Does genome size increase with water depth in marine fishes?
Data files
Apr 21, 2022 version files 15.43 MB
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_Alignments.phy
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_B17_Backbone.tre
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_B17GB_CalibratedTree_2454spp.nex
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_Readme_Medeiros_etal_2022_DATASET.txt
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B17GB_AllSpp_v2_648spp.tre
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B17GB_AllSpp_v2_651spp_outgroups.tre
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B17GB_AllSpp_v2_SppNodeLength.tre
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Carangaria_Phase1_1.csv
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Carangaria_Phase1_2.csv
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Carangaria_RRPP_ARtree.tre
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Carangaria_RRPP_R18.tre
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Database_R18Gen.csv
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EEA71_B17GB_Spp.csv
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EEA71_B17GB_Spp.tre
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EEA71_R18Sim_Spp_100_trees_SppNodeLength.csv
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EEA71_R18Sim_Spp_100_trees_SppNodeLength.tre
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EEA71_R18Sim_Spp_100_trees.tre
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EEA71_R18Sim_Spp.csv
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EEA71_Spp_B17GB_trial1.csv
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EEA71_Spp_B17GB_trial10.csv
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EEA71_Spp_B17GB_trial11.csv
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EEA71_Spp_B17GB_trial19.csv
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EEA71_Spp_B17GB_trial2.csv
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EEA71_Spp_B17GB_trial20.csv
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EEA71_Spp_B17GB_trial22.csv
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EEA71_Spp_B17GB_trial3.csv
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EEA71_Spp_B17GB_trial5.csv
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EEA71_Spp_B17GB_trial6.csv
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EEA71_Spp_B17GB_trial7.csv
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EEA71_Spp_B17GB_trial8.csv
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EEA71_Spp_B17GB_trial9.csv
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EEA71_Spp_R18Sim_trial1.csv
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EEA71_Spp_R18Sim_trial10.csv
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EEA71_Spp_R18Sim_trial11.csv
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EEA71_Spp_R18Sim_trial12.csv
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EEA71_Spp_R18Sim_trial13.csv
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EEA71_Spp_R18Sim_trial14.csv
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EEA71_Spp_R18Sim_trial15.csv
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EEA71_Spp_R18Sim_trial16.csv
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EEA71_Spp_R18Sim_trial17.csv
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EEA71_Spp_R18Sim_trial18.csv
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EEA71_Spp_R18Sim_trial19.csv
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EEA71_Spp_R18Sim_trial2.csv
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EEA71_Spp_R18Sim_trial20.csv
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EEA71_Spp_R18Sim_trial21.csv
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EEA71_Spp_R18Sim_trial22.csv
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EEA71_Spp_R18Sim_trial23.csv
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EEA71_Spp_R18Sim_trial24.csv
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EEA71_Spp_R18Sim_trial3.csv
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EEA71_Spp_R18Sim_trial4.csv
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EEA71_Spp_R18Sim_trial5.csv
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EEA71_Spp_R18Sim_trial6.csv
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EEA71_Spp_R18Sim_trial7.csv
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EEA71_Spp_R18Sim_trial8.csv
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EEA71_Spp_R18Sim_trial9.csv
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Gobiaria_B17GB.tre
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Gobiaria_R18Gen.tre
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Labriformes_B17GB.tre
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Labriformes_R18Gen.tre
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Lutjaniformes_B17GB.tre
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Lutjaniformes_R18Gen.tre
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Lutjaniformes_RiconTree_RaxML_Pruned.tre
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Ovalentaria_B17GB.tre
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Ovalentaria_R18Gen_pruned_SppNodeLength.tre
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Ovalentaria_R18Gen.tre
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Pelagiaria_B17GB.tre
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Pelagiaria_Phase1_1.csv
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Pelagiaria_Phase1_2.csv
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Pelagiaria_Phase1_5.csv
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Pelagiaria_Phase1_6.csv
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Pelagiaria_R18Gen.tre
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Perciformes_B17GB.tre
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Perciformes_Phase1_1.csv
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Perciformes_Phase1_2.csv
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Perciformes_Phase1_5.csv
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Perciformes_Phase1_6.csv
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Perciformes_R18Gen.tre
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PGLS_AllSpp_B17GB_v2_648spp_trial1.csv
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PGLS_AllSpp_B17GB_v2_648spp.csv
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PGLS_AllSpp_B17GB_v2_648spp.nex
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PGLS_AllSpp_B17GB_v2_mvmorph.csv
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PGLS_AllSpp_B17GB_v2_SppNodeLength_mvmorph.csv
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PGLS_AllSpp_B17GB_v2_SppNodeLength.csv
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PGLS_AllSpp_B17GB_v2_SppNodeLength.nex
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PGLS_AllSpp_R18Gen_592spp_SppNodeLength_mvmorph.csv
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PGLS_AllSpp_R18Gen_592spp_SppNodeLength_mvmorph.nex
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PGLS_AllSpp_R18Gen_594spp_mvmorph.csv
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PGLS_AllSpp_R18Gen_594spp_mvmorph.nex
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PGLS_AllSpp_R18Gen_594spp.csv
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PGLS_AllSpp_R18Gen_594spp.nex
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PGLS_AllSpp_R18Gen_trial1_594spp.csv
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PGLS_AllSpp_R18Gen_trial1_594spp.nex
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PGLS_AllSpp_R18Sim_705_spp_SppNodeLength_100_trees.tre
