DOI: 10.5061/dryad.w9ghx3fzf
title: Global integration of phylogenomic data and fine-scale partitioning strategies refine the evolutionary tree of Adephaga beetles (Insecta: Coleoptera)

description: Over the past decade, genomic-scale data have revolutionized insect
 phylogenomics by allowing the generation of increasingly comprehensive
 genomic and taxonomic datasets. However, because different approaches have
 been used, it is often difficult to understand to what extent these data
 can be integrated to reconstruct evolutionary trees. In this study, we
 focus on the beetle suborder Adephaga to explore whether genomic data
 produced in the past decade can be combined to reconstruct the largest
 phylogenomic tree of this clade to date. To that end, we collected
 publicly available transcriptomes, genomes, and target sequence capture
 data of Adephaga beetles to generate a global dataset. Taking advantage of
 a newly developed bioinformatic pipeline, we demonstrate the overall
 compatibility of data types, especially of ultraconserved elements and
 exon-capture data. We also examined the impact of factors such as the
 treatment of off-target flanking genomic regions, data trimming regimes
 and partitioning, as well as varying levels of taxonomic and genomic
 sampling on phylogenomic inference. Using a matrix of 2,471 loci, we
 inferred the most comprehensive fossil-based evolutionary tree of Adephaga
 beetles. Our results confirm the independent colonization of aquatic
 ecosystems by two lineages. We also reconstruct Hygrobiidae as sister to
 Amphizoidae and a paraphyletic Aspidytidae, supporting the evolutionary
 convergence of prothoracic glands in both Hygrobiidae and Dytiscidae. Our
 results suggest an origin of Adephaga in the Carboniferous, with
 subsequent diversification of major lineages in the mid-Permian. Future
 efforts should focus on expanding the taxonomic sampling in Geadephaga,
 this clade of terrestrial beetles being the most diverse lineage in
 Adephaga and paradoxically one of the least sampled. To that end, we
 introduce a new ultraconserved element probe set tailored for Geadephaga
 beetles that will help generate compatible genomic data to further refine
 the Adephaga tree of life.
description: We combined several Adephaga genomic-level datasets available
 from the National Center for Biotechnology Information (NCBI) database
 https://www.ncbi.nlm.nih.gov/, DNA Read Archive of the DNA Database of Japan (DDBJ) https://www.ddbj.nig.ac.jp/, and the Dryad Digital Repository: https://datadryad.org. Sequence data is composed of anchored hybrid enrichment data (ExC), genomic assemblies (GEN), transcriptomes (TRA), and ultraconserved elements (UCE). In an early draft of this manuscript, ExC data was referred to as AHE; in the majority of these files, AHE was changed from AHE to ExC. However, in some cases, it was not reasonable to convert AHE to ExC; e.g., the “BOLD_characterization” and “Matrices” folders. Here we provide the output and scripts used to generate the characterization of loci, locus partitioning, and the resulting joined probeset from these analyses. We also provide the Gaedephaga UCE fasta file. Additional data analysis ouptut of IQTree2 for phylogenetic inferences, PDF's of the trees generated by IQTree2, the output of the SortaDate "gene shoping" approach, the BEAST analyses, along with the BEAST output files, the conserved locus analysis, MitoFinder's logs, and the Barcode of Life Database (BOLD) input COI bycatch and resulting BOLD output are found within.
description: # Global integration of phylogenomic data and fine-scale partitioning
 strategies refine the evolutionary tree of Adephaga beetles (Insecta:
 Coleoptera) Dryad DOI: https://doi.org/10.5061/dryad.w9ghx3fzf ##
 Supplemental_Tables_dryadcorrections.xlsx Each tab in the xlsx sheet is
 described here: #### SuppFile1_Taxa Taxa accessions, Locus Recovery, and
 BOLD IDs Table of all taxa used for analyses within this manuscript.
