DOI: 10.5061/dryad.8kprr4xzr
title: Contrasting phylogeographic patterns of sandy vs. rocky sympatric sister species of supralittoral Tylos isopods in Chile

description: Sister taxa that have diverged and persisted in sympatry have likely been
 exposed to the same general environmental changes throughout their
 evolutionary history and may thus exhibit similar phylogeographies. Here
 we compare the phylogeographic patterns of two sister species of isopods
 (genus Tylos) that have broadly overlapping distributions but distinct
 habitat preferences in the supralittoral zone of Chile. The dynamic
 geoclimatic history of this region during the Quaternary has been
 implicated in shaping the evolutionary histories of other coastal taxa.
 Tylos spinulosus is found in sandy beaches at latitudes ~27–30°S, whereas
 Tylos chilensis has been found in rocky shores at ~27–33°S and at
 ~39–42°S. We sampled both species across their ranges (collectively from
 20 localities) and obtained sequences from at least one mitochondrial gene
 for 95 T. chilensis and 41 T. spinulosus. We used phylogenetics and
 population genetics methods to analyze four single-gene and one
 concatenated datasets: 12S rDNA (n=130); 16S rDNA (n=31); Cytochrome
 oxidase subunit I (n=28); Cytochrome b (n=24); concatenation of the four
 genes (n=24). Both species show high levels of isolation of local
 populations, consistent with expectations from their limited autonomous
 dispersal potential. However, they exhibit strikingly different
 mitochondrial phylogeographic patterns. Tylos chilensis shows evidence of
 multiple relatively deep divergence events leading to geographically
 restricted lineages that appear to have persisted over multiple
 glaciations. Surprisingly, one lineage of T. chilensis was found in
 geographically distant localities, suggesting the possibility of
 human-mediated dispersal. Tylos spinulosus appears to have undergone a
 relatively recent bottleneck followed by a population/range expansion.
 Differences in life histories and habitat preferences or stochasticity may
 have contributed to these striking phylogeographic differences. Finally,
 the high levels of differentiation and isolation among populations
 indicate that they are highly vulnerable to extirpation. We discuss
 threats to their persistence, and recommendations for their conservation.
 This dataset includes: details about each of the specimens used in this
 study (Supporting Table S1); input and output files used to generate the
 haplotype networks depicted in the manuscripts; input and output files of
 the analyses used to generate the rooted phylogenies depicted in this
 manuscript (5 datasets: four single-gene and one concatenated); command
 line and input files used to infer isolation by distance in Tylos
 spinulosus (Mante test); and input and output files and detailed
 methodology for testing the molecular clock hypothesis and inferring
 genetic distances for two genes.
description: # Contrasting phylogeographic patterns of sandy vs. rocky sympatric sister
 species of supralittoral Tylos isopods in Chile Dataset DOI:
 [10.5061/dryad.8kprr4xzr](10.5061/dryad.8kprr4xzr) ## Description of the
 data and file structure ### 1. SupportingDatasetS1.zip contains the files
 used to generate the haplotype networks for *Tylos chilensis* and *Tylos
 spinulosus* in the program PopArt. Files/folders included: a.
