An overview of extant conifer evolution from the perspective of the fossil record

Whole-genome-based phylogenetic analyses provide new insights into the evolution of springtails (Hexapoda: Collembola)

Springtails (Collembola) stand as one of the most abundant, widespread, and ancient terrestrial arthropods on earth. However, their evolutionary history and deep phylogenetic relationships remain elusive. In this study, we employed phylogenomic approaches to elucidate the basal relationships among Collembola. We sampled whole-genome data representing all major collembolan lineages in proportion to their known diversity. To account for potential phylogenomic biases, we implemented various data extraction, locus sampling, and signal filtering strategies to generate matrices. Subsequently, we applied a diverse array of tree-searching and rate-modelling methods to reconstruct the phylogeny. Our analyses, utilizing different matrices and methods, converged on the same unrooted relationships among collembolan ingroups, supporting the current ordinal classification and challenging the monophyly of Arthropleona and Symphypleona s.l. However, discrepancies across analyses existed in the root of Collembola. Among various root positions, those based on more informative matrices and biologically realistic models, favoring a basal topology of Entomobryomorpha + (Symphypleona s.s. + (Neelipleona + Poduromorpha)), were supported by subsequent methodological assessment, topology tests, and rooting analyses. This optimal topology suggests multiple independent reduction of the pronotum in non-poduromorph orders and aligns with the plesiomorphic status of neuroendocrine organs and epicuticular structure of Entomobryomorpha. Fossil-calibrated dating analyses based on the optimal topology indicated late-Paleozoic to mid-Mesozoic origins of the crown Collembola and four orders. In addition, our results questioned the monophyly of Isotomidae and Neanuridae, underscoring the need for further attention to the systematics of these families. Overall, this study provides novel insights into the phylogenetic backbone of Collembola, which will inform future studies on the systematics, ecology, and evolution of this significant arthropod lineage.

Evolutionary trends of reproductive phenotype in Cycadales: an analysis of morphological evolution in Ceratozamia

BACKGROUND AND AIMS

The size and shape of reproductive structures is especially relevant in evolution because these characters are directly related to the capacity for pollination and seed dispersal, a process that plays a basic role in evolutionary patterns. The evolutionary trajectories of reproductive phenotypes in gymnosperms have received special attention in terms of pollination and innovations related to the emergence of the spermatophytes. However, variability of reproductive structures, evolutionary trends and the role of environment in the evolution of cycad species have not been well documented and explored. This study considered this topic under an explicitly phylogenetic and evolutionary approach that included a broad sampling of reproductive structures in the genus Ceratozamia.

METHODS

We sampled 1400 individuals of 36 Ceratozamia species to explore the evolutionary pattern and identify and evaluate factors that potentially drove their evolution. We analysed characters for both pollen and ovulate strobili within a phylogenetic framework using different methods and characters (i.e. molecular and both quantitative and qualitative morphological) to infer phylogenetic relationships. Using this phylogenetic framework, evolutionary models of trait evolution for strobilar size were evaluated. In addition, quantitative morphological variation and its relation to environmental variables across species were analysed.

KEY RESULTS

We found contrasting phylogenetic signals between characters of pollen and ovulate strobili. These structures exhibited high morphological disparity in several characters related to size. Results of analyses of evolutionary trajectories suggested a stabilizing selection model. With regard to phenotype-environment, the analysis produced mixed results and differences for groups in the vegetation type where the species occur; however, a positive relationship with climatic variables was found.

CONCLUSIONS

The integrated approach synthesized reproductive phenotypic variation with current phylogenetic hypotheses and provided explicit statements of character evolution. The characters of volume for ovulate strobili were the most informative, and could provide a reference for further study of the evolutionary complexity in Ceratozamia. Finally, heterogeneous environments, which are under changing weather conditions, promote variability of reproductive structures.

Phylotranscriptomic and ecological analyses reveal the evolution and morphological adaptation of Abies

Coniferous forests are under severe threat of the rapid anthropogenic climate warming. Abies (firs), the fourth-largest conifer genus, is a keystone component of the boreal and temperate dark-coniferous forests and harbors a remarkably large number of relict taxa. However, the uncertainty of the phylogenetic and biogeographic history of Abies significantly impedes our prediction of future dynamics and efficient conservation of firs. In this study, using 1,533 nuclear genes generated from transcriptome sequencing and a complete sampling of all widely recognized species, we have successfully reconstructed a robust phylogeny of global firs, in which four clades are strongly supported and all intersectional relationships are resolved, although phylogenetic discordance caused mainly by incomplete lineage sorting and hybridization was detected. Molecular dating and ancestral area reconstruction suggest a Northern Hemisphere high-latitude origin of Abies during the Late Cretaceous, but all extant firs diversified during the Miocene to the Pleistocene, and multiple continental and intercontinental dispersals took place in response to the late Neogene climate cooling and orogenic movements. Notably, four critically endangered firs endemic to subtropical mountains of China, including A. beshanzuensis, A. ziyuanensis, A. fanjingshanensis and A. yuanbaoshanensis from east to west, have different origins and evolutionary histories. Moreover, three hotspots of species richness, including western North America, central Japan, and the Hengduan Mountains, were identified in Abies. Elevation and precipitation, particularly precipitation of the coldest quarter, are the most significant environmental factors driving the global distribution pattern of fir species diversity. Some morphological traits are evolutionarily constrained, and those linked to elevational variation (e.g., purple cone) and cold resistance (e.g., pubescent branch and resinous bud) may have contributed to the diversification of global firs. Our study sheds new light on the spatiotemporal evolution of global firs, which will be of great help to forest management and species conservation in a warming world.

The Systematics and Evolution of Gymnosperms with an Emphasis on a Few Problematic Taxa

Gymnosperms originated in the Middle Devonian and have experienced a long evolutionary history with pulses of speciation and extinction, which resulted in the four morphologically distinct extant groups, i.e., cycads, Ginkgo, conifers and gnetophytes. For over a century, the systematic relationships within the extant gymnosperms have been debated because different authors emphasized different characters. Recent phylogenomic studies of gymnosperms have given a consistent topology, which aligns well with extant gymnosperms classified into three classes, five subclasses, eight orders, and 13 families. Here, we review the historical opinions of systematics of gymnosperms with special reference to several problematic taxa and reconsider the evolution of some key morphological characters previously emphasized by taxonomists within a phylogenomic context. We conclude that (1) cycads contain two families, i.e., the Cycadaceae and the Zamiaceae; (2) Ginkgo is sister to cycads but not to conifers, with the similarities between Ginkgo and conifers being the result of parallel evolution including a monopodial growth pattern, pycnoxylic wood in long shoots, and the compound female cones, and the reproductive similarities between Ginkgo and cycads are either synapomorphic or plesiomorphic, e.g., the boat-shaped pollen, the branched pollen tube, and the flagellate sperms; (3) conifers are paraphyletic with gnetophytes nested within them, thus gnetophytes are derived conifers, and our newly delimited coniferophytes are equivalent to the Pinopsida and include three subclasses, i.e., Pinidae, Gnetidae, and Cupressidae; (4) fleshy cones of conifers originated multiple times, the Podocarpaceae are sister to the Araucariaceae, the Cephalotaxaceae and the Taxaceae comprise a small clade, which is sister to the Cupressaceae; (5) the Cephalotaxaceae are distinct from the Taxaceae, because the former family possesses typical female cones and the fleshy part of the seed is derived from the fleshiness of integument, while the latter family has reduced female cones and preserves no traces of the seed scale complexes.

The challenging biogeography of the Juan Fernández Islands and Coast Range of central Chile explained by new models of East Pacific tectonics

Biogeographers have often been puzzled by several unusual features in the Juan Fernández Islands (JFI) biota. These include the very high endemism density, multiple endemics that are older than the current islands, close biogeographic affinities with the central and West Pacific, and affinities with the diverse Coast Range of central Chile. We review aspects of biogeography in the JFI and the Coast Range in light of recent geological studies. These have examined the mantle below the East Pacific and South America, and have produced radical, new ideas on tectonic history. A long-lived, intraoceanic archipelago ~9000 km long is now thought to have existed in the East Pacific (passing between the JFI hotspot and mainland Chile) until the mid-Cretaceous. At this time, South America, which was moving westward with the opening of the Atlantic, collided with the archipelago. The assumption that the JFI biota is no older than its current islands is questionable, as taxa would have survived on prior islands produced at the JFI hotspot. We propose a new interpretation of evolution in the region based on tectonics rather than on island age and incorporating the following factors: the newly described East Pacific Archipelago; a long history for the JFI hotspot; metapopulation dynamics, including metapopulation vicariance; and formation of the Humboldt Current in the Cretaceous. The model accounts for many distinctive features of the JFI and Coast Range biota.

