PubMed Health⌕ Search

Biomedical subjects

Philip C J Donoghue

Publications and source records attributed to Philip C J Donoghue.

13 recordsLinked to original sources
PubMed2026

On the origin of animals and placental mammals: a critique of literalist readings of the fossil record.

The fossil record is incomplete, as evidenced by the pervasive presence of ghost lineages throughout the Tree of Life. For example, across placental mammals, at least 720 Myr of basal lineages are ghost lineages, that is, lineages that have left no fossil evidence of their past history. In contrast, some studies have suggested that the fossil record is a faithful temporal archive of evolutionary history and thus the times of diversification of clades must be close to the ages of their oldest fossils. Such literalist interpretations have been contradicted by analysis of molecular datasets which, in many cases, indicate that groups including placental mammals and animals may have originated at times substantially older than their fossil records. Some of those studies have further argued that, in the case of animals and placental mammals, molecular clocks are uninformative, suffer from characteristic pathologies, and thus cannot distinguish between recent and ancient hypotheses of diversification. Here, we reexamine these two cases and show, using Bayesian model selection theory, that the explosive diversification models previously proposed for animals and placental mammals have a posterior probability of ∼0. We show the characteristic pathologies purportedly discovered do not exist, highlight errors in previous analyses, and provide advice on best practice for molecular-clock dating analysis.

Animals↗
PubMed2007

The homology and phylogeny of chondrichthyan tooth enameloid.

A systematic SEM survey of tooth microstructure in (primarily) fossil taxa spanning chondrichthyan phylogeny demonstrates the presence of a superficial cap of single crystallite enameloid (SCE) on the teeth of several basal elasmobranchs, as well as on the tooth plates of Helodus (a basal holocephalan). This suggests that the epithelial-mesenchymal interactions required for the development of enameloid during odontogenesis are plesiomorphic in chondrichthyans, and most likely in toothed gnathostomes, and provides phylogenetic support for the homology of chondrichthyan and actinopterygian enameloid. Along the neoselachian stem, we see a crownward progression, possibly modulated by heterochrony, from a monolayer of SCE lacking microstructural differentiation to the complex triple-layered tooth enameloid fabric of neoselachians. Finally, the occurrence of fully-differentiated neoselachian enameloid microstructure (including compression-resistant tangle fibered enameloid and bending-resistant parallel fibered enameloid) in Chlamydoselachus anguineus, a basal Squalean with teeth that are functionally "cladodont," is evidence that triple-layered enameloid microstructure was a preadaption to the cutting and gouging function of many neoselachian teeth, and thus may have played an integral role in the Mesozoic radiation of the neoselachian crown group.

Animals↗
PubMed2006

Paleontological evidence to date the tree of life.

The role of fossils in dating the tree of life has been misunderstood. Fossils can provide good "minimum" age estimates for branches in the tree, but "maximum" constraints on those ages are poorer. Current debates about which are the "best" fossil dates for calibration move to consideration of the most appropriate constraints on the ages of tree nodes. Because fossil-based dates are constraints, and because molecular evolution is not perfectly clock-like, analysts should use more rather than fewer dates, but there has to be a balance between many genes and few dates versus many dates and few genes. We provide "hard" minimum and "soft" maximum age constraints for 30 divergences among key genome model organisms; these should contribute to better understanding of the dating of the animal tree of life.

Animals↗
PubMed2006

Cellular and subcellular structure of neoproterozoic animal embryos.

Stereoblastic embryos from the Doushantuo Formation of China exhibit occasional asynchronous cell division, with diminishing blastomere volume as cleavage proceeded. Asynchronous cell division is common in modern embryos, implying that sophisticated mechanisms for differential cell division timing and embryonic cell lineage differentiation evolved before 551 million years ago. Subcellular structures akin to organelles, coated yolk granules, or lipid vesicles occur in these embryos. Paired reniform structures within embryo cells may represent fossil evidence of cells about to undergo division. Embryos exhibit no evidence of epithelial organization, even in embryos composed of approximately 1000 cells. Many of these features are compatible with metazoans, but the absence of epithelialization is consistent only with a stem-metazoan affinity for Doushantuo embryos.

Animals↗
PubMed2006

Synchrotron X-ray tomographic microscopy of fossil embryos.

