DOI: 10.5061/dryad.5qfttdzcb
title: Topology testing and demographic modeling illuminate a novel speciation pathway in the Greater Caribbean Sea following the formation of the Isthmus of Panama

description: 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, we
 combine classic phylogenetic analyses with extensive topology testing and
 demographic modeling (10 site frequency replicates x 45 evolutionary
 models x 50 model simulations/replicate = 22,500 simulations) to test
 species boundaries and reconstruct the evolutionary history of what was
 expected to be a simple case study. Instead, our results indicate a
 history of allopatric divergence, secondary contact, introgression, and
 endemic hybrid speciation that we hypothesize was driven by the final
 closure of the Isthmus of Panama and the strengthening of the Gulf Stream
 Current ~3.5 million years ago. The history of this species complex
 recovered by model-based methods that allow reticulation differs from that
 recovered by standard phylogenetic analyses and is unexpected given
 contemporary distributions. The geologically and biologically meaningful
 insights gained by our model selection analyses illuminate what is likely
 a novel pathway of species formation not previously documented that
 resulted from one of the most biogeographically significant events in
 Earth’s history.
description: **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 Associated DNA sequence
 data produced for Ancylomenes pedersoni throughout the entire Tropical
 Western Atlantic. It is referred to as Dataset 1 in the manuscript and was
 used for genetic clustering and species delimitation analyses.
 *AP_spdelim_noOutgroup_Dataset3.str*- This file contains the
 Structure-formatted double digest Restriction-Site Associated DNA sequence
 data produced for Ancylomenes pedersoni used for the generation of the
 allele frequency spectrum simulation analyses in fastsimcoal2. This
 dataset is referred to as Dataset 3 in the manuscript.
 *AP_SNAPP_spTree_Dataset2.xml*- This file contains the SNAPP-formatted
 .xml file generated from double digest Restriction-Site Associated DNA
 sequence data produced for Ancylomenes pedersoni. This dataset is referred
 to as Dataset 2 in the manuscript and was used for species tree
 phylogenetic analyses in SNAPP *AP_SVDquartets_Dataset2.nexus*- This file
 contains the SVD-quartets-formatted .nexus file generated from double
 digest Restriction-Site Associated DNA sequence data produced for
 Ancylomenes pedersoni. This dataset is referred to as Dataset 2 in the
 manuscript and was used for species tree and phylogenetic analyses in
 SVD-Quartets *AP_AIC_modelselection_results.xlsx- *This file contains the
 model selection results from fastsimcoal2 demographic analyses for
 Ancylomenes pedersoni. In the file AP_AICmodelselection_results.xlsx *k* =
 number of parameters in the model, AIC = Akaike Information Criterion, ∆I
 = change in AIC scores, and *wi* = Akaike weights. Prefixes on model names
 refer to variation in model type and tree topology: A = ((Caribbean,
 (Florida, Bermuda)); B = ((Florida, (Caribbean, Bermuda)); C = ((Bermuda,
 (Caribbean, Florida)); Isl = Island Model; Hyb = Hybridization model; Sim
 = simultaneous divergence model. Models are listed according to their AIC
 rank and the highest ranked model is highlighted. Multidemensional Site
 Frequency Spectrum Replicates: The below files (.obs) represent the 10
 allele frequency spectrums that were produced for Ancylomenes pedersoni
 demographic analyses in fastsimcoal2 from Dataset 3
 (*AP_spdelim_noOutgroup_Dataset3.str).* Rep0_MSFS.obs Rep1_MSFS.obs
 Rep2_MSFS.obs Rep3_MSFS.obs Rep4_MSFS.obs Rep5_MSFS.obs Rep6_MSFS.obs
 Rep7_MSFS.obs Rep8_MSFS.obs Rep9_MSFS.obs