Biomechanics in fossil plant biology

The use of biomechanics for the analysis of the form—function relationship in palaeobotany is reviewed. Four fields of application of biomechanics are discussed and illustrated, i.e. the functional analysis of plants and plant organs (examples: lianas, leaf margin types), reconstruction of fossil plants (growth habit, tree height), functional analysis of ontogeny (lianas, trees), and evolutionary pathways (evolution of early land plants). The biomechanical analysis of ontogeny and evolution is of particular interest because it not only reveals the biomechanical constraints and functional background of these processes, but also yields information concerning the underlying mechanisms. Ontogenetic and phylogenetic changes may resemble a self-organization process constrained by laws of biomechanics.     

An overview of fossil Ginkgoales

Neither direct fossil evidence nor consensus exists on the origin of the Ginkgoales and their phylogenetic relationships with other seed plants. The bases for assigning most Palaeozoic leaf fossils to Ginkgoales are shaky. There are eight morphogenera considered more or less well defined and useful for classifying Mesozoic leaf and shoot compressions/impressions, and only two or three morphotaxa of anatomically preserved wood fossils have generally been used. About nine genera of ovulate organs, however, have been reported in the Mesozoic. Whole plant reconstructions suggested for a number of well-preserved ginkgoalean plants are enumerated. Their associated (or connected) organs, and their occurrences and distributions are cited in detail. There are three or four major evolutionary lineages so far recognized among Mesozoic Ginkgoales: the Ginkgo-Grenana-Nehvizdyella lineage, the Karkenia lineage, the Yimaia-Toretzia/Umaltolepis lineage and perhaps the Schmeissneria lineage. Ginkgoales may be classified into five to six families, with a number of accessory morphotaxa and unclassified taxa. The general evolutionary trend among ginkgoaleans is reduction of both vegetative and reproductive organs. The reduction trend is seen clearly in the genus Ginkgo and roughly recapitulated in the developmental sequences of the living species. A similar reduction sequence runs in parallel in other lineages of Ginkgoales. Ginkgoales flourished during Jurassic and Early Cretaceous, but a significant radiation of the group had occurred already in Late Triassic when Ginkgoales were present in high taxonomic diversity and showed considerable morphological innovation. Geographically, Ginkgoales are mainly distributed in Laurasia and probably originated there. The earliest records are from Laurasia as is the relict living fossil. Ginkgoales may have lived in various climates and diverse habitats, although most flourished in mesic and temperate climates, and the Late Cretaceous and Cenozoic ginkgos were largely confined to riparian environments.Advances in micro- and ultrastructure studies and chemical investigations on the cuticle and megaspore membrane of ginkgoalean fossils are also summarized. Further studies in these fields may provide useful information on the ecology and palaeoclimatology of Ginkgoales as well as their taxonomy.     

Microbe‐like inclusions in tree resins and implications for the fossil record of protists in amber

During the past two decades, a plethora of fossil micro‐organisms have been described from various Triassic to Miocene ambers. However, in addition to entrapped microbes, ambers commonly contain microscopic inclusions that sometimes resemble amoebae, ciliates, microfungi, and unicellular algae in size and shape, but do not provide further diagnostic features thereof. For a better assessment of the actual fossil record of unicellular eukaryotes in amber, we studied equivalent inclusions in modern resin of the Araucariaceae; this conifer family comprises important amber‐producers in Earth history. Using time‐of‐flight secondary ion mass spectrometry (ToF‐SIMS), we investigated the chemical nature of the inclusion matter and the resin matrix. Whereas the matrix, as expected, showed a more hydrocarbon/aromatic‐dominated composition, the inclusions contain abundant salt ions and polar organics. However, the absence of signals characteristic for cellular biomass, namely distinctive proteinaceous amino acids and lipid moieties, indicates that the inclusions do not contain microbial cellular matter but salts and hydrophilic organic substances that probably derived from the plant itself. Rather than representing protists or their remains, these microbe‐like inclusions, for which we propose the term ‘pseudoinclusions’, consist of compounds that are immiscible with the terpenoid resin matrix and were probably secreted in small amounts together with the actual resin by the plant tissue. Consequently, reports of protists from amber that are only based on the similarity of the overall shape and size to extant taxa, but do not provide relevant features at light‐microscopical and ultrastructural level, cannot be accepted as unambiguous fossil evidence for these particular groups.     