Fossilized embryos from the late Neoproterozoic and earliest Phanerozoic have caused much excitement because they preserve the earliest stages of embryology of animals that represent the initial diversification of metazoans. However, the potential of this material has not been fully realized because of reliance on traditional, non-destructive methods that allow analysis of exposed surfaces only, and destructive methods that preserve only a single two-dimensional view of the interior of the specimen. Here, we have applied synchrotron-radiation X-ray tomographic microscopy (SRXTM), obtaining complete three-dimensional recordings at submicrometre resolution. The embryos are preserved by early diagenetic impregnation and encrustation with calcium phosphate, and differences in X-ray attenuation provide information about the distribution of these two diagenetic phases. Three-dimensional visualization of blastomere arrangement and diagenetic cement in cleavage embryos resolves outstanding questions about their nature, including the identity of the columnar blastomeres. The anterior and posterior anatomy of embryos of the bilaterian worm-like Markuelia confirms its position as a scalidophoran, providing new insights into body-plan assembly among constituent phyla. The structure of the developing germ band in another bilaterian, Pseudooides, indicates a unique mode of germ-band development. SRXTM provides a method of non-invasive analysis that rivals the resolution achieved even by destructive methods, probing the very limits of fossilization and providing insight into embryology during the emergence of metazoan phyla.

Animals↗
PubMed2006

Experimental taphonomy shows the feasibility of fossil embryos.

The recent discovery of apparent fossils of embryos contemporaneous with the earliest animal remains may provide vital insights into the metazoan radiation. However, although the putative fossil remains are similar to modern marine animal embryos or larvae, their simple geometric forms also resemble other organic and inorganic structures. The potential for fossilization of animals at such developmental stages and the taphonomic processes that might affect preservation before mineralization have not been examined. Here, we report experimental taphonomy of marine embryos and larvae similar in size and inferred cleavage mode to presumptive fossil embryos. Under conditions that prevent autolysis, embryos within the fertilization envelope can be preserved with good morphology for sufficiently long periods for mineralization to occur. The reported fossil record exhibits size bias, but we show that embryo size is unlikely to be a major factor in preservation. Under some conditions of death, fossilized remains will not accurately reflect the cell structure of the living organism. Although embryos within the fertilization envelope have high preservation potential, primary larvae have negligible preservation potential. Thus the paleo-embryological record may have strong biases on developmental stages preserved. Our data provide a predictive basis for interpreting the fossil record to unravel the evolution of ontogeny in the origin of metazoans.

Animals↗
PubMed2005

Histology and affinity of the earliest armoured vertebrate.

Arandaspids are the earliest skeletonizing vertebrates known from articulated remains. Despite a wealth of data, their affinity remains questionable because they exhibit a random mixture of primitive and derived characteristics. We constrain the affinity of arandaspids by providing the first detailed characterization of their dermoskeleton which is revealed to be three-layered, composed of a basal laminated, cancellous middle and tubercular superficial layers. All three layers are composed of acellular bone but the superficial layer also includes dentine and enameloid, comprising the tubercles. As such, the composition of the arandaspid dermoskeleton is common to heterostracans and astraspids, supporting existing hypotheses of early vertebrate phylogeny. This emphasizes the peculiarity of existing interpretations of aranadaspid anatomy and there is need for a complete reappraisal of the existing anatomical data.

Animals↗
PubMed2005

Genome duplication, extinction and vertebrate evolution.

Vertebrate evolution has been punctuated by three episodes of widespread gene or genome duplication, which have been linked with the origin of vertebrates, gnathostomes and teleosts, respectively. These three events coincide with bursts of character acquisition and increases in phenotypic complexity, and many researchers have suggested a causal relationship between the two. However, this pattern is derived from data for living taxa only; we argue here that, when fossils are taken into account, bursts of character acquisition disappear and gen(om)e duplication in vertebrate phylogeny can no longer be correlated with the origin of body plans. If patterns of character acquisition or morphological gaps between higher taxa are a reflection of phenotypic complexity, then more inclusive data sets incorporating fossil taxa provide no support for hypotheses linking gen(om)e duplications and the evolution of complexity in vertebrates.

Journal Article↗
PubMed2004

Fossil embryos from the Middle and Late Cambrian period of Hunan, south China.

