Isoetes (Isoetaceae, Isoetales) is a cosmopolitan genus with an ancient and diverse evolutionary history that presumably peaked in the Palaeozoic. The age of the living clade has never been satisfactorily clarified. With little morphological (and molecular) divergence among species, megaspore morphology may provide valuable information on relationships in the group, not least among extant and extinct forms. We study megaspore ornamentation and surface texture/structure in 74 phylogenetically placed samples representing 59 species of Isoetes using scanning electron microscopy, and we discuss evolutionary implications of the results. Ornamentation (classified into 12 categories) and surface structure/texture (10 categories) were mapped onto a phylogeny constructed based on molecular data from the same samples whenever possible. All megaspores of the family are trilete with an outermost siliceous coating. There is substantial micromorphological variation, of which some appears clade specific. The megaspores of Isoetes reticulata, discovered from the late Oligocene to early Miocene of Tasmania, share remarkable similarities with those of extant species in the Australasian clade, in particular Isoetes neoguineensis and partly also Isoetes japonica. Adding a minimum age of the Australasian crown group (clade D) based on this fossil improved log marginal likelihood values of dating analyses significantly, and the fossil may provide key information for the understanding of divergence times of clades in the Isoetaceae crown group.

The long-term effects of present-day climate change on pollination are unquantified. However, distinguishing climatic drivers of ancient changes in pollination could provide valuable insights into biotic responses to near-future climate states. Herein, we show that pollination in a group of gymnosperm shrubs (Ephedra L., Gnetales) was irrevocably altered by the Cenozoic expansion of drylands on two different continents. In Asia, increased continentality during the mid-Eocene drove aridification and strong, dust-carrying storms that promoted a shift to prevailing wind pollination in the core clade of Ephedra. Surface uplift in the North American interior together with global cooling caused the expansion of aeolian deposition and placed similar evolutionary pressures on ephedras there, beginning in the latest Eocene and continuing across the Eocene–Oligocene transition (EOT). These climatic changes fundamentally altered the abundance and evolution of this ancient plant lineage on both continents and determined pollination mechanisms in the core clade of Ephedra today. Based on fossil evidence, this review demonstrates how climate change may have major and permanent impacts on plant–pollinator networks, as well as demonstrates possible evolutionary consequences of near-future climate scenarios for which we have no modern analogue.

Members of the tribe Palicoureeae of the coffee family (Rubiaceae) have a complex taxonomic history and have been the focus of few modern systematic studies. The tribe comprises about 1,100 tropical species in ten genera. To investigate phylogeny, we used a target capture approach and the angiosperm-wide Angiosperms353 bait set to produce genomic data for a representative taxon sample of Palicoureeae, with particular focus on the African genus Hymenocoleus. Using coalescent-based inference methods, we find that Puffia gerrardii (recently separated from Geophila) is sister to Hymenocoleus. The deepest split in Hymenocoleus is highly affected by incomplete lineage sorting, possibly as a consequence of rapid speciation during the early evolution of the clade. Remaining interspecific relationships in Hymenocoleus could be confidently resolved and while Robbrecht’s traditional infrageneric classification scheme based on floral features is not supported as reflecting evolution in the group, we find that several other features do, e.g. characters of pyrenes and involucral cups. Although not free of challenges, a strong advantage with our analytical approach is that gene tree heterogeneity can be taken into account. Including flanking regions yielded data sets that had the strongest power to reject polytomies and produced less gene tree error, resulting in species trees with higher normalised quartet scores and higher average support compared to trees inferred only from exon data. Presumably paralogous loci are often filtered out prior to species tree estimation but we find that they may contribute important phylogenetic information when using an inference method that actively accounts for them.

In recent phylogenetic studies of legumes the species Zygia/Ingainundata and Zygiasabatieri have been shown to not belong in neither Inga nor Zygia. Inga inundata was originally placed in the genus Inga based on morphological characters such as having pinnate leaves, but was transferred to the genus Zygia when the pod was discovered. The species was placed in its own section in Zygia, Zygia sect. Ingopsis, due to the similarity in leaf morphology to the species in Inga. Zygia sabatieri is another species placed in its own section in Zygia, Zygia sect. Pseudocojoba, due to similarity in flower morphology to the legume genus Cojoba. The genus Marmaroxylon has been synonymized under Zygia but the species Marmaroxylonocumarense has been shown to be closer related to species of the genus Macrosamanea and is not resolved within Zygia. In this study these results are compared and discussed. Zygia/Ingainundata and Zygiasabatieri are morphologically distinct from Inga and Zygia, and from each other, and taxonomic adjustments are made. Two new genera are described, Ingopsis gen. nov. to accommodate Zygia/Inga inundata and Pseudocojoba gen. nov. to accommodate Zygia sabatieri. In addition, Marmaroxylon ocumarense is transferred to the genus Macrosamanea where it fits phylogenetically and morphologically.

