DOI: 10.5061/dryad.mw6m9069d
title: Data from: The <em>Carpiodes</em> conundrum: Molecular hypothesis testing informs conservation applications for Carpsuckers (Catostomidae: Carpiodes) in Texas and beyond

description: Sufficient taxonomic understanding is critical for biodiversity
 conservation. This is particularly relevant among freshwater fishes, where
 cryptic undescribed species cause difficulties for promoting conservation
 efforts. Catostomidae (i.e., suckers) is a family of freshwater fishes
 with cryptic diversity and biological traits that make them difficult to
 classify taxonomically. Among suckers, the Carpsuckers (Carpiodes carpio,
 Carpiodes cyprinus, Carpiodes velifer) possess uncertain taxonomic
 classifications and cryptic diversity despite a rich history of research.
 Within Carpiodes, uniquely slender bodied populations occurring in Western
 Gulf of Mexico drainages suggest potential for an undescribed species.
 Originally collected in the Llano River, tributary to the Texas Colorado
 River, Llano River Carpsucker are morphologically similar to C. cyprinus.
 Our study explores how historical biogeographic scenarios may have led to
 lineage diversification of Llano River Carpsucker. We test competing
 molecular hypotheses (i.e., Native Endemic Species Hypothesis, Native
 Lineage Hypothesis) to explain the native origin of Llano River Carpsucker
 and further assess whether the taxon is non-native C. cyprinus (i.e.,
 Species Introduction Hypothesis), each carrying vastly different
 conservation and management implications. Additionally, we assessed
 phylogenetic relationships across the entire genus Carpiodes. Phylogenetic
 analyses recovered divergent lineages of C. cyprinus in Eastern Gulf of
 Mexico drainages, suggesting the presence of cryptic undescribed species.
 Llano River Carpsucker specimens were resolved in unique lineages relative
 to C. cyprinus, with mitochondrial haplotypes closely related to
 Mississippi C. cyprinus (p-distance &lt; 0.005). Our study suggests
 Llano River Carpsucker represent native C. cyprinus, supporting our Native
 Lineage Hypothesis. We further provide evidence that C. cyprinus readily
 hybridizes with C. carpio, resulting in mitochondrial introgression across
 much of their distribution. Lastly, we provide recommendations to promote
 conservation efforts and discuss further research directions to understand
 deeper evolutionary and environmental mechanisms behind morphologically
 and genetically unique C. cyprinus inhabiting Western Gulf of Mexico
 drainages of Texas.
description: # Data from: The *Carpiodes* conundrum: Molecular hypothesis testing
 informs conservation applications for Carpsuckers (Catostomidae:
 Carpiodes) in Texas and beyond Dataset DOI:
 [10.5061/dryad.mw6m9069d](https://doi.org/10.5061/dryad.mw6m9069d) ##
 Description of the data and file structure Data comprises mitochondrial
 (CYTB) and nuclear (IRBP2) sequences from tissued catostomid specimens
 collected from field work as part of this study and tissues from voucher
 specimens originating from several museums (see paper *Acknowledgements*).
 Sequences were used to create phylogenetic trees, haplotype networks and
 genetic distance estimates. All sequences herein were uploaded to GenBank
 (PV579174-PV579834) and include metadata on locality information for each
 specimen. Metadata for each specimen can also be found in Supplementary
 Table S1 of the paper. Data also includes spatial information on the
 distribution of *Carpiodes* taxa, *Carpiodes* clades, and hypothesized
 biogeographic history. ### Files and variables ##
 Roberts_et_al_2025_data.zip ### Haplotypes Folder Note that opening up
 annotated .nex files in PopART typically will rearrange haplotypes making
 them appear different than data figures (i.e., Figure 9, Figure 10) from
 related publication. Annotated haplotype networks generated for this
 manuscript were further edited in BoxySVG software to develop final
 figures. To generate haplotype networks, open up alignment .phy files
 (e.g., “CYTB_haplo.phy”) and .csv traits file (e.g.,
 Taxa_River_for_haplo_CYTB.csv). Following uploading these files, select
 Network &gt; Median Joining Network, and keep Epsilon value to default
 (i.e., zero). **Files included** 1. "CYTB_haplo.phy" (CYTB
 sequences for developing haplotype network) 1. First row of file includes
 number of sequences (308) and number of nucleotides (1140) for each
 sequence 2. All following rows include the sequence ID in the first column
 and associated nucleotide sequence in the second column 2.
