DOI: 10.5061/dryad.0cfxpnwbw
title: Data from: Landscape evolution drives continental diversification in Neotropical freshwater fishes of the family Erythrinidae (Teleostei, Characiformes)

description: Aim: Evolutionary diversification and diversity patterns in Neotropical
 freshwater fishes can, in part, be predicted by the effects of
 geomorphological settings on landscape evolution. However, studies at a
 continental scale, focusing on specific taxa that reflect the tight
 connection between their evolutionary history and orogenic uplifts on the
 tectonically active Western margin and watershed migration dynamics on the
 passive Eastern margin of South America remain limited. Here, we
 investigated biogeographical and chronological patterns of diversification
 in the geographically widespread teleost family Erythrinidae
 (Characiformes, Erythrinoidea). Location: Neotropical Region Time period:
 Late Cretaceous and Cenozoic Taxon: Erythrinidae (Characiformes) Methods:
 We used phylogenomic and parametric biogeographic methods. Our dataset
 based on ultraconserved elements (UCEs) included 29 erythrinoid lineages
 and 23 related taxa. Results: The time calibration along with ancestral
 area estimation proposes that superfamily Erythrinoidea originated in the
 Late Cretaceous ca. 80 Ma, with divergence of major clades during the
 Paleogene ca. 51–31 Ma. Erythrinidae diversified rapidly after the
 formation of the transcontinental Amazon River ca. 10 Ma, from eight
 lineages to at least 28 putative species today. A majority of erythrinid
 species (78%) are members of just three relatively young clades less than
 13 Ma: Erythrinus, Hoplerythrinus, and Hoplias malabaricus group. Results
 present contrasting temporal patterns of cladogenetic events on the two
 continental margins: a pulsed age-distribution of biogeographic events on
 the Western Margin as predicted by discrete tectonic uplifts of the
 Northern Andean cordilleras, and a more continuous age-distribution on the
 Eastern Margin as predicted by westward-propagating watershed migration.
 Main conclusions: Historical changes in landscape connectivity have
 influenced diversification in Erythrinidae, where Late Neogene uplifts of
 the Northern Andean cordilleras profoundly structured freshwater diversity
 gradients by fragmenting the aquatic faunas of cis- and trans-Andean
 basins as well as portions of the sub-Andean Foreland basin, and merging
 faunas of the Western and Eastern Amazonia with the onset of the
 transcontinental Amazon River. Alternative diversification scenarios are
 also consistent with available paleontological, paleogeographic, and
 paleoenvironmental data.
description: Representatives of each erythrinid species/lineages were selected
 to be sequenced for ultraconserved elements. Illumina sequencing libraries
 were prepared with a slightly modified version of the NEBNext(R) Ultra(TM)
 DNA Library Prep Kit for Illumina(R). Sequencing was performed across two
 Illumina HiSeq PE100 bp lanes using v4 chemistry. The pipeline used for
 processing target-enriched UCE data was conducted on PHYLUCE v1.5.0.
 Adapter contamination and low-quality bases were trimmed using the
 Illumiprocessor. We assembled reads and generated consensus contigs for
 each sample using Velvet v1.5.0. The trimmed alignment was used to
 generate two subsets, each including all taxa examined: the 75% and 95%
 complete matrices. We analyzed the 75% and 95% concatenated datasets using
 maximum likelihood (ML) in RAxML v8.1.3, Bayesian inference (BI) in
 ExaBayes v1.4, and a coalescent-based analysis in ASTRAL-III
 v.5.6.2.
description: # Data from: Landscape evolution drives continental diversification in
 Neotropical freshwater fishes of the family Erythrinidae (Teleostei,
 Characiformes)
 [https://doi.org/10.5061/dryad.0cfxpnwbw](https://doi.org/10.5061/dryad.0cfxpnwbw) ## Description of the data and file structure Data was collected from museum specimens. Sequences were obtained from captures of ultraconserved elements of 97 taxa using Illumina approaches. Data was processed by Phyluce and analyses ran through RAxML, ExaBayes, Astral, BEAST, BAMM, and BioGeoBEARs. Two matrices are available in phylip format: the 75% complete matrix and thr 95% complete matrix of ultraconserved elements. Users can use any of these matrices for running phylogenetic analyses of molecular data. ### Files and variables #### File: mafft-nexus-edge-trimmed-clean-95p.phylip **Description:** Data matrix 95% complete of ultraconserved elements. #### File: mafft-nexus-edge-trimmed-clean-75p.phylip **Description:** Data matrix 75% complete of ultraconserved elements. ## Code/software Use Geneious software (https://www.geneious.com/) or the open access MEGA (https://www.megasoftware.net/) to open phylip matrices. Analyses can be done in the following softwares. PHYLUCE v1.5.0 RAxML v8.1.3 EXABAYES v1.4 ASTRAL v5.6.2 BEAST v2.6.3 ## Access information Other publicly accessible locations of the data: * There are no other publicly accessible location of the data. Data was derived from the following sources: * Data is original and were generated using museum specimens and sequencing of ultraconserved elements. Sequencing was performed across two Illumina HiSeq PE100 bp lanes using v4 chemistry.