Conifers Concentrate Large Numbers of NLR Immune Receptor Genes on One Chromosome

Nucleotide-binding domain and leucine-rich repeat (NLR) immune receptor genes form a major line of defense in plants, acting in both pathogen recognition and resistance machinery activation. NLRs are reported to form large gene clusters in limber pine (Pinus flexilis), but it is unknown how widespread this genomic architecture may be among the extant species of conifers (Pinophyta). We used comparative genomic analyses to assess patterns in the abundance, diversity, and genomic distribution of NLR genes. Chromosome-level whole genome assemblies and high-density linkage maps in the Pinaceae, Cupressaceae, Taxaceae, and other gymnosperms were scanned for NLR genes using existing and customized pipelines. The discovered genes were mapped across chromosomes and linkage groups and analyzed phylogenetically for evolutionary history. Conifer genomes are characterized by dense clusters of NLR genes, highly localized on one chromosome. These clusters are rich in TNL-encoding genes, which seem to have formed through multiple tandem duplication events. In contrast to angiosperms and nonconiferous gymnosperms, genomic clustering of NLR genes is ubiquitous in conifers. NLR-dense genomic regions are likely to influence a large part of the plant's resistance, informing our understanding of adaptation to biotic stress and the development of genetic resources through breeding.

Development of a Target Enrichment Probe Set for Conifer (REMcon)

Conifers are an ecologically and economically important seed plant group that can provide significant insights into the evolution of land plants. Molecular phylogenetics has developed as an important approach in evolutionary studies, although there have been relatively few studies of conifers that employ large-scale data sourced from multiple nuclear genes. Target enrichment sequencing (target capture, exon capture, or Hyb-Seq) has developed as a key approach in modern phylogenomic studies. However, until now, there has been no bait set that specifically targets the entire conifer clade. REMcon is a target sequence capture probe set intended for family- and species-level phylogenetic studies of conifers that target c. 100 single-copy nuclear loci. We tested the REMcon probe set using 69 species, including 44 conifer genera across six families and four other gymnosperm taxa, to evaluate the efficiency of target capture to efficiently generate comparable DNA sequence data across conifers. The recovery of target loci was high, with, on average, 94% of the targeted regions recovered across samples with high read coverage. A phylogenetic analysis of these data produced a well-supported topology that is consistent with the current understanding of relationships among conifers. The REMcon bait set will be useful in generating relatively large-scale nuclear data sets consistently for any conifer lineage.

Evolutionary radiation of the Eurasian Pinus species under pervasive gene flow

Evolutionary radiation, a pivotal aspect of macroevolution, offers valuable insights into evolutionary processes. The genus Pinus is the largest genus in conifers withc . $$ c. $$ 90% of the extant species emerged in the Miocene, which signifies a case of rapid diversification. Despite this remarkable history, our understanding of the mechanisms driving radiation within this expansive genus has remained limited. Using exome capture sequencing and a fossil-calibrated phylogeny, we investigated the divergence history, niche diversification, and introgression among 13 closely related Eurasian species spanning climate zones from the tropics to the boreal Arctic. We detected complex introgression among lineages in subsection Pinus at all stages of the phylogeny. Despite this widespread gene exchange, each species maintained its genetic identity and showed clear niche differentiation. Demographic analysis unveiled distinct population histories among these species, which further influenced the nucleotide diversity and efficacy of purifying and positive selection in each species. Our findings suggest that radiation in the Eurasian pines was likely fueled by interspecific recombination and further reinforced by their adaptation to distinct environments. Our study highlights the constraints and opportunities for evolutionary change, and the expectations of future adaptation in response to environmental changes in different lineages.

Disparity of cycad leaves dispels the living fossil metaphor

The living fossil metaphor is tightly linked with the cycads. This group of gymnosperms is supposed to be characterised by long-term morphological stasis, particularly after their peak of diversity and disparity in the Jurassic. However, no formal test of this hypothesis exists. Here, we use a recent phylogenetic framework and an improved character matrix to reconstruct the Disparity Through Time for cycad leaves using a Principal Coordinate Analysis and employing Pre-Ordination Ancestral State Reconstruction to test the impact of sampling on the results. Our analysis shows that the cycad leaf morsphospace expanded up to the present, with numerous shifts in its general positioning, independently of sampling biases. Moreover, they also show that Zamiaceae expanded rapidly in the Early Cretaceous and continued to expand up to the present, while now-extinct clades experienced a slow contraction from their peak in the Triassic. We also show that rates of evolution were constantly high up to the Early Cretaceous, and then experienced a slight decrease in the Paleogene, followed by a Neogene acceleration. These results show a much more dynamic history for cycads, and suggest that the 'living fossil' metaphor is actually a hindrance to our understanding of their macroevolution.

Reproductive biology of the "Brazilian pine" (Araucaria angustifolia-Araucariaceae): the pollen tube growth and the seed cone development

KEY MESSAGE

In Araucaria angustifolia, the seed scale is part of the ovule, the female gametophyte presents a monosporic origin and arises from a coenocytic tetrad, and the pollen tube presents a single axis. The seed cone of conifers has many informative features, and its ontogenetic data may help interpret relationships among function, development patterns, and homology among seed plants. We reported the seed cone development, from pollination to pre-fertilization, including seed scale, ovule ontogeny, and pollen tube growth in Araucaria angustifolia. The study was performed using light microscopy, scanning electron microscopy, and X-ray microcomputed tomography (μCT). During the pollination period, the ovule arises right after the seed scale has emerged. From that event to the pre-fertilization period takes about 14 months. Megasporogenesis occurs three weeks after ovule formation, producing a coenocytic tetrad. At the same time as the female gametophyte's first nuclear division begins, the pollen tube grows through the seed scale adaxial face. Until maturity, the megagametophyte goes through the free nuclei stage, cellularization stage, and cellular growth stage. Along its development, many pollen tubes develop in the nucellar tissue extending straight toward the female gametophyte. Our observations show that the seed scale came out of the same primordia of the ovule, agreeing with past studies that this structure is part of the ovule itself. The formation of a female gametophyte with a monosporic origin that arises from a coenocytic tetrad was described for the first time in conifers, and the three-dimensional reconstruction of the ovule revealed the presence of pollen tubes with only one axis and no branches, highlighting a new pattern of pollen tube growth in Araucariaceae.

Deep learning approaches to the phylogenetic placement of extinct pollen morphotypes

The phylogenetic interpretation of pollen morphology is limited by our inability to recognize the evolutionary history embedded in pollen features. Deep learning offers tools for connecting morphology to phylogeny. Using neural networks, we developed an explicitly phylogenetic toolkit for analyzing the overall shape, internal structure, and texture of a pollen grain. Our analysis pipeline determines whether testing specimens are from known species based on uncertainty estimates. Features from specimens with uncertain taxonomy are passed to a multilayer perceptron network trained to transform these features into predicted phylogenetic distances from known taxa. We used these predicted distances to place specimens in a phylogeny using Bayesian inference. We trained and evaluated our models using optical superresolution micrographs of 30 extant Podocarpus species. We then used trained models to place nine fossil Podocarpidites specimens within the phylogeny. In doing so, we demonstrate that the phylogenetic history encoded in pollen morphology can be recognized by neural networks and that deep-learned features can be used in phylogenetic placement. Our approach makes extinction and speciation events that would otherwise be masked by the limited taxonomic resolution of the fossil pollen record visible to palynological analysis.

The ontogeny of disparity in Cupressaceae seed cones

Ontogenetic shape change has long been recognized to be important in generating patterns of morphological diversity and may be especially important in plant reproductive structures. We explore how seed cone disparity in Cupressaceae changes over ontogeny by comparing pollination-stage and mature cones. We sampled cones at pollen and seed release and measured cone scales using basic morphometric shape variables. We used multivariate statistical methods, particularly hypervolume overlap calculations, to measure morphospace occupation and disparity. Cone scales at both pollination and maturity exhibit substantial variability, although the disparity is greater at maturity. Mature cone scales are also more clustered in trait space, showing less overlap with other taxa than at pollination. These patterns reflect two growth strategies that generate closed cones over maturation, either through thin laminar scales or relatively thick, peltate scales, resulting in two distinct regions of morphospace occupation. Disparity patterns in Cupressaceae seed cones change over ontogeny, reflecting shifting functional demands that require specific patterns of cone scale growth. The evolution of Cupressaceae reproductive disparity therefore represents selection for trajectories of ontogenetic shape change, a phenomenon that should be widespread across seed plants.