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PGLS_AllSpp_R18Sim_705_spp_SppNodeLength_mvmorph.csv
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PGLS_AllSpp_R18Sim_705_spp_SppNodeLength.csv
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PGLS_AllSpp_R18Sim_708_spp_100_trees.tre
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PGLS_AllSpp_R18Sim_708spp_1tree.tre
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PGLS_AllSpp_R18Sim_SppNodeLength.csv
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PGLS_AllSpp_R18Sim_tree69.nex
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PGLS_AllSpp_R18Sim_trial1.csv
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PGLS_AllSpp_R18Sim.csv
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PGLS_Carangaria_B17GB.csv
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PGLS_Carangaria_B17GB.nex
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PGLS_Carangaria_R18Gen.csv
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PGLS_Carangaria_R18Gen.nex
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PGLS_Carangaria_R18Sim_tree69.nex
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PGLS_Carangaria_R18Sim.csv
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PGLS_Gobiaria_B17GB.csv
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PGLS_Gobiaria_R18Gen.csv
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PGLS_Gobiaria_R18Sim.csv
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PGLS_Labriformes_B17GB.csv
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PGLS_Labriformes_R18Gen.csv
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PGLS_Labriformes_R18Sim_tree69.nex
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PGLS_Labriformes_R18Sim_trial1.csv
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PGLS_Labriformes_R18Sim.csv
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PGLS_Lutjaniformes_B17GB.csv
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PGLS_Lutjaniformes_R18Gen.csv
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PGLS_Lutjaniformes_R18Sim_tree69.nex
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PGLS_Lutjaniformes_R18Sim.csv
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PGLS_Lutjaniformes_Rincon.csv
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PGLS_Ovalentaria_B17GB.csv
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PGLS_Ovalentaria_B17GB.nex
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PGLS_Ovalentaria_R18Gen_SppNodeLength.csv
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PGLS_Ovalentaria_R18Gen_SppNodeLength.nex
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PGLS_Ovalentaria_R18Gen.csv
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PGLS_Ovalentaria_R18Gen.nex
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PGLS_Ovalentaria_R18Sim_SppNodeLength.csv
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PGLS_Ovalentaria_R18Sim_tree69.nex
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PGLS_Ovalentaria_R18Sim.csv
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PGLS_Pelagiaria_B17GB.csv
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PGLS_Pelagiaria_B17GB.nex
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PGLS_Pelagiaria_R18Gen.csv
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PGLS_Pelagiaria_R18Gen.nex
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PGLS_Pelagiaria_R18Sim_tree69.nex
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PGLS_Pelagiaria_R18Sim.csv
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PGLS_Perciformes_B17GB.csv
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PGLS_Perciformes_B17GB.nex
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PGLS_Perciformes_R18Gen.csv
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PGLS_Perciformes_R18Sim_tree69.nex
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PGLS_Perciformes_R18Sim.csv
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PGLS_Spariformes_B17GB.csv
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PGLS_Spariformes_R18Gen.csv
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PGLS_Spariformes_R18Sim_tree69.nex
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PGLS_Spariformes_R18Sim.csv
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PGLS_Syngnatharia_B17GB.csv
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PGLS_Syngnatharia_R18Gen.csv
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PGLS_Syngnatharia_R18Sim_tree69.nex
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PGLS_Syngnatharia_R18Sim.csv
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PGLS_Tetraodontiformes_B17GB.csv
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PGLS_Tetraodontiformes_R18Gen.csv
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R18Gen_592spp_SppNodeLength.tre
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R18Gen_594spp.tre
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R18Gen_trial1_594spp.tre
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R18Sim_AllTrees_Carangaria.tre
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R18Sim_AllTrees_Gobiaria.tre
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R18Sim_AllTrees_Labriformes.tre
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R18Sim_AllTrees_Lutjaniformes.tre
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R18Sim_AllTrees_Ovalentaria_SppNodeLength.tre
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R18Sim_AllTrees_Ovalentaria.tre
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R18Sim_AllTrees_Pelagiaria.tre
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R18Sim_AllTrees_Perciformes.tre
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R18Sim_AllTrees_Spariformes.tre
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R18Sim_AllTrees_Syngnatharia.tre
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R18Sim_AllTrees_Tetraodontiformes.tre
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R18Sim_AllTrees_Zeiogadaria.tre
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Spariformes_B17GB.tre
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Spariformes_R18Gen.tre
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Tetraodontiformes_B17GB.tre
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Abstract
A growing body of research suggests that genome size in animals can be affected by ecological factors. Half a century ago, Ebeling et al. (1971; EEA71) proposed that genome size increases with depth in some teleost fish groups and discussed a number of biological mechanisms that may explain this pattern (e.g., passive accumulation, adaptive acclimation). Using phylogenetic comparative approaches, we revisit this hypothesis based on genome size and ecological data from up to 708 marine fish species in combination with a set of large-scale phylogenies, including a newly inferred tree. We also conduct modelling approaches of trait evolution and implement a variety of regression analyses to assess the relationship between genome size and depth. Our reanalysis of the EEA71 dataset shows a weak association between these variables, but the overall pattern in their data is driven by a single clade. While analyses based on the new dataset resulted in positive correlations, providing some evidence that genome size evolves adaptively as a function of depth, only a fraction of individual subclade analyses yielded statistically significant results. By contrast, negative correlations are rare and largely non-significant. All in all, we find modest evidence for an increase in genome size along the depth axis in marine fishes. We discuss some mechanistic explanations for the observed trends.