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Aim: Pleistocene (2.58 Ma–11.7 ka) climatic fluctuations have shaped intraspecific genetic patterns worldwide; however, their impact on species in many regions remains unknown. In order to determine the impact of Pleistocene climatic fluctuations on the tropical rain forests of western Ecuador, we explored the evolutionary history of the endemic palm Phytelephas aequatorialis. Location: Western Ecuador, north‐western South America. Taxon: Phytelephas aequatorialis (Arecaceae). Methods: One hundred and seventy‐six nuclear genes were sequenced in 91 individuals for phylogenomic and population structure analyses. The time of divergence between identified genetic lineages was estimated using a coalescent phylogenomic analysis. Palaeoecological niche modelling analyses were performed to determine areas of historical climatic suitability since the Last Glacial Maximum (LGM; 22 ka) that potentially acted as forest refugia during the Pleistocene. A Wilcoxon test and Pearson correlations were used to explore how current levels of genetic diversity, in terms of expected heterozygosity (Hs), have been shaped by several palaeoclimatic and geographic factors. Results: Phylogenomic and population structure analyses revealed two main genetic lineages with a north–south distribution, which diverged 1.14 Ma during the Pleistocene. Two potential Pleistocene refugia were identified, one along the Pacific coast of Ecuador and one in the Andean foothills of south‐western Ecuador. The location of these refugia agrees with the spatial location of the two genetic lineages. Within the Andean foothills, Hs was lower for the southern lineage than for the northern lineage. Hs significantly increased with decreasing latitude across the species as a whole. Main conclusions: Pleistocene climatic fluctuations promoted intraspecific divergence in P. aequatorialis within the rain forests of western Ecuador. The Andean foothills of south‐western Ecuador could be an important area for rain forest evolution because they potentially remained climatically suitable throughout the Pleistocene. Lower genetic diversity in the southern lineage, which apparently remained isolated in the Andean foothills during glacial cycles, adds evidence to the presence of a forest refugium in south‐western Ecuador. The geographic pattern in genetic diversity suggests that P. aequatorialis colonized western Ecuador from the north. This study supports the role of Pleistocene climatic fluctuations in promoting intraspecific divergence, and for the first time, we show their impact west of the Andes. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

[Display omitted] • Confirmation of eight species within the palm tribe Phytelepheae. • Phytelephas seemannii and Phytelephas schottii are not closely related to Phytelephas macrocarpa , and should not be treated as the same species. • The ancestor of the Phytelepheae was widely distributed in the Chocó, the inter-Andean valley of the Magdalena River, and the Amazonia. • Andean uplift potentially promoted early diversification in the genus Phytelephas by isolating the Chocó/Magdalena from the Amazonia. The palm tribe Phytelepheae form a clade of three genera and eight species whose phylogenetic relationships and historical biogeography are not fully understood. Based on morphological similarities and phylogenetic relatedness, it has been suggested that Phytelephas seemannii and Phytelephas schottii are synonyms of Phytelephas macrocarpa , implying the existence of only six species within the Phytelepheae. In addition, uncertainty in their phylogenetic relationships in turn results in blurred biogeographic history. We inferred the phylogenomic relationships in the Phytelepheae by target-capturing 176 nuclear genes and estimated divergence times by using four fossils for time calibration. We lastly explored the biogeographic history of the tribe by inferring its ancestral range evolution. Our phylogenomic trees showed that P. seemannii and P. schottii are not closely related with P. macrocarpa , and therefore, support the existence of eight species in the Phytelepheae. The ancestor of the tribe was widely-distributed in the Chocó, Magdalena, and Amazonia during the Miocene at 19.25 Ma. Early diversification in Phytelephas at 5.27 Ma could have occurred by trans -Andean vicariance after the western Andes uplifted rapidly at ∼ 10 Ma. Our results show the utility of phylogenomic approaches to shed light on species relationships and their biogeographic history. [ABSTRACT FROM AUTHOR]

African rainforests (ARFs) are species rich and occur in two main rainforest blocks: West/Central and East Africa. This diversity is suggested to be the result of recent diversification, high extinction rates and multiple vicariance events between west/central and East African forests. We reconstructed the diversification history of two subtribes (Annickieae and Piptostigmateae) from the ecologically dominant and diverse tropical rainforest plant family Annonaceae. Both tribes contain endemic taxa in the rainforests of West/Central and East Africa. Using a dated molecular phylogeny based on 32 nuclear markers, we estimated the timing of the origin of East African species. We then undertook several diversification analyses focusing on Piptostigmateae to infer variation in speciation and extinction rates, and test the impact of extinction events. Speciation in both tribes dated to the Pliocene and Pleistocene. In particular, Piptostigma (13 species) diversified mainly during the Pleistocene, representing one of the few examples of Pleistocene speciation in an African tree genus. Our results also provide evidence of an ARF fragmentation at the mid-Miocene linked to climatic changes across the region. Overall, our results suggest that continental-wide forest fragmentation during the Neogene (23.03–2.58 Myr), and potentially during the Pliocene, led to one or possibly two vicariance events within the ARF clade Piptostigmateae, in line with other studies. Among those tested, the best fitting diversification model was the one with an exponential speciation rate and no extinction. We did not detect any evidence of mass extinction events. This study gives weight to the idea that the ARF might not have been so negatively impacted by extinction during the Neogene, and that speciation mainly took place during the Pliocene and Pleistocene. [ABSTRACT FROM AUTHOR]

Palms are conspicuous floristic elements across the tropics. In continental Africa, even though there are less than 70 documented species, they are omnipresent across the tropical landscape. The genus Raphia has 20 accepted species in Africa and one species endemic to the Neotropics. It is the most economically important genus of African palms with most of its species producing food and construction material. Raphia is divided into five sections based on inflorescence morphology. Nevertheless, the taxonomy of Raphia is problematic with no intra-generic phylogenetic study available. We present a phylogenetic study of the genus using a targeted exon capture approach sequencing of 56 individuals representing 18 out of the 21 species. Our results recovered five well supported clades within the genus. Three sections correspond to those based on inflorescence morphology. R. regalis is strongly supported as sister to all other Raphia species and is placed into a newly described section: Erectae. Overall, morphological based identifications agreed well with our phylogenetic analyses, with 12 species recovered as monophyletic based on our sampling. Species delimitation analyses recovered 17 or 23 species depending on the confidence level used. Species delimitation is especially problematic in the Raphiate and Temulentae sections. In addition, our clustering analysis using SNP data suggested that individual clusters matched geographic distribution. The Neotropical species R. taedigera is supported as a distinct species, rejecting the hypothesis of a recent introduction into South America. Our analyses support the hypothesis that the Raphia individuals from Madagascar are potentially a distinct species different from the widely distributed R. farinifera. In conclusion, our results support the infra generic classification of Raphia based on inflorescence morphology, which is shown to be phylogenetically useful. Classification and species delimitation within sections remains problematic even with our phylogenomic approach. Certain widely distributed species could potentially contain cryptic species. More in-depth studies should be undertaken using morphometrics, increased sampling, and more variable markers. Our study provides a robust phylogenomic framework that enables further investigation on the biogeographic history, morphological evolution, and other eco-evolutionary aspects of this charismatic, socially, and economically important palm genus. [ABSTRACT FROM AUTHOR]