Detailed Seed Cone Morpho-Anatomy Provides New Insights into Seed Cone Origin and Evolution of Podocarpaceae; Podocarpoid and Dacrydioid Clades

The study of reproductive morphology and trait evolution provides a vital insight to understand the evolutionary history of plants. The conifer family Podocarpaceae has a remarkable diversity of seed cones, with distinct morphology among the genera and with conifers in general. However, we lack a good understanding of the seed cone morpho-anatomy and trait evolution of Podocarpaceae. We investigated detailed seed cone morpho-anatomy using staining and sectioning techniques to clarify the anatomical, morphological diversity and evolution of functional traits. The presence of a fleshy receptaculum is a characteristic feature of both clades. However, species of Retrophyllum, Afrocarpus and some species of Nageia and Podocarpus form a fleshy sarcotesta-like seed coat, lacking a fleshy receptaculum. The ancestral state reconstructions show a shift between and sometimes within the genus. Although both clades demonstrate fleshiness as an ancestral trait, the shift in fleshy structures provides evidence for complex multiple evolutions of fleshy morphologies. These seed cone traits (e.g., fleshiness and size), along with the broad, flattened and well-adapted (leaf dimorphism) foliage in both clades, are largely congruent with efficient light harvesting and bird dispersal. These traits make these two clades well adapted to their environment, when growing in communities including tall and broad-leaved angiosperms (closed-canopy angiosperm forests), compared to other podocarps, making them more successful in achieving a wider distribution and species richness.

Quantifying the complexity of plant reproductive structures reveals a history of morphological and functional integration

Vascular plant reproductive structures have undoubtedly become more complex through time, evolving highly differentiated parts that interact in specialized ways. But quantifying these patterns at broad scales is challenging because lineages produce disparate reproductive structures that are often difficult to compare and homologize. We develop a novel approach for analysing interactions within reproductive structures using networks, treating component parts as nodes and a suite of physical and functional interactions among parts as edges. We apply this approach to the plant fossil record, showing that interactions have generally increased through time and that the concentration of these interactions has shifted towards differentiated surrounding organs, resulting in more compact, functionally integrated structures. These processes are widespread across plant lineages, but their extent and timing vary with reproductive biology; in particular, seed-producing structures show them more strongly than spore or pollen-producing structures. Our results demonstrate that major reproductive innovations like the origin of seeds and angiospermy were associated with increased integration through greater interactions among parts. But they also reveal that for certain groups, particularly Mesozoic gymnosperms, millions of years elapsed between the origin of reproductive innovations and increased interactions among parts within their reproductive structures.

A novel seed cone of Pinus from the Miocene of coastal Southeast China indicates kinship with Southeast Asian pines

Pinus is an economically and ecologically important genus whose members are dominant components globally in low-latitude mountainous and mid-latitude temperate forests. Pinus species richness is currently concentrated in subtropical mid-low latitudes of the Northern Hemisphere, differing from the latitudinal diversity gradient mostly recognized in woody angiosperms. How the present pattern was developing in Earth's past is still poorly studied, particularly in eastern Asia. Here, a new fossil species, Pinus shengxianica sp. nov. is described based on a fossil seed cone from the Late Miocene Shengxian Formation in Zhejiang, southeast China. A co-occurring cone is recognized as a known fossil species, Pinus speciosa Li. Extensive comparison of extant and fossil members of Pinus suggests P. shengxianica shares a striking cone similarity to Pinus merkusii and Pinus latteri (subsection Pinus) from tropical Southeast Asia in having annular bulges around the umbo on the apophysis. The morphological resemblance indicates these two extant low-latitude pines probably possess a close affinity with the present newly-discovered P. shengxianica and originated from East Asian mid-low latitude ancestors during this generic re-diversification in the Miocene. This scenario is consistent with the evolutionary trajectory reflected by the pine fossil history and molecular data, marking the Miocene as a key period for the origin and evolution of most extant pines globally. The co-occurrences of diverse conifers and broadleaved angiosperms preferring diverse niches demonstrate Late Miocene eastern Zhejiang was one of the hot spots for coniferophyte diversity and hosted a needled-broadleaved mixed forest with complex vegetation structure and an altitudinal zonation.

Rearranging and completing the puzzle: Phylogenomic analysis of bark beetles Dendroctonus reveals new hypotheses about genus diversification

Studies carried out on bark beetles within Dendroctonus have been extensive and revealed diverse information in different areas of their natural history, taxonomy, evolution, and interactions, among others. Despite these efforts, phylogenetic hypotheses have remained obscured mainly due to limited information analyzed (taxonomic, gene sampling, or both) in studies focused on obtaining evolutionary hypotheses for this genus. With the aim of filling these gaps in the evolutionary history for Dendroctonus, we analyzed ∼1800 loci mapped to a reference genome obtained for 20 of the 21 species recognized to date, minimizing the impact of missing information and improving the assumption of orthology in a phylogenomic framework. We obtained congruent phylogenetic topologies from two phylogenomic inference strategies: loci concatenation (ML framework) and a multispecies coalescent model (MSC) through the analysis of site pattern frequencies (SNPs). Dendroctonus is composed of two major clades (A and B), each containing five and four subclades, respectively. According to our divergence dating analysis, the MRCA for Dendroctonus dates back to the early Eocene, while the MRCA for each major clade diverged in the mid-Eocene. Interestingly, most of the speciation events of extant species occurred during the Miocene, which could be correlated with the diversification of pine trees (Pinus). The MRCA for Dendroctonus inhabited large regions of North America, with all ancestors and descendants of clade A having diversified within this region. The Mexican Transition Zone is important in the diversification processes for the majority of clade A species. For clade B, we identified two important colonization events to the Old World from America: the first in the early Oligocene from the Arctic to Asia (via Beringia), and the second during the Miocene from the Arctic-Western-Alleghany region to Europe and Siberia (also via Beringia). Our genomic analyses also supported the existence of hidden structured lineages within the frontalis complex, and also that D. beckeri represent a lineage independent from D. valens, as previously suggested. The information presented here updates the knowledge concerning the diversification of a genus with remarkable ecological and economic importance.

A new fossil Acmopyle with accessory transfusion tissue and potential reproductive buds: Direct evidence for ever-wet rainforests in Eocene Patagonia

PREMISE

Acmopyle (Podocarpaceae) comprises two extant species from Oceania that are physiologically restricted to ever-wet rainforests, a confirmed fossil record based on leaf adpressions and cuticles in Australia since the Paleocene, and a few uncertain reports from New Zealand, Antarctica, and South America. We investigated fossil specimens with Acmopyle affinities from the early Eocene Laguna del Hunco site in Patagonia, Argentina.

METHODS

We studied 42 adpression leafy-shoot fossils and included them in a total evidence phylogenetic analysis.

RESULTS

Acmopyle grayae sp. nov. is based on heterophyllous leafy shoots with three distinct leaf types. Among these, bilaterally flattened leaves uniquely preserve subparallel, linear features that we interpret as accessory transfusion tissue (ATT, an extra-venous water-conducting tissue). Some apical morphologies of A. grayae shoots are compatible with the early stages of ovuliferous cone development. Our phylogenetic analysis recovers the new species in a polytomy with the two extant Acmopyle species. We report several types of insect-herbivory damage. We also transfer Acmopyle engelhardti from the middle Eocene Río Pichileufú flora to Dacrycarpus engelhardti comb. nov.

CONCLUSIONS

We confirm the biogeographically significant presence of the endangered West Pacific genus Acmopyle in Eocene Patagonia. Acmopyle is one of the most drought-intolerant genera in Podocarpaceae, possibly due to the high collapse risk of the ATT, and thus the new fossil species provides physiological evidence for the presence of an ever-wet rainforest environment at Laguna del Hunco during the Early Eocene Climatic Optimum.

Exploring the Seasonal Dynamics and Molecular Mechanism of Wood Formation in Gymnosperm Trees

Forests, comprising 31% of the Earth's surface, play pivotal roles in regulating the carbon, water, and energy cycles. Despite being far less diverse than angiosperms, gymnosperms account for over 50% of the global woody biomass production. To sustain growth and development, gymnosperms have evolved the capacity to sense and respond to cyclical environmental signals, such as changes in photoperiod and seasonal temperature, which initiate growth (spring and summer) and dormancy (fall and winter). Cambium, the lateral meristem responsible for wood formation, is reactivated through a complex interplay among hormonal, genetic, and epigenetic factors. Temperature signals perceived in early spring induce the synthesis of several phytohormones, including auxins, cytokinins, and gibberellins, which in turn reactivate cambium cells. Additionally, microRNA-mediated genetic and epigenetic pathways modulate cambial function. As a result, the cambium becomes active during the summer, resulting in active secondary xylem (i.e., wood) production, and starts to become inactive in autumn. This review summarizes and discusses recent findings regarding the climatic, hormonal, genetic, and epigenetic regulation of wood formation in gymnosperm trees (i.e., conifers) in response to seasonal changes.

