Improved phylogenetic resolution within the Neotropical rainforest genus Zygia (Mimoseae, Fabaceae) using phylogenomic data
Introduction: The Neotropical legume genus Zygia consists of approximately 60 species of small, cauliflorous trees. Phylogenetic relationships within Zygia are not fully known since previous phylogenies were for the most part poorly supported and unresolved with non-monophyletic species. Previous studies have shown that the genus Marmaroxylon is nested within Zygia, but a full sample of Marmaroxylon has yet to be included in analyses. This study aims to resolve taxonomic limits of Zygia and to test if phylogenomic data and more sampling of taxa improves resolution within the genus.   Methods: We utilize data from 1315 nuclear loci sequenced from 134 accessions, representing 47 species of Zygia, as well as four species of the closely related genus Macrosamanea, the poorly known Marmaroxylon magdalenae, endemic to the Magdalena Valley in Colombia and Marmaroxylon eperuetorum, which is the last remaining species of Marmaroxylon not tested with DNA data. The data is analyzed using species tree reconstruction based on the multispecies coalescent model and maximum likelihood analyses of concatenated datasets.  Results: Our phylogenetic analysis showed that the core Zygia clade is sister to a clade consisting of Macrosamanea, Zygia turneri, Marmaroxylon magdalenae, Inga, Ingopsis and Pseudocojoba. Zygia is non-monophyletic since Z. turneri is more closely related to Marmaroxylon magdalenae and Macrosamanea than to remaining species of Zygia. Marmaroxylon eperuetorum is found within the core Zygia clade. Resolution within Zygia clearly improved with phylogenomic data and denser sampling of taxa, but non-monophyletic species are still present. Discussion: The core Zygia clade is strongly supported statistically and relationships within it are well-resolved. However, 13 species of Zygia are non-monophyletic and the reasons for this are not yet fully known but could be due to e.g., misidentification, hybridization or incomplete lineage sorting. Both species trees reconstructed based on the multispecies coalescent model and phylogenetic trees inferred from maximum likelihood analyses of the concatenated datasets show similar topologies. Gene tree discordance is high for many branches within Zygia and is in most cases due to incomplete lineage sorting. To render Zygia monophyletic new combinations in Macrosamanea are given for Z. turneri and Marmaroxylon magdalenae.
Introduction: The Neotropical legume genus Zygia consists of approximately 60 species of small, cauliflorous trees. Phylogenetic relationships within Zygia are not fully known since previous phylogenies were for the most part poorly supported and unresolved with non-monophyletic species. Previous studies have shown that the genus Marmaroxylon is nested within Zygia, but a full sample of Marmaroxylon has yet to be included in analyses. This study aims to resolve taxonomic limits of Zygia and to test if phylogenomic data and more sampling of taxa improves resolution within the genus.   Methods: We utilize data from 1315 nuclear loci sequenced from 134 accessions, representing 47 species of Zygia, as well as four species of the closely related genus Macrosamanea, the poorly known Marmaroxylon magdalenae, endemic to the Magdalena Valley in Colombia and Marmaroxylon eperuetorum, which is the last remaining species of Marmaroxylon not tested with DNA data. The data is analyzed using species tree reconstruction based on the multispecies coalescent model and maximum likelihood analyses of concatenated datasets.  Results: Our phylogenetic analysis showed that the core Zygia clade is sister to a clade consisting of Macrosamanea, Zygia turneri, Marmaroxylon magdalenae, Inga, Ingopsis and Pseudocojoba. Zygia is non-monophyletic since Z. turneri is more closely related to Marmaroxylon magdalenae and Macrosamanea than to remaining species of Zygia. Marmaroxylon eperuetorum is found within the core Zygia clade. Resolution within Zygia clearly improved with phylogenomic data and denser sampling of taxa, but non-monophyletic species are still present. Discussion: The core Zygia clade is strongly supported statistically and relationships within it are well-resolved. However, 13 species of Zygia are non-monophyletic and the reasons for this are not yet fully known but could be due to e.g., misidentification, hybridization or incomplete lineage sorting. Both species trees reconstructed based on the multispecies coalescent model and phylogenetic trees inferred from maximum likelihood analyses of the concatenated datasets show similar topologies. Gene tree discordance is high for many branches within Zygia and is in most cases due to incomplete lineage sorting. To render Zygia monophyletic new combinations in Macrosamanea are given for Z. turneri and Marmaroxylon magdalenae.
Department of Ecology, Environment and Plant Sciences