Phylogenomic evidence for multiple losses of flight in ratite birds

Molecular insights into region-specific sexual dichromatism: Comparative transcriptome analysis of red cheek pigmentation in zebra finches

Feathers, the primary skin appendage covering the avian body, undergo dynamic phenotypic changes throughout a bird's life. Males and females of the same species can exhibit sexually dichromatic plumage colors which play a critical role in mating choice, survival, and ecological interactions. In this study, we investigate the molecular mechanisms underlying the changes of color that occur during the transition from juvenile to adult feathers, known as the secondary transition. We focus on sexual dichromatism of craniofacial plumage and use the male cheek domain of the zebra finch (Taeniopygia guttata) as the major model. The transcriptome of the cheek and scalp (crown) domains in males and females of wild-type and genetic color variants were compared. We found that (1) Craniofacial color patterning operates through two regulatory layers. The first layer involves transcription factor (TF) genes that define the cheek domain such as PITX1, PAX1, PAX6. The second layer comprises pigment-related genes responsible for specific colors, including male-biased TFs (SOX10 and DMRT1) and transporters associated with red pigment synthesis. (2) Surprisingly, ASIP, which controls pheomelanin production in other species, was expressed in both male (red) and female (gray) cheeks. Instead, PAX1 in cheek dermal fibroblasts may serve as an upstream regulator, potentially triggering the male-biased color pattern through PAX6 and SOX10. PAX6 and SOX10 in melanocytes potentially enhance the expression of GPR143, SLC45A2, and TMEM163, driving increased pheomelanin production in males. (3) Sexual dichromatism is associated with sex-linked genes on the Z chromosome, notably SLC45A2. In addition, motif analysis comparing the binding strength between regional transcription factors and melanogenesis genes suggests that craniofacial pigmentation may have evolved convergently in passerine birds. These findings provide novel insights into the molecular control of color patterning and lay the groundwork for further studies on avian sexual dichromatism and secondary feather transition.

Practical Guidance and Workflows for Identifying Fast Evolving Non-Coding Genomic Elements Using PhyloAcc

Comparative genomics provides ample ways to study genome evolution and its relationship to phenotypic traits. By developing and testing alternate models of evolution throughout a phylogeny, one can estimate rates of molecular evolution along different lineages in a phylogeny and link these rates with observations in extant species, such as convergent phenotypes. Pipelines for such work can help identify when and where genomic changes may be associated with, or possibly influence, phenotypic traits. We recently developed a set of models called PhyloAcc, using a Bayesian framework to estimate rates of nucleotide substitution on different branches of a phylogenetic tree and evaluate their association with pre-defined or estimated phenotypic traits. PhyloAcc-ST and PhyloAcc-GT both allow users to define a priori a set of target lineages and then compare different models to identify loci accelerating in one or more target lineages. Whereas ST considers only one species tree across all input loci, GT considers alternate topologies for every locus. PhyloAcc-C simultaneously models molecular rates and rates of continuous trait evolution, allowing the user to ask whether the two are associated. Here, we describe these models and provide tips and workflows on how to prepare the input data and run PhyloAcc.

Fast and Simple Molecular Test for Sex Determination of the Monomorphic Eudromia elegans Individuals

Sex determination based just on morphological traits such as plumage dichromatism, sexual size dimorphism, behavior, or vocalizations is really challenging because of the sexual monomorphism present in more than half of avian species. Currently, a lot of them can be tested through DNA-based procedures, but they do not fit all the avian species, such as Eudromia elegans. The aim of this study was to design a new molecular method suitable for routine sex determination for that species that is fast, simple, and cost- and time- effective. DNA was isolated from dry blood stain and/or chest feather samples of E. elegans species. We used two sets of sex-specific primers (ZF/ZR and WF/WR) to amplify the expected fragments localized on the highly conserved CHD1 gene to distinguish between sexes due to the W-specific DNA sequence present only in females. We confirmed the accuracy and consistency of the PCR-based method based on length differences to distinguish between the sexes of E. elegans, which amplified two fragments in females and one fragment in males.