Cretaceous pollen cone with three-dimensional preservation sheds light on the morphological evolution of cycads in deep time

The Cycadales are an ancient and charismatic group of seed plants. However, their morphological evolution in deep time is poorly understood. While molecular divergence time analyses estimate a Cretaceous origin for most major living cycad clades, much of the extant diversity is inferred to be a result of Neogene diversifications. This leads to long branches throughout the cycadalean phylogeny that, with few exceptions, have yet to be rectified by unequivocal fossil cycads. We report a permineralized pollen cone from the Campanian Holz Shale located in Silverado Canyon, CA, USA (c. 80 million yr ago). This fossil was studied via serial sectioning, SEM, 3D reconstruction and phylogenetic analyses. Microsporophyll and pollen morphology indicate this cone is assignable to Skyttegaardia, a recently described genus based on disarticulated lignitized microsporophylls from the Early Cretaceous of Denmark. Data from this new species, including a simple cone architecture, anatomical details and vasculature organization, indicate cycadalean affinities for Skyttegaardia. Phylogenetic analyses support this assignment and recover Skyttegaardia as crown-group Cycadales, nested within Zamiaceae. Our findings support a Cretaceous diversification for crown-group Zamiaceae, which included the evolution of morphological divergent extinct taxa with unique traits that have yet to be widely identified in the fossil record.

Wood from Hardwood Angiosperms and Coniferous Gymnosperms Shows Distinctive Lignin Peaks in Direct Analysis in Real Time (DART) Mass Spectra

A data set was constructed consisting of 3021 mass spectra randomly selected from all available families in the ForeST© (Forensic Spectra of Trees) database of mass spectra for wood analyzed by Direct Analysis in Real Time ionization coupled with time-of-flight mass spectrometry (DART-TOFMS). Clear and reproducible differences were observed between the lignin peaks for hardwood angiosperms and coniferous gymnosperms, with DART-TOFMS spectra of angiosperms showing significantly higher relative abundances for peaks associated with syringyl subunits. Application of the method to processed wood samples demonstrated that these differences can be used to provide support for enforcing trade laws by accurately identifying the source of finished wood products from hardwood angiosperms and coniferous gymnosperms.

Diversity, Distribution, Systematics and Conservation Status of Podocarpaceae

Among conifer families, Podocarpaceae is the second largest, with amazing diversity and functional traits, and it is the dominant Southern Hemisphere conifer family. However, comprehensive studies on diversity, distribution, systematic and ecophysiological aspects of the Podocarpaceae are sparse. We aim to outline and evaluate the current and past diversity, distribution, systematics, ecophysiological adaptations, endemism, and conservation status of podocarps. We analyzed data on the diversity and distribution of living and extinct macrofossil taxa and combined it with genetic data to reconstruct an updated phylogeny and understand historical biogeography. Podocarpaceae today contains 20 genera and approximately 219 taxa (201 species, 2 subspecies, 14 varieties and 2 hybrids) placed in three clades, plus a paraphyletic group/grade of four distinct genera. Macrofossil records show the presence of more than 100 podocarp taxa globally, dominantly from the Eocene-Miocene. Australasia (New Caledonia, Tasmania, New Zealand, and Malesia) is the hotspot of living podocarps diversity. Podocarps also show remarkable adaptations from broad to scale leaves, fleshy seed cones, animal dispersal, shrubs to large trees, from lowland to alpine regions and rheophyte to a parasite (including the only parasitic gymnosperm-Parasitaxus) and a complex pattern of seed and leaf functional trait evolution.

Phylogenetic risk assessment is robust for forecasting the impact of European insects on North American conifers

Some introduced species cause severe damage, although the majority have little impact. Robust predictions of which species are most likely to cause substantial impacts could focus efforts to mitigate those impacts or prevent certain invasions entirely. Introduced herbivorous insects can reduce crop yield, fundamentally alter natural and managed forest ecosystems, and are unique among invasive species in that they require certain host plants to succeed. Recent studies have demonstrated that understanding the evolutionary history of introduced herbivores and their host plants can provide robust predictions of impact. Specifically, divergence times between hosts in the native and introduced ranges of a nonnative insect can be used to predict the potential impact of the insect should it establish in a novel ecosystem. However, divergence time estimates vary among published phylogenetic datasets, making it crucial to understand if and how the choice of phylogeny affects prediction of impact. Here, we tested the robustness of impact prediction to variation in host phylogeny by using insects that feed on conifers and predicting the likelihood of high impact using four different published phylogenies. Our analyses ranked 62 insects that are not established in North America and 47 North American conifer species according to overall risk and vulnerability, respectively. We found that results were robust to the choice of phylogeny. Although published vascular plant phylogenies continue to be refined, our analysis indicates that those differences are not substantial enough to alter the predictions of invader impact. Our results can assist in focusing biosecurity programs for conifer pests and can be more generally applied to nonnative insects and their potential hosts by prioritizing surveillance for those insects most likely to be damaging invaders.

No cell is an island: characterising the leaf epidermis using epidermalmorph, a new R package

The leaf epidermis is the interface between a plant and its environment. The epidermis is highly variable in morphology, with links to both phylogeny and environment, and this diversity is relevant to several fields, including physiology, functional traits, palaeobotany, taxonomy and developmental biology. Describing and measuring leaf epidermal traits remains challenging. Current approaches are either extremely labour-intensive and not feasible for large studies or limited to measurements of individual cells. Here, we present a method to characterise individual cell size, shape (including the effect of neighbouring cells) and arrangement from light microscope images. We provide the first automated characterisation of cell arrangement (from traced images) as well as multiple new shape characteristics. We have implemented this method in an R package, epidermalmorph, and provide an example workflow using this package, which includes functions to evaluate trait reliability and optimal sampling effort for any given group of plants. We demonstrate that our new metrics of cell shape are independent of gross cell shape, unlike existing metrics. epidermalmorph provides a broadly applicable method for quantifying epidermal traits that we hope can be used to disentangle the fundamental relationships between form and function in the leaf epidermis.

Miocene Cupressinoxylon from Gökçeada (Imbros), Turkey with Protophytobia cambium mining and the study of ecological signals of wood anatomy

Premise

The recognition of the Miocene Climate Optimum (MCO) in terrestrial palaeoenvironments of the Eastern Mediterranean is restricted to Lesbos and Lemnos Islands, Greece. This area is significant for its wood microfossils. A recently-discovered fossil wood assemblage from Gökçeada (Imbros) Island, Turkey, including tree species similar to the Greek findings, is thought to have an early Miocene age. Here, we revise the age of the latter plant fossiliferous locality, re-evaluate the area for the study of MCO for the terrestrial palaeoecosystems of the Eastern Mediterranean and the nomenclature errors referring to the occurrence of fossil wood. We present the plant-insect-environment interactions using detailed anatomical descriptions, of an extinct conifer and its extinct cambium miner feeding traces observed in its secondary xylem.

Methods

Three thin sections were prepared with standard palaeoxylotomical techniques from a small section of the silicified wood; the sections were observed under a light microscope. The anatomy of the conifer and its damage patterns were compared with those of extant and fossil Cupressaceae and Agromyzidae, respectively.

Pivotal results

The common anatomical features of the studied wood specimen and Hesperocyparis macrocarpa (Hartw.) Bartel and a shared characteristic (the number of the cross-field pits - a feature we consider of diagnostic value) with Xanthocyparis vietnamensis Farjon & T.H. Nguyên led to its assignment to the Hesperocyparis-Xanthocyparis-Callitropsis clade. The detailed study of the wound scars and anatomical abnormalities, the anatomical-environmental associations, and structural-functional reactions follow the identification of the wood's anatomy sensu Carlquist providing decisive results.

Conclusions

Based on the distinctive characteristics presented, we identify our macrofossil as Cupressinoxylon matromnense Grambast, a stem or an extinct lineage of the Hesperocyparis-Xanthocyparis vietnamensis-Callitropsis nootkatensis clade with feeding traces of the fossil cambium miner of the genus Protophytobia Süss (Diptera: Agromyzidae), and anatomical damage and reaction tissue on adventitious shoots. The use of Protopinaceae and Pinoxylon F. H. Knowlton from the eastern Mediterranean are re-evaluated and corrections are provided. The age of the studied plant fossiliferous locality in Gökçeada is revised as middle Miocene, allowing the proposal of an eastern Mediterranean MCO hotspot, including Lesbos, Lemnos, and Gökçeada (Imbros) Islands.

The Jurassic epiphytic macrolichen Daohugouthallus reveals the oldest lichen-plant interaction in a Mesozoic forest ecosystem

Lichens are well known as pioneer organisms or stress-tolerant extremophiles, potentially playing a core role in the early formation of terrestrial ecosystems. Epiphytic macrolichens are known to contribute to the water- and nutrient cycles in forest ecosystem. But due to the scarcity of fossil record, the evolutionary history of epiphytic macrolichens is poorly documented. Based on new fossil of Jurassic Daohugouthallus ciliiferus, we demonstrate the hitherto oldest known macrolichen inhabited a gymnosperm branch. We applied energy dispersive X-ray spectroscopy and geometric morphometric analysis to complementarily verify lichen affinity of D. ciliiferus and quantitatively assess the potential relationships with extant lichenized lineages, providing new approaches for study of this lichen adpression fossil. Considering the results, and the inferred age of D. ciliiferus, a new family, Daohugouthallaceae, is established. This work updates current knowledge to the early evolution of epiphytic macrolichens and reveals more complex lichen-plant interactions in a Jurassic forest ecosystem.

