DOI: 10.5061/dryad.ht76hdrm0
title: Supplementary data from: Species delimitation under allopatry: Genomic insights within and across continents in Lepidoptera

description: Delimitation of allopatric populations into species remains subjective and
 largely arbitrary. Many cold-adapted species from the subarctic and
 Central and Southern European Mountain systems display frequent allopatry
 with disjunct distributions of their populations. The same concerns
 Holarctic species which are many and which almost regularly show various
 degrees of differentiation between the continents. In this study, we
 analyze high-throughput target enrichment data for ten groups of
 arctic-alpine and Holarctic lepidopteran species sampled from four main
 regions across the Holarctic realm – Fennoscandia, North America, Alps and
 Altai. We first aimed to assess whether the genetic differences in the
 nuclear genome reflect observed DNA barcode divergences and second,
 whether the gap between population and species-level differences can be
 dissected using genomic data. We compared the phylogenetic trees and
 uncorrected pairwise genetic distances obtained from target enrichment and
 the mitochondrial cytochrome oxidase I (COI) barcodes for each of the
 study species. Additionally, we also performed a suite of population
 genetic and species delimitation analyses to further shed light on
 patterns of intraspecific variation using a large number of nuclear
 markers. We observed that in about one half of the cases, DNA barcodes
 tended to show phylogenetic relationships similar to the target enrichment
 markers. We report varying levels of nuclear genetic differentiation among
 the populations analyzed, starting from low differentiation of
 geographically separated populations to the deeper separation of some
 Nearctic population and further arctic-alpine disjunction. Given that no
 single consistent pattern emerged across different case studies, we
 demonstrate that the delimitation of allopatric populations into species
 could be done much more efficiently and in a consistent manner if based on
 a large set of universal genetic loci, which would help in reaching
 standards for taxonomic delimitation of allopatric populations.
description: The nuclear genomic data was generated using target enrichment
 method. Barcodes were generated through standard barcoding lab protocol
 and sanger sequencing. The raw target enrichment data was processed using
 TEnriAn pipeline (Mayer et al. 2021) which is specifically designed for
 processing of target enrichment data. The downstream phylogenetic and
 other analyses were carried out using commonly used programs such as
 IQtree (version 2), STRUCTURE, etc., and species delimitation analyses
 were carried out using programs tr2 and SODA.  The
 barcode sequences were processed using Geneious Prime to generate the
 multiple sequence alignments and phylogenetic trees were generated using
 IQtree 2.  For other analyses such as PCA and
 generating P-distance plots, R packages <em>adegenet</em> and
 <em>ggplot2 </em>were used. 
description: To open the Maximum likelihood phylogenetic trees and ASTRAL
 trees (ending with .treefile or .tre), FigTree program would be needed.
 Nucleotide alignments can be viewed using any alignment editor such as
 AliView, Geneious. The vcf files can be read using vcfR package in
 R. 
description: # Supplementary data from: Species delimitation under allopatry: Genomic
 insights within and across continents in Lepidoptera ### Description of
 files This folder contains the data files associated with the manuscript
 titled 'Species Delimitation Under Allopatry: Genomic Divergences
 Within and Across Continents in Lepidoptera'. The description of the
 contents of the folder is given below. (NOTE: Upon secondary inspection of
 individual locus alignments for Arctia caja, non-homologous sequences
 corresponding to the sample represented by a long-branch in ML
 phylogenetic tree were found for *Arctia caja*. Such sequences were
 removed and the concatenated and loci files were constructed again for
 *Arctia caja*).  1. Files ending with '_new_astral.tre' -
 Contains phylogenetic trees inferred using ASTRAL for all 9 species except
 *Arctia caja*. The ASTRAL tree for *Arctia caja* is represented in
 file 'Arctia_caja_astral_corrected_filtered.tre' 2. Files ending
 with '_Barcode_alignment_with_outgroup.fas' - Contains barcode
 alignments used as an input to infer barcode tree 3. Files ending with
 '_Barcodes_alignment_with_outgroup.fas.treefile' - Contains
 Maximum Likelihood phylogenetic trees inferred for barcodes using IQtree
 4. Files ending with '_new_concat.fas' - Concatenated
 supermatrix and input file used to infer Maximum likelihood tree for
 target enrichment dataset using IQtree 5. Files ending with
 '_new_loci.treefile' - Gene trees inferred for each study
 species using IQtree 6. Files ending with
 '_partitioned_tree.treefile' - Maximum Likelihood phylogenetic
 trees inferred for each study species using IQtree 7. vcf files - SNPs in
 vcf file format for each study species after first and second filtering
 (ending with \_filtered) step respectively 8. Supplementary_file_v.2.docx
 - Supplementary file 9. tsv files ending with '_species_samples'
 contains a key for each species linking specimen names from treefiles
 above to their respective sample codes 10. File
 'Arctia_caja_new_concat_corrected.fas' is corrected concatenated
 supermatrix file for *Arctia caja* after removing non-homologous sequences
 from its alignment. Similarly,
 'Arctia_caja_loci_corrected.treefile' is corrected loci file and
 'Arctia_caja_astral_corrected_filtered.tre' is ASTRAL tree based
 on these loci.  The target enrichment raw data is available from SRA under
 BioProject PRJNA922447. All the newly generated barcodes from this study
 have been deposited on BOLD database.