Biology subjects

Donoghue, P.

Publications and source records attributed to Donoghue, P..

7 recordsLinked to original sources

bioRxiv2026

Transposable element-mediated co-option drives the evolution of the miRNA regulatory system in Oryza AA-genome species

MicroRNAs (miRNAs) are key post-transcriptional regulators in plants, yet the evolutionary dynamics of the entire miRNA-mediated regulatory system remain poorly understood. We performed small RNA sequencing and comparative genomics analyses across all eight AA-genome species of Oryza within a well-resolved phylogenetic framework. We found that miRNA gene (MIRNA) families evolve with low birth-death rates, while individual paralogous MIRNAs turn over rapidly. We identified a novel mechanism in which transposable element (TE) insertions de novo generates functional miRNA target sites. miRNA target genes are characterized by distinct evolutionary signatures, including greater sequence length, lower GC content, moderately highly expression, reduced expression variability, and higher evolutionary conservation, which is consistent with their role as a conserved kernel regulatory subsystem. In contrast, the majority of recently evolved target genes that have acquired their miRNA binding sites through TE insertions tend to exhibit the opposite set of features. Furthermore, we uncovered co-evolutionary signatures between duplicated MIRNAs and their target genes, as well as between MIRNAs and phased siRNAs (phasiRNAs). Taken together, our study reveals multi-level evolutionary dynamics driven by TEs that rapidly generate new regulatory circuit and proposes a generalizable TE-MIRNA co-option model for regulatory network expansion in plants.

genomics↗

bioRxiv2024

Independent origins of spicules reconcile the evolutionary history of sponges

Sponges (Porifera) play a critical role in global biogeochemical processes. However, their evolutionary timeline remains unclear hampering our understanding of Neoproterozoic paleoecology. Molecular data suggest a Tonian or Cryogenian origin, while the oldest confirmed sponge fossils, represented by siliceous spicules, date to the Ediacaran. To understand this 150-million-year discrepancy, we compiled a new phylogenomic dataset, revised fossil evidence, derived a new dated sponge phylogeny, and tested whether ancestral sponges were aspiculated or not. We infer the last common sponge ancestor to have been early Ediacaran in age and aspiculated. Siliceous spicules evolved independently at least four times, and calcareous spicules at least two times in crown sponges. We performed a diversification rate analysis showing that siliceous spicules did not drive species radiations. Our study reconciles molecular and fossil evidence, indicating that while sponges emerged in the early Ediacaran, they are largely absent from the Neoproterozoic fossil record because they had not yet evolved spicules. TeaserSponges emerged in the Precambrian, were soft-bodied and did not produce mineralized spicules, which emerged multiple times independently.

evolutionary biology↗

bioRxiv2023

The three-dimensionally articulated oral apparatus of a Devonian heterostracan sheds light on feeding in Palaeozoic jawless fishes

Attempts to explain the origin and diversification of vertebrates have commonly invoked the evolution of feeding ecology, contrasting the passive suspension feeding of invertebrate chordates and larval lampreys with active predation in living jawed vertebrates. Of the extinct jawless vertebrates that phylogenetically intercalate these living groups, the feeding apparatus is preserved only in the early diverging stem-gnathostome heterostracans and its anatomy remains poorly understood. Here we use X-ray microtomography to characterise the feeding apparatus of the pteraspid heterostracan Rhinopteraspis dunensis (Roemer, 1855). We show that the apparatus is composed of thirteen plates arranged approximately bilaterally, the majority of which articulate from the postoral plate. Our reconstruction of the apparatus shows that the oral plates would have been capable of movement within the dorso-ventral plane, but their degree of movement was limited. The functional morphology of the apparatus in Rhinopteraspis precludes all proposed interpretations of feeding except for suspension/deposit feeding and we interpret the apparatus as having served primarily to moderate the oral gape. This is consistent with evidence that at least some early jawless gnathostomes were suspension feeders and runs contrary to macroecological scenarios that envisage early vertebrate evolution as characterised by a directional trend towards increasingly active food acquisition.

paleontology↗

bioRxiv2023

An evolutionary timescale for Bacteria calibrated using the Great Oxidation Event