Mass extinction events and the plant fossil record

Five mass extinction events have punctuated the geological record of marine invertebrate life. They are characterized by faunal extinction rates and magnitudes that far exceed those observed elsewhere in the geological record. Despite compelling evidence that these extinction events were probably driven by dramatic global environmental change, they were originally thought to have little macroecological or evolutionary consequence for terrestrial plants. New high-resolution regional palaeoecological studies are beginning to challenge this orthodoxy, providing evidence for extensive ecological upheaval, high species-level turnover and recovery intervals lasting millions of years. The challenge ahead is to establish the geographical extent of the ecological upheaval, because reconstructing the vegetation dynamics associated with these events will elucidate the role of floral change in faunal mass extinction and provide a better understanding of how plants have historically responded to global environmental change similar to that anticipated for our future.     

Amplification and analysis of Miocene plant fossil DNA.

Ancient DNA has been extracted and sequenced from several animal and plant specimens. Previous considerations of the damage to ancient DNA have suggested that both the age and size of DNA fragments that can be retrieved and sequenced may be limited, the former to between several thousand and at most tens of thousands of years old, and the latter to at most a few hundred bases. A recent report of a 770 base pair (b.p.) sequence from the chloroplast gene rbcL from a Miocene Magnolia latahensis leaf indicates that both estimated limitations may be too conservative. Further work has indicated that analysis of Miocene fossil DNA can be replicated, and can, therefore, open up the prospects for future development of the field of molecular palaeontology. Successful amplification of fossil DNA is sometimes confounded by factors inherent to fossil DNA or to samples with minimal amounts of target DNA. Techniques that alter denaturation, reduce inhibitors and the problem of contaminants, and repair DNA prior to polymerase chain reaction amplification can increase the probability of success.     

Autophagy in protists

Autophagy is the degradative process by which eukaryotic cells digest their own components using acid hydrolases within the lysosome. Originally thought to function almost exclusively in providing starving cells with nutrients taken from their own cellular constituents, autophagy is in fact involved in numerous cellular events including differentiation, turnover of macromolecules and organelles, and defense against parasitic invaders. During the last 10-20 years, molecular components of the autophagic machinery have been discovered, revealing a complex interactome of proteins and lipids, which, in a concerted way, induce membrane formation to engulf cellular material and target it for lysosomal degradation. Here, our emphasis is autophagy in protists. We discuss experimental and genomic data indicating that the canonical autophagy machinery characterized in animals and fungi appeared prior to the radiation of major eukaryotic lineages. Moreover, we describe how comparative bioinformatics revealed that this canonical machinery has been subject to moderation, outright loss or elaboration on multiple occasions in protist lineages, most probably as a consequence of diverse lifestyle adaptations. We also review experimental studies illustrating how several pathogenic protists either utilize autophagy mechanisms or manipulate host-cell autophagy in order to establish or maintain infection within a host. The essentiality of autophagy for the pathogenicity of many parasites, and the unique features of some of the autophagy-related proteins involved, suggest possible new targets for drug discovery. Further studies of the molecular details of autophagy in protists will undoubtedly enhance our understanding of the diversity and complexity of this cellular phenomenon and the opportunities it offers as a drug target.     

Differential responses of soil bacteria,fungi, archaea and protists to plant species richness and plant functional group identity

Plants are known to influence belowground microbial community structure along their roots, but the impacts of plant species richness and plant functional group (FG) identity on microbial communities in the bulk soil are still not well understood. Here, we used 454‐pyrosequencing to analyse the soil microbial community composition in a long‐term biodiversity experiment at Jena, Germany. We examined responses of bacteria, fungi, archaea, and protists to plant species richness (communities varying from 1 to 60 sown species) and plant FG identity (grasses, legumes, small herbs, tall herbs) in bulk soil. We hypothesized that plant species richness and FG identity would alter microbial community composition and have a positive impact on microbial species richness. Plant species richness had a marginal positive effect on the richness of fungi, but we observed no such effect on bacteria, archaea and protists. Plant species richness also did not have a large impact on microbial community composition. Rather, abiotic soil properties partially explained the community composition of bacteria, fungi, arbuscular mycorrhizal fungi (AMF), archaea and protists. Plant FG richness did not impact microbial community composition; however, plant FG identity was more effective. Bacterial richness was highest in legume plots and lowest in small herb plots, and AMF and archaeal community composition in legume plant communities was distinct from that in communities composed of other plant FGs. We conclude that soil microbial community composition in bulk soil is influenced more by changes in plant FG composition and abiotic soil properties, than by changes in plant species richness per se.     

New insights into the reading of Paleozoic plant fossil record discontinuities

Studying the discontinuity patterns of Paleozoic vascular plants provides a global vision of these key events from the multivariate methods viewpoint. Non-metric multidimensional scaling, detrended correspondence analysis and cluster analysis have been employed together with a set of diversity and abundance measures and an evaluation of the geologic constraints from the plant fossil record data. The results reveal four clear significant discontinuities in terms of taxonomic composition and record representativeness during the early-middle Devonian, Devonian–Carboniferous, Mississippian–Pennsylvanian and early-late Permian. Due to the controversial character of the plant fossil record data and the effect of mass extinction events, the results can be explained in taxonomic turnover and ecological reorganisation terms which emphasise the crucial role of the geologic constrains in paleobiological inference.     

