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We have generated matK, rbcL, and nrITS2 DNA barcodes for 320 specimens representing all 18 extant genera of the conifer family Podocarpaceae. The sample includes 145 of the 198 recognized species. Comparative analyses of sequence quality and species discrimination were conducted on the 159 individuals from which all three markers were recovered (representing 15 genera and 97 species). The vast majority of sequences were of high quality (B30 = 0.596-0.989). Even the lowest quality sequences exceeded the minimum requirements of the BARCODE data standard. In the few instances that low quality sequences were generated, the responsible mechanism could not be discerned. There were no statistically significant differences in the discriminatory power of markers or marker combinations (p = 0.05). The discriminatory power of the barcode markers individually and in combination is low (56.7% of species at maximum). In some instances, species discrimination failed in spite of ostensibly useful variation being present (genotypes were shared among species), but in many cases there was simply an absence of sequence variation. Barcode gaps (maximum intraspecific p-distance > minimum interspecific p-distance) were observed in 50.5% of species when all three markers were considered simultaneously. The presence of a barcode gap was not predictive of discrimination success (p = 0.02) and there was no statistically significant difference in the frequency of barcode gaps among markers (p = 0.05). In addition, there was no correlation between number of individuals sampled per species and the presence of a barcode gap (p = 0.27).

Premise of the Study Conifers are an important living seed plant lineage with an extensive fossil record spanning more than 300 million years. The group therefore provides an excellent opportunity to explore congruence and conflict between dated molecular phylogenies and the fossil record. Methods We surveyed the current state of knowledge in conifer phylogenetics to present a new time‐calibrated molecular tree that samples ~90% of extant species diversity. We compared phylogenetic relationships and estimated divergence ages in this new phylogeny with the paleobotanical record, focusing on clades that are species‐rich and well known from fossils. Key Results Molecular topologies and estimated divergence ages largely agree with the fossil record in Cupressaceae, conflict with it in Araucariaceae, and are ambiguous in Pinaceae and Podocarpaceae. Molecular phylogenies provide insights into some fundamental questions in conifer evolution, such as the origin of their seed cones, but using them to reconstruct the evolutionary history of specific traits can be challenging. Conclusions Molecular phylogenies are useful for answering deep questions in conifer evolution if they depend on understanding relationships among extant lineages. Because of extinction, however, molecular datasets poorly sample diversity from periods much earlier than the Late Cretaceous. This fundamentally limits their utility for understanding deep patterns of character evolution and resolving the overall pattern of conifer phylogeny.

The ability of lineages to disperse long distances over evolutionary timescales may be influenced by the gain or loss of traits adapted to enhance local, ecological dispersal. For example, some species in the southern conifer family Podocarpaceae have fleshy cones that encourage bird dispersal, but it is unknown how this trait has influenced the clade’s historical biogeography, or its importance compared with other predictors of dispersal such as the geographic distance between regions. We answer these questions quantitatively by using a dated phylogeny of 197 species of southern conifers (Podocarpaceae and their sister family Araucariaceae) to statistically compare standard, trait-independent biogeography models with new BioGeoBEARS models where an evolving trait can influence dispersal probability, and trait history, biogeographical history, and model parameters are jointly inferred. We validate the method with simulation-inference experiments. Comparing all models, those that include trait-dependent dispersal accrue 87.5% of the corrected Akaike Information Criterion (AICc) model weight. Averaged across all models, lineages with nonfleshy cones had a dispersal probability multiplier of 0.49 compared with lineages with fleshy cones. Distance is included as a predictor of dispersal in all credible models (100% model weight). However, models with changing geography earned only 22.0% of the model weight, and models submerging New Caledonia/New Zealand earned only 0.01%. The importance of traits and distance suggests that long-distance dispersal over macroevolutionary timespans should not be thought of as a highly unpredictable chance event. Instead, long-distance dispersal can be modeled, allowing statistical model comparison to quantify support for different hypotheses.

Endophytic fungi have been considered as a repertoire for bioactive secondary metabolites with potential application in medicine, agriculture and food industry. The biosynthetic pathways by fungal endophytes raise the argument of acquisition of these machineries of such complex metabolites from the plant host. Diterpenoids “Taxol” is the most effective anticancer drug with highest annual sale, since its discovery in 1970 from the Pacific yew tree, Taxus brevifolia. However, the lower yield of Taxol from this natural source (bark of T. brevifolia), availability and vulnerability of this plant to unpredicted fluctuation with the ecological and environmental conditions are the challenges. Endophytic fungi from Taxus spp. opened a new avenue for industrial Taxol production due to their fast growth, cost effectiveness, independence on climatic changes, feasibility of genetic manipulation. However, the anticipation of endophytic fungi for industrial Taxol production has been challenged by the loss of its productivity, due to the metabolic reprograming of cells, downregulating the expression of its encoding genes with subculturing and storage. Thus, the objectives of this review were to (1) Nominate the endophytic fungal isolates with the Taxol producing potency from Taxaceae and Podocarpaceae; (2) Emphasize the different approaches such as molecular manipulation, cultural optimization, co-cultivation for enhancing the Taxol productivities; (3) Accentuate the genome mining of the rate-limiting enzymes for rapid screening the Taxol biosynthetic machinery; (4) Triggering the silenced rate-limiting genes and transcriptional factors to activates the biosynthetic gene cluster of Taxol.