 Associated ID (Other Code), Accession codes (Code), references, species
 identity, locality, data source (type of data), locus recovery by probe
 source, assembly statistics (length, min, max, average length), and BOLD
 identification are available for each taxon results: queryID, best genus
 guess, best species guess, database search, percentage match, and lowest
 percentage match for bold ID. NA's in this sheet are data that are
 unavailable or not applicable. #### SuppFile1_MLTreeStats Four tables of
 maximum likelihood and information criterion values of trees generated in
 IQ-TREE2 Four tables presenting the results of phylogenomic tree
 inferences of the all and subset taxon sets split by partitioning scheme
 and locus coverage: A) locus partitioning and A) 30 % locus coverage and
 B) 40% locus coverage, followed by gene partitioning and C) 30% locus
 coverage and D) 40% locus coverage. Each subtable contains LL:
 Log-likelihood of the tree; unconstrained LL: Unconstrained log-likelihood
 (without tree); Free parameters: Number of free parameters (# branches + #
 model parameters); AIC: Akaike information criterion (AIC) score; AICc:
 Corrected Akaike information criterion (AICc) score; BIC: Bayesian
 information criterion (BIC) score; Consensus LL: Log-likelihood of
 consensus tree; RF dist: Robinson-Foulds distance between ML tree and
 consensus tree; lastly any sub header with (*) indicates that the
 consensus tree has higher likelihood than the ML tree found and the
 consensus tree should be used over ML tree. #### SuppFile1_prelim_notrim
 Preliminary aligned locus statistics, no trimming. Columns are standard
 output from
 [AMAS](https://github.com/marekborowiec/AMAS/tree/master) summary. All
 loci recovered from all taxa using the joined probeset without any
 trimming, with a number of summary statistics. ####
 SuppFile1_prelim_trimalauto Preliminary aligned locus statistics, trimAl
 auto trimming. Columns are standard output from
 [AMAS](https://github.com/marekborowiec/AMAS/tree/master) summary. All
 loci recovered from all taxa using the joined probeset with trimAl auto
 trimming, including a number of summary statistics. ####
 SuppFile1_prelim_gblocks Preliminary aligned locus statistics, Gblocks
 trimming. Columns are standard output from
 [AMAS](https://github.com/marekborowiec/AMAS/tree/master) summary. All
 loci recovered from AllTAxa using the joined probeset with Gblocks
 trimming set to default phyluce parameters, including a number of summary
 statistics if available. #### SuppFile1_AllTaxa-core AllTaxa core data
 Joined probest loci statistics Sequence count and length by locus before
 and after trimming with Gblocks and trimAl for the core curation dataset.
 Columns are the locus ID, the number of sequences, and length for the
 notrim, the number of sequences and length for the gblocks, the number of
 sequences and length for the trimal, the difference in sequences from the
 untrimmed and gblocks, the difference in sequence length of the untrimmed
 and gblocks, the difference in sequences from the untrimmed and trimal,
 the difference in sequence length of the untrimmed and trimal, and the
 probe source.  Any NA means the locus was not present or recovered in that
 probe set. #### SuppFile1_AllTaxa-core+flanking AllTaxa core+flanking data
 Joined probest loci statistics Sequence count and length by locus before
 and after trimming with Gblocks and trimAl for the core+flanking curation
 dataset. Columns indicate the locus ID, the number of sequences and length
 for the notrim, the number of sequences and length for the gblocks, the
 number of sequences and length for the trimal, the difference in sequences
 from the untrimmed and gblocks, the difference in sequence length of the
 untrimmed and gblocks, the difference in sequences from the untrimmed and
 trimal, the difference in sequence length of the untrimmed and trimal, and
 the probe source. Any NA means the locus was not present or recovered in
 that probe set. #### SuppFile1_AllTaxa-flanking AllTaxa flanking data
 Joined probest loci statistics Sequence count and length by locus before
 and after trimming with Gblocks and trimAl for the flanking curation
 dataset. Columns indicate the locus ID, the number of sequences and length
 for the notrim, the number of sequences and length for the gblocks, the
 number of sequences and length for the trimal, the difference in sequences
 from the untrimmed and gblocks, the difference in sequence length of the
 untrimmed and gblocks, the difference in sequences from the untrimmed and
 trimal, the difference in sequence length of the untrimmed and trimal, and
 the probe source. Any NA means the locus was not present or recovered in
 that probe set. #### SuppFile1_curation_notrim Two tables of alignment
 sequence counts and length pre-trimming A table of the alignment
 statistics before and after trimming for sequence curation methods and by
 probe origin in the joined probe set. Columns indicate the locus ID, the
 number of sequences and length for the notrim, the number of sequences and
 length for the gblocks, the number of sequences and length for the trimal,
