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Time-calibrated phylogeny of neotropical freshwater fishes

https://doi.org/10.3389/fbinf.2024.1433995

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What this work says

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

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Global diversity of fish (Pisces) in freshwater

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Neotropical Riverine Cichlids: Adaptive Radiation and Macroevolution at Continental Scales

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Approaches to Macroevolution: 1. General Concepts and Origin of Variation

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Time-calibrated molecular phylogeny reveals a Miocene–Pliocene diversification in the Amazon miniature killifish genus Fluviphylax (Cyprinodontiformes: Cyprinodontoidei)

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Patterns in Freshwater Fish Diversity

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Late Neogene megariver captures and the Great Amazonian Biotic Interchange

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The dorsal and pectoral fin spines of catfishes (Ostariophysi: Siluriformes) from the Bauru Group (Late Cretaceous), Brazil: A comparative and critical analysis

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Paleogeographic influences on freshwater fish distributions in northeastern Brazil

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The Great Ordovician Biodiversification Event (GOBE): The palaeoecological dimension

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Phylogenetic analysis of community assembly and structure over space and time

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Phylogenetic diversity and nature conservation: where are we?

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Evolution in a Community Context: On Integrating Ecological Interactions and Macroevolution

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A phylogenetic analysis of the major groups of catfishes (Teleostei: Siluriformes) using rag1 and rag2 nuclear gene sequences

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Molecular phylogeny and biogeography of the Neotropical cichlid fish tribe Cichlasomatini (Teleostei: Cichlidae: Cichlasomatinae)

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Multilocus phylogeny and rapid radiations in Neotropical cichlid fishes (Perciformes: Cichlidae: Cichlinae)

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Molecular phylogeny of the Neoplecostominae and Hypoptopomatinae (Siluriformes: Loricariidae) using multiple genes

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Molecular phylogeny of Aphyocharacinae (Characiformes, Characidae) with morphological diagnoses for the subfamily and recognized genera

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Life history and biogeographic diversification of an endemic western North American freshwater fish clade using a comparative species tree approach

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Model-based total evidence phylogeny of Neotropical electric knifefishes (Teleostei, Gymnotiformes)

inferredcites →https://doi.org/10.1016/j.ympev.2017.07.007openalex-snapshot

Multilocus analysis of the catfish family Trichomycteridae (Teleostei: Ostariophysi: Siluriformes) supporting a monophyletic Trichomycterinae

inferredcites →https://doi.org/10.1016/j.ympev.2017.10.008openalex-snapshot

Exon-based phylogenomics strengthens the phylogeny of Neotropical cichlids and identifies remaining conflicting clades (Cichliformes: Cichlidae: Cichlinae)

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Molecular phylogenetics of Neotropical detritivorous fishes of the family Curimatidae (Teleostei: Characiformes)

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Galapagos Gore, NazCoPac Triple Junction and Carnegie/Cocos Ridges

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Accelerated body size evolution in upland environments is correlated with recent speciation in South American freshwater fishes

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Global priorities for conserving the evolutionary history of sharks, rays and chimaeras

inferredcites →https://doi.org/10.1038/s41559-023-02220-8openalex-snapshot

Freshwater fish diversity in the western Amazon basin shaped by Andean uplift since the Late Cretaceous

inferredcites →https://doi.org/10.1038/s41598-020-59519-wopenalex-snapshot

Phylogenomic analysis of trichomycterid catfishes (Teleostei: Siluriformes) inferred from ultraconserved elements

inferredcites →https://doi.org/10.1073/pnas.1206625109openalex-snapshot

Resolution of ray-finned fish phylogeny and timing of diversification

inferredcites →https://doi.org/10.1073/pnas.1423853112openalex-snapshot

Biological evidence supports an early and complex emergence of the Isthmus of Panama

inferredcites →https://doi.org/10.1073/pnas.1719358115openalex-snapshot

Comprehensive phylogeny of ray-finned fishes (Actinopterygii) based on transcriptomic and genomic data

inferredcites →https://doi.org/10.1073/pnas.1818058116openalex-snapshot

Macroevolutionary diversification rates show time dependency

inferredcites →https://doi.org/10.1073/pnas.2211974120openalex-snapshot

Landscape dynamics and diversification of the megadiverse South American freshwater fish fauna

inferredcites →https://doi.org/10.1080/10635150701472164openalex-snapshot

Improvement of Phylogenies after Removing Divergent and Ambiguously Aligned Blocks from Protein Sequence Alignments

inferredcites →https://doi.org/10.1093/bib/bbn013openalex-snapshot

Recent developments in the MAFFT multiple sequence alignment program

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treePL: divergence time estimation using penalized likelihood for large phylogenies

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RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

