Topology testing and demographic modeling illuminate a novel speciation pathway in the Greater Caribbean Sea following the formation of the Isthmus of Panama

Recent genomic analyses have highlighted the prevalence of speciation with gene flow in many taxa and have underscored the importance of accounting for these reticulate evolutionary processes when constructing species trees and generating parameter estimates. This is especially important for deepening our understanding of speciation in the sea where fast-moving ocean currents, expanses of deep water, and periodic episodes of sea level rise and fall act as soft and temporary allopatric barriers that facilitate both divergence and secondary contact. Under these conditions, gene flow is not expected to cease completely while contemporary distributions are expected to differ from historical ones. Here we conduct range-wide sampling for Pederson’s cleaner shrimp (Ancylomenes pedersoni), a species complex from the Greater Caribbean that contains three clearly delimited mitochondrial lineages with both allopatric and sympatric distributions. Using mtDNA barcodes and a genomic ddRADseq approach..., , , **README:** The following supplementary material, methods, and data accompany the manuscript below which has been submitted for peer review at Systematic Biology

**Title:** Topology Testing and Demographic Modeling Illuminate a Novel Speciation Pathway in the Greater Caribbean Sea Following the Formation of the Isthmus of Panama.
**Authors:** Benjamin M. Titus, H. Lisle Gibbs, Nuno Simões, Marymegan Daly

**Supplemental Methods, Tables S1 and S3-S7, Figures S1:** Titus_etal_Aped_SysBiol_SuppMat.docx
**Supplemental TableS2:** TableS2_Aped_ddRADseq_stats.xlsx

**Datasets:**

*AP_COI_all_wOutgroups.fasta* - This file contains the aligned DNA barcode sequence data (mitochondrial cytochrome oxidase subunit I- COI) used for single locus species delimitation analyses for Ancylomenes pedersoni throughout the entire Tropical Western Atlantic, including outgroup taxa.

*Apedersoni_all_samples_Dataset1_SystBiol.str-* This file contains the Structure-formatted double digest Restriction-Site Asso...