Three chromosome-level duck genome assemblies provide insights into genomic variation during domestication

Domestic ducks are raised for meat, eggs and feather down, and almost all varieties are descended from the Mallard (Anas platyrhynchos). Here, we report chromosome-level high-quality genome assemblies for meat and laying duck breeds, and the Mallard. Our new genomic databases contain annotations for thousands of new protein-coding genes and recover a major percentage of the presumed “missing genes” in birds. We obtain the entire genomic sequences for the C-type lectin (CTL) family members that regulate eggshell biomineralization. Our population and comparative genomics analyses provide more than 36 million sequence variants between duck populations. Furthermore, a mutant cell line allows confirmation of the predicted anti-adipogenic function of NR2F2 in the duck, and uncovered mutations specific to Pekin duck that potentially affect adipose deposition. Our study provides insights into avian evolution and the genetics of oviparity, and will be a rich resource for the future genetic improvement of commercial traits in the duck.

Early origin of sweet perception in the songbird radiation

Early events in the evolutionary history of a clade can shape the sensory systems of descendant lineages. Although the avian ancestor may not have had a sweet receptor, the widespread incidence of nectar-feeding birds suggests multiple acquisitions of sugar detection. In this study, we identify a single early sensory shift of the umami receptor (the T1R1-T1R3 heterodimer) that conferred sweet-sensing abilities in songbirds, a large evolutionary radiation containing nearly half of all living birds. We demonstrate sugar responses across species with diverse diets, uncover critical sites underlying carbohydrate detection, and identify the molecular basis of sensory convergence between songbirds and nectar-specialist hummingbirds. This early shift shaped the sensory biology of an entire radiation, emphasizing the role of contingency and providing an example of the genetic basis of convergence in avian evolution.

Quantitative Analysis of Morphometric Data of Pre-modern Birds: Phylogenetic Versus Ecological Signal

Birds are one of the most diverse clades of extant terrestrial vertebrates, a diversity that first arose during the Mesozoic as a multitude of lineages of pre-neornithine (stem) birds appeared but did not survive into the Cenozoic Era. Modern birds (Neornithes) inhabit an extensive array of ecologically distinct habitats and have specific and varied foraging strategies. Likewise, the morphological disparity among Mesozoic lineages appears to underscore a significant degree of ecological diversity, yet attempts to determine lineage-specific ecologies have mainly been limited to superficial narratives. In recent years, numerous studies have used various morphometric proxies to interpret the paleoecology of Mesozoic bird lineages, but largely without evaluating the interplay between ecological and phylogenetic signals. Moreover, most studies of this sort transform the original data into logarithms to control dimensionality, underestimating the biases induced upon such transformations. The goal of this study is to quantitatively address the ecomorphology of crown-group Neornithes using a dense sample of raw forelimb and hindlimb measurements, and to examine if such results can be used to infer the ecologies of Mesozoic bird lineages. To that end, scaling of limb measurements and ecological data from modern birds was assessed statistically using phylogenetic comparative methods, followed by the inclusion of fossil taxa. A strong relationship was recovered between humerus and hindlimb allometric scaling and phylogeny. Our results indicate that while some ecological classes of modern birds can be discriminated from each other, phylogenetic signature can overwhelm ecological signal in morphometric data, potentially limiting the inferences that can be made from ecomorphological studies. Furthermore, we found differential scaling of leg bones among Early Cretaceous enantiornithines and ornithuromorphs, a result hinting that habitat partitioning among different lineages could be a pervasive phenomenon in avian evolution.

On the Multifunctionality of Feathers and the Evolution of BIrds

The ability feathers have to perform many functions simultaneously and at different times is integral to the evolutionary history of all birds. Many studies focus on single functions of feathers; but any given feather performs many functions over its lifetime. Here, we review the known functions of feathers and discuss the interactions of these functions with avian evolution. Recent years have seen an increase in research on the evolution and development of feather functions because of an increase in high quality fossils with preserved feathers, new tools for understanding genetic mechanisms of feather development, new tools for measuring and analyzing feather color, availability of phylogenies and phylogenetic comparative methods, and an increase in interest in feather molt. Here, we aim to review how feather functions interact with avian evolution, with a focus on recent technological and discovery-based advances. By synthesizing research into feather functions over hierarchical scales, we aim to provide a broad context for how the adaptability and multifunctionality of feathers have allowed birds to diversify into the astounding array of environments and life-history strategies. Overall, we suggest research into avian evolution that involves feather function in any way should consider all aspects of a feathers’ functionality, including multiple functions, molt patterns, ecological/mechanical interactions, and feather wear over time. With this more holistic view, processes such as the evolution of avian coloration and flight can be understood in a broader and more nuanced context.