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geiger v2.0: an expanded suite of methods for fitting macroevolutionary models to phylogenetic trees

inferredcites →https://doi.org/10.1093/database/baaa062openalex-snapshot

NCBI Taxonomy: a comprehensive update on curation, resources and tools

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TimeTree 5: An Expanded Resource for Species Divergence Times

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PartitionFinder 2: New Methods for Selecting Partitioned Models of Evolution for Molecular and Morphological Phylogenetic Analyses

inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a026334openalex-snapshot

Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis

inferredcites →https://doi.org/10.1093/sysbio/syab040openalex-snapshot

Accelerated Diversification Explains the Exceptional Species Richness of Tropical Characoid Fishes

inferredcites →https://doi.org/10.1093/sysbio/sys004openalex-snapshot

Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales

inferredcites →https://doi.org/10.1093/sysbio/syv064openalex-snapshot

Coordinated Dispersal and Pre-Isthmian Assembly of the Central American Ichthyofauna

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inferredcites →https://doi.org/10.1093/zoolinnean/zlae101openalex-snapshot

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inferredcites →https://doi.org/10.1093/zoolinnean/zly025openalex-snapshot

Multilocus phylogeny, diagnosis and generic revision of the Guiana Shield endemic suckermouth armoured catfish tribe Lithoxini (Loricariidae: Hypostominae)

inferredcites →https://doi.org/10.1109/gce.2010.5676129openalex-snapshot

Creating the CIPRES Science Gateway for inference of large phylogenetic trees

inferredcites →https://doi.org/10.1111/1755-0998.12449openalex-snapshot

Exon capture phylogenomics: efficacy across scales of divergence

inferredcites →https://doi.org/10.1111/2041-210x.12051openalex-snapshot

Congruification: support for time scaling large phylogenetic trees

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A guide to phylogenetic metrics for conservation, community ecology and macroecology

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Phylogeny of the North American catfish family Ictaluridae (Teleostei: Siluriformes) combining morphology, genes and fossils

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Morphology, molecules and the phylogeny of Characidae (Teleostei, Characiformes)

inferredcites →https://doi.org/10.1111/evo.13649openalex-snapshot

Phylogenomic incongruence, hypothesis testing, and taxonomic sampling: The monophyly of characiform fishes*

inferredcites →https://doi.org/10.1111/geb.12686openalex-snapshot

Phylogenetic scale in ecology and evolution

inferredcites →https://doi.org/10.1111/geb.12843openalex-snapshot

Morphological diversity of freshwater fishes differs between realms, but morphologically extreme species are widespread

inferredcites →https://doi.org/10.1111/geb.13253openalex-snapshot

Evolutionary time best explains the latitudinal diversity gradient of living freshwater fish diversity

inferredcites →https://doi.org/10.1111/jbi.12594openalex-snapshot

Biogeographical signature of river capture events in Amazonian lowlands

inferredcites →https://doi.org/10.1111/jbi.14086openalex-snapshot

Biogeography of the neotropical freshwater stingrays (Myliobatiformes: Potamotrygoninae) reveals effects of continent‐scale paleogeographic change and drainage evolution

inferredcites →https://doi.org/10.1111/jfb.13016openalex-snapshot

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inferredcites →https://doi.org/10.1111/jfb.14572openalex-snapshot

Hidden or unnoticed? Multiple lines of evidence support the recognition of a new species of Pseudocorynopoma (Characidae: Corynopomini)

inferredcites →https://doi.org/10.1111/mec.13583openalex-snapshot

Transcontinental dispersal, ecological opportunity and origins of an adaptive radiation in the Neotropical catfish genus Hypostomus (Siluriformes: Loricariidae)

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

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

inferredcites →https://doi.org/10.1130/0-8137-2356-6.363openalex-snapshot

End-Permian mass extinctions: A review

inferredcites →https://doi.org/10.1146/annurev-ecolsys-011620-031032openalex-snapshot

Diversification of Neotropical Freshwater Fishes

inferredcites →https://doi.org/10.1146/annurev-ecolsys-122120-122554openalex-snapshot

The Emerging Phylogenetic Perspective on the Evolution of Actinopterygian Fishes

inferredcites →https://doi.org/10.11646/zootaxa.4299.3.2openalex-snapshot

Taxonomic review of Trans-Andean species of Pimelodus (Siluriformes: Pimelodidae), with the descriptions of two new species

inferredcites →https://doi.org/10.1186/1471-2105-11-538openalex-snapshot

pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree

inferredcites →https://doi.org/10.1186/1471-2148-11-275openalex-snapshot

Phylogenetic relationships within the speciose family Characidae (Teleostei: Ostariophysi: Characiformes) based on multilocus analysis and extensive ingroup sampling

inferredcites →https://doi.org/10.1186/1471-2148-14-152openalex-snapshot

Systematic and historical biogeography of the Bryconidae (Ostariophysi: Characiformes) suggesting a new rearrangement of its genera and an old origin of Mesoamerican ichthyofauna