 "IRBP2_haplo.phy" (IRBP2 sequences for developing haplotype
 network) 1. First row of file includes number of sequences (616) and
 number of nucleotides (839) for each sequence 2. All following rows
 include the sequence ID in the first column and associated nucleotide
 sequence in the second column 3. "CYTB_haplo_annotated.nex"
 (Annotated haplotype network) 1. Data includes sequence IDs with
 associated nucleotides as in CYTB_haplo.phy 2. Following this trait data
 includes which "TraitLabels" each sequence belongs to in binary
 3. Following trait information annotation information on the haplotype
 network are included. 1. "ntax" number of unique haplotypes 2.
 "nvertices" number of unique vertices in haplotype network 3.
 "nedges" number of unique edges in haplotype network 4.
 "plotDim" plot dimensions 5. "Font" - font used for
 haplotype labels 6. "LegendFont" - font used for legend 4.
 "IRBP2_haplo_annotated.nex" (Annotated haplotype network) 1.
 Data includes sequence IDs with associated nucleotides as in
 IRBP2_haplo.phy 2. Following this trait data includes which
 "TraitLabels" each sequence belongs to in binary 3. Following
 trait information annotation information on the haplotype network are
 included. 1. "ntax" number of unique haplotypes 2.
 "nvertices" number of unique vertices in haplotype network 3.
 "nedges" number of unique edges in haplotype network 4.
 "plotDim" plot dimensions 5. "Font" - font used for
 haplotype labels 6. "LegendFont" - font used for legend 5.
 "Taxa_River_for_haplo_CYTB.csv" (File for developing CYTB
 haplotype network) 1. First column is sequence IDs 2. Remaining columns
 includes the specimen taxa code and drainage it was collected in coded in
 binary. Column headers are shifted to the left one column for formatting
 for PopArt. Column one has no header. 1. Carpiodes carpio from Sabine
 drainage (Cc_SR)  2. Carpiodes carpio from Colorado drainage (Cc_CR) 3.
 Carpiodes carpio from Brazos drainage (Cc_BR) 4. Carpiodes carpio from Rio
 Grande drainage (CC_RG) 5. Carpiodes carpio from Mississippi drainage
 (Cc_MS) 6. Carpiodes cyprinus from Mississippi drainage (Ccy_MS) 7. Llano
 River Carpsucker from Colorado drainage (LRCS_CR) 8. Llano River
 Carpsucker from Guadalupe drainage (LRCS_GR) 9. Llano River Carpsucker
 from San Bernard drainage (LRCS_SBR) 6.
 "Taxa_River_for_haplo_IRBP2.csv" (File for developing IRBP2
 haplotype network) 1. First column is sequence IDs 2. Remaining columns
 includes the specimen taxa code and drainage it was collected in coded in
 binary. Column headers are shifted to the left one column for formatting
 for PopArt. Column one has no header. 1. Carpiodes carpio from Sabine
 drainage (Cc_SR)  2. Carpiodes carpio from Colorado drainage (Cc_CR) 3.
 Carpiodes carpio from Brazos drainage (Cc_BR) 4. Carpiodes carpio from Rio
 Grande drainage (CC_RG) 5. Carpiodes carpio from Mississippi drainage
 (Cc_MS) 6. Carpiodes cyprinus from Mississippi drainage (Ccy_MS) 7. Llano
 River Carpsucker from Colorado drainage (LRCS_CR) 8. Llano River
 Carpsucker from Guadalupe drainage (LRCS_GR) 9. Llano River Carpsucker
 from San Bernard drainage (LRCS_SBR) ### P_distance Folder 1.