 chilensis_haplotype_network folder contains: *
 Tylos_Chile_12S_90taxa_chilensis_for_popart.nex input file for PopArt:
 *Tylos chilensis* 12S rDNA alignment file in nexus format including the
 “traits” block where individuals are assigned to populations *
 ylos_Chile_12S_90taxa_chilensis_for_popartMJN.nex output file for PopArt
 for the preceding file. b. Spinulosus_haplotype_network folder contains: *
 Tylos_Chile_12S_spinulosus_for_DNAsp_39tax.nex input file for PopArt:
 *Tylos spinulosus* 12S rDNA alignment file in nexus format including the
 “traits” block where individuals are assigned to populations *
 Tylos_Chile_12S_spinulosus_forpopart40tax.nex output file for PopArt for
 the preceding file. ### 2. SupportingTableS1.zip Empty cells mean that
 data are not applicable. **a. File: TableS1_Sheet_11Jul2025.csv** (csv
 format of the first sheet in TableS1_Workbook_11Jul2025.xlxs) Descriptions
 of columns * Specimen_voucher: Identification number used to distinguish
 individual specimens in our lab * GenBank_Acc_12S: GenBank Accession
 Number of the 12S rDNA sequence (if applicable) * GenBank_Acc_16S: GenBank
 Accession Number of the 16S rDNA sequence (if applicable) *
 GenBank_Acc_COI: GenBank Accession Number of the Cytochrome Oxidase
 Subunit I sequence (if applicable) * GenBank_Acc_Cytb GenBank Accession
 Number of the Cytochrome b sequence (if applicable) * Included in
 concatenated dataset: * Yes = individual was included in the dataset that
 concatenated the four genes listed in preceding columns * No = individual
 was not included in the dataset that concatenated the four genes listed in
 preceding columns * Lat_Lon: Geographical coordinates of locality where
 specimen was collected in decimal units * TipLabelwithGB: One of the
 options for labeling individual in other files (e.g. in trees). *
 Locality_simple_name: Simplified name of collection locality * Organism:
 Species name * Name as in nexus file: Specimen label used in DNA sequence
 alignment file * Name as in fasta for GenBank: Specimen label used for
 submission of sequences to GenBank * TipLabelDraft: Another option for
 labeling individual in other files (e.g. in trees). * Desired Tip Label no
 spaces: Another option for labeling individual in other files (e.g. in
 trees). * Names: Another option for labeling individual in other files
 (e.g. in trees). * Desired Tip Label spaces: Another option for labeling
 individual in other files (e.g. in trees). * Locality Group: name given to
 nearby localities grouped into a single locality in maps and figures *
 species_ind_locality_gp: Another option for labeling individual in other
 files (e.g. in trees). * TipLabel_no_species: Another option for labeling
 individual in other files (e.g. in trees). * Date: date specimen was
 collected in the field * Site: Locality name with additional details for
 some specimens in parenthesis * Lat: Latitudinal coordinates of locality
 where specimen was collected in Degrees, Minutes, and Decimal Seconds *
 Long: Longitudinal coordinates of locality where specimen was collected in
 Degrees, Minutes, and Decimal Seconds * Fixation: when known, specimen
 preservation method. ETOH = ethanol * Collectors: names of individuals who
 collected specimens. In parenthesis, their institutions. Ulagos =
 Universidad de los Lagos; UCN = Universidad Catolica del Norte * Remarks:
 remarks on the specimens or the collection site during the time of
 collection * Molecular Work: First name of individual lab member who
 performed molecular work * “Lat Degrees” through “long decimal”: series of
 columns with used to convert formats of geographical coordinates *
 Sequence_ID: Another option for labeling individual in other files (e.g.
 in trees). * Fwd_primer_name: name of the forward primer used to amplify
 and sequence the 12S rDNA gene * Fwd_primer_seq: sequence of the forward
 primer used to amplify and sequence the 12S rDNA gene * Rev_primer_name:
 name of the reverse primer used to amplify and sequence the 12S rDNA gene
 * Rev_primer_seq: sequence of the reverse primer used to amplify and
 sequence the 12S rDNA gene * Collected_by: names of individuals who
 collected specimens. In parenthesis, their institutions. Ulagos =
 Universidad de los Lagos; UCN = Universidad Catolica del Norte *
 Collection_date: date specimen was collected in the field * Country:
 country where specimen was collected * Haplotype_Label_12SrDNA: 12S rDNA
 gene haplotype label * Haplotype label unique: list of unique 12S rDNA
 gene haplotypes * counts per haplotype: number of individuals per
 haplotype in the preceding column * haplotype frequency: frequency of
 haplotype in the preceding column (6 decimals) * frequency rounded: values
 in the preceding column rounded to 2 decimals **b. File:
 TableS1_Sheet_11Jul2025.csv** (csv format of the first sheet in
 TableS1_Workbook_11Jul2025.xlxs) * Sheet “TableS1” contains essentially
 the same data as “TableS1_Sheet_11Jul2025.csv”, but contains Excel
 formulas used to generate some of the contents. For description of
 columns, see for file “TableS1_Sheet_11Jul2025.csv”. * Sheet
 “sorted_by_sp_lat_date” contains essentially the same data as Sheet
 “TableS1” but reordered by species, latitude, and date, and color coded.