Most of lifes diversity and history is microbial but it has left a meagre fossil record, greatly hindering understanding of evolution in deep time. However, the co-evolution of life and the Earth system has left signatures of bacterial metabolism in the geochemical record, most conspicuously the Great Oxidation Event (GOE) [~]2.33 billion years ago (Ga, (Poulton et al. 2021)), in which oxygenic photosynthesis and tectonism (Eguchi, Seales, and Dasgupta 2019) transformed Earths biosphere from dominantly anaerobic to aerobic. Here, we combine machine learning and phylogenetic reconciliation to infer ancestral transitions to aerobic lifestyles during bacterial evolution. Linking these transitions to the GOE provides new constraints to infer the timetree of Bacteria. We find that extant bacterial phyla are truly ancient, having radiated in the Archaean and the Proterozoic: the oldest include Bacillota (Firmicutes), which radiated 3.1-3.7 Ga, Cyanobacteria (3.3-3.5 Ga) and Patescibacteria (3-3.5 Ga). We show that most bacterial phyla were ancestrally anaerobic and that most transitions to an aerobic lifestyle post-dated the GOE. Our analyses trace oxygen production and consumption back to Cyanobacteria. From that starting point, horizontal transfer seeded aerobic lifestyles across bacterial diversity over hundreds of millions of years. Our analyses demonstrate that the diversification of aerobes proceeded in two waves corresponding to the GOE and to a second sustained rise in atmospheric O2 at the dawn of the Palezoic (Krause et al. 2022).

evolutionary biology↗

bioRxiv2023

ATP synthase evolution on a cross-braced dated tree of life

The timing of early cellular evolution from the divergence of Archaea and Bacteria to the origin of eukaryotes remains poorly constrained. The ATP synthase complex is thought to have originated prior to the Last Universal Common Ancestor (LUCA) and analyses of ATP synthase genes, together with ribosomes, have played a key role in inferring and rooting the tree of life. Here we reconstruct the evolutionary history of ATP synthases using an expanded sampling of Archaea, Bacteria, and eukaryotes. We developed a phylogenetic cross-bracing approach making use of endosymbioses and ancient gene duplications of the major ATP synthase subunits to infer a highly resolved, dated species tree and establish an absolute timeline for ATP synthase evolution. Our analyses show that the divergence of the ATP synthase into F- and A/V-type lineages, was a very early event in cellular evolution dating back to more than 4Ga potentially predating the diversification of Archaea and Bacteria. Our cross-braced, dated tree of life also provides insight into more recent evolutionary transitions including eukaryogenesis, showing that the eukaryotic nuclear and mitochondrial lineages diverged from their closest archaeal (2.67-2.19Ga) and bacterial (2.58-2.12Ga) relatives at roughly the same time, with the nuclear stem being moderately longer.

evolutionary biology↗

bioRxiv2021

Divergent evolutionary trajectories of bryophytes and tracheophytes from a complex common ancestor of land plants

The origin of plants and their colonization of land resulted in the transformation of the terrestrial environment. Here we investigate the evolution of the land plants (embryophytes) and their two main lineages, the tracheophytes (vascular plants) and bryophytes (non-vascular plants). We used new fossil calibrations, relative lineage dating implied by horizontal gene transfer, and new phylogenomic methods for mapping gene family origins. Distinct rooting strategies resolve tracheophytes and bryophytes as monophyletic sister groups that diverged during the Cambrian, 515-494 Ma. The embryophyte stem is characterised by a burst of gene innovation, while bryophytes subsequently experienced a no less dramatic episode of reductive genome evolution in which they lost genes associated with the elaboration of vasculature and the stomatal complex. Overall, our analyses confirm that extant tracheophytes and bryophytes are both highly derived; as a result, understanding the origin of land plants requires tracing character evolution across the diversity of modern lineages.

evolutionary biology↗

bioRxiv2021

Compositional phylogenomic modelling resolves the 'Zoraptera problem': Zoraptera are sister to all other polyneopteran insects

The evolution of wings propelled insects to their present mega-diversity. However, interordinal relationships of early-diverging winged insects and the timescale of their evolution are difficult to resolve, in part due to uncertainties in the placement of the enigmatic and species-poor order Zoraptera. The Zoraptera problem has remained a contentious issue in insect evolution since its discovery more than a century ago. This is a key issue because different placements of Zoraptera imply dramatically different scenarios of diversification and character evolution among polyneopteran. Here, we investigate the systematic placement of Zoraptera using the largest protein-coding gene dataset available to date, deploying methods to mitigate common sources of error in phylogenomic inference, and testing historically proposed hypotheses of zorapteran evolution. We recover Zoraptera as the earliest-diverging polyneopteran order, while earwigs (Dermaptera) and stoneflies (Plecoptera) form a monophyletic clade (Dermoplectopterida) sister to the remainder of Polyneoptera. The morphology and palaeobiology of stem-zorapterans are informed by Mesozoic fossils. The gut content and mouthparts of a male specimen of Zorotypus nascimbenei from Kachin amber (Cretaceous) reveal a fungivorous diet of Mesozoic zorapterans, akin to extant species. Based on a set of 42 justified fossil and stratigraphic calibrations, we recover a Devonian origin of winged insects and Polyneoptera, suggesting that these groups coincided with the rise of arborescence during the diversification of early terrestrial plants, fungi, and animals. Our results provide a robust framework for understanding the pattern and timescale of early winged insect diversification.

zoology↗