Phylogenomic relationships and historical biogeography in the South American vegetable ivory palms (Phytelepheae).

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 âˆ¼ 10 Ma. Our results show the utility of phylogenomic approaches to shed light on species relationships and their biogeographic history.

Palm seed and fruit lipid composition: phylogenetic and ecological perspectives.

BACKGROUND AND AIMS: Palms are vital to worldwide human nutrition, in particular as major sources of vegetable oils. However, our knowledge of seed and fruit lipid diversity in the family Arecaceae is limited. We therefore aimed to explore relationships between seed and fruit lipid content, fatty acid composition in the respective tissues, phylogenetic factors and biogeographical parameters. METHODS: Oil content and fatty acid composition were characterized in seeds and fruits of 174 and 144 palm species respectively. Distribution, linear regression and multivariate analyses allowed an evaluation of the chemotaxonomic value of these traits and their potential relationship with ecological factors. KEY RESULTS: A considerable intra-family diversity for lipid traits was revealed. Species with the most lipid-rich seeds belonged to the tribe Cocoseae, while species accumulating oil in the mesocarp occurred in all subfamilies and two-thirds of the tribes studied. Seed and fruit lipid contents were not correlated. Fatty acid composition of mesocarp oil was highly variable within tribes. By contrast, within-tribe diversity for seed lipid traits was low, whereas between-tribe variability was high. Consequently, multivariate analyses of seed lipid traits produced groupings of species belonging to the same tribe. Medium-chain fatty acids predominated in seeds of most palm species, but they were also accumulated in the mesocarp in some cases. Seed unsaturated fatty acid content correlated with temperature at the coldest latitude of natural occurrence. CONCLUSION: Several previously uncharacterized palms were identified as potential new sources of vegetable oils for comestible or non-food use. Seed lipid traits reflect genetic drift that occurred during the radiation of the family and therefore are highly relevant to palm chemotaxonomy. Our data also suggest that seed unsaturated fatty acids may provide an adaptive advantage in the coldest environments colonized by palms by maintaining storage lipids in liquid form for efficient mobilization during germination.

Three Amazonian palms as underestimated and little-known sources of nutrients, bioactive compounds and edible insects.

Mauritia flexuosa, Bactris gasipaes, and Oenocarpus bataua are among the main palms in the Amazon used for food and medicinal purposes. The food most commonly derived from these are fruits, oil, and the larvae of the insect Rhynchophorus palmarum reared in their trunks. Palm fruits are used for oil extraction as they are rich in saturated fatty acids, fiber, pro-vitamin A, carotenoids, tocopherols, macro and microelements, and polyphenols. Furthermore, the larvae of R. palmarum are rich in lipids, vitamin E, and proteins. This review analyzes the chemical composition of the fruit and oil of these palm species, as well as the R. palmarum larvae that breed in them. Our aim is to present information that is not widely known in order to demonstrate the potential of these palms as sources of plant-based and animal food with high nutritional and functional values.

Bactris gasipaes Kunth var. gasipaes complete plastome and phylogenetic analysis.

Bactris gasipaes var. gasipaes (Arecaceae, Palmae) is an economically and socially important plant species for populations across tropical South and Central America. It has been domesticated from its wild variety, B. gasipaes var. chichagui, since pre-Columbian times. In this study, we sequenced the plastome of the cultivated variety, B. gasipaes Kunth var. gasipaes and compared it with the published plastome of the wild variety. The chloroplast sequence obtained was 156,580 bp. The cultivated chloroplast sequence was conserved compared to the wild type sequence with 99.8% of nucleotide identity. We did, however, identify multiple Single Nucleotide Variants (SNVs), insertions, microsatellites and a resolved region of missing nucleotides. A SNV in one of the core barcode markers (matK) was detected between the wild and cultivated accessions. Phylogenetic analysis was carried out across the Arecaceae family and compared to previous reports, resulting in an identical topology. This study is a step forward in understanding the genome evolution of this species.

Perceptions of agrodiversity and seed-saving practices in the northern Andes of Ecuador.

BACKGROUND: As concerns about agrodiversity loss and its impact on food security increase, interest in seed-saving practices and motivations has risen, especially in regions characterized by ancestral farming. Agroecology practitioners in the northern Andes of Ecuador (n = 65) participated in this study to describe (1) the dynamics of intergenerational agrodiversity, (2) perceptions of relevance of the crops they grow, (3) criteria for characterizing the differences between conventional and non-conventional seeds, and (4) their seed-saving practices. METHODS: This exploratory study incorporated a community-based participatory research approach using mixed methods. We conducted (1) a timeline mapping for exploring the dynamics of intergenerational agrodiversity and (2) structured interviews to explore the perception of relevance of crops grown to identify criteria for characterizing conventional and non-conventional seeds and for identifying seed-saving practices. We computed ranks and frequencies from free listing data derived from the interviews to detect the most salient patterns for crop diversity and seed-saving practices. A principal component analysis was performed to illustrate crops distribution within the study area. RESULTS AND DISCUSSION: Based on the timeline-mapping tool, we found that participants perceive an intergenerational loss of agrodiversity. Data derived from free listing determined that salient crops differ in each location of the study area, mostly due to geographic (altitude, climate), market factors, and crop management limitations. Responses from open-ended interview questions revealed that farmers discriminate conventional from non-conventional seeds using yield, adaptation to local conditions, pest tolerance, taste, and crop management as criteria. Analysis of free listing data determined that the most salient reported practices related to seed saving were soil fertility management, seed selection, safe seed storage, tilling and rowing, and weeding. CONCLUSIONS: This study contributes to raising awareness of intergenerational agrodiversity loss and replacement with modern crops. We found the relevance of crops and practices is subject to cultural and environmental context, and few agricultural practices are exclusively used for seed saving. Further, farmers clearly discriminate conventional from non-conventional seeds based on advantages and disadvantages, cultural motivation, and produce destination. The community-based participatory approach resulted in positive engagement from participants and promoted commitment from farmers to preserve agrodiversity and support practices at the community level.

