DOI: 10.5061/dryad.37pvmcvm1
title: Widespread sympatry in a species-rich clade of marine fishes (Carangoidei)

description: A universal paradigm describing patterns of speciation across the tree of
 life has been debated for decades. In marine organisms, patterns of
 speciation are largely unknown due to the deficiency of species-level
 phylogenies and information on species’ distributions, as well as
 conflicting relationships between species’ dispersal, range size and
 co-occurrence. Most research on global patterns of marine fish speciation
 has focused on coral reef or pelagic species. Carangoidei is an
 ecologically important clade of marine fishes that utilize both coral reef
 and pelagic environments. We used sequence capture of 1314 ultraconserved
 elements (UCEs) from 154 taxa to generate a phylogeny of Carangoidei and
 its parent clade, Carangiformes. Age-range correlation analyses of the
 geographic distributions and divergence times of sister species pairs
 reveal widespread sympatry, with 73% of sister species pairs exhibiting a
 sympatric geographic distribution, regardless of node age, and most
 species pairs co-existing across large portions of their ranges. We also
 observe greater disparity in body size and water column depth utilization
 between sympatric than allopatric sister species. These and other
 ecological or behavioral attributes likely facilitate sympatry among the
 most closely related carangoids.
description: We obtained tissues for 154 species including nine outgroup
 species of Carangiformes through field collection and museum loans. We
 prepared dual-indexed libraries for targeted enrichment using the
 HyperPrep Kit (KAPA Biosystems, Wilmington, MA) following the
 manufacturer’s protocols. We used a probe set targeting 1314 UCE loci
 informative for phylogenetic analyses of Carangiformes and other
 acanthomorph fishes across evolutionary time scales. UCE sequence data
 were processed prior to phylogenetic analyses with
 <em>phyluce</em> v1.6, which we used to construct alignments
 of individual UCE loci and perform edge trimming. We generated two data
 matrices for phylogenetic analyses to compare tree topologies with
 different amounts of missing data – one where 75% of taxa (115 out of 154)
 were present in each alignment and one where 95% of taxa (146 out of 154)
 were present.
description: UCE sequence data were processed prior to phylogenetic analyses
 with <em>phyluce</em> v1.6. Downstream
 analyses were conducted in R v3.5.2. 
description: Data descriptions for: Glass, J.R., R.C. Harrington, P.F. Cowman, B.C.
 Faircloth, and T.J. Near. Widespread sympatry in a species-rich clade of
 marine fishes (Carangoidea). *Proc. R. Soc. B 20230657.*
 Carangiform\_75p.phylip Concatenated phylip alignment for the dataset for
 which 95% of taxa were present in each alignment (146 out of 154 taxa).
 CharPartitions\_75p.nex Partition file for 75% complete matrix generated
 in PartitionFinder v2. Carangiform\_95p.phylip Concatenated phylip
 alignment for the dataset for which 75% of taxa were present in each
 alignment (115 out of 154 taxa). CharPartitions\_95p.nex Partition file
 for 95% complete matrix generated in PartitionFinder v2.
 Carangiformes.Depth.csv List of species, DepthRangeShallow (m),
 DepthRangeDeep (m), species code (FishBase), and data source (FishBase or
 FishNet2). Carangiformes.Length.csv List of species, maximum length (cm),
 common length (cm), and species code (FishBase), and data source
 (FishBase). sis.pairs.df.csv Data frame containing the following columns:
 A. Number: Identifying Number B. Species1: Sister Species 1 Scientific
 Name C. Species2: Sister Species 2 Scientific Name D. daughter.node:
 Daughter node label E. RangeOverlap: Range Overlap Value F. RangeSymetry:
 Range Symmetry Value G. parental.node: Parental node label H. sister.node:
 Sister Node Age I. mrca.age: Age of the MRCA (Most Recent Common Ancestor)
 of the Sister Node J. Sp1Habitat: Habitat Classification for Sister
 Species 1 (Reef [R] or NonReef [NR]) K. Sp1Piscivory: Piscivory
 classification for Sister Species 1 (Y = piscivorous, N = non-piscivorous)
 L. Sp1\_ln.maxdepth: Sister Species 1 ln.maxdepth from FishBase (max depth
 in meters) M. Sp1\_ln.maxlength: Sister Species 1 ln.maxlength (max length
 in centimeters) N. Sp1\_ln.maxdepth.IUCN: Sister Species 1 ln.maxdepth
 from IUCN (max depth in meters) O. Sp2Habitat: Habitat Classification for
 Species 2 (Reef [R] or NonReef [NR]) P. Sp2Piscivory: Piscivory
 classification for Species 2 (Y = piscivorous, N = non-piscivorous) Q.
 Sp2\_ln.maxdepth: Sister Species 2 ln.maxdepth from FishBase (max depth in
 meters) R. Sp2\_ln.maxlength: Sister Species 2 ln.maxlength (max length in
 centimeters) S. Sp2\_ln.maxdepth.IUCN: Sister Species 2 ln.maxdepth from
 IUCN (max depth in meters)