Biology subjects

Cooney, C. R.

Publications and source records attributed to Cooney, C. R..

10 recordsLinked to original sources

bioRxiv2026

The avian colourscape is disproportionately threatened by species extinctions

The impact of projected extinctions on global animal colour diversity remains unknown. Combining citizen science with self-supervised deep learning, we built novel representations of bird plumage colour patterning based on >125,000 museum specimen images covering 9,143 species. We demonstrate that losing currently threatened bird species will drive a disproportionate reduction in avian plumage diversity, with the most severe losses occurring in tropical and subtropical regions. Furthermore, while humans generally find non-typical plumage phenotypes more aesthetically attractive, threatened species are unexpectedly deemed less visually appealing despite their comparatively unusual plumages. Overall, our results highlight severe, imminent threats to the existing avian colourscape and raise critical questions about the future of animal colour diversity in a changing world.

ecology↗

bioRxiv2026

Sexual selection does not predict long-term population trends in birds

Sexual selection is a major evolutionary force, yet its demographic consequences remain unclear. While experimental studies often report positive effects of sexual selection on traits linked to population performance, comparative studies often find null or negative associations with population persistence. One explanation for this discrepancy is that the demographic consequences of sexual selection depend on ecological context, particularly variation in mortality and fecundity. Here, we used six decades of abundance data and test whether sexual selection predicts population trends across 738 bird species from Europe and North America. We quantify sexual selection using complementary proxies capturing different components of sexual selection: mating system, sexual dichromatism, sexual size dimorphism and relative testes mass. We further assess whether the effect of sexual selection in population trends is mediated by mortality and fecundity. Across all proxies, we found no evidence that sexual selection is associated with population trends. This result is consistent across continents and robust to variation in mortality and fecundity. Our findings suggest that, despite its central role in shaping phenotypic evolution, sexual selection does not translate into consistent effects on long-term population trends at macroecological scales. More broadly, these results highlight a potential disconnect between evolutionary processes and population dynamics.

evolutionary biology↗

bioRxiv2023

Historical contingency influences the diversity of feather nanostructures in cuckoos

Structural coloration is widespread in animals, yet we know relatively little about its evolution and development. While previous studies have explored adaptive functions of structural color, a key gap is our lack of understanding of how historical contingency (path-dependency of biological processes) influences the loss and gain of this complex trait. We shed light on this question by describing feather nanostructures responsible for plumage colors in the cuckoos (family Cuculidae), a group with widespread occurrence of shiny, metallic plumage (metallic luster). The melanosomes found in feathers with metallic luster have specialized shapes: hollow rods, thin solid rods, hollow platelets, or solid platelets. In contrast, it is generally assumed that drably colored feathers possess thick, rod-shaped melanosomes. However, we uncover that this assumption is unfounded in cuckoos. We describe metallic luster in the plumages of 126 cuckoo species and map its phylogenetic distribution. This reveals that metallic luster is widespread in cuckoos but has likely been lost several times. We then use transmission electron microscopy to describe the feather nanostructures of 21 cuckoo species. Surprisingly, the drab feathers of many cuckoo species contain melanosomes with specialized shapes. We propose that historical contingency greatly influences nanostructure diversity in cuckoos. Specialized melanosome shapes can be retained in the plumages of drab species, potentially making it easier for metallic luster to evolve again in the future. This discovery supports the idea that historical contingency plays a key role in shaping the evolution of plumage color diversity.

evolutionary biology↗

bioRxiv2023

The mechanistic basis of evolutionary transitions between grey, slate, and blue colour in Tanagers (Thraupidae)