Long-fragment targeted capture for long-read sequencing of plastomes.

PREMISE: Third-generation sequencing methods generate significantly longer reads than those produced using alternative sequencing methods. This provides increased possibilities for the study of biodiversity, phylogeography, and population genetics. We developed a protocol for in-solution enrichment hybridization capture of long DNA fragments applicable to complete plastid genomes. METHODS AND RESULTS: The protocol uses cost-effective in-house probes developed via long-range PCR and was used in six non-model monocot species (Poaceae: African rice, pearl millet, fonio; and three palm species). DNA was extracted from fresh and silica gel-dried leaves. Our protocol successfully captured long-read plastome fragments (3151 bp median on average), with an enrichment rate ranging from 15% to 98%. DNA extracted from silica gel-dried leaves led to low-quality plastome assemblies when compared to DNA extracted from fresh tissue. CONCLUSIONS: Our protocol could also be generalized to capture long sequences from specific nuclear fragments.

Genetic divergence and fine scale population structure of the common bottlenose dolphin (Tursiops truncatus, Montagu) found in the Gulf of Guayaquil, Ecuador.

The common bottlenose dolphin, Tursiops truncatus, is widely distributed along the western coast of South America. In Ecuador, a resident population of bottlenose dolphins inhabits the inner estuarine area of the Gulf of Guayaquil located in the southwestern part of the country and is under threat from different human activities in the area. Only one genetic study on South American common bottlenose dolphins has been carried out to date, and understanding genetic variation of wildlife populations, especially species that are identified as threatened, is crucial for defining conservation units and developing appropriate conservation strategies. In order to evaluate the evolutionary link of this population, we assessed the phylogenetic relationships, phylogeographic patterns, and population structure using mitochondrial DNA (mtDNA). The sampling comprised: (i) 31 skin samples collected from free-ranging dolphins at three locations in the Gulf of Guayaquil inner estuary, (ii) 38 samples from stranded dolphins available at the collection of the "Museo de Ballenas de Salinas," (iii) 549 mtDNA control region (mtDNA CR) sequences from GenBank, and (iv) 66 concatenated sequences from 7-mtDNA regions (12S rRNA, 16S rRNA, NADH dehydrogenase subunit I-II, cytochrome oxidase I and II, cytochrome b, and CR) obtained from mitogenomes available in GenBank. Our analyses indicated population structure between both inner and outer estuary dolphin populations as well as with distinct populations of T. truncatus using mtDNA CR. Moreover, the inner estuary bottlenose dolphin (estuarine bottlenose dolphin) population exhibited lower levels of genetic diversity than the outer estuary dolphin population according to the mtDNA CR. Finally, the estuarine bottlenose dolphin population was genetically distinct from other T. truncatus populations based on mtDNA CR and 7-mtDNA regions. From these results, we suggest that the estuarine bottlenose dolphin population should be considered a distinct lineage. This dolphin population faces a variety of anthropogenic threats in this area; thus, we highlight its fragility and urge authorities to issue prompt management and conservation measures.

Genetic structuring in a Neotropical palm analyzed through an Andean orogenesis-scenario.

Andean orogenesis has driven the development of very high plant diversity in the Neotropics through its impact on landscape evolution and climate. The analysis of the intraspecific patterns of genetic structure in plants would permit inferring the effects of Andean uplift on the evolution and diversification of Neotropical flora. In this study, using microsatellite markers and Bayesian clustering analyses, we report the presence of four genetic clusters for the palm Oenocarpus bataua var. bataua which are located within four biogeographic regions in northwestern South America: (a) Chocó rain forest, (b) Amotape-Huancabamba Zone, (c) northwestern Amazonian rain forest, and (d) southwestern Amazonian rain forest. We hypothesize that these clusters developed following three genetic diversification events mainly promoted by Andean orogenic events. Additionally, the distinct current climate dynamics among northwestern and southwestern Amazonia may maintain the genetic diversification detected in the western Amazon basin. Genetic exchange was identified between the clusters, including across the Andes region, discarding the possibility of any cluster to diversify as a distinct intraspecific variety. We identified a hot spot of genetic diversity in the northern Peruvian Amazon around the locality of Iquitos. We also detected a decrease in diversity with distance from this area in westward and southward direction within the Amazon basin and the eastern Andean foothills. Additionally, we confirmed the existence and divergence of O. bataua var. bataua from var. oligocarpus in northern South America, possibly expanding the distributional range of the latter variety beyond eastern Venezuela, to the central and eastern Andean cordilleras of Colombia. Based on our results, we suggest that Andean orogenesis is the main driver of genetic structuring and diversification in O. bataua within northwestern South America.