inferredcites →https://doi.org/10.1186/1471-2148-7-44openalex-snapshot

A practical approach to phylogenomics: the phylogeny of ray-finned fish (Actinopterygii) as a case study

inferredcites →https://doi.org/10.1186/s12862-015-0403-4openalex-snapshot

Molecular phylogeny of the subfamily Stevardiinae Gill, 1858 (Characiformes: Characidae): classification and the evolution of reproductive traits

inferredcites →https://doi.org/10.1186/s12862-017-0958-3openalex-snapshot

Phylogenetic classification of bony fishes

inferredcites →https://doi.org/10.1371/journal.pone.0071162openalex-snapshot

Temporal Patterns of Diversification across Global Cichlid Biodiversity (Acanthomorpha: Cichlidae)

inferredcites →https://doi.org/10.1371/journal.pone.0161680openalex-snapshot

Phylogenetic Systematics, Biogeography, and Ecology of the Electric Fish Genus Brachyhypopomus (Ostariophysi: Gymnotiformes)

inferredcites →https://doi.org/10.1371/journal.pone.0166988openalex-snapshot

A Time-Calibrated Mitogenome Phylogeny of Catfish (Teleostei: Siluriformes)

inferredcites →https://doi.org/10.1525/california/9780520268685.003.0002openalex-snapshot

Major Biogeographic and Phylogenetic Patterns

inferredcites →https://doi.org/10.1525/california/9780520268685.003.0008openalex-snapshot

The Biogeography of Marine Incursions in South America

inferredcites →https://doi.org/10.1525/california/9780520268685.003.0010openalex-snapshot

An Ecological Perspective on Diversity and Distributions

inferredcites →https://doi.org/10.15381/rpb.v28iespecial.21911openalex-snapshot

Checklist of freshwater fishes from Loreto, Peru

inferredcites →https://doi.org/10.1590/1676-0611-bn-2021-1296openalex-snapshot

Building knowledge to save species: 20 years of ichthyological studies in the Tocantins-Araguaia River basin

inferredcites →https://doi.org/10.1590/1982-0224-20160067openalex-snapshot

Checklist of Gymnotiformes (Osteichthyes: Ostariophysi) and catalogue of primary types

inferredcites →https://doi.org/10.1590/1982-0224-2019-0081openalex-snapshot

Systematic revision of the Neotropical catfish genus Scleronema (Siluriformes: Trichomycteridae), with descriptions of six new species from Pampa grasslands

inferredcites →https://doi.org/10.1590/1982-0224-2020-0060openalex-snapshot

New species of the Corumbataia cuestae group (Siluriformes: Loricariidae) from the Rio Tocantins basin, with comments on its phylogenetic relationships

inferredcites →https://doi.org/10.1590/1982-0224-2021-0079openalex-snapshot

Assessing extinction risk from geographic distribution data in Neotropical freshwater fishes

inferredcites →https://doi.org/10.1590/1982-0224-2022-0002openalex-snapshot

A new genus of armored catfish (Siluriformes: Loricariidae) from the Greater Amazon, with a review of the species and description of five new species

inferredcites →https://doi.org/10.1590/1982-0224-2023-0066openalex-snapshot

Fishes of the upper rio Paraná basin: diversity, biogeography and conservation

inferredcites →https://doi.org/10.1635/053.162.0106openalex-snapshot

Phylogenetic Relationships and Molecular Dating of the Major Groups of Catfishes of the Neotropical Superfamily Pimelodoidea (Teleostei, Siluriformes)

inferredcites →https://doi.org/10.2307/2937046openalex-snapshot

Ecomorphological Diversification in Lowland Freshwater Fish Assemblages from Five Biotic Regions

inferredcites →https://doi.org/10.32942/x2n59nopenalex-snapshot

The ecomorphological diversity of Amazonian stream fishes is constrained by phylogenetic relationships

inferredcites →https://doi.org/10.3389/fevo.2021.788328openalex-snapshot

Landscape Evolution as a Diversification Driver in Freshwater Fishes

inferredcites →https://doi.org/10.3389/fgene.2018.00030openalex-snapshot

Detection of Potential Problematic Cytb Gene Sequences of Fishes in GenBank

inferredcites →https://doi.org/10.3389/fgene.2021.662254openalex-snapshot

Next-Generation Sequencing in Newborn Screening: A Review of Current State

inferredcites →https://doi.org/10.3390/life8020020openalex-snapshot

phylotaR: An Automated Pipeline for Retrieving Orthologous DNA Sequences from GenBank in R

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Three new species of saddled loricariid catfishes, and a review of Hemiancistrus, Peckoltia, and allied genera (Siluriformes)

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Checklist of the ichthyofauna of the Rio Negro basin in the Brazilian Amazon

inferredcites →https://doi.org/10.5281/zenodo.16430758openalex-snapshot

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

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