The Lower Cretaceous (likely upper Barremian to lower Aptian) flora of the Crato Formation in the Araripe Basin in NE Brazil opens a unique window to a late Mesozoic low latitude paleo-ecosystem. Therefore, the taxonomic-systematic and floristic investigation of the Crato Formation flora and the combined interpretation of its geological background gives the fascinating opportunity to explore the environmental and climatic conditions under which flowering plants (angiosperms) began to diversify. Besides, gymnosperms are still the predominant group of vascular plants in the vegetation mirrored by the fossil taphocoenosis. Gnetalean-like plants had the highest diversity in Earth’s history during the Early Cretaceous. In this chapter, all gymnosperm taxa based on formally published macrofossils are compiled and briefly discussed in terms of their phylogenetic position and paleo-ecology. Data from the pollen record are added but they must be handled cautiously as their lithostratigraphic position within the Crato Formation is not entirely settled. Gymnospermous plants were growing either as large trees (araucarias), shrubs (likely frenelopsids), or subshrubs and herbaceous plants (gnetalean-like taxa). Not all groups (orders and families) recognized from the pollen assemblage are also in the macrofossil component. However, the macrofossil assemblage still contains many undescribed fossil plants of various affinities.

Genome skimming (shallow whole-genome sequencing) offers time- and cost-efficient production of large amounts of DNA data that can be used to address unsolved evolutionary questions. Here we address phylogenetic relationships and topological incongruence in the tribe Anthospermeae (Rubiaceae), using phylogenomic data from the mitochondrion, the nuclear ribosomal cistron, and the plastome. All three genomic compartments resolve relationships in the Anthospermeae; the tribe is monophyletic and consists of three major subclades. Carpacoce Sond. is sister to the remaining clade, which comprises an African subclade and a Pacific subclade. Most results, from all three genomic compartments, are statistically well supported; however, not fully consistent. Intergenomic topological incongruence is most notable in the Pacific subclade but present also in the African subclade. Hybridization and introgression followed by organelle capture may explain these conflicts but other processes, such as incomplete lineage sorting (ILS), can yield similar patterns and cannot be ruled out based on the results. Whereas the null hypothesis of congruence among all sequenced loci in the individual genomes could not be rejected for nuclear and mitochondrial data, it was rejected for plastid data. Phylogenetic analyses of three subsets of plastid loci identified using the hierarchical likelihood ratio test demonstrated statistically supported intragenomic topological incongruence. Given that plastid genes are thought to be fully linked, this result is surprising and may suggest modeling or sampling error. However, biological processes such as biparental inheritance and inter-plastome recombination have been reported and may be responsible for the observed intragenomic incongruence. Mitochondrial insertions into the plastome are rarely documented in angiosperms. Our results indicate that a mitochondrial insertion event in the plastid trnSGGA - rps4 IGS region occurred in the common ancestor of the Pacific clade of Anthospermeae. Exclusion/inclusion of this locus in phylogenetic analyses had a strong impact on topological results in the Pacific clade. Genomic data have provided new opportunities to address phylogenetic incongruence and its bases. Our work shows notable intergenomic incongruence in a tribe of the coffee family, and the null hypothesis of congruence among all sequenced loci in the individual genomes was surprisingly rejected for plastid data. We further detected a (rarely reported) insertion of mitochondrial data into the plastome that had a decisive impact on tree topology.image

The use of molecular data in phylogenetic reconstruction during more than three decades has greatly improved our understanding of the macroevolutionary history of the coffee family (Rubiaceae) and has provided a solid basis for improvement of its classification. Based on the results of 130 studies, among them most recent phylogenomic works, we present a consensus phylogeny and a robust classification of Rubiaceae that shed light on the evolutionary success of this highly diverse angiosperm family and can serve as a framework for ecological and evolutionary studies. There are more than 14,000 species and about 580 accepted genera of Rubiaceae that are assigned to 71 tribes, of which 68 are classified in two subfamilies (Dialypetalanthoideae with 38 tribes and Rubioideae with 30 tribes). Three tribes (Acranthereae, Coptosapelteae, Luculieae) remain unclassified as to subfamily. Sixty-three of these 71 tribes are assigned to nine informal alliances (four in Rubioideae and five in Dialypetalanthoideae). These tribes are listed in alphabetical order within their respective alliances. Five tribes, one (Coussareeae) in Rubioideae and four (Airospermeae, Jackieae, Retiniphylleae, Steenisieae) in Dialypetalanthoideae, are excluded from these alliances due to unclear or conflicting phylogenetic positions. Thirty-six tribes retain their tribal status but receive new generic limits to remedy their previous para- or polyphyletic nature. Twenty-nine tribes not implemented in previous classifications have been added, of which three (Chioneae, Glionnetieae, Temnopterygeae) are newly described here. Basic information on phylogenies, distributions, former classifications, and useful references to previous works are provided for all accepted tribes, and future perspectives are discussed.