Comparative embryology is integral to uncovering the pattern and process of metazoan phylogeny, but it relies on the assumption that life histories of living taxa are representative of their antecedents. Fossil embryos provide a crucial test of this assumption and, potentially, insight into the evolution of development, but because discoveries so far lack phylogenetic constraint, their significance is moot. Here we describe a collection of embryos from the Middle and Late Cambrian period (500 million years ago) of Hunan, south China, that preserves stages of development from cleavage to the pre-hatching embryo of a direct-developing animal comparable to living Scalidophora (phyla Priapulida, Kinorhyncha, Loricifera). The latest-stage embryos show affinity to the Lower Cambrian embryo Markuelia, whose life-history strategy contrasts both with the primitive condition inferred for metazoan phyla and with many proposed hypotheses of affinity, all of which prescribe indirect development. Phylogenetic tests based on these embryological data suggest a stem Scalidophora affinity. These discoveries corroborate, rather than contradict, the predictions of comparative embryology, providing direct historical support for the view that the life-history strategies of living taxa are representative of their stem lineages.

Animals↗
PubMed2002

Origin and early evolution of vertebrate skeletonization.

Data from living and extinct faunas of primitive vertebrates imply very different scenarios for the origin and evolution of the dermal and oral skeletal developmental system. A direct reading of the evolutionary relationships of living primitive vertebrates implies that the dermal scales, teeth, and jaws arose synchronously with a cohort of other characters that could be considered unique to jawed vertebrates: the dermoskeleton is primitively composed of numerous scales, each derived from an individual dental papilla; teeth are primitively patterned such that they are replaced in a classical conveyor-belt system. The paleontological record provides a unique but complementary perspective in that: 1) the organisms in which the skeletal system evolved are extinct and we have no recourse but to fossils if we aim to address this problem; 2) extinct organisms can be classified among, and in the same way as, living relatives; 3) a holistic approach to the incorporation of all data provides a more complete perspective on early vertebrate evolution. This combined approach is of no greater significance than in dealing with the origin of the skeleton and, combined with recent discoveries and new phylogenetic analyses, we have been able to test and reject existing hypotheses for the origin of the skeleton and erect a new model in their place.

Animals↗
PubMedDate not supplied

The anatomy, affinity, and phylogenetic significance of Markuelia.

The fossil record provides a paucity of data on the development of extinct organisms, particularly for their embryology. The recovery of fossilized embryos heralds new insight into the evolution of development but advances are limited by an almost complete absence of phylogenetic constraint. Markuelia is an exception to this, known from cleavage and pre-hatchling stages as a vermiform and profusely annulated direct-developing bilaterian with terminal circumoral and posterior radial arrays of spines. Phylogenetic analyses have hitherto suggested assignment to stem-Scalidophora (phyla Kinorhyncha, Loricifera, Priapulida). We test this assumption with additional data and through the inclusion of additional taxa. The available evidence supports stem-Scalidophora affinity, leading to the conclusion that scalidophorans, cyclonerualians, and ecdysozoans are primitive direct developers, and the likelihood that scalidophorans are primitively metameric.

Animals↗
PubMedDate not supplied

Fossilized embryos are widespread but the record is temporally and taxonomically biased.

We report new discoveries of embryos and egg capsules from the Lower Cambrian of Siberia, Middle Cambrian of Australia and Lower Ordovician of North America. Together with existing records, embryos have now been recorded from four of the seven continents. However, the new discoveries highlight secular and systematic biases in the fossil record of embryonic stages. The temporal window within which the embryos and egg capsules are found is of relatively short duration; it ends in the Early Ordovician and is roughly coincident with that of typical "Orsten"-type faunas. The reduced occurrence of such fossils has been attributed to reducing levels of phosphate in marine waters during the early Paleozoic, but may also be owing to the increasing depth of sediment mixing by infaunal metazoans. Furthermore, most records younger than the earliest Cambrian are of a single kind-large eggs and embryos of the priapulid-like scalidophoran Markuelia. We explore alternative explanations for the low taxonomic diversity of embryos recovered thus far, including sampling, size, anatomy, ecology, and environment, concluding that the preponderance of Markuelia embryos is due to its precocious development of cuticle at an embryonic stage, predisposing it to preservation through action as a substrate on which microbially mediated precipitation of authigenic calcium phosphate may occur. The fossil record of embryos may be limited to a late Neoproterozoic to early Ordovician snapshot that is subject to dramatic systematic bias. Together, these biases must be considered seriously in attempts to use the fossil record to arbitrate between hypotheses of developmental and life history evolution implicated in the origin of metazoan clades.

Animals↗