Introgression across evolutionary scales suggests reticulation contributes to Amazonian tree diversity

This is the final version. Available from Wiley via the DOI in this record.The data that support the findings of this study are openly available from online repositories. All raw reads generated with the targeted bait capture and ddRADseq methods are available on the NCBI Sequence Read Archive with the Accession nos SAMN13439069‐SAMN13439140 and SAMN13441804‐SAMN13441974, respectively, under the BioProject number PRJNA592723. All full phylogenomic sequence alignments, single‐accession‐per‐species alignments and tree files, bgc input files, Stacks output files and the Detarioideae bait kit sequence file are found on Dryad (https://doi.org/10.5061/dryad.k3j9kd53w). Data are under embargo until publication, and any further data required are available from the corresponding author upon reasonable request.Hybridization has the potential to generate or homogenize biodiversity and is a particularly common phenomenon in plants, with an estimated 25% of plant species undergoing interspecific gene flow. However, hybridization in Amazonia's megadiverse tree flora was assumed to be extremely rare despite extensive sympatry between closely related species, and its role in diversification remains enigmatic because it has not yet been examined empirically. Using members of a dominant Amazonian tree family (Brownea, Fabaceae) as a model to address this knowledge gap, our study recovered extensive evidence of hybridization among multiple lineages across phylogenetic scales. More specifically, using targeted sequence capture our results uncovered several historical introgression events between Brownea lineages and indicated that gene tree incongruence in Brownea is best explained by reticulation, rather than solely by incomplete lineage sorting. Furthermore, investigation of recent hybridization using ~19,000 ddRAD loci recovered a high degree of shared variation between two Brownea species that co-occur in the Ecuadorian Amazon. Our analyses also showed that these sympatric lineages exhibit homogeneous rates of introgression among loci relative to the genome-wide average, implying a lack of selection against hybrid genotypes and persistent hybridization. Our results demonstrate that gene flow between multiple Amazonian tree species has occurred across temporal scales, and contrasts with the prevailing view of hybridization's rarity in Amazonia. Overall, our results provide novel evidence that reticulate evolution influenced diversification in part of the Amazonian tree flora, which is the most diverse on Earth.Natural Environment Research Council (NERC)Genetics Societ

Epitypification with an emended description of Tropidia connata (Orchidaceae, Epidendroideae, Tropidieae)

We found several specimens of Tropidia connata, a mycoheterotrophic orchid from Borneo, with features which have never been described in any of the existing literature, namely subterranean tubers. We mainly focus on the importance of the subterranean structures in comparison with the mycoheterotrophic genus Kalimantanorchis from the tribe Tropidieae. This finding of the tuberous structure gives a new insight into the classification of mycoheterotrohic species of Tropidieae and might affect the generic placement of Kalimantanorchis. We made a detailed study on the newly discovered specimens as well as the type, and found more diagnostic characters of T. connata than the previous description. Considering that the type specimen lacks the whole tuberous character, we consequently designate an epitype with a drawing and emend the description

Molecular phylogenetic study of the tribe Tropidieae (Orchidaceae, Epidendroideae) with taxonomic and evolutionary implications

Volume: 140Start Page: 11-2

Molecular phylogenetic study of the tribe Tropidieae (Orchidaceae, Epidendroideae) with taxonomic and evolutionary implications

The orchid tribe Tropidieae comprises three genera, Tropidia, Corymborkis and Kalimantanorchis. There are three fully mycoheterotrophic species within Tropidieae: Tropidia saprophytica, T. connata and Kalimantanorchis nagamasui. A previous phylogenetic study of K. nagamasui, based only on plastid matK data, placed K. nagamasui outside the clade of Tropidia and Corymborkis without support. In this study, we performed phylogenetic analyses using a nuclear ribosomal DNA spacer (ITS1-5.8S-ITS2), a low-copy nuclear coding gene (Xdh) and a mitochondrial intron (nad1b-c intron) to study the phylogenetic relationships within Tropidieae. We included six photosynthetic and all three fully mycoheterotrophic Tropidieae species. The resulting phylogenetic trees placed these fully mycoheterotrophic species inside the Tropidia clade with high support. In our trees, these three species do not form a monophyletic group together, because the photosynthetic T. graminea is nested amongst them. Our results also suggest that the loss of photosynthetic ability occurred at least twice in Tropidia

Molecular phylogenetic study of the tribe Tropidieae (Orchidaceae, Epidendroideae) with taxonomic and evolutionary implications

The orchid tribe Tropidieae comprises three genera, Tropidia, Corymborkis and Kalimantanorchis. There are three fully mycoheterotrophic species within Tropidieae: Tropidia saprophytica, T. connata and Kalimantanorchis nagamasui. A previous phylogenetic study of K. nagamasui, based only on plastid matK data, placed K. nagamasui outside the clade of Tropidia and Corymborkis without support. In this study, we performed phylogenetic analyses using a nuclear ribosomal DNA spacer (ITS1-5.8S-ITS2), a low-copy nuclear coding gene (Xdh) and a mitochondrial intron (nad1b-c intron) to study the phylogenetic relationships within Tropidieae. We included six photosynthetic and all three fully mycoheterotrophic Tropidieae species. The resulting phylogenetic trees placed these fully mycoheterotrophic species inside the Tropidia clade with high support. In our trees, these three species do not form a monophyletic group together, because the photosynthetic T. graminea is nested amongst them. Our results also suggest that the loss of photosynthetic ability occurred at least twice in Tropidia