Biology subjects

Clarke, J. A.

Publications and source records attributed to Clarke, J. A..

5 recordsLinked to original sources

bioRxiv2024

Integration of sexual dimorphism and left-right asymmetry in the development of the duck syrinx

Embryonic morphogenesis is regulated across multiple dimensions. In ducks, the syrinx, the avian vocal organ, undergoes morphogenic processes that result in both left-right asymmetric and sexually dimorphic development. Although these properties are thought to be controlled by the NODAL-PITX2 left-right signaling cascade and the sex steroid pathways, how these mechanisms work together to produce an asymmetric structure in a sexually dimorphic manner remains unclear. Here, we first establish evidence for sexual selection driving the evolution of the duck syrinx. During its development, we observe that PITX2 is expressed on the left side in both male and female ducks, although not in other birds. Asymmetric activation of PITX2 in this domain is triggered by bilateral BMP signaling but is limited to the left side by left-specific stably accessible chromatin established during an earlier asymmetric wave of PITX2 expression. Ultimately, there is an induction of left-specific WNT and BMP signaling in the syrinx primordium, which synergistically elevates cell proliferation on the left, leading to asymmetric growth. Estrogen receptor expression is also shown to be induced on the left side of the forming syrinx. This has no effect in males, but in females where the hormone is present, estrogen signaling reduces left-sided cell proliferation, thus promoting bilaterally symmetric growth. These data demonstrate how sexually dimorphic left-right asymmetry can be integrated to produce an adaptive trait.

developmental biology↗

bioRxiv2023

Taphonomic damage obfuscates interpretation of the retroarticular region of the Asteriornis mandible

Asteriornis maastrichtensis, from the latest Cretaceous of Belgium, is among the oldest known crown bird fossils, and its three-dimensionally preserved skull provides the most substantial insights into the cranial morphology of early crown birds to date. Phylogenetic analyses recovered Asteriornis as a total-group member of Galloanserae (the clade uniting Galliformes and Anseriformes. One important feature supporting this placement was enlargement of the retroarticular processes, which form elongate caudal extensions of the mandible in extant Galloanserae. Here, we reinterpret the jaw of Asteriornis and illustrate that the caudalmost portion of the mandibles are in fact not preserved. Instead, the caudal extremities of both the left and right mandibular rami extend to the surface of the fossil block containing the holotype skull, where they have eroded away. The originally identified retroarticular process of the right mandible--which exhibits a morphology and orientation strikingly similar to the retroarticular processes of certain extant and fossil galloanserans, including the early Palaeogene total-clade anseriforms Conflicto and Nettapterornis--instead represents a twisted and caudally displaced medial process. Nonetheless, anatomical comparisons with extant taxa reveal that we are unable to exclude the possibility that Asteriornis exhibited robust retroarticular processes comparable to those of extant Galloanserae. In light of the reinterpreted morphology of the Asteriornis mandible, we update the original anatomical character matrix used to investigate its phylogenetic relationships, and our revised phylogenetic analyses continue to support its position as a total-group galloanseran, as initially interpreted. We demonstrate additional morphological traits of the mandible supporting this phylogenetic position and provide new data on the nature and distribution of retroarticular processes among early crown birds.

paleontology↗

bioRxiv2022

A new Paleogene fossil and a new dataset for waterfowl (Aves: Anseriformes) clarify phylogeny, ecological evolution, and avian evolution at the K-Pg Boundary.

AbstractDespite making up one of the most ecologically diverse groups of living birds, comprising soaring, diving and giant flightless taxa, the evolutionary relationships and ecological evolution of Anseriformes (waterfowl) remain unresolved. Although Anseriformes have a comparatively rich, global Cretaceous and Paleogene fossil record, morphological datasets for this group that include extinct taxa report conflicting relationships for all known extinct taxa. Correct placement of extinct taxa is necessary to understand whether ancestral anseriform feeding ecology was more terrestrial or one of a set of diverse aquatic ecologies and to better understand avian evolution around the K-T boundary. Here, we present a new morphological dataset for Anseriformes that includes more extant and extinct taxa than any previous anseriform-focused dataset and describe a new anseriform species from the early Eocene Green River Formation of North America. The new taxon has a mediolaterally narrow bill which is not known in any previously described anseriform fossils other than portions of the pseudotoothed Pelagornithidae. The matrix created to assess the placement of this taxon comprises 41 taxa and 719 discrete morphological characters describing skeletal morphology, musculature, syringeal morphology, ecology, and behavior. We additionally combine the morphological dataset with published sequences using Bayesian methods and perform ancestral state reconstruction for ecological and behavioral characters. We recover the new Eocene taxon as a stem anseranatid across all analyses, and find that the new taxon represents a novel ecology within known Anseriformes and the Green River taxa. Results indicate that Anseriformes were likely ancestrally aquatic herbivores with rhamphothecal lamellae and provide insight into avian evolution during and following the K-Pg mass extinction.

evolutionary biology↗

bioRxiv2020

The first dinosaur egg remains a mystery

A recent study by Norell et al. (2020) described new egg specimens for two dinosaur species, identified as the first soft-shelled dinosaur eggs. The authors used phylogenetic comparative methods to reconstruct eggshell type in a sample of reptiles, and identified the eggs of dinosaurs and archosaurs as ancestrally soft-shelled, with three independent acquisitions of a hard eggshell among dinosaurs. This result contradicts previous hypotheses of hard-shelled eggs as ancestral to archosaurs and dinosaurs. Here we estimate the ancestral condition for dinosaur and archosaur eggs by reanalyzing the original data from Norell et al. and that from a recent study on reptile eggshells (Legendre et al., 2020) with the addition of these new dinosaur specimens. We show that the recovery of dinosaur eggs as ancestrally soft-shelled is conditioned by the discretization of a continuous character (eggshell thickness), the exclusion of turtle outgroups from the original sample, and a lack of branch length information. When using a larger sample, calibrated trees, and a definition of hard-shelled eggs referencing their unique prismatic structure, we recover dinosaur and archosaur eggs as either hard-shelled or uncertain (i.e. equal probability for hard- and soft-shelled). This remaining ambiguity is due to uncertainty in the assessment of eggshell type in two dinosaur species, i.e. [~]1% of the total sample. We conclude that more reptile egg specimens and a strict comparative framework are necessary to decipher the evolution of dinosaur eggs in a phylogenetic context.

paleontology↗

bioRxiv2018

Convergent regulatory evolution and the origin of flightlessness in palaeognathous birds

The relative roles of regulatory and protein evolution in the origin and loss of convergent phenotypic traits is a core question in evolutionary biology. Here we combine phylogenomic, epigenomic and developmental data to show that convergent evolution of regulatory regions, but not protein-coding genes, is associated with flightlessness in palaeognathous birds, a classic example of a convergent phenotype. Eleven new genomes, including a draft genome from an extinct moa, resolve palaeognath phylogeny and show that the incidence of independent, convergent accelerations among 284,000 conserved non-exonic elements is significantly more frequent in ratites than other bird lineages. Ratite-specific acceleration of conserved regions and measures of open chromatin across eight tissues in the developing chick identify candidate regulatory regions that may have modified or lost function in ratites. Enhancer activity assays conducted in the early developing chicken forelimb confirm that volant versions of a conserved element in the first intron of the TEAD1 gene display conserved enhancer activity, whereas an accelerated flightless version fails to drive reporter gene expression. Our results show that convergent molecular changes associated with loss of flight are largely regulatory in nature.

evolutionary biology↗