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Somatic embryogenesis (SE) in conifers is usually characterized as a multi-step process starting with the development of proembryogenic cell masses and followed by histodifferentiation, somatic embryo development, maturation, desiccation, and plant regeneration. Our current understanding of conifers' SE is mainly derived from studies using Pinaceae species as a model. However, the evolutionary relationships between conifers are not clear. Some hypotheses consider conifers as a paraphyletic group and Gnetales as a closely related clade. In this review, we used an integrated approach in order to cover the advances in knowledge on SE in conifers and Gnetales, discussing the state-of-the-art and shedding light on similarities and current bottlenecks. With this approach, we expect to be able to better understand the integration of these clades within current studies on SE. Finally, the points discussed raise an intriguing question: are non-Pinaceae conifers less prone to expressing embryogenic competence and generating somatic embryos as compared to Pinaceae species? The development of fundamental studies focused on this morphogenetic route in the coming years could be the key to finding a higher number of points in common between these species, allowing the success of the SE of one species to positively affect the success of another.

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BACKGROUND: Amber has been reported from the Early Cretaceous Crato Formation, as isolated clasts or within plant tissues. Undescribed cones of uncertain gymnosperm affinity have also been recovered with amber preserved in situ. Here, we provide multiple lines of evidence to determine the botanical affinity of this enigmatic, conspicuous cone type, and to better understand the diversity of amber-source plants present in the Crato Formation and beyond. RESULTS: A new taxon of amber-bearing pollen cone Araripestrobus resinosus gen. nov. et sp. nov. is described here from complete cones and characteristic disarticulated portions. The best-preserved cone portion has both in situ amber infilling the resin canals inside the preserved microsporophyll tissues and pollen of the Eucommiidites-type. This places this genus within the Erdtmanithecales, an incompletely known gymnosperm group from the Mesozoic. FTIR analysis of the in situ amber indicates a potential araucariacean conifer affinity, although affinity with cupressacean conifers cannot be definitely ruled out. Pyr-GC-MS analysis of the Araripestrobus resinosus gen. nov. et sp. nov. in situ fossil resin shows that it is a mature class Ib amber, thought to indicate affinities with araucariacean and cupressacean, but not pinaceous, conifers. This is the first confirmed occurrence of this class of amber in the Crato Formation flora and in South America, except for an archaeological sample from Laguna Guatavita, Colombia. CONCLUSIONS: The combined results of the cones' novel gross morphology and the analyses of the in situ amber and pollen clearly indicate that the new taxon of resinous gymnosperm pollen cones from the Crato Formation is affiliated with Erdtmanithecales. The cone morphology is very distinct from all known pollen cone types of this extinct plant group. We therefore assume that the plant group that produced Eucommiidites-type pollen is much more diverse in habits than previously thought. Moreover, the diversity of potential amber source plants from the Crato Formation is now expanded beyond the Araucariaceae and the Cheirolepidiaceae to include this member of the Erdtmanithecales. Despite dispersed Eucommiidites pollen being noted from the Crato Formation, this is the first time macrofossils of Erdtmanithecales have been recognized from the Early Cretaceous of South America.

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PREMISE: Eocene floras of Patagonia document biotic response to the final separation of Gondwana. The conifer genus Araucaria, distributed worldwide during the Mesozoic, has a disjunct extant distribution between South America and Australasia. Fossils assigned to Australasian Araucaria Sect. Eutacta usually are represented by isolated organs, making diagnosis difficult. Araucaria pichileufensis E.W. Berry, from the middle Eocene Río Pichileufú (RP) site in Argentine Patagonia, was originally placed in Sect. Eutacta and later reported from the early Eocene Laguna del Hunco (LH) locality. However, the relationship of A. pichileufensis to Sect. Eutacta and the conspecificity of the Araucaria material among these Patagonian floras have not been tested using modern methods. METHODS: We review the type material of A. pichileufensis alongside large (n = 192) new fossil collections of Araucaria from LH and RP, including multi-organ preservation of leafy branches, ovuliferous complexes, and pollen cones. We use a total evidence phylogenetic analysis to analyze relationships of the fossils to Sect. Eutacta. RESULTS: We describe Araucaria huncoensis sp. nov. from LH and improve the whole-plant concept for Araucaria pichileufensis from RP. The two species respectively resolve in the crown and stem of Sect. Eutacta. CONCLUSIONS: Our results confirm the presence and indicate the survival of Sect. Eutacta in South America during early Antarctic separation. The exceptionally complete fossils significantly predate several molecular age estimates for crown Eutacta. The differentiation of two Araucaria species demonstrates conifer turnover during climate change and initial South American isolation from the early to middle Eocene.