 "CYTB_full_clades.mdsx" (MEGA file used to determine *Carpiodes*
 clade genetic p-distances for CYTB) 1. includes column for sequence IDs
 ("Name"). Remaining columns are nucleotides associated with each
 sequence ID. 2. "CYTB_full_subclades.mdsx" (MEGA file used to
 determine *Carpiodes* subclade genetic p-distances for CYTB) 1. includes
 column for sequence IDs ("Name"). Remaining columns are
 nucleotides associated with each sequence ID. 3. "IRBP2.mdsx"
 (MEGA file used to determine individual based IRBP2 genetic distances) 1.
 includes column for sequence IDs ("Name"). Remaining columns are
 nucleotides associated with each sequence ID. ### Phylogenetics Folder
 Includes four subfolders (Concatenated_Subset, CYTB_full, CYTB_subset,
 IRBP2_Subset) corresponding to consensus trees developed in paper. Each
 subfolder contains the following. Sequences in Nexus and PHYLIP files
 associated with this folder are formatted like those in Haplotypes folder
 which includes a column for the sequence ID and column for nucleotides
 associated with each sequence ID. Nexus files including "Bayes"
 in name include AIC results of top model of nucleotide evolution and
 mrbayes code block "begin mrbayes". 1. Jmodel test results (.txt
 format) 1. includes model selection results for best models of nucleotide
 evolution using Akaike Information Criterion (AIC) Akaike Information
 Criterion corrected for small sample size (AICc), Bayesian Information
 Criterion (BIC), and Decision Theory Performance-Based Selection (DT) 2.
 Files used for Jmodel test (.phy format) 3. Files used for MrBayes (.nex
 format) 4. MrBayes Output. Additional folder including. 1. Output files
 (.t, .p, .trprobs, .tstat, .vstat, .parts files) 1. .t files 1. includes
 names for tip labels coded as integers  2. each "tree gen"
 includes results of the topology of each tree in Newick format 2. .p files
 1. results of parameters from each sampled tree. 2. Column 1: includes the
 tree generation sampled "Gen" 3. Column 2: is log likelihood of
 tree "LnL" 4. Column 3: Log Prior Probability of tree
 "LnPr" 5. Column 4: Tree length "TL"  6. Remaining
 columns include rate parameter values of nucleotide substitutions (e.g,
 "r(A &lt;-&gt;C), Gamma parameter "alpha", proportion of
 variables sites "pinvar" 1. Note that not all the same
 parameters will be represented in each tree as it depends on top model of
 nucleotide evolution determined through AIC 3. .trprobs 1. file showing
 the posterior probaility "P" of each tree 4. .tstat 1. file
 containing summaries of partition statistics 5. .vstat 1. file containing
 mean, median, variance, and 95% credible intervals for estimated branch
 lengths. 6. .parts 1. a file that contains the key to taxon bipartitions,
 meaning it lists the splits or branches of a phylogenetic tree and their
 associated posterior probabilities 2. Tip labels for tree anotation (.txt)
 1. includes tip labels from .t files and modified names
 "Tip_Label" 3. infile (.nex) 4. output consensus tree (.tre) 5.
 Annotated full and condensed trees (.tre) ### R_script 1.
 "infile.nex.con" (Output CYTB full consensus tree from MrBayes)
 2. "Roberts_et_al_25_master_.xlsx" (Excel file with data for R)
 1. Sheet 1 - datasheet containing the proportion of basins resolved in
 each clade for the CYTB full tree 1. Column 1: "Clade" - Clade
 ID  2. Column 2: "Region" - Basin name 3. Column 3:
 "value" - proportion of specimens resolved in a given clade
 associated with the basin they were collected in  2. Sheet 2 - datasheet
 containing the proportion of basins resolved in each clade for the CYTB
 subsetted and concatenated trees 1. Column 1: "Clade" - Clade
 ID  2. Column 2: "Region" - Basin name 3. Column 3:
 "value" - proportion of specimens resolved in a given clade
 associated with the basin they were collected in  3. Sheet 3: datasheet
 used to determine Nei's D genetic distance estimates for Carpiodes
 major clades and subclades using specimens from CYTB full tree 1. Column
 1: "Order" - Order used for organization 2. Column 2:
 "Name" - Name of specimen 3. Column 3: "Taxa" - Taxa
 code 4. Column 4: "Phylocount" - order of specimens as they are
 listed in CYTB full tree 5. Colum 5: "Clade" - Major clade each
 specimen is resolved in 6. Column 6: "SubClade" - Subclade each
 specimen is resolved in 7. Column 7: "SubClade_Num" - Subclades
 coded as numbers 8. Column 8: "Population" - Population each
 specimen was collected from 9. Column 9: "Basin" - Coded basin
 each specimen was collected from 10. Remaining columns - Column headers L1
 - L201 include sites from mitochondrial CYTB sequences where single
 nucleotide polymorphisms (SNPs) were observed. Each colulm possesses
 categorical codes for nucleotides ("A", "C",
 "G", "T") 3. "Roberts_et_al_2025_Master.r"
 (R file with script) ### Spatial All files associated with these the
 shared map packages below were developed using ArcGIS Pro (v 3.4.0).