Neontological and paleontological congruence in the evolution of Podocarpaceae (coniferales) reproductive morphology

Introduction

Podocarpaceae are a diverse, primarily tropical conifer family that commonly produce large leaves and highly reduced, fleshy seed cones bearing large seeds. These features may result from relatively recent adaptation to closed-canopy angiosperm forests and bird-mediated seed dispersal, although determining precisely when shifts in leaf and seed cone morphology occurred is difficult due to a sparse fossil record and relatively few surviving deep lineages.

Methods

We compare the fossil record of Podocarpaceae with results from ancestral state reconstruction methods and correlated character models using neontological data and a previously published molecular time-tree.

Results

Ancestral state reconstructions suggest that small leaves, small seeds, and multi-seeded cones are ancestral in crown Podocarpaceae, with reduced cones bearing few seeds appearing in the Early Cretaceous and the correlated evolution of large leaves and large seeds occurring from the Late Cretaceous onwards. The exact timing of these shifts based on neontological data alone are poorly constrained, however, and estimates of leaf and seed size are imprecise.

Discussion

The fossil record is largely congruent with results based on the molecular time-tree, but provide important constraints on the range of leaf and seed sizes that were present in Cretaceous Podocarpaceae and the time by which changes in cone morphology and seed size likely occurred. We suggest in particular that reduced seed cones appeared in the Early Cretaceous and are linked to the contemporaneous diversification of small bodied avialans (birds), with shifts to larger seed sizes occurring after the Cretaceous in association with the spread of closed-canopy angiosperm forests.

Detailed seed cone morpho-anatomy of the Prumnopityoid clade: an insight into the origin and evolution of Podocarpaceae seed cones

BACKGROUND AND AIMS

Seed cone traits are significant for understanding the evolutionary history of conifers. Podocarpaceae has fleshy cones with a distinct morphology compared with other conifers. However, we have a poor understanding of the seed cone morphology of the Prumnopityoid clade and within Podocarpaceae. This study presents detailed seed cone morpho-anatomy and the evolution of fleshy structures traits in the Prumnopityoid clade.

METHODS

We investigated the detailed seed cone morpho-anatomy of selected species from the nine genera using the histological method. The evolution of morpho-anatomical traits was assessed using ancestral state reconstruction methods.

KEY RESULTS

The Prumnopityoid clade has evolved fleshy seed cones using different functional structures (e.g. aril, epimatium, bracts or receptaculum) and fleshiness is an ancestral trait in the clade. An epimatium is present in all genera except Phyllocladus, but with different structural morphologies (e.g. a fleshy asymmetrical cup-like epimatium or an epimatium that is fused with the integument, forming a fleshy sarcotesta-like seed coat). In all species with fleshy sarcotesta-like seed coats, the endotesta is hard and woody, forming a sclerotesta-like structure and the epimatium and exotesta are fused, forming a fleshy sarcotesta-like structure.

CONCLUSIONS

This study highlights that the Prumnopityoid clade has an amazing diversity of structures and complex evolutionary patterns. Fleshiness is an ancestral trait of the clade and has been achieved via diverse evolutionary pathways and structures. This clade has four distinct seed cone types, i.e. drupe-like, receptaculate, arilloid and dacrydioid cones, based on morpho-anatomical structures and traits. The macrofossil record also demonstrates the presence of several structures and traits.

How many ways can you build a conifer cone? A commentary on 'Origin and evolution of Podocarpaceae seed cones'

This article comments on:

Raees Khan, Robert S. Hill, Veit M. Dörken and Ed Biffin, Detailed seed cone morpho-anatomy of the Prumnopityoid clade: an insight into the origin and evolution of Podocarpaceae seed cones, Annals of Botany, Volume 130, Issue 5, 1 November 2022, Pages 637–655 https://doi.org/10.1093/aob/mcac097

The evolution of diffusive and biochemical capacities for photosynthesis was predominantly shaped by [CO2] with a smaller contribution from [O2]

The atmospheric concentration of carbon dioxide ([CO₂]) and oxygen ([O₂]) directly influence rates of photosynthesis (P_N) and photorespiration (R_PR) through the enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO). Levels of [CO₂] and [O₂] have varied over Earth history affecting rates of both CO₂ uptake and loss, alongside associated transpirative water-loss. The availability of CO₂ has likely acted as a stronger selective pressure than [O₂] due to the greater specificity of RubisCO for CO₂. The role of [O₂], and the interaction of [O₂] and [CO₂], in plant evolutionary history is less understood. We exposed twelve phylogenetically diverse species to combinations of sub-ambient, ambient and super-ambient [O₂] and [CO₂] to examine the biochemical and diffusive components of P_N and the possible role of [O₂] as a selective pressure. Photosynthesis, photosynthetic capacity and stomatal, mesophyll and total conductance to CO₂ were higher in the derived eudicot and monocot angiosperms than the more basal ferns, gymnosperms and basal angiosperms which originated in atmospheres characterised by higher CO₂:O₂ ratios. The ratio of R_PR:P_N was lower in the monocots, consistent with greater carboxylation capacity and higher stomatal and mesophyll conductance making easier CO₂ delivery to chloroplasts. The effect of [O₂] and [CO₂] on P_N/R_PR was less evident in more derived species with a higher conductance to CO₂. The effect of [O₂] was less apparent at high [CO₂], suggesting that atmospheric [O₂] may only have exerted a strong selective pressure on plant photosynthetic processes during periods characterised by low atmospheric CO₂:O₂ ratios. Current rising [CO₂] will predominantly enhance P_N rates in species with low diffusive conductance to CO₂.

Phylogeny and evolution of Cupressaceae: Updates on intergeneric relationships and new insights on ancient intergeneric hybridization

After the merger of the former Taxodiaceae and Cupressaceae s.s., currently the conifer family Cupressaceae (sensu lato) comprises seven subfamilies and 32 genera, most of which are important components of temperate and mountainous forests. With the exception of a recently published genus-level phylogeny of gymnosperms inferred from sequence analysis of 790 orthologs, previous phylogenetic studies of Cupressaceae were based mainly on morphological characters or a few molecular markers, and did not completely resolve the intergeneric relationships. In this study, we reconstructed a robust and well-resolved phylogeny of Cupressaceae represented by all 32 genera, using 1944 genes (Orthogroups) generated from transcriptome sequencing. Reticulate evolution analyses detected a possible ancient hybridization that occurred between ancestors of two subclades of Cupressoideae, including Microbiota-Platycladus-Tetraclinis (MPT) and Juniperus-Cupressus-Hesperocyparis-Callitropsis-Xanthocyparis (JCHCX), although both concatenation and coalescent trees are highly supported. Moreover, divergence time estimation and ancestral area reconstruction indicate that Cupressaceae very likely originated in Asia in the Triassic, and geographic isolation caused by continental separation drove the vicariant evolution of the two subfamilies Cupressoideae and Callitroideae in the northern and southern hemispheres, respectively. Evolutionary analyses of some morphological characters suggest that helically arranged linear-acicular leaves and imbricate bract-scale complexes represent ancestral states, and the shift from linear-acicular leaves to scale-like leaves was associated with the shift from helical to decussate arrangement. Our study sheds new light on phylogeny and evolutionary history of Cupressaceae, and strongly suggests that both dichotomous phylogenetic and reticulate evolution analyses be conducted in phylogenomic studies.

Mummified Wood of Juniperus (Cupressaceae) from the Late Miocene of Taman Peninsula, South Russia

Juniperus L. is the second-largest genus of conifers, having the widest distribution of all conifer genera. Its phytogeographic history is, however, obscure due to its very poor fossil record. We described a wood of Juniperus sp. from the lower Maeotian sediments of the Popov Kamen section, Taman Peninsula, South Russia, in order to clarify its taxonomic position shedding light on the phytogeographic history of the genus. This fossil wood was well-preserved by mummification, which allowed for it to be studied by the same methods as used for the anatomical examination of modern woods. The wood from the Popov Kamen section shows the greatest similarity to the extant Mediterranean species J. excelsa, belonging to the section Sabina. This is the first reliable macrofossil evidence of the sect. Sabina from Eurasia convincingly dated to the Miocene. The age of the mummified wood from the Popov Kamen section is consistent with molecular dating of diversification of the lineage comprising juniper species of the sect. Sabina from Europe, Asia and eastern Africa. The wood of Juniperus sp. has not been buried in situ, as it was found in the relatively deep-water marine sediments. The available coeval pollen series and macrofossils of Cupressaceae from the surrounding regions suggest that this wood was likely transferred by sea current from the northwestern side of the Black Sea, which was a part of the Eastern Paratethys.