 the difference in sequences from the untrimmed and gblocks, the difference
 in sequence length of the untrimmed and gblocks, the difference in
 sequences from the untrimmed and trimal, the difference in sequence length
 of the untrimmed and trimal, and the probe source. Any NA means the locus
 was not present or recovered in that probe set. ####
 SuppFile1_curation_stats Four tables of alignment sequence count and
 length differences post-trimming A table of the alignment differences
 after trimming for sequence curation methods and probe origin in the
 joined probe set after trimming. The difference is expressed as the number
 of sequences for the respective trimming methods data subtracted from the
 number of sequences from the untrimmed data. #### SuppFile1_gCFsCF Gene
 and Site concordance factor analysis results as output by IQTree
 concordance analysis. The resulting output of gene and site concordance
 factors with IQ-TREE2 using the 30% trimAL gene SubTaxa dataset. IQTree2
 concordance factor column information (from IQTree2): ID: Branch ID, gCF:
 Gene concordance factor (=gCF_N/gN %), gCF_N: Number of trees concordant
 with the branch, gDF1: Gene discordance factor for NNI-1 branch
 (=gDF1_N/gN %), gDF1_N: Number of trees concordant with NNI-1 branch,
 gDF2: Gene discordance factor for NNI-2 branch (=gDF2_N/gN %), gDF2_N:
 Number of trees concordant with NNI-2 branch, gDFP: Gene discordance
 factor due to polyphyly (=gDFP_N/gN %), gDFP_N: Number of trees decisive
 but discordant due to polyphyly, gN: Number of trees decisive for the
 branch, sCF: Site concordance factor averaged over 1000 quartets
 (=sCF_N/sN %), sCF_N: sCF in absolute number of sites, sDF1: Site
 discordance factor for alternative quartet 1 (=sDF1_N/sN %), sDF1_N: sDF1
 in absolute number of sites, sDF2: Site discordance factor for alternative
 quartet 2 (=sDF2_N/sN %), sDF2_N: sDF2 in absolute number of sites, sN:
 Number of informative sites averaged over 1000 quartets, Label: Existing
 branch label, and Length: Branch length. #### SuppFile1_Fossils Table of
 expanded fossil taxa. An expanded fossil table including the fossil name,
 number, suborder, placement, minimum age, family, subfamily, fossil code,
 deposit, reference, and exponential and lognormal prior settings for
 BEAUti and BEAST analyses. Column information: fossil: fossil name,
 Number: fossil ID on tree, Suborder: suborder, Placement Min. Age: minimum
 age (My), Family: family, Subfamily: subfamily, Fossil Code: if available,
 Fossil code/ID; deposit: geological deposition fossil was identified,
 References: fossil journal reference, BEAUti Exponential Prior Settings:
 exponential prior settings, and BEAUti Lognormal Prior Settings: log
 normal prior settings. N/A= not applicable. #### SuppFile1_ExpTime
 Exponential divergence time analysis time estimates Estimated dates of the
 fossils used to calibrate the Bayesian timetree in the exponential
 analysis. Columns include: lognormal_taxon: fossils, tree number: node in
 tree, mean (Ma), stderr of mean: standard error of mean, stdev: standard
 deviation, variance, median (Ma), value range: rante of divergence
 estimates, geometric mean 95%, HPD interval: highest posterior density
 interval, auto-correlation time (ACT), effective sample size (ESS), number
 of samples. #### SuppFile1_LogNormTime Log normal divergence time analysis
 time estimates Estimated dates of the fossils used to calibrate the
 Bayesian timetree in the log-normal analysis. Columns include:
 lognormal_taxon: fossils, tree number: node in tree, mean (Ma), stderr of
 mean: standard error of mean, stdev: standard deviation, variance, median
 (Ma), value range: rante of divergence estimates, geometric mean 95%, HPD
 interval: highest posterior density interval, auto-correlation time (ACT),
 effective sample size (ESS), number of samples. #### SuppFile1_cogenic
 Cogenic loci found in the Pterostichus madidus genome. Counts for
 annotated genes in the *P. madidus* genome where more than one probe from
 the joined probe set map. Includes the partition ID and count of cogenic
 loci. #### SuppFile1_LMM Table of linear mixed effects model of the
 conservedness of loci The resulting summaries of the most likely linear
 mixed effect model (LMM) fit by maximum likelihood are presented for the
 (A) informative sites and (B) invariant sites. Estimated variance of the
 LMM for the (C) informative and (D) invariant sites. Significance testing
 of the LMM for the (E) informative and (F) invariant sites. --- ##
 Supplemental_pdf's ### Supplemental_1.pdf supplemental analyses,
 figures, and tables. ### Supplemental_2.pdf Phylogenetic trees from the
 all data set analyses. Trees are named in the top right with the data set,
 partitioning scheme, curation method, and locus occupancy; e.g.,
 all_gene_core_trimal_30p. ### Supplemental_3.pdf Phylogenetic trees from
 the subset data set analyses. Trees are named in the top right with the
 data set, partitioning scheme, curation method, and locus occupancy; e.g.,
 subset_gene_core_trimal_30p. ### Supplemental_4.pdf Phylogenetic analyses
 of the subset data set, analyses for the wASTRAL, and the gene and site
