Target-capture phylogenomics provide insights on gene and species tree discordances in Old World Treefrogs (Anura: Rhacophoridae)
Data files
Aug 20, 2020 version files 1.44 GB
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alignment_75complete_exon.phy
92.77 MB
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alignment_75complete_intron.phy
169.56 MB
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alignment_75complete_uce.phy
17.89 MB
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alignment_all-combined.phy
309.17 MB
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alignment_legacy.phy
1.73 MB
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alignment_pis50_exon.phy
85.75 MB
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alignment_pis50_intron.phy
162.79 MB
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alignment_pis50_uce.phy
14.27 MB
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alignment_unf_exon.phy
128.96 MB
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alignment_unf_intron.phy
259.56 MB
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alignment_unf_uce.phy
24.19 MB
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astral_75complete_exon.tre
2.49 KB
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astral_75complete_intron.tre
2.46 KB
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astral_75complete_uce.tre
2.48 KB
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astral_all-combined.tre
2.48 KB
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astral_legacy.tre
2.52 KB
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astral_pis50_exon.tre
2.48 KB
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astral_pis50_intron.tre
2.47 KB
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astral_pis50_uce.tre
2.48 KB
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astral_unf_exon.tre
2.49 KB
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astral_unf_intron.tre
2.47 KB
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astral_unf_uce.tre
2.49 KB
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genetrees_50PIS_exon
14.63 MB
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genetrees_50PIS_intron
14.25 MB
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genetrees_50PIS_uce
874.71 KB
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genetrees_75complete_exon
18.66 MB
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genetrees_75complete_intron
18.45 MB
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genetrees_75complete_uce
1.43 MB
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genetrees_all-combined
50.36 MB
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genetrees_legacy
74.52 KB
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genetrees_unf_exon
23.17 MB
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genetrees_unf_intron
25.59 MB
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genetrees_unf_uce
1.59 MB
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iqtree_75complete_exon.contree
2.92 KB
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iqtree_75complete_intron.contree
2.92 KB
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iqtree_75complete_uce.contree
2.92 KB
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iqtree_all-combined.contree
2.92 KB
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iqtree_legacy.contree
2.91 KB
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iqtree_pis50_exon.contree
2.92 KB
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iqtree_pis50_intron.contree
2.92 KB
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iqtree_pis50_uce.contree
2.92 KB
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iqtree_unf_exon.contree
2.92 KB
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iqtree_unf_intron.contree
2.92 KB
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iqtree_unf_uce.contree
2.92 KB
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partitions_75complete_exon.txt.txt
413.22 KB
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partitions_75complete_uce.txt.txt
21.70 KB
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partitions_all-combined.txt.txt
620.24 KB
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partitions_legacy.txt.txt
1.41 KB
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partitions_pis50_exon.txt.txt
314.11 KB
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partitions_pis50_intron.txt.txt
314.71 KB
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partitions_pis50_uce.txt.txt
15.04 KB
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partitions_unf_exon.txt.txt
638.61 KB
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partitions_unf_intron.txt.txt
637.68 KB
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partitions_unf_uce.txt.txt
30.32 KB
Aug 26, 2020 version files 364.98 MB
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Alignments.zip
293.68 MB
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ASTRAL_species_trees_GTR.zip
13.53 KB
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ASTRAL_species_trees_modeltest.zip
14.98 KB
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Genetrees_GTR.zip
29 MB
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Genetrees_modeltest.zip
41.27 MB
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IQTREE_consensus_trees_partitioned.zip
12.02 KB
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IQTREE_consensus_trees_unpartitioned.zip
16.45 KB
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Partitions.zip
974.38 KB
Oct 29, 2020 version files 364.98 MB
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Alignments.zip
293.68 MB
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ASTRAL_species_trees_GTR.zip
13.53 KB
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ASTRAL_species_trees_modeltest.zip
14.98 KB
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Genetrees_GTR.zip
29 MB
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Genetrees_modeltest.zip
41.27 MB
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IQTREE_consensus_trees_partitioned.zip
12.02 KB
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IQTREE_consensus_trees_unpartitioned.zip
16.45 KB
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Partitions.zip
974.38 KB
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SVDQuartets_T5.tre
2.09 KB
Abstract
Genome-scale data have greatly facilitated the resolution of recalcitrant nodes that Sanger-based datasets have been unable to resolve. However, phylogenomic studies continue to utilize traditional methods such as bootstrapping to estimate branch support; and high bootstrap values are still interpreted as providing strong support for the correct topology. Furthermore, relatively little attention is given to assessing discordances between gene and species trees, and the underlying processes that produce phylogenetic conflict. We generated novel genomic datasets to characterize and determine the causes of discordance in Old World Treefrogs (Family: Rhacophoridae)—a group that is fraught with conflicting and poorly supported topologies among major clades. We showed that incomplete lineage sorting was present at all nodes that exhibited high levels of discordance, which was caused by extremely short internal branches. We also clearly demonstrate that bootstrap values do not reflect uncertainty or confidence for the correct topology, and hence, should not be used as a measure of branch support in phylogenomic datasets. Overall, we showed that species tree inference can be improved using a total-evidence and multi-faceted approach that utilizes the most amount of data and considers results from different analytical methods and datasets.
This repository includes all relevant files required for reproducibility of the study:
1) Alignments (phylip format)
2) Partition files (for partitioned analysis of concatenated data)
3) IQ-TREE consensus trees
4) ASTRAL-III species trees
5) SVDQuartets species trees
6) Individual gene trees (estimated using IQ-TREE).