DOI: 10.5061/dryad.mw6m905xb
title: Dugesia (Tricladida, Platyhelminthes) Cox1, 18S, 28S, ITS-1, DUNUC3, DUNUC5 datasets for worldwide biogeographic study

description: Aim: Freshwater planarians may have a wide geographic range despite their
 assumed low vagility. Found across four continents, Dugesia may have
 either an ancient origin on a large paleo landmass, followed by
 colonisation in different regions before continental fragmentation, or a
 more recent origin and subsequent transoceanic dispersal. We seek to
 resolve between these two hypotheses. Location: Africa, Eurasia, and
 Australasia Taxon: Genus Dugesia (Platyhelminthes: Tricladida: Dugesiidae)
 Methods: We used data from the sequencing of six gene fragments and
 comprehensive taxonomic sampling of Dugesia from across its distribution
 range to reconstruct the phylogeny of this genus using maximum likelihood
 and bayesian inference methods. We conducted two phylogenetic dating
 analyses using Platyhelminthes fossils and palaeogeological events. Basing
 on the time-calibrated molecular phylogenetic framework we evaluated the
 contribution of vicariance and dispersal to the biogeographic evolution of
 Dugesia. By reconstructing the ancestral areas and present-day potential
 distribution using BioGeoBEARS and niche modelling, we elucidated the
 biogeographic history of the genus. Results: The present-day distribution
 of Dugesia is a result of different vicariance and dispersal events.
 However, we also found evidence of transoceanic dispersal. Consistent with
 previous hypotheses, Dugesia dates to the Upper Jurassic in the
 Afro-Malagasy Gondwana region. We unveiled a novel biogeographic scenario
 for the genus, involving multiple events of colonisation in Eurasia from
 continental Africa via at least three dispersal routes. Main conclusions:
 Dugesia is an ancient genus having reached its present distribution
 through a complex history of dispersal and vicariant events following its
 origin in southern Gondwana. Despite the low vagility of Dugesia, we found
 evidence of their overseas dispersal.
description: <strong>DNA extraction, PCR and
 sequencing.</strong> Total genomic DNA extraction was carried out
 using either DNAzol® (Molecular Research Center Inc. Cincinnati, OH) or
 the Wizard® Genomic DNA Purification Kit (Promega, Madison, WI, USA),
 following the manufacturer's instructions. The following gene
 fragments were amplified by polymerase chain reaction (PCR): (1) the
 mitochondrial gene cytochrome c oxidase subunit I (Cox1); from the nuclear
 ribosomal cluster (2) 18S ribosomal gene (18S), (3) 28S ribosomal gene
 (28S), and (4) the ribosomal internal transcribed spacer-1 (ITS−1);
 finally, two other anonymous nuclear makers coined elsewhere as (5) DUNUC3
 and (6) DUNUC5 (Leria et al., 2020.
 https://doi.org/10.1016/j.ympev.2019.05.010). 
 <strong>Alignment.</strong> Nuclear genes were
 aligned using the online software MAFFT version 7 under the G-INS-i
 algorithm (Katoh & Standley, 2013.
 https://doi.org/10.1093/molbev/mst010). The intronic region of DUNUC5 was
 curated by eye after alignment using Geneious 10.2.3
 (https://www.geneious.com,  Kearse et al., 2012). The Cox1 sequences were
 translated into amino acid sequences (genetic code 9 in NCBI) to verify
 the absence of stop codons. Thereafter, Cox1 sequences were aligned using
 the translation align function in Geneious 10.2.3 ('MAFFT
 alignment' option). All alignments were also inspected by eye in
 Geneious 10.2.3. Four datasets were prepared for the
 different analyses. Dataset I included 18S, 28S, DUNUC3, Cox1 for
 <em>Dugesia</em> representatives and used
 <em>Recurva</em> and <em>Schmidtea</em> as
 outgroups, to root the <em>Dugesia</em> (Sluys et al., 2013.
 https://doi.org/10.1111/zoj.12077). Dataset II included Cox1, 18S, 28S,
 ITS-1, DUNUC3, DUNUC5 analysed concatenated or independently (no outgroup
 included), to obtain the phylogenetic trees and to carry out dating
 analyses. Dataset III is constituted by 18S gene sequences from Catenulida
 and Rhabditophora (including Tricladida) representatives, and a
 chaetognath species as outgroup to run a dating analysis. Dataset IV, to
 run biogeographical analyses, was obtained by pruning dataset II to
 include only one representative per biogeographical region but including
 at least one representative per clade (species of
 <em>Recurva</em> and <em>Schmidtea</em> were used
 as outgroup representatives), in this dataset each gene was analysed
 independently.
description: Four datasets were prepared
 for the different analyses: Dataset I includes 18S, 28S,
 DUNUC3, Cox1 concatenated for <em>Dugesia</em> representatives
 and used <em>Recurva</em> and <em>Schmidtea</em>
 genera as outgroups, to root the <em>Dugesia </em>(Sluys et
 al., 2013).<em> </em> Dataset I (4,444
 bp): 18S - 1 -
 1,737 28S - 1,738 -
 3,316 Dunuc3 - 3,317 -
 3,688 Cox1 - 3,689 -
 4,444 Dataset II includes 18S, 28S,
 Cox1, DUNUC3, DUNUC5, ITS-1 concatenated (no outgroup included), to obtain
 the phylogenetic trees and to carry out dating analyses.
 Dataset II (5,501
 bp): 18S - 1 -
 1,607 28S - 1,608 -
 3,184 Cox1 - 3,185 -
 3,934 Dunuc3 - 3,935 -
 4,300 Dunuc5 - 4,301 -
 4,622 ITS-1 - 4,623 -
 5,501 Dataset III is constituted by 18S
 gene sequences from Catenulida and Rhabditophora (including Tricladida)
 representatives, and a chaetognath species as outgroup to run a dating
 analysis. Dataset
 IV, to run biogeographical analyses, was obtained by pruning dataset II to
 include only one representative per biogeographical region but including
 at least one representative per clade (species of <em>Recurva
 </em>and <em>Schmidtea</em> were used as outgroup
 representatives). Dunuc2 alignment includes the
 sequences obtained for these nuclear gene fragment. Since few sequences
 were obtained they were not analysed in the paper, nonetheless they have
 been uploaded to GenBank, and the data on exon and intron limits is given
 in a table on the paper. See readme file for more details
 on the datasets