Molecular fingerprints resolve affinities of Rhynie chert organic fossils

Proterozoic microfossils continue to provide new insights into the rise of complex eukaryotic life

Eukaryotes have evolved to dominate the biosphere today, accounting for most documented living species and the vast majority of the Earth's biomass. Consequently, understanding how these biologically complex organisms initially diversified in the Proterozoic Eon over 539 million years ago is a foundational question in evolutionary biology. Over the last 70 years, palaeontologists have sought to document the rise of eukaryotes with fossil evidence. However, the delicate and microscopic nature of their sub-cellular features affords early eukaryotes diminished preservation potential. Chemical biomarker signatures of eukaryotes and the genetics of living eukaryotes have emerged as complementary tools for reconstructing eukaryote ancestry. In this review, we argue that exceptionally preserved Proterozoic microfossils are critical to interpreting these complementary tools, providing crucial calibrations to molecular clocks and testing hypotheses of palaeoecology. We highlight recent research on their preservation and biomolecular composition that offers new ways to enhance their utility.

Plastome evolution of Engelhardia facilitates phylogeny of Juglandaceae

BACKGROUND

Engelhardia (Juglandaceae) is a genus of significant ecological and economic importance, prevalent in the tropics and subtropics of East Asia. Although previous efforts based on multiple molecular markers providing profound insights into species delimitation and phylogeography of Engelhardia, the maternal genome evolution and phylogeny of Engelhardia in Juglandaceae still need to be comprehensively evaluated. In this study, we sequenced plastomes from 14 samples of eight Engelhardia species and the outgroup Rhoiptelea chiliantha, and incorporated published data from 36 Juglandaceae and six outgroup species to test phylogenetic resolution. Moreover, comparative analyses of the plastomes were conducted to investigate the plastomes evolution of Engelhardia and the whole Juglandaceae family.

RESULTS

The 13 Engelhardia plastomes were highly similar in genome size, gene content, and order. They exhibited a typical quadripartite structure, with lengths from 161,069 bp to 162,336 bp. Three mutation hotspot regions (TrnK-rps16, ndhF-rpl32, and ycf1) could be used as effective molecular markers for further phylogenetic analyses and species identification. Insertion and deletion (InDels) may be an important driving factor for the evolution of plastomes in Juglandoideae and Engelhardioideae. A total of ten codons were identified as the optimal codons in Juglandaceae. The mutation pressure mostly contributed to shaping codon usage. Seventy-eight protein-coding genes in Juglandaceae experienced relaxed purifying selection, only rpl22 and psaI genes showed positive selection (Ka/Ks > 1). Phylogenetic results fully supported Engelhardia as a monophyletic group including two sects and the division of Juglandaceae into three subfamilies. The Engelhardia originated in the Late Cretaceous and diversified in the Late Eocene, and Juglandaceae originated in the Early Cretaceous and differentiated in Middle Cretaceous. The phylogeny and divergence times didn't support rapid radiation occurred in the evolution history of Engelhardia.

CONCLUSION

Our study fully supported the taxonomic treatment of at the section for Engelhardia species and three subfamilies for Juglandaceae and confirmed the power of phylogenetic resolution using plastome sequences. Moreover, our results also laid the foundation for further studying the course, tempo and mode of plastome evolution of Engelhardia and the whole Juglandaceae family.

A mathematical description of fossilization

Fossils constitute an inestimable archive of past life on the Earth. However, the stochastic processes driving decay and fossilization and overwhelmingly distorting this archive, are challenging to interpret. Consequently, concepts of exceptional or poor preservation are often subjective or arbitrarily defined. Here, we offer an alternative way to think about fossilization. We propose a mathematical description of decay and fossilization relying on the change in the relative frequency and characteristics of biogenic objects (e.g. atoms, functional groups, molecules, body parts and organisms) within an organism-fossil system. This description partitions taphonomic changes into three categories: gain, loss and alteration of state. Although the changes undergone by organisms through decay, preservation and alteration vary a lot for different organisms under different conditions, we provide a unified formalism which can be applied directly in the comparison of different assemblages, experiments and fossils. Our expression is closely related to George R. Price's famous equation for the change in evolutionary traits and can be adapted to the study of palaeontological systems and many others.

Human brains preserve in diverse environments for at least 12 000 years

The brain is thought to be among the first human organs to decompose after death. The discovery of brains preserved in the archaeological record is therefore regarded as unusual. Although mechanisms such as dehydration, freezing, saponification, and tanning are known to allow for the preservation of the brain on short time scales in association with other soft tissues (≲4000 years), discoveries of older brains, especially in the absence of other soft tissues, are rare. Here, we collated an archive of more than 4400 human brains preserved in the archaeological record across approximately 12 000 years, more than 1300 of which constitute the only soft tissue preserved amongst otherwise skeletonized remains. We found that brains of this type persist on time scales exceeding those preserved by other means, which suggests an unknown mechanism may be responsible for preservation particular to the central nervous system. The untapped archive of preserved ancient brains represents an opportunity for bioarchaeological studies of human evolution, health and disease.

Visualization and identification of components in a gigantic spherical dolomite concretion by Raman imaging in combination with MCR or CLS methods

The combination of Raman imaging and multivariate curve resolution (MCR) or classical least squares (CLS) has allowed us to explore the distribution and identification of components in a gigantic spherical dolomite concretion. It has been found by the MCR and CLS analyses of imaging data that the concretion contains dolomite, kerogen, anatase, quartz, plagioclase, and carbon materials with considerably large distribution of dolomite. The existence of these components has also been confirmed by the point-by-point analysis of imaging data. The distributions of these components were clearly observed by Raman images. Of note is that the amount of carbon materials is considerably large, and they are buried among the matrix sedimentary grains in the concretion, suggesting that there exist soft tissues with biological origin. Moreover, one of the loading spectra of CLS shows intense bands in the region of 3000-2800 cm-1, and bands at ca. 1658, ca. 1585, 1455, 1323, and 1261 cm-1. These bands indicate the existence of decomposed organic materials in the concretion. Raman imaging of concretions provides direct evidence that concretions are of biological organic origin.

Hapalosiphonacean cyanobacteria (Nostocales) thrived amid emerging embryophytes in an early Devonian (407-million-year-old) landscape

Cyanobacteria have a long evolutionary history, well documented in marine rocks. They are also abundant and diverse in terrestrial environments; however, although phylogenies suggest that the group colonized land early in its history, paleontological documentation of this remains limited. The Rhynie chert (407 Ma), our best preserved record of early terrestrial ecosystems, provides an opportunity to illuminate aspects of cyanobacterial diversity and ecology as plants began to radiate across the land surface. We used light microscopy and super-resolution confocal laser scanning microscopy to study a new population of Rhynie cyanobacteria; we also reinvestigated previously described specimens that resemble the new fossils. Our study demonstrates that all are part of a single fossil species belonging to the Hapalosiphonaceae (Nostocales). Along with other Rhynie microfossils, these remains show that the accommodation of morphologically complex cyanobacteria to terrestrial ecosystems transformed by embryophytes was well underway more than 400 million years ago.