The empire disintegrates

This short article comments on the Symposium in ERS vol. 37/10 in which current scholars revisited the book The Empire Strikes Back and its legacy. The article comments on the book's assertion that a historical background is necessary to understand the absorption of migrant labour into capitalist societies, and notes the prevailing ignorance of the history of imperialism in UK schools and society. It discusses the current assumptions that if schools teach ‘fundamental British values’, racial and religious conflicts will somehow be minimized.     

Endosymbiotic associations within protists

The establishment of an endosymbiotic relationship typically seems to be driven through complementation of the host''s limited metabolic capabilities by the biochemical versatility of the endosymbiont. The most significant examples of endosymbiosis are represented by the endosymbiotic acquisition of plastids and mitochondria, introducing photosynthesis and respiration to eukaryotes. However, there are numerous other endosymbioses that evolved more recently and repeatedly across the tree of life. Recent advances in genome sequencing technology have led to a better understanding of the physiological basis of many endosymbiotic associations. This review focuses on endosymbionts in protists (unicellular eukaryotes). Selected examples illustrate the incorporation of various new biochemical functions, such as photosynthesis, nitrogen fixation and recycling, and methanogenesis, into protist hosts by prokaryotic endosymbionts. Furthermore, photosynthetic eukaryotic endosymbionts display a great diversity of modes of integration into different protist hosts.In conclusion, endosymbiosis seems to represent a general evolutionary strategy of protists to acquire novel biochemical functions and is thus an important source of genetic innovation.     

Protein kinases in protists

Summary The vast preponderance of our understanding of protein kinases comes from studies of mammalian or of other higher eukaryotic systems. A survey of the Wilson reference databank yielded 3,807 citations for protein kinases; only nine of these were reports of protein kinases in protists. It is apparent, nonetheless, that this understudied group offers unique opportunities for resolving the mechanisms by which protein kinases mediate a variety of cellular processes. Moreover, generalities about cofactor requirements (e.g., Ca²⁺ alone activates many protist protein kinases), substrate specificity, and the nature of the enzymes themselves (monomeric versus dimeric cyclic-nucleotide dependent protein kinases) will certainly need to be modified.     

The mitochondrial genome of protists

The data on the structure and functions of the mitochondrial genomes of protists (Protozoa and unicellular red and green algae) are reviewed. It is emphasized that mitochondrial gene structure and composition, as well as organization of mitochondrial genomes in protists are more diverse than in multicellular eukaryotes. The gene content of mitochondrial genomes of protists are closer to those of plants than animals or fungi. In the protist mitochondrial DNA, both the universal (as in higher plants) and modified (as in animals and fungi) genetic codes are used. In the overwhelming majority of cases, protist mitochondrial genomes code for the major and minor rRNA components, some tRNAs, and about 30 proteins of the respiratory chain and ribosomes. Based on comparison of the mitochondrial genomes of various protists, the origin and evolution of mitochondria are briefly discussed.     

An alternative interpretation ofAustralopithecus afarensis fossil material

Hominoid fossils from Hadar, in Ethiopia and Laetoli, in Tanzania, and dated from the late Pliocene, were described as a new species of hominid, “Australopithecus afarensis,”Johanson, White andCoppens, 1978. A comparative morphological analysis of the lectotype and several paralectotypes reveal that that two taxa were synthesized and that “Australopithecus afarensis” represents a hominid and a pongid. The hominid is relatively unspecialized, and the pongid is remarkably similar toDryopithecus (Sivapithecus) sivalensis (Lydekker), 1879. The pongid is the first anthropoid ape recorded from the late Pliocene in Africa.     

Challenging the empire

This paper considers how Paul Gilroy transformed hitherto dominant understandings of the relationship between race and class by developing an innovative account that foregrounded questions of racist oppression and collective resistance amid the organic crisis of British capitalism. The returns from this rethinking were profound in that he was able to make transparent both the structuring power of racism within the working class, and the necessity for autonomous black resistance. At the same time, significant lacunae in his account are identified, including the neglect of the episodic emergence of working-class anti-racism and the part played by socialists, particularly those of racialized minority descent in fashioning a major anti-racist social movement. The paper concludes with a lament for the disappearance of such work informed by a ‘Marxism without guarantees’ in the contemporary field of racism studies, and asks readers to consider the gains to be derived from such a re-engagement.