Phylogenetics of Olea (Oleaceae) based on plastid and nuclear ribosomal DNA sequences: Tertiary climatic shifts and lineage differentiation times

Background and Aims The genus Olea (Oleaceae) includes approx. 40 taxa of evergreen shrubs and trees classified in three subgenera, Olea, Paniculatae and Tetrapilus, the first of which has two sections (Olea and Ligustroides). Olive trees (the O. europaea complex) have been the subject of intensive research, whereas little is known about the phylogenetic relationships among the other species. To clarify the biogeographical history of this group, a molecular analysis of Olea and related genera of Oleaceae is thus necessary. Methods A phylogeny was built of Olea and related genera based on sequences of the nuclear ribosomal internal transcribed spacer-1 and four plastid regions. Lineage divergence and the evolution of abaxial peltate scales, the latter character linked to drought adaptation, were dated using a Bayesian method. Key Results Olea is polyphyletic, with O. ambrensis and subgenus Tetrapilus not sharing a most recent common ancestor with the main Olea clade. Partial incongruence between nuclear and plastid phylogenetic reconstructions suggests a reticulation process in the evolution of subgenus Olea. Estimates of divergence times for major groups of Olea during the Tertiary were obtained. Conclusions This study indicates the necessity of revising current taxonomic boundaries in Olea. The results also suggest that main lines of evolution were promoted by major Tertiary climatic shifts: (1) the split between subgenera Olea and Paniculatae appears to have taken place at the Miocene-Oligocene boundary; (2) the separation of sections Ligustroides and Olea may have occurred during the Early Miocene following the Mi-1 glaciation; and (3) the diversification within these sections (and the origin of dense abaxial indumentum in section Olea) was concomitant with the aridification of Africa in the Late Miocen

Lack of ITS sequence homogenization in Erysimum species (Brassicaceae) with different ploidy levels

Funding This research is supported by grants from FEDER/Junta de Andalucía-Consejería de Economía y Conocimiento A-RNM-505-UGR18 and P18-FR-3641. This research was also funded by the Spanish Ministry of Science and Innovation (CGL2013-47558-P and PID2021-126456NB-C22), including EU FEDER funds. COM was supported by the Ministry of Economy and Competitiveness (BES-2014-069022). This is a contribution to the Research Unit Modeling Nature, funded by the Consejería de Economía, Conocimiento, Empresas y Universidad, and European Regional Development Fund (ERDF), reference QUALIFICA 00011.Acknowledgements The authors thank the Tatiana López Pérez and the Evoflor group for helping us during several phases of the study. We also thank the Sierra Nevada National Park headquarters for providing access to sampling in the National Park.The internal transcribed spacers (ITS) exhibit concerted evolution by the fast homogenization of these sequences at the intragenomic level. However, the rate and extension of this process are unclear and might be conditioned by the number and divergence of the different ITS copies. In some cases, such as hybrid species and polyploids, ITS sequence homogenization appears incomplete, resulting in multiple haplotypes within the same organism. Here, we studied the dynamics of concerted evolution in 85 individuals of seven plant species of the genus Erysimum (Brassicaceae) with multiple ploidy levels. We estimated the rate of concerted evolution and the degree of sequence homogenization separately for ITS1 and ITS2 and whether these varied with ploidy. Our results showed incomplete sequence homogenization, especially for polyploid samples, indicating a lack of concerted evolution in these taxa. Homogenization was usually higher in ITS2 than in ITS1, suggesting that concerted evolution operates more efficiently on the former. Furthermore, the hybrid origin of several species appears to contribute to the maintenance of high haplotype diversity, regardless of the level of ploidy. These findings indicate that sequence homogenization of ITS is a dynamic and complex process that might result in varying intra- and inter-genomic diversity levels.FEDER/Junta de Andalucía-Consejería de Economía y Conocimiento A-RNM-505-UGR18 and P18-FR-3641Spanish Ministry of Science and Innovation (CGL2013-47558-P and PID2021-126456NB-C22)Ministry of Economy and Competitiveness (BES-2014-069022)Research Unit Modeling Nature, funded by the Consejería de Economía, Conocimiento, Empresas y Universidad, and European Regional Development Fund (ERDF), reference QUALIFICA 0001

Genomic Resources for Erysimum spp. (Brassicaceae): Transcriptome and Chloroplast Genomes