Confirmation of ovarian follicles in an enantiornithine (Aves) from the Jehol biota using soft tissue analyses

The remains of ovarian follicles reported in nine specimens of basal birds represents one of the most remarkable examples of soft-tissue preservation in the Early Cretaceous Jehol Biota. This discovery was immediately contested and the structures alternatively interpreted as ingested seeds. Fragments of the purported follicles preserved in an enantiornithine (STM10-12) were extracted and subjected to multiple high-resolution analyses. The structures in STM10-12 possess the histological and histochemical characteristics of smooth muscles fibers intertwined together with collagen fibers, resembling the contractile structure in the perifollicular membrane (PFM) of living birds. Fossilized blood vessels, very abundant in extant PFMs, are also preserved. Energy Dispersive Spectroscopy shows the preserved tissues primarily underwent alumino-silicification, with minor mineralization via iron oxides. No evidence of plant tissue was found. These results confirm the original interpretation as follicles within the left ovary, supporting the interpretation that the right ovary was functionally lost early in avian evolution.

Anatomy of Parahesperornis: Evolutionary Mosaicism in the Cretaceous Hesperornithiformes (Aves)

The Hesperornithiformes constitute the first known avian lineage to secondarily lose flight in exchange for the evolution of a highly derived foot-propelled diving lifestyle, thus representing the first lineage of truly aquatic birds. First unearthed in the 19th century, and today known from numerous Late Cretaceous (Cenomanian-Maastrichtian) sites distributed across the northern hemisphere, these toothed birds have become icons of early avian evolution. Initially erected as a taxon in 1984 by L. D. Martin, Parahesperornis alexi is known from the two most complete hesperornithiform specimens discovered to date and has yet to be fully described. P. alexi thus contributes significantly to our understanding of hesperornithiform birds, despite often being neglected in favor of the iconic Hesperornis. Here, we present a full anatomical description of P. alexi based upon the two nearly complete specimens in the collections of the University of Kansas Natural History Museum, as well as an extensive comparison to other hesperornithiform taxa. This study reveals P. alexi to possess a mosaic of basal and derived traits found among other hesperornithiform taxa, indicating a transitional form in the evolution of these foot-propelled diving birds. This study describes broad evolutionary patterns within the Hesperornithiformes, highlighting the significance of these birds as not only an incredible example of the evolution of ecological specializations, but also for understanding modern bird evolution, as they are the last known divergence of pre-modern bird diversification.

To Hop or Not to Hop? The Answer Is in the Bird Trees

Birds can use different types of gaits to move on the ground: they either walk, hop, or run. Although velocity can easily explain a preference for running, it remains unclear what drives a bird species to favor hopping over walking. As many hopping birds are relatively small and arboreal, we wanted to test the link between size, arboreality, and hopping ability. First, we carried out ancestral character state reconstructions of size range, hopping ability, and habitat traits on over 1000 species of birds. We found that both hopping ability and arboreality were derived and significantly correlated traits in avian evolution. Second, we tested the influence of hopping ability on the morphology of the lower appendicular skeleton by quantifying the shape differences of the pelvis and the three long bones of the hind limbs in 47 avian species with different habitats and gait preferences. We used geometric morphometrics on 3D landmarks, digitized on micro–computed tomography (micro-CT) and surface scans of the pelvis, femur, tibiotarsus, and tarsometatarsus. Locomotion habits significantly influence the conformation of the pelvis, especially at the origin of hip and knee muscle extensors. Interestingly, habitat, more than locomotion habits, significantly changed tarsometatarsus conformation. The morphology of the distal part of the tarsometatarsus constrains digit orientation, which leads to a greater ability to perch, an advantageous trait in arboreality. The results of this work suggest an arboreal origin of hopping and illuminate the evolution of avian terrestrial locomotion.[Anatomy; avian; gait; leg; lifestyle; pelvis; tree-dwelling.]

Evolution and distribution of medullary bone: evidence from a new Early Cretaceous enantiornithine bird

Living birds are unique among vertebrates in the formation of a female-specific bone tissue called medullary bone (MB) that is strictly associated with reproductive activity. MB is a rapidly mobilized source of calcium and phosphorus for the production of eggshell. Among living taxa, its skeletal distribution can be highly extensive such that it even exists in the ribs of some species. Due to its ephemeral nature, MB is rarely fossilized and so little is understood with regard to the origin of MB and its skeletal distribution in early taxa. Here we describe a new Early Cretaceous enantiornithine bird, Mirusavis parvus, gen. et. sp. nov., indicating that skeleton-wide distribution of MB appeared early in avian evolution. We suggest that this represents the plesiomorphic condition for the Aves and that the distribution of MB observed among extant neornithines is a product of increased pneumatization in this lineage and natural selection for more efficient distribution of MB.