DOI: 10.5061/dryad.0gb5mkmff
title: Integrating host use and dispersal ability with species delimitation to unravel a cryptic radiation of photosynthetic sea slugs

description: Species delimitation models are important quantitative tools for
 facilitating the discovery of cryptic species and clarifying the
 boundaries between focal taxa. However, distinct evolutionary processes
 may promote diversification at different points in a radiation,
 complicating efforts to identify speciation processes and diagnostic
 characters. Moreover, traits like dispersal ability can have opposing
 effects on diversification rate versus population subdivision, which
 causes coalescent models to oversplit samples. In this study, we examined
 the effects of larval dispersal and host use on population structure and
 diversity in a Caribbean radiation of photosynthetic herbivores, sea slugs
 in the genus Elysia. We applied five species delimitation models (SDMs) to
 molecular datasets, and also performed phylogenetic analyses of
 evolutionary relationships and population-genetic structure within
 species. We further modeled ancestral use of host algae using Bayesian
 Inference methods. Datafiles archived here include input files for
 analyses such as DNA sequence alignments and Arlequin input files, and
 also output files generated by the
 program BayesTraits during ancestral state
 reconstruction of host use. The findings broadly supported six
 described taxa as well as a 7th, previously unrecognized taxon. However,
 species with less dispersive offspring were often oversplit by SDMs based
 on the multispecies coalescent. Surprisingly, species that spanned a major
 phylogeographic break were also likely to be split into multiple taxa by
 coalescent models, regardless of their dispersal ability. Some host shifts
 may have contributed to divergence, but others predated speciation,
 suggesting ecological specialization can promote reproductive isolation
 but often acted at deeper timescales; recent speciation was more often
 driven by sea level fluctuations and changes in reproductive anatomy,
 potentially reinforced by dispersal limitation.
description: # Integrating host use and dispersal ability with species delimitation to
 unravel a cryptic radiation of photosynthetic sea slugs Dataset DOI:
 [10.5061/dryad.0gb5mkmff](https://doi.org/10.5061/dryad.0gb5mkmff) ##
 Description of the data and file structure Index and description of DRYAD
 supporting data and output files associated with the article Krug et al.,
 “Integrating host use and dispersal ability with species delimitation to
 unravel a cryptic radiation of photosynthetic sea slugs”, ***Biological
 Journal of the Linnean Society*** (https:10.1093/biolinnean/blaf111). ###
 Files and variables #### File: 1_7spp_collapsed_outgroups.nex
 **Description:** Phylip-format input file for RaXML analysis containing
 collapsed COI haplotypes from candidate *Elysia* species (234 unique
 ingroup haplotypes) plus three related *Elysia* spp. as outgroups (3
 additional haplotypes). #### File: 2_7sppCOI.nex
 **Description:** Nexus-format *BayesPhylogenies* input file containing the
 same 237 COI haplotypes. #### File: 3_4runs_burnin_7sppCOI.nex.trees
 **Description:** Combined output of four runs of *BayesPhylogenies* after
 deleting the first 75% of each run as burnin, and pooling the remaining
 trees into one file to average phylogenetic uncertainty across runs; used
 to calculate posterior probability support for nodes, and as input for
 downstream comparative analyses. #### File: 4_7_spp__collapsed.fasta
 **Description:** Fasta-format input file of collapsed COI haplotypes used
 to calculate pairwise K80-corrected COI distances as input for ABGD and
 ASAP analyses. #### File: 5_Arlequin_input_2022_papillosa_v2.arp
 **Description:** Arlequin input file for *Elysia papillosa* population
 genetic structure based on COI haplotypes #### File:
 6_Arlequin_input_2022_patina.arp **Description:** Arlequin input file for
 *Elysia patina* population genetic structure based on COI haplotypes ####
 File: 7_Arlequin_input_2022_taino.arp **Description:** Arlequin input file
 for *Elysia taino* population genetic structure based on COI haplotypes
 #### File: 8_Arlequin_input_2022_zuleicae_v3.arp **Description:** Arlequin
 input file for *Elysia zuleicae* population genetic structure based on COI
 haplotypes #### File: 9_papillosa_network_v4_graphic.nex
 **Description:** POPART input file for the *Elysia papillosa* COI
 haplotype network, color-coding by sampling site. #### File:
 10_patina_network_v1_graphic.nex **Description:** POPART input file for
 the *Elysia patina* COI haplotype network, color-coding by sampling site.
 #### File: 11_taino_network_v2_graphic.nex **Description:** POPART input
 file for the *Elysia taino* COI haplotype network, color-coding by
 sampling site. #### File: 12_zuleicae_network_v4_graphic.nex
 **Description:** POPART input file for the *Elysia zuleicae* COI haplotype
 network, color-coding by sampling site. #### File:
 13b._host.txt.Log_3runs_pooledNEW.csv **Description:** Output of
 *BayesTraits* ancestral host reconstruction analyses for key nodes,
 estimating posterior probability of four possible host states using the
 pooled post-burnin tree sample to incorporate phylogenetic uncertainty
 into analyses. The command block at the top of the file includes portions
 of the output that indicate how the “AddNode” commands were set up to
 fossilize (fix) specific nodes for the analysis by indicating the tips
 (samples) contained within the nodes of interest. ## Access information
 Other publicly accessible locations of the data: * All gene sequences are
 deposited in the NCBI repository; full details are provided in
 Supplementary Table S1. Data was derived from the following sources: * NA