 concordance factor analyses of the subset. Trees are named in the top
 right with the data set with the preferred tree and analysis; e.g.,
 subset-gene-core-trimal-30p_wASTRAL. --- ## Supplemental_data2.zip In this
 zip folder, in the directory `_data`, there is one file and several
 subdirectories described here. The joined probe set used in all analyses
 is found here * **Note** \ In an early draft of this manuscript, ExC data
 were referred to as AHE. In the majority of these files, AHE was changed
 from AHE to ExC. However, in some cases it was not reasonable to convert
 AHE to ExC; e.g. the “BOLD_characterization” and “Matrices” folders. ###
 BEAST Within this directory, there are: * Combined log files * combined
 time and treeannattator tree files * XML files generated by BEAUTi for the
 exponential and lognormal analyses. * chrono tree used in the analyses ###
 BOLD_Taxonomy_ID Within this directory, there are: * Multi-fasta of COI
 genes * BOLD trees of select taxa * BOLD Search report as a PDF & XLS
 * BLAST search results of select taxa * MitoFinder logs for all samples *
 GenBank mitochondrial genome references for MitoFinder search As a note,
 the XLS files generated by BOLD are output from the BOLD database search
 and contain empty cells. ### characterization Within this directory are:
 ##### 1genefeatures output from processing of the genomic fasta files to
 generate introns and intergenic gene features ##### 2mapping output of the
 mapping of probes to the genome ##### 3intersect output of the
 identification of intersecting robes ##### 4probe-reduction output of the
 identification and subset of probes that do intersect the preferred probe
 set (Adephaga, UCE-Ade) ##### 5join-probes output of the probes that
 remain and are used to create the joined probe set ##### 6group-by output
 of remapping the probes to the preferred genome and creation of the
 modified partition file based on probes that are found to be on the same
 gene ##### Characterization_analysis R script to process and describe the
 joined and Adephaga probe sets ##### cogenic-loci R script to describe the
 number of cogenic loci found (from the 6-group-by output) #####
 mapping_analysis R script to describe the number of loci recovered by
 probe set for all taxa ### Matrices General directory structure: ``` . ├──
 all-gene │ └── core+flanking │ └── gblocks_30p ├── subset-loci │ └──
 core+flanking │ └── gblocks_30p ``` All data here are loci recovered using
 the joined probe set designed for in-silico capture/recovery of sequence
 data with Phyluce for alignment and trimming. Sub-directories for IQ-TREE2
 analyses for all and subset taxon data sets, for both the loci and gene
 partitioning. Each contains the CORE, CORE+FLANKING, FLANKING, and 30%
 & 40% taxa per locus. All taxon data sets have both trimal and gblocks
 data. The subset taxon set has only trimal. For example: ``` all-gene ├──
 core │ ├── gblocks_30p │ ├── gblocks_40p │ ├── trimal_30p │ └── trimal_40p
 ├── core+flanking │ ├── gblocks_30p │ ├── gblocks_40p │ ├── trimal_30p │
 └── trimal_40p └── flanking ├── gblocks_30p ├── gblocks_40p ├── trimal_30p
 └── trimal_40p ``` Within each taxon set, "all" directories
 contain output files from IQTree2 * the associated nexus matrix and
 partition files used as input for partition analyses -the resulting
 partition analyses partitions * IQ-TREE2 log files * IQ-TREE2 iqtree file
 * IQ-TREE2 newick tree files Taxon subset data has a slightly different
 data prefix due to additional analyses that are described in the next
 section. #### subset data Within the Subset taxon data sets in the same
 directory containing the IQ-TREE2 files are the associated wASTRAL and
 concordance analyses files (`subset-gene-core-trimal_30p`). * concatenated
 locus/gene IQ-TREE2 log file (`gene-tree.*`) * concatenated locus/gene
 iqtree file (`gene-tree.iqtree`) * concatenated locus/gene newick tree
 files generated by IQ-TREE2 (`gene-tree.treefile`) * concordance analysis
 log file (`concordance_*`) * concordance analysis tree file * wASTRAL tree
 file (`wASTRAL_*`) Because there is a slightly different workflow for
 concordance and wASTRAL analyses, there is a different prefix. Loci with
 similar partitioning models are not merged to create locus/gene trees.
 Files prefixed with `nomerege_*` indicate that during the search for the
 optimal partition, the loci were not merged after. Files prefixed with
 `UFB_*` indicate that the partition search was performed with
 IQ0-TREE2's *MF+MERGE* option. ### SortaDate Contains subdirectories
 ##### IQ-TREE2 output of IQTREE2 for the model finder of the partition
 finder2 output ##### partitionfinder2 output of the partitioning scheme of
 partition finder ##### SortaDate output of the sort date analysis #####
 These are the files and outputs used for the SortaDate analysis.
 `core_parti-gene_30p.rr.tree` The tree file used in the sortadate analysis
 ##### `core_SORTADATE.*` Files were generated using AMAS after identifying
 the best partitioning scheme from PartitionFinder2 and IQ-TREE2 --- ##
 GeaSub_2.9kv1.fasta The new ultra-conserved element probe set designed for
 Geadephaga