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The knowledge about plant miRNAs has increased exponentially, with thousands of miRNAs been reported in different plant taxa using high throughput sequencing technologies and bioinformatic tools. Nevertheless, several groups of plants remain unexplored, and the gap of knowledge about conifer miRNAs is considerable. There is no sequence or functional information available on miRNAs in Araucariaceae. This group is represented in Brazil by only one species, Araucaria angustifolia, an endangered species known as Brazilian pine. In the present study, Brazilian pine has its transcriptome explored with respect to small RNAs, representing the first description in a member of the Araucariaceae family. The screening for conserved miRNAs in Brazilian pine revealed 115 sequences of 30 miRNA families. A total of 106 precursors sequences were predicted. Forty one comprised conserved miRNAs from 16 families, whereas 65 were annotated as novel miRNAs. The comparison of Brazilian pine precursors with sRNA libraries of other five conifer species indicates that 9 out 65 novel miRNAs are conserved among gymnosperms, while 56 seems to be specific for Brazilian pine or restricted to Araucariaceae family. Analysis comparing novel Brazilian pine miRNAs precursors and Araucaria cunninghamii RNA-seq data identified seven orthologs between both species. Mature miRNA identified by bioinformatics predictions were validated using stem-loop RT-qPCR assays. The expression pattern of conserved and novel miRNAs was analyzed in five different tissues of 3-month-old Araucaria seedlings. The present study provides insights about the nature and composition of miRNAs in an Araucariaceae species, with valuable information on miRNAs diversity and conservation in this taxon.

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PREMISE OF THE STUDY: The fossil record of Agathis historically has been restricted to Australasia. Recently described fossils from the Eocene of Patagonian Argentina showed a broader distribution than found previously, which is reinforced here with a new early Paleocene Agathis species from Patagonia. No previous phylogenetic analyses have included fossil Agathis species. METHODS: We describe macrofossils from Patagonia of Agathis vegetative and reproductive organs from the early Danian, as well as leaves with Agathis affinities from the latest Maastrichtian. A total evidence phylogenetic analysis is performed, including the new Danian species together with other fossil species having agathioid affinities. KEY RESULTS: Early Danian Agathis immortalis sp. nov. is the oldest definite occurrence of Agathis and one of the most complete Agathis species in the fossil record. Leafy twigs, leaves, pollen cones, pollen, ovuliferous complexes, and seeds show features that are extremely similar to the living genus. Dilwynites pollen grains, associated today with both Wollemia and Agathis and known since the Turonian, were found in situ within the pollen cones. CONCLUSIONS: Agathis was present in Patagonia ca. 2 million years after the K-Pg boundary, and the putative latest Cretaceous fossils suggest that the genus survived the K-Pg extinction. Agathis immortalis sp nov. is recovered in a stem position for the genus, while A. zamunerae (Eocene, Patagonia) is recovered as part of the crown. A Mesozoic divergence for the Araucariaceae crown group, previously challenged by molecular divergence estimates, is supported by the combined phylogenetic analyses including the fossil taxa.

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PREMISE OF THE STUDY: We describe a new araucarian species, Araucaria lefipanensis, from the Late Cretaceous flora of the Lefipán Formation, in Patagonia (Argentina) based on reproductive and vegetative remains, with a combination of characters that suggest mosaic evolution in the Araucaria lineage. METHODS: The studied fossils were found at the Cañadón del Loro locality. Specimens were separated into two leaf morphotypes, and their morphological differences were tested with MANOVA. KEY RESULTS: The new species Araucaria lefipanensis is erected based on the association of dimorphic leaves with cuticle remains and isolated cone scale complexes. The reproductive morphology is characteristic of the extant section Eutacta, whereas the vegetative organs resemble those of the sections Intermedia, Bunya, and Araucaria (the broad-leaved clade). CONCLUSIONS: The leaf dimorphism of A. lefipanensis is similar to that of extant A. bidwillii, where dimorphism is considered to be related to seasonal growth. The leaf dimorphism in A. lefipanensis is consistent with the paleoclimatic and paleoenvironmental reconstructions previously suggested for the Lefipán Formation, which is thought to have been a seasonal subtropical forest. The new species shows evidence of mosaic evolution, with cone scale complexes morphologically similar to section Eutacta and leaves similar to the sections of the broad-leaved clade, constituting a possible transitional form between these two well-defined lineages. More complete plant concepts, especially those including both reproductive and vegetative remains are necessary to understand the evolution of ancient plant lineages. This work contributes to this aim by documenting a new species that may add to the understanding of the early evolution of the sections of Araucaria.

