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.

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 phyluce 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.

UCE sequence data were processed prior to phylogenetic analyses with phyluce v1.6.

Downstream analyses were conducted in R v3.5.2.