In this study of evolutionary relationships in the subfamily Rubioideae (Rubiaceae), we take advantage of the off-target proportion of reads generated via previous target capture sequencing projects based on nuclear genomic data to build a plastome phylogeny and investigate cytonuclear discordance. The assembly of off-target reads resulted in a comprehensive plastome dataset and robust inference of phylogenetic relationships, where most intratribal and intertribal relationships are resolved with strong support. While the phylogenetic results were mostly in agreement with previous studies based on plastome data, novel relationships in the plastid perspective were also detected. For example, our analyses of plastome data provide strong support for the SCOUT clade and its sister relationship to the remaining members of the subfamily, which differs from previous results based on plastid data but agrees with recent results based on nuclear genomic data. However, several instances of highly supported cytonuclear discordance were identified across the Rubioideae phylogeny. Coalescent simulation analysis indicates that while ILS could, by itself, explain the majority of the discordant relationships, plastome introgression may be the better explanation in some cases. Our study further indicates that plastomes across the Rubioideae are, with few exceptions, highly conserved and mainly conform to the structure, gene content, and gene order present in the majority of the flowering plants.

Premise: The isoetalean lineage has a rich fossil record that extends to the Devonian, but the age of the living clade is unclear. Recent results indicate that it is young, from the Cenozoic, whereas earlier work based on less data from a denser taxon sampling yielded Mesozoic median ages.

Methods: We analyzed node ages in Isoetes using two genomic data sets (plastome and nuclear ribosomal cistron), three clock models implemented in MrBayes (ILN, WN, and TK02 models), and a conservative approach to calibration.

Results: While topological results were consistently resolved in Isoetes estimated crown group ages range from the latest Paleozoic (mid-Permian) to the Mesozoic depending on data type and clock model. The oldest estimates were retrieved using the autocorrelated TK02 clock model. An (early) Cenozoic age was only obtained under one specific condition (plastome data analyzed with the uncorrelated ILN clock model). That same plastome data set also yielded the oldest (mid-Permian) age estimate when analyzed with the autocorrelated TK02 clock model. Adding the highly divergent, recently established sister species Isoetes wormaldii to the data set approximately doubled the average median node depth to the Isoetes crown group.

Conclusions: There is no consistent support for a Cenozoic origin of the living clade Isoetes. We obtained seemingly well-founded, yet strongly deviating results depending on data type and clock model. The single most important future improvement is probably to add calibration points, which requires an improved understanding of the isoetalean fossil record or alternative bases for calibration.

Background: Merlin's grass (Isoetes, Isoetaceae, Lycopsida), is the extant remnant of the isoetalean wood-producing lycopsids that originated during the Paleozoic, possibly in aquatic or boggy habitats. Modern day species are aquatic, semi-aquatic or terrestrial and occur almost worldwide. They display little morphological variation; the lobed corm has helically arranged leaves with internal air channels and basal sporangia. Genetic variation has also proven limited, which has hampered phylogenetic inference. We investigate evolutionary relationships in Isoetes, using molecular data and an extended sample of species compared to previous work, adding species that have never before been included in a phylogenetic study.

Results: Our results reveal an unexpected discovery of an Amborella syndrome in Isoetaceae: a single poorly known species is sister to the remaining family. The species, Isoetes wormaldii, is a rare endemic to the Eastern Cape of South Africa. Its leaves are flattened with a rounded point, which sharply contrasts with the awl-shaped leaves of most other species of Isoetes. The remaining species of Isoetes are resolved in five major clades, also indicated in previous work. While the phylogeny shows geographic structure, the patterns are complex. For example, tropical-southern African species occur in at least five clades, and Indian, Australian and Mediterranean species in at least three clades each.

Conclusion: The evolutionary and biogeographical history of Isoetes is not easily explained, and may conceivably include ample extinction and a mixture of ancient and more recent processes. Previously shown difficulties with node age estimation increase the problem. The here demonstrated sister-relationship between the phylogenetically, morphologically and genetically distinct Isoetes wormaldii and the remaining family appears to bridge the morphological gap between Isoetes and its extinct relatives, although further studies are needed. Moreover, it shortens the branch length to its living sister genus Selaginella, and may enhance node age estimation in future studies. Isoetes wormaldii is critically endangered, known only from one (to a few) minor populations. Immediate actions need to be taken if we want to prevent this unique species from going extinct.