Afromontane forests host a unique biodiversity distributed in isolated high elevation habitats within a matrix of rain forests or savannahs, yet they share a remarkable flora that raises questions about past connectivity between currently isolated forests. Here, we focused on the Podocarpus latifolius - P. milanjianus complex (Podocarpaceae), the most widely distributed conifers throughout sub-Saharan African highlands, to infer its demographic history from genetic data. We sequenced the whole plastid genome, mitochondrial DNA regions, and nuclear ribosomal DNA of 88 samples from Cameroon to Angola in western Central Africa and from Kenya to the Cape region in eastern and southern Africa to reconstruct time-calibrated phylogenies and perform demographic inferences. We show that P. latifolius and P. milanjianus form a single species, whose lineages diverged during the Pleistocene, mostly between c. 200 and 300 kyrs BP, after which they underwent a wide range expansion leading to their current distributions. Confronting phylogenomic and palaeoecological data, we argue that the species originated in East Africa and reached the highlands of the Atlantic side of Africa through two probable latitudinal migration corridors: a northern one towards the Cameroon volcanic line, and a southern one towards Angola. Although the species is now rare in large parts of its range, no demographic decline was detected, probably because it occurred too recently to have left a genetic signature in our DNA sequences. Despite the ancient and highly fluctuating history of podocarps in Africa revealed by palaeobotanical records, the extended distribution of current P. latifolius/milanjianus lineages is shown to result from a more recent history, mostly during the mid-late Pleistocene, when Afromontane forests were once far more widespread and continuous.

Research on ancient adhesives from the South African Stone Age is expanding, driven by excellent preservation conditions of adhesives and the potential to address diverse archaeological questions. These adhesives are primarily characterized through microscopic and chemical analysis. Despite geographic variability, a consistently identified component is Podocarpus resin or tar. We challenge these identifications, considering another Podocarpaceae genus, Afrocarpus , and the Cupressaceae genus Widdringtonia . Gas Chromatography-Mass Spectrometry was employed to analyze molecular signatures of modern wood, tar, resin, and seed cones from these genera. The results form an extensive reference database and reveal challenges in distinguishing these genera based on the diterpenoid signature. While Podocarpus is frequently cited, we advocate for a broader classification as Podocarpaceae when phenolic diterpenoids are found in high abundances and pimaranes and abietanes in lower abundances, and Widdringtonia when the opposite is true. The study differentiates materials used in adhesive production, including leaves and wood, highlighting the significance of α,ω-dicarboxylic acids, hydroxy acids, n -alkanes, and alcohols. Tars produced from leaves are characterized by odd-numbered n -alkanes, while tars produced from twigs and branches are characterized by long-chain α,ω-dicarboxylic acids, hydroxy acids, and alcohols. Because the differences between these adhesives in terms of raw material procurement and production are great, a more nuanced and cautious approach that acknowledges the challenges in differentiating tree species on a molecular level and considers archaeological and environmental context is required.

Despite much interest and studies toward the genus Podocarpus, the anti-malarial evaluation of Podocarpus polystachyus’s phytoconstituents remains lacking. Herein, the phytoconstituents of P. polystachyus leaves and their anti-malarial effect against Plasmodium falciparum were investigated for the first time. One new natural product, 8ß,13ß-kaur-15-en-17-al (1), along with three known compounds, 8ß,13ß-kaur-15-en-17-ol (2) and 13ß-kaur-16-ene (3), and α-tocopherol hydroquinone (4) were isolated via HR-ESI-MS and NMR analyses. Compounds 1 and 2 inhibited P. falciparum growth at 12 and 52 µM of IC50, respectively. Their anti-malarial activity was associated with the in silico P. falciparum lactate dehydrogenase (PfLDH) inhibition. Molecular docking of ligands 1 and 2 with the putative target PfLDH revealed ~−2 kcal/mol of binding energies more negative than the control. Molecular dynamic simulations (100 ns) showed equal or smaller deviation values (RMSD, RMSF, Rg) and stronger interactions of PfLDH-1 and PfLDH-2 complexes via at least one consistent H-bond than the control. Additionally, a slightly increased PfLDH H-bond profile in their interactions improved the PfLDH dynamic and structural stabilities. Overall, this study supports the relevance of 1 and 2 as plasmodial growth inhibitors with their putative anti-PfLDH activity, which could be a potential scaffold for developing anti-malarial drugs.