Both pigmentary and structural colours share many common elements of their feather anatomy, i.e. keratin, air and melanin packed in the melanosomes, despite utilizing different mechanisms of the colour production. This means that evolutionary transitions between pigmentary and structural colours can be achieved through a simple adjustment of these elements. Recently, an evolutionary hypothesis for the transition between pigmentary grey, through slate and finally to structural blue colour has been proposed and confirmed in the clade Tanagers on a macroevolutionary level. Here, we investigate mechanistic basis of this evolutionary pathway. By using SAXS (small-angle X-ray scattering) we have quantified important elements of spongy layer in medullary cells that is crucial for colour production by coherent scattering of light wavelengths. We have quantified five elements of the spongy layer: nanostructure complexity, average hard block thickness, average soft block thickness, filling fraction and Io value. We report that across different categories of feather colour, i.e. blue, slate and grey, nanostructure complexity, filling fraction and Io value explained variation in the chromatic component of the colour (between the three colour categories). Chromatic variation within the colour category was explained by filling fraction in the case of slate colour and by nanostructure complexity and average hard block thickness in the case of blue colour. We propose that variation in different elements or combination of elements of the spongy nanostructure has been utilised in feather colour evolution, both within and between colour categories, to overcome developmental constraints imposed by self-assembly processes.

evolutionary biology↗

bioRxiv2023

Evolutionary dynamics of pigmentary grey and non- iridescent structural blue colouration in Tanagers (family: Thraupidae)

3.1Birds are one of the most colourful animal groups in the world and there are multiple ways by which they achieve this feature. Mechanisms of colour production range from pigmentary (pigment deposition) to structural (nanostructural arrangements), or the combination of both. Despite the huge breadth of colour gamut, the basic components of feathers are shared across all of them (keratin, air and presence of pigments in accordance with the colour produced). It has been shown that in some instances, colour evolution between pigmentary and structural colours can proceed by rearrangement of the nano-structural elements of feathers. Here, we investigated evolutionary transitions between pigmentary grey and non-iridescent structural blue. We focus on the Thraupidae (tanagers and allies) that display a variety of blues and greys including a potential transition state that we refer to as slate. We used digitally calibrated images of birds to quantify colour and determine the distinctiveness of slate colour in colourspace. Following, we identify the most likely pathway for the evolution of the colour blue: from grey via slate colour. Our research reveals a new pathway in the evolution of blue colour.

evolutionary biology↗

bioRxiv2023

Long-term selection on mitocoding genes buried in mammalian and avian nuclear genomes

Sporadically genetic material that originates from an organelle genome integrates into the nuclear genome. However it is unclear what processes maintain such an integration over longer evolutionary time. Recently it was shown that nuclear DNA of mitochondrial origin (NUMTs) may harbour genes with intact mitochondrial reading frames despite the fact that they are highly divergent to the hosts mitochondrial genome. Two major hypotheses have been put forward to explain the existence of such mitocoding nuclear genes: (A) recent introgression from another species and (B) long-term selection. To address whether these intriguing possibilities do play a role we scanned the genomes of more than 1,000 avian and mammalian species for NUMTs. We indeed identified that the subclass of divergent NUMTs harbouring mitogenes with intact reading frames are widespread across mammals and birds. We can show that for these NUMTs signatures of cross-species introgression are widespread in birds, but not mammals with the exception of ungulates. We can also show that a substantial fraction of deeply divergent NUMTs are maintained by selection. For a small number of NUMT genes we identify an evolutionary signature that is consistent with adaptive evolution including one human NUMT that is shared among seven ape species. This highlights the intriguing possibility that NUMT insertions occasionally may be functional.

evolutionary biology↗

bioRxiv2021

Segmenting biological specimens from photos to understand the evolution of UV plumage in passerine birds

Ultraviolet (UV) colouration is thought to be an important signalling mechanism in many bird species, yet broad insights regarding the prevalence of UV plumage colouration and the factors promoting its evolution are currently lacking. Here, we develop a novel image segmentation pipeline based on deep learning that considerably outperforms classical (i.e. non-deep learning) segmentation methods, and use this to extract accurate information on whole-body plumage colouration from photographs of >24,000 museum specimens covering >4,500 species of passerine birds. Our results demonstrate that UV reflectance, particularly as a component of other colours, is widespread across the passerine radiation but is strongly phylogenetically conserved. We also find clear evidence in support of the role of light environment in promoting the evolution of UV plumage colouration, and a weak trend towards higher UV plumage reflectance among bird species with ultraviolet rather than violet-sensitive visual systems. Overall, our study provides important broad-scale insight into an enigmatic component of avian colouration, as well as demonstrating that deep learning has considerable promise for allowing new data to be bought to bear on long-standing questions in ecology and evolution.