Funding was provided by the Spanish Ministry of Science and Competitiveness (CGL2016-79950-R; CGL2017-86626-C22-P), including FEDER funds. This research was also funded by the Consejeria de Economia, Conocimiento, Empresas y Universidad, and European Regional Development Fund (ERDF), ref. SOMM17/6109/UGR and A-RNM-505-UGR18. COM was supported by the Ministry of Economy and Competitiveness (BES-2014-069022).We are grateful to Modesto Berbel Cascales and José M. Gómez for their help in sampling and DNA/RNA extractions.Erysimum (Brassicaceae) is a genus of more than 200 species (Al-Shehbaz, 2012). It is widely distributed in the Northern Hemisphere and has been the focus of active research in ecology, evolution, and genetics (Gómez and Perfectti, 2010; Gómez, 2012; Valverde et al., 2016). Despite long-standing interest in Erysimum, its taxonomy has yet to be properly established, partly due to a complex and reticulated evolutionary history that renders phylogenetic reconstructions highly challenging (Ancev, 2006; Marhold and Lihová, 2006; Abdelaziz et al., 2014; Gomez et al., 2014; Moazzeni et al., 2014; Züst et al., 2020). The Baetic Mountains (South-Eastern Iberia) are among the most critical glacial refugia in Europe. The waxing and waning of plant populations following climatic fluctuations have likely complicated the distribution and genetic variation of extant diversity in this region. Isolation and posterior secondary contact between taxa may have favored hybridization and introgression (Médail and Diadema, 2009). The Erysimum species that inhabit these mountains have been a particularly fruitful system for plant evolutionary ecology [e.g., Gómez et al., 2006, 2008; Gómez and Perfectti, 2010; Gómez, 2012; Valverde et al., 2016]. However, the relationships among these species remain unresolved, hampering comparative and evolutionary studies. Genome duplications, incomplete lineage sorting, and hybridization have compromised the phylogenetic reconstructions within Erysimum (Marhold and Lihová, 2006; Osuna-Mascaró, 2020). Additionally, clarifying this group's complex evolution requires extensive genomic resources, which are currently being produced but are mostly lacking. The fast development of high-throughput sequencing technologies has led to a rapid increase in genomic and transcriptomic for many plant species (Dong et al., 2004; Duvick et al., 2007; Sundell et al., 2015; Boyles et al., 2019). However, obtaining complete genome sequencing remains a challenge with large, repetitive-DNA enriched genomes. Transcriptome sequencing is comparatively more accessible, providing a relatively cheap and fast method to obtain large amounts of functional genomic data (Timme et al., 2012; Yang and Smith, 2013; Wickett et al., 2014; Léveillé-Bourret et al., 2017). Accordingly, global initiatives such as the 1,000 plants (1KP) project have generated transcriptomic resources for over 1,000 plant species (Matasci et al., 2014; Leebens-Mack et al., 2019). In addition, the use of RNA-Seq could be useful in obtaining complete chloroplast genomes in a reliable and accessible way, making possible the use of complete molecules in phylogenomic analyses (Smith, 2013; Osuna-Mascaró et al., 2018; Morales-Briones et al., 2021). Here, we report the annotation of 18 floral transcriptomes assembled de novo from total RNA-Seq libraries and nine chloroplast genomes from seven Erysimum species inhabiting the Baetic Mountains. The chloroplast genomes were assembled from total RNA-Seq data following a previously-validated reference assemble approach (Osuna-Mascaró et al., 2018). The data presented here represent reliable genomic resources for transcriptomic, proteomic, and phylotranscriptomic studies. These data contribute to the ecological and genetic resources available for Brassicaceae in general and the genus Erysimum in particular, being the only genomic resources for these species coming from flower buds.Spanish Ministry of Science and Competitiveness CGL2016-79950-R CGL2017-86626-C22-PEuropean CommissionConsejeria de Economia, Conocimiento, Empresas y UniversidadEuropean Commission SOMM17/6109/UGR A-RNM-505-UGR18Ministry of Economy and Competitiveness BES-2014-06902

Forest Restoration in a Fog Oasis: Evidence Indicates Need for Cultural Awareness in Constructing the Reference

Background: In the Peruvian Coastal Desert, an archipelago of fog oases, locally called lomas, are centers of biodiversity and of past human activity. Fog interception by a tree canopy, dominated by the legume tree tara (Caesalpinia spinosa), enables the occurrence in the Atiquipa lomas (southern Peru) of an environmental island with a diverse flora and high productivity. Although this forest provides essential services to the local population, it has suffered 90% anthropogenic reduction in area. Restoration efforts are now getting under way, including discussion as to the most appropriate reference ecosystem to use. Methodology/Principal Findings: Genetic diversity of tara was studied in the Atiquipa population and over a wide geographical and ecological range. Neither exclusive plastid haplotypes to loma formations nor clear geographical structuring of the genetic diversity was found. Photosynthetic performance and growth of seedlings naturally recruited in remnant patches of loma forest were compared with those of seedlings recruited or planted in the adjacent deforested area. Despite the greater water and nitrogen availability under tree canopy, growth of forest seedlings did not differ from that of those recruited into the deforested area, and was lower than that of planted seedlings. Tara seedlings exhibited tight stomatal control of photosynthesis, and a structural photoprotection by leaflet closure. These drought-avoiding mechanisms did not optimize seedling performance under the conditions produced by forest interception of fog moisture. Conclusions/Significance: Both weak geographic partitioning of genetic variation and lack of physiological specialization of seedlings to the forest water regime strongly suggest that tara was introduced to lomas by humans. Therefore, the most diverse fragment of lomas is the result of landscape management and resource use by pre-Columbian cultures. We argue that an appropriate reference ecosystem for ecological restoration of lomas should include sustainable agroforestry practices that emulate the outcomes of ancient uses

Universidad y sociedad: comunicación e integración en empresas e instituciones públicas y organizaciones no lucrativas. Nuevos avances

Depto. de Teorías y Análisis de la ComunicaciónFac. de Ciencias de la InformaciónFALSEsubmitte

Universidad y sociedad: comunicación e integración en empresas e instituciones públicas y organizaciones no lucrativas: innovación y progreso

Depto. de Teorías y Análisis de la ComunicaciónFac. de Ciencias de la InformaciónFALSEsubmitte