Aim: The genus Podocarpus (Podocarpaceae) provides an opportunity to contrast biogeographical hypotheses within and among continents, and to analyse divergence between disjunct tropical and temperate forests of South America. We developed a calibrated phylogeny of Podocarpus to reconstruct the ancestral areas and potential expansion routes within Podocarpaceae. Location: Podocarpus consists of two extant subgenera: Foliolatus from Asia and Oceania, and Podocarpus located in Gondwanan continents and north to the Caribbean. The paper focuses mainly on the area occupied by the latter subgenus. Methods: We combined previously published and novel DNA sequences with fossil records. New species sequenced are members of Podocarpus subgenus Podocarpus from South and Central America. We assembled DNA sequences of the chloroplast (matK and rbcL) and nuclear (ITS1 and ITS2) to analyse phylogenetic relationships within Podocarpus subgenus Podocarpus by Bayesian methods, which were calibrated using macrofossils that could be confidently identified as modern genera. Ancestral areas were inferred using the dispersal–extinction–cladogenesis model. Results: The phylogenetic reconstruction inferred a minimum age for the origin of Podocarpus s.l. in the late Cretaceous–early Palaeogene (63 Ma) and strongly supported monophyly of the genus Podocarpus and of subgenera Podocarpus and Foliolatus. Subgenus Podocarpus consists of two monophyletic, latitudinally structured clades. One clade consists of temperate American species while the other includes species from tropical-subtropical Africa and South America. Main conclusions: The history of the subgenera within Podocarpus is older than previously reported: they can be traced back to late Cretaceous–early Palaeocene biogeographical connections between Australasia and South America through Antarctica. Latitudinally disjunct lineages within South America most probably diverged from widespread ancestors as a result of a persistent arid barrier that was established prior to the late Palaeogene. The calibrated age for the Tropical–Subtropical clade suggests an Atlantic–subtropical biogeographical corridor between South America and Africa long after the breakup of Gondwana and the stabilization of the circum-Antarctic current.

Background Caleosins are lipid-associated proteins that exist in plants and fungi. Its molecules and biological functions have been extensively characterized, particularly in some economic crops. Different caleosins have various physiological roles in plant growth, development, and plant-environment interactions. However, a comprehensive investigation into their evolutionary history and patterns has yet to be undertaken. Results Here, we identified 922 caleosins from 203 species comprising green algae and other plant taxa, followed by large-scale phylogenetic analysis. Phylogenetic analysis indicates that the plant caleosin family gave rise to the H and L branches after the emergence of aquatic algae and before the appearance of land plants. Hornworts and liverworts lost the L- caleosin during the evolutionary process. Caleosins from Araucariaceae, Podocarpaceae, Sciadopityaceae, and Stangeriaceae are absent in the H clade, and those from Ginkgoaceae, Gnetaceae, Pinaceae, and Zamiaceae are missing in the L clade. This suggests that the H and L clades were lost at the family level. In addition, we present a more comprehensive phylogenetic structure of angiosperm caleosin . The H and L branches of angiosperm caleosin expanded once each, generating two branches, respectively. We also explored the diversification of caleosin in Brassicaceae and Poaceae, respectively. Conclusion Our study offers a comprehensive understanding of the evolutionary trajectory of the caleosin gene family in green plants at a genome-wide level. These findings establish a crucial groundwork for future research to conduct thorough functional characterization.

PREMISE OF THE STUDY: The flip‐leaved podocarp Retrophyllum has a disjunct extant distribution in South American and Australasian tropical rainforests and a Gondwanic fossil record since the Eocene. Evolutionary, biogeographic, and paleoecological insights from previously described fossils are limited because they preserve little foliar variation and no reproductive structures. METHODS: We investigated new Retrophyllum material from the terminal Cretaceous Lefipán, the early Eocene Laguna del Hunco, and the early/middle Eocene Río Pichileufú floras of Patagonian Argentina. We also reviewed type material of historical Eocene fossils from southern Chile. KEY RESULTS: Cretaceous Retrophyllum superstes sp. nov. is described from a leafy twig, while Eocene R. spiralifolium sp. nov. includes several foliage forms and a peduncle with 13 pollen cones. Both species preserve extensive damage from sap‐feeding insects associated with foliar transfusion tissue. The Eocene species exhibits a suite of characters linking it to both Neotropical and West Pacific Retrophyllum, along with several novel features. Retrophyllum araucoensis (Berry) comb. nov. stabilizes the nomenclature for the Chilean fossils. CONCLUSIONS: Retrophyllum is considerably older than previously thought and is a survivor of the end‐Cretaceous extinction. Much of the characteristic foliar variation and pollen‐cone morphology of the genus evolved by the early Eocene. The mixed biogeographic signal of R. spiralifolium supports vicariance and represents a rare Neotropical connection for terminal‐Gondwanan Patagonia, which is predominantly linked to extant Australasian floras due to South American extinctions. The leaf morphology of the fossils suggests significant drought vulnerability as in living Retrophyllum, indicating humid paleoenvironments.