Evolution of the coniferous seed scale

BACKGROUND

The Florin model is the commonly accepted theory of coniferous seed scale evolution. It describes the derivation of extant seed scale morphology from the morphology of fossil conifers via the reduction of complex to simple axillary structures. In this framework the seed scale is composed of a reduced lateral shoot with fertile and sterile appendages which are interpreted as leaf homologues.

SCOPE

The Florin model has three crucial problems that we address here: (1) the original derivation series does not take the ontogeny of extant conifers into account, (2) it cannot explain the morphology of all extant conifers and (3) Taxaceae were originally excluded. Examination of seed cones of extant conifers shows that ovules occur in three different positions in the cone: in an axillary position, replacing a leaf or terminating the cone axis. By interpreting the fertile appendage or seed-bearing structure as a leaf, not all positions are possible. The exclusion of Taxaceae from conifers is in stark contrast to recent molecular phylogenetic studies, which include Taxaceae in conifers as sister to Cupressaceae. Therefore, the Florin model does not offer an adequate explanation for taxaceous morphology.

CONCLUSION

We conclude that the seed-bearing structure of conifers cannot be interpreted as homologous to a leaf. In the interpretation we present here, the seed-bearing structure is the modified funiculus of the ovule, multiples of which laterally fuse to form the seed scale. The seed scales of all extant conifers can be derived from a Cunninghamia-like morphology via fusion and reduction of individual funiculi.

A novel cupulate seed plant, Xadzigacalix quatsinoensis gen. et sp. nov., provides new insight into the Mesozoic radiation of gymnosperms

PREMISE

Anatomically preserved evidence for a novel clade of gymnosperms emphasizes diversity of seed plants immediately prior to the appearance of angiosperm fossils in the paleontological record.

METHODS

Cupulate seeds from the Early Cretaceous Apple Bay locality (Vancouver Island) are described from serial cellulose acetate peels and three-dimensional reconstruction. Phylogenetic context is assessed through the comparative analysis of gymnosperm seed producing fructifications and maximum parsimony analysis of a revised morphological data set for seed plant phylogeny.

RESULTS

Xadzigacalix quatsinoensis gen. et sp. nov. is characterized by an orthotropous ovule with an elongated micropyle and complex integument, enclosed within a radial cupule. The micropylar canal is elongated; and the nucellus extends into the micropyle to seal the post pollination ovule. Except at the apex of the micropyle, the seed is completely enclosed by a parenchymatous cupule with ca. 20 axially elongated secretory ducts. The cupulate seed is produced upon a triangular woody stele, consisting of a parenchymatous pith surrounded by radially aligned tracheids. The stele produces three short terete traces that terminate within the base of the cupule as transfusion tissue at the seed chalaza.

CONCLUSIONS

Organography, vascularization, nature of the integument and nucellus, and configuration of the micropylar canal distinguish Xadzigacalix quatsinoensis from all other gymnosperm clades. Cladistic analyses suggest the new plant may have affinities with gnetophytes or angiosperms. These results are complemented with a critical re-evaluation of ovulate structures for Mesozoic gymnosperms, providing new insight into plant diversity immediately antecedent to the explosive diversification of flowering plants.

Phylotranscriptomics reveals the evolutionary history of subtropical East Asian white pines: further insights into gymnosperm diversification

Floristic composition within a geographic area is driven by a wide array of factors from local biotic interactions to biogeographical processes. Subtropical East Asia is a key biodiversity hotspot of the world, and harbors the most families of extant gymnosperms and a large number of endemic genera with ancient origins, but rare phylogenetic studies explored whether it served as a diversification center for gymnosperms. Here, we investigated the evolutionary and biogeographical history of subtropical East Asian white pines using an integrative approach that combines phylotranscriptomic and ecological analyses. Using 2,606 orthologous nuclear genes, we reconstructed a fully resolved and dated phylogeny of these species. Two main clades first diverged in the early Miocene, and by the late Miocene, all species appeared. Two white pines endemic to Taiwan Island experienced independent colonization events and regional extinction, which resulted in the present disjunctive distribution from mainland China. Ecological and biogeographical analyses indicate that the monsoon-driven assembly of evergreen broadleaved forests (EBLFs) might have significantly affected the diversification of subtropical East Asian white pines. Our study highlights the interactions of biotic and abiotic forces in the diversification and speciation of subtropical East Asian white pines. These findings indicate that subtropical East Asia is not only a floristic museum, but also a diversification center for gymnosperms. Our study also demonstrates the importance of phylotranscriptomics on species delimitation and biodiversity conservation, particularly for closely related species.

Morpho-anatomical affinities and evolutionary relationships of three paleoendemic podocarp genera based on seed cone traits

BACKGROUND AND AIMS

The three relict genera Pherosphaera, Microcachrys and Saxegothaea in Podocarpaceae produce quite distinct seed cone types in comparison with other genera and do not form a clade along with Acmopyle. The detailed seed cone morpho-anatomy of these three relict genera and affinities with other podocarps are poorly known. This study aims to understand the seed cone morpho-anatomy and affinities among these three disjunct relict genera and with other podocarps.

METHODS

We comparatively analysed the seed cone morpho-anatomical traits of the three podocarps genera and used ancestral state reconstruction to understand the evolution of these traits.

KEY RESULTS

We described the seed cone morpho-anatomical structures of the three relict genera in detail. The three genera produce aggregated multiovulate cones. Both Microcachrys and Saxegothaea have an asymmetrical free cup-like epimatium. Both species of Pherosphaera lack an epimatium. The ancestral state reconstruction implies that the presence of an epimatium is an ancestral trait in podocarps and is independently lost in Pherosphaera and Phyllocladus. The seed cones are fleshy in Microcachrys and non-fleshy in Saxegothaea and Pherosphaera. The seed cone macrofossils of both extinct and living podocarps also show the presence of an epimatium and fleshiness in podocarps.

CONCLUSIONS

Altogether, the morpho-anatomy suggests that Pherosphaera, Microcachrys and Saxegothaea present affinities with each other and other podocarps, but the reconstruction of the ancestral seed cone in Podcarpaceae is quite complex due to multiple convergent evolutions of several structures. These structures (e.g. epimatium, aril and receptaculum) are of low taxonomic value but of great evolutionary and ecological significance, and are responsive adaptations to ever-changing environmental conditions.

New insights into the phylogeny and evolution of Podocarpaceae inferred from transcriptomic data

Phylogenies of an increasing number of taxa have been resolved with the development of phylogenomics. However, the intergeneric relationships of Podocarpaceae, the second largest family of conifers comprising 19 genera and approximately 187 species mainly distributed in the Southern Hemisphere, have not been well disentangled in previous studies, even when genome-scale data sets were used. Here we used 993 nuclear orthologous groups (OGs) and 54 chloroplast OGs (genes), which were generated from 47 transcriptomes of Podocarpaceae and its sister group Araucariaceae, to reconstruct the phylogeny of Podocarpaceae. Our study completely resolved the intergeneric relationships of Podocarpaceae represented by all extant genera and revealed that topological conflicts among phylogenetic trees could be attributed to synonymous substitutions. Moreover, we found that two morphological traits, fleshy seed cones and flattened leaves, might be important for Podocarpaceae to adapt to angiosperm-dominated forests and thus could have promoted its species diversification. In addition, our results indicate that Podocarpaceae originated in Gondwana in the late Triassic and both vicariance and dispersal have contributed to its current biogeographic patterns. Our study provides the first robust transcriptome-based phylogeny of Podocarpaceae, an evolutionary framework important for future studies of this family.

Early Cretaceous abietoid Pinaceae from Mongolia and the history of seed scale shedding

PREMISE

Seed cones of extant Pinaceae exhibit two mechanisms of seed release. In "flexers" the cone scales remain attached to the central axis, while flexing and separating from each other to release the seeds. In "shedders" scales are shed from the axis, with the seeds either remaining attached to the scale or becoming detached. The early fossil history of Pinaceae from the Jurassic to Early Cretaceous is dominated by flexing seed cones, while the systematic information provided by shedding fossil cones has been overlooked and rarely integrated with data based on compression and permineralized specimens. We describe the earliest and best-documented evidence of a "shedder" seed cone from the Aptian-Albian of Mongolia.

METHODS

Lignite samples from Tevshiin Govi locality were disaggregated in water, washed, and dried in air. Fossils were compared to material of extant Pinaceae using LM and CT scans.

RESULTS

Lepidocasus mellonae gen. et sp. nov. is characterized by a seed cone that disarticulated at maturity and shed obovate bract-scale complexes that have a distinctive ribbed surface and an abaxial surface covered with abundant trichomes. The ovuliferous scale has ca. 30-40 resin canals, but only scarce xylem near the attachment to the cone axis. Resin vesicles are present in the seed integument. Phylogenetic analysis places Lepidocasus as sister to extant Cedrus within the abietoid grade.

