dominant and Codominant Markers: A Bayesian Perspective

inferredcites →https://doi.org/10.1534/genetics.113.151670openalex-snapshot

Rates and Genomic Consequences of Spontaneous Mutational Events in Drosophila melanogaster

inferredcites →https://doi.org/10.1534/genetics.117.200493openalex-snapshot

Inferring the Joint Demographic History of Multiple Populations: Beyond the Diffusion Approximation

inferredcites →https://doi.org/10.1590/0001-3765201420130030openalex-snapshot

Morphology of the first zoeal stages of five species of the portunid genus Callinectes (Decapoda, Brachyura) hatched at the laboratory

inferredcites →https://doi.org/10.1590/s1679-87592000000200008openalex-snapshot

A corrente do Brasil ao largo da costa leste brasileira

inferredcites →https://doi.org/10.2307/1352367openalex-snapshot

Dispersal of River Sediments in Coastal Seas: Six Contrasting Cases

inferredcites →https://doi.org/10.2307/1538947openalex-snapshot

THE LARVAL DEVELOPMENT OF CALLINECTES SAPIDUS RATHBUN REARED IN THE LABORATORY

inferredcites →https://doi.org/10.2307/1540792openalex-snapshot

AN EXPERIMENTAL GRADIENT ANALYSIS : HYPOSALINITY AS AN "UPSTRESS" DISTRIBUTIONAL DETERMINANT FOR CARIBBEAN PORTUNID CRABS

inferredcites →https://doi.org/10.2307/j.ctv1nzfgj7openalex-snapshot

Phylogeography

inferredcites →https://doi.org/10.3354/meps08287openalex-snapshot

Population genetics, larval dispersal, and connectivity in marine systems

inferredcites →https://doi.org/10.3354/meps09248openalex-snapshot

Comparative phylogeography of four Indo-Pacific moray eel species (Muraenidae) reveals comparable ocean-wide genetic connectivity despite five-fold differences in available adult habitat

inferredcites →https://doi.org/10.3354/meps310119openalex-snapshot

Pelagic conditions affect larval behavior, survival, and settlement patterns in the Caribbean coral Montastraea faveolata

inferredcites →https://doi.org/10.3389/fmars.2020.574455openalex-snapshot

Genetic Connectivity of the West Indian Manatee in the Southern Range and Limited Evidence of Hybridization With Amazonian Manatees

inferredcites →https://doi.org/10.5281/zenodo.5400459openalex-snapshot

Molecular analysis of the taxonomic and distributional status for the hermit crab genera Loxopagurus Forest, 1964 and Isocheles Stimpson, 1858 (Decapoda, Anomura, Diogenidae)

inferredcites →https://doi.org/10.5343/bms.2013.1007openalex-snapshot

Phylogeography unplugged: comparative surveys in the genomic era

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

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