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Hybridization can facilitate both evolutionary diversification and extinction and has had a critical role in plant evolution, with c. 25% of species known to hybridize in some temperate floras. However, in the species-rich Neotropical flora, the role of hybridization in the evolution of diversity remains unclear. Our review examines studies of hybridization in seed plants from across the Neotropics and explores its outcomes on Neotropical plant evolution. We review studies on a per-biome basis and a spectrum of evolutionary outcomes from hybridization are evident across Neotropical biomes and taxa. These range from short-term impacts, such as the broadening of ecological amplitude in hybrid progeny with transgressive phenotypes and genetic swamping, through to long term impacts, such as the generation of new lineages. Among these studies certain themes emerge, such as the pervasive hybridization among species-rich plant radiations from the Andean páramos, suggesting a role for hybridization in rapid diversification events. Finally, we highlight that hybridization is relatively understudied in the Neotropical flora, despite its remarkable species richness. The advent of genomic techniques can facilitate the study of hybridization and its effects in understudied biomes and plant groups. The increasing availability of genomic resources will eventually allow comparisons between tropical and temperate floras and therefore shed light on the evolutionary impacts of hybridization across the latitudinal biodiversity gradient.

The date palm, Phoenix dactylifera, has been a cornerstone of Middle Eastern and North African agriculture for millennia. It was first domesticated in the Persian Gulf, and its evolution appears to have been influenced by gene flow from two wild relatives, P. theophrasti, currently restricted to Crete and Turkey, and P. sylvestris, widespread from Bangladesh to the West Himalayas. Genomes of ancient date palm seeds show that gene flow from P. theophrasti to P. dactylifera may have occurred by ∼2,200 years ago, but traces of P. sylvestris could not be detected. We here integrate archeogenomics of a ∼2,100-year-old P. dactylifera leaf from Saqqara (Egypt), molecular-clock dating, and coalescence approaches with population genomic tests, to probe the hybridization between the date palm and its two closest relatives and provide minimum and maximum timestamps for its reticulated evolution. The Saqqara date palm shares a close genetic affinity with North African date palm populations, and we find clear genomic admixture from both P. theophrasti, and P. sylvestris, indicating that both had contributed to the date palm genome by 2,100 years ago. Molecular-clocks placed the divergence of P. theophrasti from P. dactylifera/P. sylvestris and that of P. dactylifera from P. sylvestris in the Upper Miocene, but strongly supported, conflicting topologies point to older gene flow between P. theophrasti and P. dactylifera, and P. sylvestris and P. dactylifera. Our work highlights the ancient hybrid origin of the date palms, and prompts the investigation of the functional significance of genetic material introgressed from both close relatives, which in turn could prove useful for modern date palm breeding., Molecular Biology and Evolution, 38 (10), ISSN:0737-4038, ISSN:1537-1719

Well-supported phylogenies are a prerequisite for the study of the evolution and diversity of life on earth. The subfamily Calamoideae accounts for more than one fifth of the palm family (Arecaceae), occurs in tropical rainforests across the world, and supports a billion-dollar industry in rattan products. It contains ca. 550 species in 17 genera, 10 subtribes and three tribes, but their phylogenetic relationships remain insufficiently understood. Here, we sequenced almost one thousand nuclear genomic regions for 75 systematically selected Calamoideae, representing the taxonomic diversity within all calamoid genera. Our phylogenomic analyses resolved a maximally supported phylogenetic backbone for the Calamoideae, including several higher-level relationships not previously inferred. In-depth analysis revealed low gene tree conflict for the backbone but complex deep evolutionary histories within several subtribes. Overall, our phylogenomic framework sheds new light on the evolution of palms and provides a robust foundation for future comparative studies, such as taxonomy, systematics, biogeography, and macroevolutionary research.

Poor morphological and molecular differentiation in recently diversified lineages is a widespread phenomenon in plants. Phylogenetic relationships within such species complexes are often difficult to resolve because of the low variability in traditional molecular loci, as well as various other biological phenomena responsible for topological incongruence such as ILS and hybridization. In this study, we employ a Genotyping-by-sequencing (GBS) approach to disentangle evolutionary relationships within a species complex belonging to the Neotropical orchid genus Cycnoches. The complex includes seven taxa distributed in Central America and the adjacent Chocó biogeographic region, nested within a clade estimated to have first diversified in the early Quaternary. Previous phylogenies inferred from a handful of loci failed to provide support for internal relationships within the complex. Our Neighbor-net and coalescent-based analyses inferred from ca. 13,000 GBS loci obtained from 31 individuals belonging to six of the seven traditionally accepted Cycnoches species provided a robustly supported network. The resulting three main clades are corroborated by morphological traits and geographical distributions. Similarly, Maximum Likelihood (ML) inferences of concatenated GBS-loci produced results comparable with those derived from coalescence and network-based methods, albeit always with poor statistical support. The low support evident in the ML phylogeny might be attributed to the abundance of uninformative GBS loci, which can account for up to 50% of the total number of loci recovered. The phylogenomic framework provided here, as well as morphological evidence and geographical patterns, suggest that the six entities previously thought to be different species might actually represent only three distinct segregates. Our study is the first to demonstrate the utility of GBS data in phylogenomic research of a very young Neotropical plant clade (~2 Ma), and it paves the way for the study of the many other species complexes that populate the species-rich orchid family.