CONCLUSIONS

The exquisite preservation of the trichomes in L. mellonae raises questions about their potential ecological function in the cones of fossil and living Pinaceae. Lepidocasus mellonae also shows that a shedding dispersal syndrome, a feature that has often been overlooked, evolved early in the history of Pinaceae during the Early Cretaceous.

On tree longevity

Large, majestic trees are iconic symbols of great age among living organisms. Published evidence suggests that trees do not die because of genetically programmed senescence in their meristems, but rather are killed by an external agent or a disturbance event. Long tree lifespans are therefore allowed by specific combinations of life history traits within realized niches that support resistance to, or avoidance of, extrinsic mortality. Another requirement for trees to achieve their maximum longevity is either sustained growth over extended periods of time or at least the capacity to increase their growth rates when conditions allow it. The growth plasticity and modularity of trees can then be viewed as an evolutionary advantage that allows them to survive and reproduce for centuries and millennia. As more and more scientific information is systematically collected on tree ages under various ecological settings, it is becoming clear that tree longevity is a key trait for global syntheses of life history strategies, especially in connection with disturbance regimes and their possible future modifications. In addition, we challenge the long-held notion that shade-tolerant, late-successional species have longer lifespans than early-successional species by pointing out that tree species with extreme longevity do not fit this paradigm. Identifying extremely old trees is therefore the groundwork not only for protecting and/or restoring entire landscapes, but also to revisit and update classic ecological theories that shape our understanding of environmental change.

Plastome phylogenomics of Cephalotaxus (Cephalotaxaceae) and allied genera

BACKGROUND AND AIMS

Cephalotaxus is a paleo-endemic genus in East Asia that consists of about 7-9 conifer species. Despite its great economic and ecological importance, the relationships between Cephalotaxus and related genera, as well as the interspecific relationships within Cephalotaxus, have long been controversial, resulting in contrasting taxonomic proposals in delimitation of Cephalotaxaceae and Taxaceae. Based on plastome data, this study aims to reconstruct a robust phylogeny to infer the systematic placement and the evolutionary history of Cephalotaxus.

METHODS

A total of 11 plastomes, representing all species currently recognized in Cephalotaxus and two Torreya species, were sequenced and assembled. Combining these with previously published plastomes, we reconstructed a phylogeny of Cephalotaxaceae and Taxaceae with nearly full taxonomic sampling. Under a phylogenetic framework and molecular dating, the diversification history of Cephalotaxus and allied genera was explored.

KEY RESULTS

Phylogenetic analyses of 81 plastid protein-coding genes recovered robust relationships between Cephalotaxus and related genera, as well as providing a well-supported resolution of interspecific relationships within Cephalotaxus, Taxus, Torreya and Amentotaxus. Divergence time estimation indicated that most extant species of these genera are relatively young, although fossil and other molecular evidence consistently show that these genera are ancient plant lineages.

CONCLUSIONS

Our results justify the taxonomic proposal that recognizes Cephalotaxaceae as a monotypic family, and contribute to a clear-cut delineation between Cephalotaxaceae and Taxaceae. Given that extant species of Cephalotaxus are derived from recent divergence events associated with the establishment of monsoonal climates in East Asia and Pleistocene climatic fluctuations, they are not evolutionary relics.

Sareomycetes: more diverse than meets the eye

Since its resurrection, the resinicolous discomycete genus Sarea has been accepted as containing two species, one with black apothecia and pycnidia, and one with orange. We investigate this hypothesis using three ribosomal (nuITS, nuLSU, mtSSU) regions from and morphological examination of 70 specimens collected primarily in Europe and North America. The results of our analyses support separation of the traditional Sarea difformis s.lat. and Sarea resinae s.lat. into two distinct genera, Sarea and Zythia. Sarea as circumscribed is shown to conservatively comprise three phylospecies, with one corresponding to Sarea difformis s.str. and two, morphologically indistinguishable, corresponding to the newly combined Sarea coeloplata. Zythia is provisionally maintained as monotypic, containing only a genetically and morphologically variable Z. resinae. The new genus Atrozythia is erected for the new species A. klamathica. Arthrographis lignicola is placed in this genus on molecular grounds, expanding the concept of Sareomycetes by inclusion of a previously unknown type of asexual morph. Dating analyses using additional marker regions indicate the emergence of the Sareomycetes was roughly concurrent with the diversification of the genus Pinus, suggesting that this group of fungi emerged to exploit the newly-available resinous ecological niche supplied by Pinus or another, extinct group of conifers. Our phylogeographic studies also permitted us to study the introductions of these fungi to areas where they are not native, including Antarctica, Cape Verde, and New Zealand and are consistent with historical hypotheses of introduction.

Integrating stomatal physiology and morphology: evolution of stomatal control and development of future crops

Stomata are central players in the hydrological and carbon cycles, regulating the uptake of carbon dioxide (CO₂) for photosynthesis and transpirative loss of water (H₂O) between plants and the atmosphere. The necessity to balance water-loss and CO₂-uptake has played a key role in the evolution of plants, and is increasingly important in a hotter and drier world. The conductance of CO₂ and water vapour across the leaf surface is determined by epidermal and stomatal morphology (the number, size, and spacing of stomatal pores) and stomatal physiology (the regulation of stomatal pore aperture in response to environmental conditions). The proportion of the epidermis allocated to stomata and the evolution of amphistomaty are linked to the physiological function of stomata. Moreover, the relationship between stomatal density and [CO₂] is mediated by physiological stomatal behaviour; species with less responsive stomata to light and [CO₂] are most likely to adjust stomatal initiation. These differences in the sensitivity of the stomatal density—[CO₂] relationship between species influence the efficacy of the ‘stomatal method’ that is widely used to infer the palaeo-atmospheric [CO₂] in which fossil leaves developed. Many studies have investigated stomatal physiology or morphology in isolation, which may result in the loss of the ‘overall picture’ as these traits operate in a coordinated manner to produce distinct mechanisms for stomatal control. Consideration of the interaction between stomatal morphology and physiology is critical to our understanding of plant evolutionary history, plant responses to on-going climate change and the production of more efficient and climate-resilient food and bio-fuel crops.

A Total-Group Phylogenetic Metatree for Cetacea and the Importance of Fossil Data in Diversification Analyses

Phylogenetic trees provide a powerful framework for testing macroevolutionary hypotheses, but it is becoming increasingly apparent that inferences derived from extant species alone can be highly misleading. Trees incorporating living and extinct taxa are are needed to address fundamental questions about the origins of diversity and disparity but it has proved challenging to generate robust, species-rich phylogenies that include large numbers of fossil taxa. As a result, most studies of diversification dynamics continue to rely on molecular phylogenies. Here, we extend and apply a recently developed meta-analytic approach for synthesizing previously published phylogenetic studies to infer a well-resolved set of species level, time-scaled phylogenetic hypotheses for extinct and extant cetaceans (whales, dolphins and allies). Our trees extend sampling from the ∼ 90 extant species to over 500 living and extinct species, and therefore allow for more robust inference of macroevolutionary dynamics. While the diversification scenarios we recover are broadly concordant with those inferred from molecular phylogenies they differ in critical ways, notably in the relative contributions of extinction and speciation rate shifts in driving rapid radiations. The metatree approach provides the most immediate route for generating higher level phylogenies of extinct taxa, and opens the door to re-evaluation of macroevolutionary hypotheses derived only from extant taxa.

Tight association of genome rearrangements with gene expression in conifer plastomes

BACKGROUND

Our understanding of plastid transcriptomes is limited to a few model plants whose plastid genomes (plastomes) have a highly conserved gene order. Consequently, little is known about how gene expression changes in response to genomic rearrangements in plastids. This is particularly important in the highly rearranged conifer plastomes.

RESULTS

We sequenced and reported the plastomes and plastid transcriptomes of six conifer species, representing all six extant families. Strand-specific RNAseq data show a nearly full transcription of both plastomic strands and detect C-to-U RNA-editing sites at both sense and antisense transcripts. We demonstrate that the expression of plastid coding genes is strongly functionally dependent among conifer species. However, the strength of this association declines as the number of plastomic rearrangements increases. This finding indicates that plastomic rearrangement influences gene expression.

CONCLUSIONS

Our data provide the first line of evidence that plastomic rearrangements not only complicate the plastomic architecture but also drive the dynamics of plastid transcriptomes in conifers.