 Individual shapefiles can be downloaded and mapped on free software such
 as QGIS. 1. "Carpiodes_conceptual_biogeography.ppkx" (Shared map
 package associated with input spatial files for Figure 5) Figure 5 main
 text. Conceptual diagram illustrating ancestral Carpiodes hypothesized
 biogeographic patterns leading to colonization of the Western Gulf of
 Mexico (i.e., Western Gulf) basin. Western Gulf drainages illustrated
 include the Brazos, Colorado, Guadalupe, Neches, Rio Grande, Sabine, San
 Bernard, and Trinity. The Pecos drainage is also illustrated nested within
 the Rio Grande drainage. Colored arrows denote ancestral C. carpio and C.
 cyprinus hypothesized dispersal routes. Shaded basins were derived from
 the North American Atlas Basin Watersheds dataset. 2.
 "Carpiodes_Distribution_Maps.ppkx" (Shared map package with
 input spatial files for Figures 2 and 4) Figure 2 main text. Distribution
 of recognized species of Carpiodes. Occurrences (i.e., points) were
 derived from the Global Biodiversity Information Facility database and
 represent native distributions of each species. Shaded basins were
 modified from the North American Atlas Basin Watersheds dataset. Figure 4
 main text. Distribution of Llano River Carpsucker. Crosses display
 locations where the taxon has been collected across Colorado, Guadalupe,
 and San Bernard drainages. Observations stem from collections conducted in
 this study, confirmed records of the taxon housed at the Fishes of Texas
 Database, and specimens collected in the San Bernard drainage (Adam Cohen,
 Personal communication). The grey shaded region denotes the Edwards
 Plateau ecoregion where the taxon is predominantly found. 3.
 "Carpiodes_Phylogeny_Maps.ppkx" (Shared map package with input
 spatial files for Figure 8 Figure 8 main text. Distribution of Carpiodes
 major clades and subclades. Specimens are shape coded based on taxonomic
 assignment. (a) Distribution of Carpiodes cyprinus in the Eastern Gulf
 basin. (b) Distribution of C. cyprinus and Carpiodes velifer in Atlantic
 Slope and Eastern Gulf basins. (c) Distribution of Carpiodes carpio and C.
 velifer inhabiting Mississippi and Western Gulf basins. (d) Distribution
 of specimens resolved in Subclade 3i across Great Lakes, Hudson Bay,
 Mississippi, and Western Gulf basins. Shaded basins were modified from the
 North American Atlas Basin Watersheds dataset. ## Code/software ###
 Rstudio (v4.4.2) Packages used
 (ggplot2,ggpubr,tidytree,adegenet,hierfstat,phangorn,LEA,tidyr,dplyr,vegan,readxl,teeio) Script includes code to generate pie charts for phylogenetic trees, pruned consensus tree (Figure S3), and Nei's genetic distances ### ArcGIS Pro (v 3.4.0) ## PopArt (v1.7) ### MEGA (v11.0.13) ### CIPRES (v3.3) 1. jModelTest2 (v2.1.6) 2. MrBayes (v3.2.7a) ### MrBayes - Desktop (v3.2.7a) ### Tracer (v1.7.2) ### FigTree (v1.4.4) ## Access information