 Cell colors are intended to closely match locality/region colors used in
 figures. Different font colors within the same cell color are used to
 distinguish different localities within a region or different collection
 years within the same locality/region. * Sheet “Lat_Longs_Unique_Counts”
 contains the commands used to find unique geographic coordinates among the
 rows of sheet “TableS1”, and counts of the rows per each unique geographic
 coordinate values * Sheet “T_spi_01&05haps_individuals” contains a
 list of the specimens of *Tylos spinulosus* assigned to haplotypes
 T_spi_01 and T_spi_05 * Sheet “summary_table” was used to generate the
 Table 1 in the main text. ### 3. SupportingDatasetS2.zip contains 5
 folders. Each folder groups the files associated with the phylogenetic
 analyses of the four single-gene datasets and the concatenated dataset.
 Files names ending with “.phy” are the Phylip-formatted alignment files
 used in each analysis. In some cases, nexus- (.nex) and fasta- (.fas)
 formatted alignment files are also included. Files including “TipLabels”
 in the name, were used to replace tip label names in the resulting trees
 using the FigTree app. All remaining files are output files of the IQTree
 analyses. File names ending with “.log” provide the command line used and
 details on the output file names and contents. List of 5 folders: a.
 12S_rDNA_gene b. 16SrDNA_gene c. COI_gene d. Concatenated e. Cytb_gene ###
 4. SupportingDatasetS3.zip contains the input files and commands used to
 run the Mantel test. List of files: a.
 SuccessfulMantel_commands_results.txt contains the command line used in R
 b. Fst_matrix.txt contains the pairwise Fst distances used in the Mantel
 test (.txt format) c. Fst_matrix.csv contains the pairwise Fst distances
 used in the Mantel test (.csv format) d. geog_matrix.csv contains the
 pairwise geographic distances used in the Mantel test (.csv format) e.
 geog__no_L_matrix.csv contains the same information as “geog_matrix.csv”,
 but excludes the Lagunillas locality f. Fst_matrix_no_L.csv contains the
 same information as “Fst_matrix.csv”, but excludes the Lagunillas locality
 ### 5. SupportingDatasetS4.zip contains 3 folders and 2 files that
 collectively include the input files, commands, and formulas used to run
 the test the molecular clock hypothesis for the Cytb and COI genes, and
 the estimated Kimura-2-parameter (K2P) distances. List of files/folders:
 a. Methods_to_test_molecular_clock_and_estimate_pairwise_distances folder:
 contains the instructions and file names of the pipeline followed for
 these analyses in two formats * i.
 Methods_to_test_molecular_clock_and_estimate_pairwise_distances.md in
 MarkDown format * ii.
 Methods_to_test_molecular_clock_and_estimate_pairwise_distances.pdf in pdf
 format b. COI_dataset contains the files used to generate the tree used to
 test the molecular clock hypothesis for the COI gene dataset. Please see
 description of Supporting Dataset S2 for interpretation of files names. c.
 Cytb_dataset contains the files used to generate the tree used to test the
 molecular clock hypothesis for the Cytb gene dataset. Please see
 description of Supporting Dataset S2 for interpretation of files names. d.
 lrt_k2p_coi_cytb.xlsx is an Excel workbook containing processed output of
 Paup*. List of sheets: * i. k2p_cytb_271chars_24taxa contains the
 Kimura-2-parameter (K2P) distances inferred by Paup* for the Cytb dataset.
 * ii. k2p_coi_159chars contains the Kimura-2-parameter (K2P) distances
 inferred by Paup* for the COI dataset * iii. molec_clock_tests contains
 the Excel formulas used to conduct the Likelihood ratio test (LRT) to test
 the molecular clock hypothesis. e. k2p_cytb_271chars_24taxa.csv has
 identical contents to sheet “k2p_cytb_271chars_24taxa”, but in csv format
 f. k2p_coi_159chars.csv has identical contents to sheet
 “k2p_coi_159chars”, but in csv format.