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PREMISE OF THE STUDY: Agathis is an iconic genus of large, ecologically important, and economically valuable conifers that range over lowland to upper montane rainforests from New Zealand to Sumatra. Exploitation of its timber and copal has greatly reduced the genus's numbers. The early fossil record of Agathis comes entirely from Australia, often presumed to be its area of origin. Agathis has no previous record from South America. METHODS: We describe abundant macrofossils of Agathis vegetative and reproductive organs, from early and middle Eocene rainforest paleofloras of Patagonia, Argentina. The leaves were formerly assigned to the New World cycad genus Zamia. KEY RESULTS: Agathis zamunerae sp. nov. is the first South American occurrence and the most complete representation of Agathis in the fossil record. Its morphological features are fully consistent with the living genus. The most similar living species is A. lenticula, endemic to lower montane rainforests of northern Borneo. CONCLUSIONS: Agathis zamunerae sp. nov. demonstrates the presence of modern-aspect Agathis by 52.2 mya and vastly increases the early range and possible areas of origin of the genus. The revision from Zamia breaks another link between the Eocene and living floras of South America. Agathis was a dominant, keystone element of the Patagonian Eocene floras, alongside numerous other plant taxa that still associate with it in Australasia and Southeast Asia. Agathis extinction in South America was an integral part of the transformation of Patagonian biomes over millions of years, but the living species are disappearing from their ranges at a far greater rate.

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Embryogenic cultures of Araucaria angustifolia were established in a BM liquid medium supplemented with 2 µM 2,4-dichlorophenoxyacetic acid, 1 µM 6-benzylaminopurine and 1 µM kinetin (BM2) and in a BM medium free of growth regulators (BM0). During 42 days in culture, the cell growth pattern of both cultures was similar. The pH of the culture medium of both BM0 and BM2 underwent progressive reduction during culture time. For both the embryogenic cultures a preferential uptake of glucose in the late stages of cell growth kinetics was observed. The extracellular protein content was similar for both the embryogenic cultures. Acetocarmine and Evan's blue double stain showed major differences for early somatic embryo organisation, in which only the embryogenic culture grown in a liquid culture medium free of plant growth regulators showed the presence of bipolar somatic pro-embryos.

Culturas embriogênicas de Araucaria angustifolia foram estabelecidas em meio de cultura líquido BM suplementado com 2 µM Ácido 2,4 Diclorofenoxiacético, 1 µM 6-Benzilaminopurina e 1 µM Cinetina (BM2) e em meio BM isento de reguladores de crescimento (BM0). Durante 42 dias de cultivo, o padrão de crescimento celular em ambas as culturas foi similar. O pH do meio de cultura BM0 e BM2 sofreu uma progressiva redução durante o período de cultivo. Em ambas as culturas embriogênicas foram observadas um consumo preferencial de glicose no período final da curva de crescimento celular. O nível de proteínas extracelulares foi similar para ambas as culturas embriogênicas. A dupla coloração com carmin acético e azul de Evans revelou diferenças na organização das linhagens celulares embriogênicas, sendo que a presença de proembriões somáticos bipolares foi apenas evidenciada nas culturas embriogênicas mantidas em meio de cultura líquido sem reguladores de crescimento.

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Habitat fragmentation and a decrease in population size may lead to a loss in population genetic diversity. For the first time, the reduction in genetic diversity in the northernmost limit of natural occurence (southeastern Brazil) of Araucaria angustifolia in comparison with populations in the main area of the species continuous natural distribution (southern Brazil), was tested. The 673 AFLPs markers revealed a high level of genetic diversity for the species (Ht = 0.27), despite anthropogenic influence throughout the last century, and a decrease of H in isolated populations of southeastern Brazil (H = 0.16), thereby indicating the tendency for higher genetic diversity in remnant populations of continuous forests in southern Brazil, when compared to natural isolated populations in the southeastern region. A strong differentiation among southern and southeastern populations was detected (AMOVA variance ranged from 10%-15%). From Bayesian analysis, it is suggested that the nine populations tested form five "genetic clusters" (K = 5). Five of these populations, located in the northernmost limit of distribution of the species, represent three "genetic clusters". These results are in agreement with the pattern of geographic distribution of the studied populations.

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Habitat fragmentation and a decrease in population size may lead to a loss in population genetic diversity. For the first time, the reduction in genetic diversity in the northernmost limit of natural occurence (southeastern Brazil) of Araucaria angustifolia in comparison with populations in the main area of the species continuous natural distribution (southern Brazil), was tested. The 673 AFLPs markers revealed a high level of genetic diversity for the species (Ht = 0.27), despite anthropogenic influence throughout the last century, and a decrease of H in isolated populations of southeastern Brazil (H = 0.16), thereby indicating the tendency for higher genetic diversity in remnant populations of continuous forests in southern Brazil, when compared to natural isolated populations in the southeastern region. A strong differentiation among southern and southeastern populations was detected (AMOVA variance ranged from 10 percent-15 percent). From Bayesian analysis, it is suggested that the nine populations tested form five "genetic clusters" (K = 5). Five of these populations, located in the northernmost limit of distribution of the species, represent three "genetic clusters". These results are in agreement with the pattern of geographic distribution of the studied populations.

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