Phylotranscriptomics reveals the complex evolutionary and biogeographic history of the genus Tsuga with an East Asian-North American disjunct distribution

The disjunct distribution between East Asia and North America is one of the best established biogeographic patterns. A robust phylogeny is fundamental for understanding the biogeographic histories of taxa with this distribution pattern. Tsuga (hemlock) is a genus of Pinaceae with a typical intercontinental disjunct distribution in East Asia and eastern and western North America, and its phylogeny has not been completely reconstructed in previous studies. In this study, we reconstructed a highly resolved phylogeny of Tsuga using 881 nuclear genes, 60 chloroplast genes and 23 mitochondrial genes and explored its biogeographic and reticulate evolutionary history. The results of phylogenetic analysis, molecular dating and ancestral area reconstruction indicate that Tsuga very likely originated from North America in the late Oligocene and dispersed from America to East Asia via the Bering Land Bridge during the middle Miocene. In particular, we found complex reticulate evolutionary pattern among the East Asian hemlock species. T. sieboldii possibly originated from hybridization with the ancestor of T. chinensis from mainland China and T. forrestii as the paternal donor and the ancestor of T. diversifolia and T. ulleungensis as the maternal donor. T. chinensis (Taiwan) could have originated by hybridization together with T. sieboldii and then evolved independently after dispersal to the Taiwan Island, subsequently experiencing mitochondrial DNA introgression with T. chinensis from mainland China. Moreover, our study found that T. chinensis from western China is more closely related to T. forrestii than to T. chinensis from eastern China. The nonmonophyletic T. chinensis needs taxonomic reconsideration.

The rise of angiosperms pushed conifers to decline during global cooling

Competition among species and entire clades can impact species diversification and extinction, which can shape macroevolutionary patterns. The fossil record shows successive biotic turnovers such that a dominant group is replaced by another. One striking example involves the decline of gymnosperms and the rapid diversification and ecological dominance of angiosperms in the Cretaceous. It is generally believed that angiosperms outcompeted gymnosperms, but the macroevolutionary processes and alternative drivers explaining this pattern remain elusive. Using extant time trees and vetted fossil occurrences for conifers, we tested the hypotheses that clade competition or climate change led to the decline of conifers at the expense of angiosperms. Here, we find that both fossil and molecular data show high congruence in revealing 1) low diversification rates, punctuated by speciation pulses, during warming events throughout the Phanerozoic and 2) that conifer extinction increased significantly in the Mid-Cretaceous (100 to 110 Ma) and remained high ever since. Their extinction rates are best explained by the rise of angiosperms, rejecting alternative models based on either climate change or time alone. Our results support the hypothesis of an active clade replacement, implying that direct competition with angiosperms increased the extinction of conifers by pushing their remaining species diversity and dominance out of the warm tropics. This study illustrates how entire branches on the Tree of Life may actively compete for ecological dominance under changing climates.

A Reference Genome Sequence for Giant Sequoia

The giant sequoia (Sequoiadendron giganteum) of California are massive, long-lived trees that grow along the U.S. Sierra Nevada mountains. Genomic data are limited in giant sequoia and producing a reference genome sequence has been an important goal to allow marker development for restoration and management. Using deep-coverage Illumina and Oxford Nanopore sequencing, combined with Dovetail chromosome conformation capture libraries, the genome was assembled into eleven chromosome-scale scaffolds containing 8.125 Gbp of sequence. Iso-Seq transcripts, assembled from three distinct tissues, was used as evidence to annotate a total of 41,632 protein-coding genes. The genome was found to contain, distributed unevenly across all 11 chromosomes and in 63 orthogroups, over 900 complete or partial predicted NLR genes, of which 375 are supported by annotation derived from protein evidence and gene modeling. This giant sequoia reference genome sequence represents the first genome sequenced in the Cupressaceae family, and lays a foundation for using genomic tools to aid in giant sequoia conservation and management.

Resin ducts as resistance traits in conifers: linking dendrochronology and resin-based defences

Conifers have evolved different chemical and anatomical defences against a wide range of antagonists. Resin ducts produce, store and translocate oleoresin, a complex terpenoid mixture that acts as both a physical and a chemical defence. Although resin duct characteristics (e.g., number, density, area) have been positively related to biotic resistance in several conifer species, the literature reporting this association remains inconclusive. Axial resin ducts recorded in annual growth rings are an archive of annual defensive investment in trees. This whole-life record of defence investment can be analysed using standard dendrochronological procedures, which allows us to assess interannual variability and the effect of understudied drivers of phenotypic variation on resin-based defences. Understanding the sources of phenotypic variation in defences, such as genetic differentiation and environmental plasticity, is essential for assessing the adaptive potential of forest tree populations to resist pests under climate change. Here, we reviewed the evidence supporting the importance of resin ducts in conifer resistance, and summarized current knowledge about the sources of variation in resin duct production. We propose a standardized methodology to measure resin duct production by means of dendrochronological procedures. This approach will illuminate the roles of resin ducts in tree defence across species, while helping to fill pivotal knowledge gaps in plant defence theory, and leading to a robust understanding of the patterns of variation in resin-based defences throughout the tree's lifespan.

The Mitogenome of Norway Spruce and a Reappraisal of Mitochondrial Recombination in Plants

Plant mitogenomes can be difficult to assemble because they are structurally dynamic and prone to intergenomic DNA transfers, leading to the unusual situation where an organelle genome is far outnumbered by its nuclear counterparts. As a result, comparative mitogenome studies are in their infancy and some key aspects of genome evolution are still known mainly from pregenomic, qualitative methods. To help address these limitations, we combined machine learning and in silico enrichment of mitochondrial-like long reads to assemble the bacterial-sized mitogenome of Norway spruce (Pinaceae: Picea abies). We conducted comparative analyses of repeat abundance, intergenomic transfers, substitution and rearrangement rates, and estimated repeat-by-repeat homologous recombination rates. Prompted by our discovery of highly recombinogenic small repeats in P. abies, we assessed the genomic support for the prevailing hypothesis that intramolecular recombination is predominantly driven by repeat length, with larger repeats facilitating DNA exchange more readily. Overall, we found mixed support for this view: Recombination dynamics were heterogeneous across vascular plants and highly active small repeats (ca. 200 bp) were present in about one-third of studied mitogenomes. As in previous studies, we did not observe any robust relationships among commonly studied genome attributes, but we identify variation in recombination rates as a underinvestigated source of plant mitogenome diversity.

Evolutionary diversification of taiwanioid conifers: evidence from a new Upper Cretaceous seed cone from Hokkaido, Japan

A single cylindrical seed cone 2 cm long, 1.1 cm wide has been found preserved in a calcium carbonate marine concretion from the Hakobuchi Formation (late Campanian-early Maastrichtian) of Hobetsu, Hokkaido, Japan. The cone, attached to a bent peduncle lacking leaves, has helically arranged bract/scale complexes that arise at right angles from the cone axis in the middle of the cone. The cone axis, ca. 1 mm wide, has a broad cylinder of secondary vascular tissue, and lacks a continuous resin canal system. Bract-scale complexes are laminar, cordate-orbiculate, and upturned distally, consisting primarily of bract tissue with no visible scale tip. The vascular trace to the bract/scale complex originates as a rod that divides laterally into several traces at the level of seed attachment. A single resin canal originates at the base of the bract-scale complex abaxial to the vascular strand, but more distally there are up to ca. 15 large resin canals that form a single row. Two to three inverted winged seeds are attached adaxially near the cone periphery. Cone structure and vascularization are most similar to those in the Cupressaceae, Subfamily Taiwanioideae, differing from living Taiwania cryptomerioides by having up to three seeds/scale rather than two, an abruptly upturned bract tip, in details of bract/scale vasculature, and a cone peduncle lacking leaves. This cone is described as Mukawastrobus satoi Stockey, Nishida and Rothwell. Together with previously described Early to Late Cretaceous taiwanioid seed cones from Mongolia and Hokkaido the new species demonstrates that the taxonomically diagnostic characters of such conifers are as subtle as those of Cretaceous and Cenozoic sequoioid Cupressaceae. This realization emphasizes that evolutionary diversification and turnover among taiwanioid conifers during the Cretaceous and Paleogene are probably far greater than currently recognized.

Adaptation and coordinated evolution of plant hydraulic traits

Hydraulic properties control plant responses to climate and are likely to be under strong selective pressure, but their macro-evolutionary history remains poorly characterised. To fill this gap, we compiled a global dataset of hydraulic traits describing xylem conductivity (K_s ), xylem resistance to embolism (P50), sapwood allocation relative to leaf area (Hv) and drought exposure (ψ_min ), and matched it with global seed plant phylogenies. Individually, these traits present medium to high levels of phylogenetic signal, partly related to environmental selective pressures shaping lineage evolution. Most of these traits evolved independently of each other, being co-selected by the same environmental pressures. However, the evolutionary correlations between P50 and ψ_min and between K_s and Hv show signs of deeper evolutionary integration because of functional, developmental or genetic constraints, conforming to evolutionary modules. We do not detect evolutionary integration between conductivity and resistance to embolism, rejecting a hardwired trade-off for this pair of traits.