Biology subjects

Hanley, D.

Publications and source records attributed to Hanley, D..

5 recordsLinked to original sources

bioRxiv2026

Design-Evolution Synergy Enables New-to-Nature Enzyme Chemistry

Directed evolution and machine-learning-assisted evolution have transformed biocatalysis by enabling rapid optimisation of catalytic performance within compatible protein scaffolds. In parallel, advances in deep-learning-driven de novo protein design have expanded accessible protein architectural space, enabling the generation of functional catalysts for increasingly challenging transformations. We herein report a synergistic design-evolution strategy to encode new-to-nature regio- and enantioselective C-H amination reactions using engineered de novo haemproteins to synthesise chiral piperidines, a privileged pharmacophore in drug discovery. By integrating motif scaffolding, computational re-design, and directed evolution, we demonstrate de novo enzyme design can enable challenging, high-energy-barrier enzyme chemistry with programmable regio- and enantioselectivity, high catalytic efficiency, excellent enzyme stability, and scaffold diversity.

synthetic biology↗

bioRxiv2025

Egg colour mimicry in the common cuckoo results from coevolutionary alternation, not coevolutionary arms races

The exquisite eggshell mimicry found in many cuckoo-host systems has been the textbook example of a coevolutionary arms race1. In this system, cuckoos lay their eggs in their hosts nests leaving these foster parents to rear their young2. In defence, most of these hosts have evolved the ability to recognize cuckoo eggs. It is long-assumed that these interactions select for ever-improving eggshell mimicry in cuckoo host-races laying distinct eggs that specifically mimic their hosts eggshell, regardless of its particular colour3,4. We challenge this paradigm and demonstrate that coevolutionary arms races and egg colour mimicry are the exception to the rule. Here, using eggshell reflectance spectra from 39 host species and the specific cuckoo eggs found in their nests, we show that eggshell colour mimicry is very uncommon even among frequent hosts. Although cuckoo eggs display considerable variation in eggshell colour, their hosts eggshell colours occupy 6 times their colour volume. As a result, mimicry is only achieved for a small subset of the egg colour gamut. Furthermore, cuckoo host-races rarely lay eggs that match their hosts eggs better than those of other potential hosts or that are distinct from those laid by other cuckoo host-races. These patterns are inconsistent with the long-held assumption of coevolutionary arms races, but consistent with coevolutionary alternation that is defined by a process of continual host-switching. These findings open new avenues for research in a system that has long served as a model for studying coevolutionary processes.

evolutionary biology↗

bioRxiv2022

Recording animal-view videos of the natural world

Plants, animals, and fungi display a rich tapestry of colors. Animals, in particular, use colors in dynamic displays performed in spatially complex environments. In such natural settings, light is reflected or refracted from objects with complex shapes that cast shadows and generate highlights. In addition, the illuminating light changes continuously as viewers and targets move through heterogeneous, continually fluctuating, light conditions. Although traditional spectrophotometric approaches for studying colors are objective and repeatable, they fail to document this complexity. Worse, they miss the temporal variation of color signals entirely. Here, we introduce hardware and software that provide ecologists and filmmakers the ability to accurately record animal-perceived colors in motion. Specifically, our Python codes transform photos or videos into perceivable units (quantum catches) for any animal of known photoreceptor sensitivity. We provide the plans, codes, and validation tests necessary for end-users to capture animal-view videos. This approach will allow ecologists to investigate how animals use colors in dynamic behavioral displays, the ways natural illumination alters perceived colors, and other questions that remained unaddressed until now due to a lack of suitable tools. Finally, our pipeline provides scientists and filmmakers with a new, empirically grounded approach for depicting the perceptual worlds of non-human animals.

animal behavior and cognition↗

bioRxiv2022

Consistent differences in eggshell phenotypes select for bluer eggs in an avian host-parasite system

Avian brood parasitism is a well-recognized model for studying coevolution. In this model, hosts adapt the ability to recognize and remove parasitic young to avoid the costs of rearing foreign offspring, while parasites counter-adapt phenotypes to evade detection. A classic example of host-parasite coevolutionary arms race is the great reed warbler and its parasite the common cuckoo (hereafter warbler and cuckoo, respectively). Recent work has found that cuckoo eggs are more likely to be accepted by warblers when those are bluer than their own eggs. Therefore, hosts would select for bluer cuckoo eggs; in turn, this provides directional selection for hosts eggs to remain bluer than cuckoo eggs. Here, we tested whether there were consistent differences in eggshell appearance between cuckoo and warbler eggs using a dataset which provides eggshell coloration of both warblers and cuckoos from the same nest. Despite being a textbook example of mimicry, we found that the cuckoos have significantly browner eggs than the warblers. These findings most likely suggest that this warbler-cuckoo system is experiencing negative frequency-dependent selection, as expected under red queen dynamics. Future research comparing warbler-cuckoo interactions over time would advance our understanding of the coevolution between avian brood parasites and their hosts.

evolutionary biology↗

bioRxiv2019

Temperature drives the evolution and global distribution of avian eggshell colour

The survival of a birds egg depends upon their ability to maintain within strict thermal limits. Avian eggshell colours have long been considered a phenotype that can help them stay within these thermal limits, with dark eggs absorbing heat more rapidly than bright eggs. Although long disputed, evidence suggests that darker eggs do increase in temperature more rapidly than lighter eggs, explaining why dark eggs are often considered as a cost to trade-off against crypsis. Although studies have considered whether eggshell colours can confer an adaptive benefit, no study has demonstrated evidence that eggshell colours have actually adapted for this function. This would require data spanning a wide phylogenetic diversity of birds and a global spatial scale. Here we show evidence that darker and browner eggs have indeed evolved in cold climes, and that the thermoregulatory advantage for avian eggs is a stronger selective pressure in cold climates. Temperature alone predicted more than 80% of the global variation in eggshell colour and luminance. These patterns were directly related to avian nesting strategy, such that all relationships were stronger when eggs were exposed to incident solar radiation. Our data provide strong evidence that sunlight and nesting strategies are important selection pressures driving egg pigment evolution through their role in thermoregulation. Moreover, our study advances understanding of how traits have adapted to local temperatures, which is essential if we are to understand how organisms will be impacted by global climate change.

ecology↗