DOI: 10.5061/dryad.6t1g1jx6b
title: Data from: Sources of gene tree discordance and their implications for systematics and evolution of a megadiverse Australian plant radiation (subtribe Hakeinae, Proteaceae)

description: Resolving phylogenetic relationships in the presence of conflicting signal
 across genes is one of the major challenges of the phylogenomic era.
 Conflicting signals can emerge from biological processes, such as
 incomplete lineage sorting or introgression, or have technical origins,
 such as from misaligned sequences. As such, decisions made in the process
 of estimating species trees may result in alternative tree topologies and
 large variation in branch support values with important systematic
 consequences. Here we compare alternative strategies for alignment
 cleaning, loci filtering, and phylogenetic estimation in 551 taxa in the
 Proteaceae subtribe Hakeinae, to explore how these methodological choices
 affect the estimation of relationships. We found that node support values
 across gene trees were low and gene discordance was high in the Hakeinae,
 particularly in lineages from the Temperate Forests biome of southeastern
 Australia. Higher stringency of alignment cleaning tended to decrease node
 support and filtering desirable loci tended to increase gene concordance.
 Cleaning, filtering, and phylogenetic estimation method (short-cut
 coalescent or concatenation) have significant effects of tree topologies
 with distinct clusters of similar tree topologies detected in tree space.
 Of note, when using concatenated approaches, the two largest Hakeinae
 genera, Hakea and Grevillea, were reciprocally monophyletic. However,
 using coalescent approaches, we regularly found that Hakea was nested
 within Grevillea. Our results suggest that widespread gene discordance may
 be the result of rapid radiation and incomplete lineage sorting,
 demonstrating the importance of assessing the drivers of discordance to
 understand phylogenetic relationships.
description: In short, This study used 551 sequences for 482 Proteaceae taxa,
 of which 186 sequences were obtained from an earlier study (Cardillo et
 al. 2017). These 186 sequences include 151 species of <em>Hakea,
 </em>four species of<em> Grevillea</em> (<em>G.
 dimorpha</em>, <em>G. evanescens</em>, <em>G.
 hookeriana</em>, and <em>G. batrachiodes</em>), and
 <em>Opisthiolepis heterophylla</em> of the Hakeinae, together
 with eight Proteaceae outgroup taxa: <em>Lomatia
 silaifolia</em>, <em>Stenocarpus davallioides</em>,
 <em>Alloxylon pinnatum</em>, <em>A. flammeum</em>,
 <em>Telopea speciosissima</em>, <em>Banksia
 paludosa</em>, <em>B. rufa</em>, and <em>Lambertia
 formosa</em>. In addition, 368 samples were collected for novel DNA
 extraction and sequencing, sourced from fresh plant tissue obtained from
 wild or cultivated plants, or from dried herbarium specimens (see Table S1
 for a list of samples). These included 320 species of
 <em>Grevillea</em> and <em>Finschia
 chloroxantha</em> from the Hakeinae, and additional Proteaceae
 outgroups: <em>Stenocarpus milnei</em>, <em>Oreocallis
 mucronata</em>, <em>Macadamia integrifolia</em>,
 <em>Adenanthos glabrescens</em>, <em>Lambertia
 formosa</em>, <em>Isopogon formosus</em>. Samples were
 sequenced using Anchored Hybrid Enrichment.