evolutionary biology↗

bioRxiv2019

Non-coding rather than coding regions underpin avian bill shape diversification at macroevolutionary scales

Recent progress has been made in identifying genomic regions implicated in trait evolution on a microevolutionary scale in many species, but whether these are relevant over macroevolutionary time remains unclear. Here, we directly address this fundamental question using bird beak shape, a key evolutionary innovation linked to patterns of resource use, divergence and speciation, as a model trait. We integrate class-wide geometric-morphometric analyses with evolutionary sequence analyses of 10,322 protein coding genes as well as 229,001 genomic regions spanning 72 species. We identify 1,434 protein coding genes and 39,806 noncoding regions for which molecular rates were significantly related to rates of bill shape evolution. We show that homologs of the identified protein coding genes as well as genes in close proximity to the identified noncoding regions are involved in craniofacial embryo development in mammals. They are associated with embryonic stem cells pathways, including BMP and Wnt signalling, both of which have repeatedly been implicated in the morphological development of avian beaks. This suggests that identifying genotype-phenotype association on a genome wide scale over macroevolutionary time is feasible. While the coding and noncoding gene sets are associated with similar pathways, the actual genes are highly distinct, with significantly reduced overlap between them and bill-related phenotype associations specific to noncoding loci. Evidence for signatures of recent diversifying selection on our identified noncoding loci in Darwin finch populations further suggests that regulatory rather than coding changes are major drivers of morphological diversification over macroevolutionary times.

evolutionary biology↗

bioRxiv2019

Ecology, phylogeny, and the evolution of developmental duration in birds

The duration of the developmental period represents a fundamental axis of life history variation in animals, yet broad insights regarding the drivers of this diversity are currently lacking. Here using embryological data combined with information on incubation and fledging periods for 3096 species, we test key mechanistic and adaptive explanations for the evolutionary diversification of developmental durations in birds. First, using data on embryonic development for 20 model species, we show that developmental phases associated primarily with growth are longer and more variable than earlier phases, consistent with a role for allometric constraint in determining the duration of development. Second, using phylogenetic comparative methods, we find that avian developmental durations retain a strong imprint of deep evolutionary history, and that after accounting for these effects, body size differences among species explain less variation (5-22%) in developmental period lengths than previously thought. Finally, by collecting data for a suite of potential explanatory variables, our analyses reveal broad-scale ecological correlates of developmental durations, including variables associated with the relative safety of the developmental environment (e.g. nest height, insularity) and pressures of breeding phenology (e.g. migration). Overall, our results reveal that the combined effects of species body size, ecology, and phylogenetic history can account for 62-93% of the variation in developmental durations across birds, providing broad-scale quantitative insight into the relative importance of mechanistic constraints, adaptive evolution and evolutionary constraints in shaping the diversification of this key life-history trait.

evolutionary biology↗

bioRxiv2017

Sex-biased gene expression resolves sexual conflict through the evolution of sex-specific genetic architecture

Many genes are subject to contradictory selection pressures in males and females, and balancing selection resulting from sexual conflict has the potential to substantially increase standing genetic diversity in populations and thereby act as an important force in adaptation. However, the underlying causes of sexual conflict, and the potential for resolution, remains hotly debated. Using transcriptome resequencing data from male and female guppies, we use a novel approach, combining patterns of genetic diversity and inter-sexual divergence in allele frequency, to distinguish the different scenarios that give rise to sexual conflict, and how this conflict may be resolved through regulatory evolution. We show that reproductive fitness is the main source of sexual conflict, and this is resolved via the evolution of male-biased expression. Furthermore, resolution of sexual conflict produces significant differences in genetic architecture between males and females, which in turn leads to specific alleles influencing sex-specific viability. Together, our findings suggest an important role for sexual conflict in shaping broad patterns of genome diversity, and show that regulatory evolution is a rapid and efficient route to the resolution of conflict.

evolutionary biology↗