description: This README.txt file was generated 22.10.2024 by Alexander Skeels ##
 GENERAL INFORMATION 1\. Title of Dataset: Data from:
 'Paleoenvironments shaped biotic exchange of terrestrial vertebrates
 across Wallace’s Line' 2\. Author Information Corresponding
 Investigator Name: Dr Alexander Skeels Institution: Research School of
 Biology, Australian National University, 46 Sullivans Creek Rd, Acton, ACT
 0200, Australia Email:
 [alexander.skeels@gmail.com](mailto:alexander.skeels@gmail.com)
 Co-investigator 1 Name: Hervé Sauquet Institution: National Herbarium of
 NSW, Botanic Gardens of Sydney, Mount Annan, NSW, Australia / Evolution
 and Ecology Research Centre, School of Biological, Earth and Environmental
 Sciences, University of New South Wales, Sydney, NSW, 2052 Australia
 Co-investigator 2 Name: Austin Mast Institution: Department of Biological
 Science, Florida State University, 319 Stadium Drive, Tallahassee 32306,
 Florida, USA Co-investigator 3 Name: Peter H. Weston Institution: National
 Herbarium of NSW, Botanic Gardens of Sydney, Mount Annan, NSW, Australia
 Co-investigator 4 Name: Peter M. Olde Institution: National Herbarium of
 NSW, Botanic Gardens of Sydney, Mount Annan, NSW, Australia
 Co-investigator 5 Name: Zoe K.M. Reynolds Institution: Research School of
 Biology, Australian National University, 46 Sullivans Creek Rd, Acton, ACT
 0200, Australia Co-investigator 6 Name: Jéssica Fenker Institution:
 Research School of Biology, Australian National University, 46 Sullivans
 Creek Rd, Acton, ACT 0200, Australia / Sciences Department, Museums
 Victoria, 11 Nicholson Street, Carlton, VIC 3053, Australia
 Co-investigator 7 Name: Alan Lemmon Institution: Department of Scientific
 Computing, Florida State University, Tallahassee, Florida, USA
 Co-investigator 8 Name: Marcel Cardillo Institution: Research School of
 Biology, Australian National University, 46 Sullivans Creek Rd, Acton, ACT
 0200, Australia 3\. Date of data collation: 2015-2024 4\. Geographic
 location of data collection: Australia 5\. Recommended citation for this
 dataset: Skeels et al. (2024), Data from: Sources of gene tree discordance
 and their implications for systematics and evolution of a megadiverse
 Australian plant radiation (subtribe Hakeinae, Proteaceae) ## DATA &
 FILE OVERVIEW Description of dataset These data and R scripts were
 produced to infer the phylogenetic relationships among Proteaceae taxa in
 the subtribe Hakeinae and to investigate variation in node support and
 gene concordance.. Files: ### 1. Table\_S1\_R1.csv: Sequence labels for
 Hakeinae taxa ### 2. Data folder: includes all data used in this study
 2.1: data/AHE_March2022_TrimmedAlignments Description: 216 Anchored Hybrid
 Enrichment loci for 551 Hakeinae taxa and outgroups in fasta format 2.2:
 data/Hakeinae_ALA_records_cleaned.csv Description: Point occurence records
 for Hakeinae taxa from the Atlas of Living Australia 2.3:
 data/Hakeinae_biome_pam.csv Description: Presence/Absence Matrix across
 biomes in bioegoragphic realms for Hakeinae taxa. ### 3. Scripts folder:
 Contins R scripts used to replicate analyses 3.1:
 scripts/script_0_discordance_ms_functions.R Description: Custom functions
 used throughout R scripts. 3.2: scripts/script_1a_AHE_cleaning_H.R
 Description: Cleaning AHE alignments with the "heavy" treatment
 3.3: scripts/script_1a_AHE_cleaning_M.R Description: Cleaning AHE
 alignments with the "moderate" treatment 3.4:
 scripts/script_1c_AHE_cleaning_summary.R Description: Summarising cleaned
 AHE alignments with different statistics 3.5:
 scripts/script_2a_node_support_gene_trees.R Description: Getting node
 support values from gene trees 3.6:
 scripts/script_2b_node_support_concatenated.R Description: Getting node
 support valuers from concatenated trees 3.7:
 scripts/script_3a_filtering_gene_trees.R Description: Filtering gene trees
 3.8: scripts/script_4a_concordance_factors.R Description: Exploring gene
 and site concordance factors 3.9: scripts/script_5a_tree_space.R
 Description: Estimating and visualising topological differences in tree
 space 3.10: scripts/Script_6a_tip_concordance.R Description: Tip
 concordance factors across phylogeny and geography 3.11:
 scripts/script_7a_introgression_tests.R Description: ABBA-BABA tests for
 introgression ### 4. Outputs folder: Contains 8 subfolders. Each subfolder
 is generated and populated using the R scripts and Data 4.1:
 output/alignment_summaries Description: Two tables with summary statistics
 from multiple sequence alignment treatments. 4.2.1:
 node_support_LMH_raw.csv conatins summary metrics of node support values
 estimated in IQ-Tree. Columns are as follows: * tree = the tree ID
 corresponding to the position of that tree in the gene_trees set for L, M,
 and H alignment clenaing strategies (below); * locus = the correpsonding
 locus for each gene tree * mean_UFBoot= the mean ultrafast bootstrap value
 accross all nodes in the tree, estimated in IQ-Tree * mean_SHaLRT= the
 mean SH-like approximate likelihood ratio test value accross all nodes in
 the tree, estimated in IQ-Tree * prop_UFBoot = the proportion of ultrafast
 bootstrap value accross all nodes in the tree that are greater than 90,
 estimated in IQ-Tree * prop_SHaLRT= the proportion of SH-like approximate
 likelihood ratio test value accross all nodes in the tree that are greater
 than 80, estimated in IQ-Tree * all_set = the version of the cleaned
 alignment set (Low [L], Medium [M], and High [H]) 4.2.2:
 alignment_summary_LMH.csv contains summary statistics for the sampling
 density, length, and phylogenetic infromtion in each cleaned alignment
 set. Columns are as follows: * locus = the correpsonding locus for each
 alignment * n_seq = number of sequences in alignment * n_sites= length of
 the alignment * PIS_frac = fraction of sites with parsimony infromative
 characters * PIS_abs= absolute number of parsimony infromative sites *
 n_gaps = total number of missing data across all sequences * prop_gaps =
 proportion of total alignment that is missing data * mean_gaps = mean
 number of gaps per locus * n_amb = total number of ambigously called bases
 across all sequences * prop_amb = proportion of total alignment that is
 ambigously called bases * mean_amb = mean number of ambigously called
 bases per locus * n_invariant = number of invariant sites in each locus *
 n_partial_invariant = number of partially invaraint sites in each locus *
 prop_invariant = proportion of invaraint sites in each locus *
 prop_partial_invariant = proportion of partially invariant sites in each
 locus * version = the version of the cleaned alignment set (Low [L],
 Medium [M], and High [H]) 4.2: output/gene_trees Description: 14
 alternative sets of gene trees for the Hakeinae and outgroups estimated in
 IQ-Tree with different data prepparation methods. Phylogenetic trees are
 in Newick format. 4.3: output/species_trees Description: 12 species trees
 for the Hakeinae and outgroups. Three species trees were estimated with
 concatenated loci under different data cleaning strategies in IQTree
 (concatenated) and nine species trees were estimated from the gene tree
 sets with ASTRAL-III (coalescent) 4.4: output/cvR2T Description:
 coefficient of variation of root-to-tip distances for each gene tree
 estimated from three alternative alignment sets (Low [L], Medium [M], and
 High [H]). The data is organised as a seperated .rds file containing a
 list, with each list element corresponding the the tree ID (e.g.,
 placement of tree in the gene_trees and the "tree" column of the
 alignment_summary.csv) 4.5: output/gCF Description: Gene concordance
 factors estimated with IQ-Tree (--gcf) and associated standard outputs.
 4.6: output/sCF Description: Site concordance factors estimated with
 IQ-Tree (--scf) and associated standard outputs. 4.7: output/TCF
 Description: Tip Concordance Factors (TCF) null model results. This folder
 contains a table which shows the TCF value for each species based on each
 species tree with alternative phylogenetic inference methods (IQ-Tree =
 con), data cleaning (Low [L], Medium [M], and High [H]), and loci
 filtering (FL0, FL1, FL2). 4.8: output/ABBA_BABA Description: ABBA-BABA
 test results on cleaning and filtering treatments. The results for the
 ABBA-BABA test based on each of the 12 species-trees topologies are
 contained in seperate .rds files. Each file contans a list, with each
 element representing a ABBA-BABA test on a different triad and standadr
 output from the method of Rancilhac et al., 2021 (see main text for
 details). The folder also contains two further .rds files which show the
 results from 10,000 ABBA-BABA tests for deeper divergences across the tree
 for the H-FL2 and M-FL1 treatments. These files have a suffix
 "_10K.rds". ### 5. Figure\_S5 Cladograms of Hakeinae with
 alternative phylogenetic inference methods (ASTRAL-III and IQ-Tree), data
 cleaning (Low [L], Medium [M], and High [H]), and loci filtering (FL0,
 FL1, FL2) ### 6. Version Changes **Dec 2024:** Added addition accession
 numbers in Table S1 from backlogged samples