Paleoneurology of stem palaeognaths clarifies the plesiomorphic condition of the crown bird central nervous system

Lithornithidae, an assemblage of volant Palaeogene fossil birds, provide our clearest insights into the early evolutionary history of Palaeognathae, the clade that today includes the flightless ratites and volant tinamous. The neotype specimen of Lithornis vulturinus, from the early Eocene (approximately 53 million years ago) of Europe, includes a partial neurocranium that has never been thoroughly investigated. Here, we describe these cranial remains including the nearly complete digital endocasts of the brain and bony labyrinth. The telencephalon of Lithornis is expanded and its optic lobes are ventrally shifted, as is typical for crown birds. The foramen magnum is positioned caudally, rather than flexed ventrally as in some crown birds, with the optic lobes, cerebellum, and foramen magnum shifted further ventrally. The overall brain shape is similar to that of tinamous, the only extant clade of flying palaeognaths, suggesting that several aspects of tinamou neuroanatomy may have been evolutionarily conserved since at least the early Cenozoic. The estimated ratio of the optic lobe's surface area relative to the total brain suggests a diurnal ecology. Lithornis may provide the clearest insights to date into the neuroanatomy of the ancestral crown bird, combining an ancestrally unflexed brain with a caudally oriented connection with the spinal cord, a moderately enlarged telencephalon, and ventrally shifted, enlarged optic lobes.

A nuclear genome assembly of an extinct flightless bird, the little bush moa

We present a draft genome of the little bush moa (Anomalopteryx didiformis)-one of approximately nine species of extinct flightless birds from Aotearoa, New Zealand-using ancient DNA recovered from a fossil bone from the South Island. We recover a complete mitochondrial genome at 249.9× depth of coverage and almost 900 megabases of a male moa nuclear genome at ~4 to 5× coverage, with sequence contiguity sufficient to identify more than 85% of avian universal single-copy orthologs. We describe a diverse landscape of transposable elements and satellite repeats, estimate a long-term effective population size of ~240,000, identify a diverse suite of olfactory receptor genes and an opsin repertoire with sensitivity in the ultraviolet range, show that the wingless moa phenotype is likely not attributable to gene loss or pseudogenization, and identify potential function-altering coding sequence variants in moa that could be synthesized for future functional assays. This genomic resource should support further studies of avian evolution and morphological divergence.

Evolution of bird sex chromosomes: a cytogenomic approach in Palaeognathae species

BACKGROUND

Different patterns of sex chromosome differentiation are seen in Palaeognathae birds, a lineage that includes the ratites (Struthioniformes, Rheiformes, Apterygiformes, Casuariiformes, and the sister group Tinamiformes). While some Tinamiform species have well-differentiated W chromosomes, both Z and W of all the flightless ratites are still morphologically undifferentiated. Here, we conducted a comprehensive analysis of the ZW differentiation in birds using a combination of cytogenetic, genomic, and bioinformatic approaches. The whole set of satDNAs from the emu (Dromaius novaehollandiae) was described and characterized. Furthermore, we examined the in situ locations of these satDNAs alongside several microsatellite repeats and carried out Comparative Genomic Hybridizations in two related species: the greater rhea (Rhea americana) and the tataupa tinamou (Crypturellus tataupa).

RESULTS

From the 24 satDNA families identified (which represent the greatest diversity of satDNAs ever uncovered in any bird species), only three of them were found to accumulate on the emu's sex chromosomes, with no discernible accumulation observed on the W chromosome. The W chromosomes of both the greater rhea and the emu did not exhibit a significant buildup of either C-positive heterochromatin or repetitive DNAs, indicating their large undifferentiation both at morphological and molecular levels. In contrast, the tataupa tinamou has a highly differentiated W chromosome that accumulates several DNA repeats.

CONCLUSION

The findings provide new information on the architecture of the avian genome and an inside look at the starting points of sex chromosome differentiation in birds.

Ostrich (Struthio camelus) syrinx morphology and vocal repertoire across postnatal ontogeny and sex: Implications for understanding vocal evolution in birds

Vocal production in birds has been the target of considerable research that mostly has focused on phylogenetically well-nested songbirds. Anatomical descriptions and recordings of many non-songbirds have often only focused on a single ontogenetic stage or sex. While basic morphology of the vocal organ (syrinx) of ostrich (Palaeognathae, Struthio camelus) has been known since the 1800s, descriptions of its vocal repertoire and syrinx anatomy since then have been incomplete or inconsistent. New toolkits now enable detailed qualitative description of internal anatomy and meristic data and allow it to be compared to vocal production. Here we describe the anatomy of the syrinx in Struthio camelus for three post-hatching ontogenetic stages and both an adult male and female utilizing dissection and contrast enhanced X-ray computed tomography (diceCT). We find changes in ring geometry and spacing through ontogeny as well as lateral labia thickness. We document a small unpaired, midline, cartilaginous structure, a "pessuliform process" at the tracheobronchial juncture present throughout ontogeny and in both males and females. Investigation of the vocal repertoire of ostriches across ontogeny using a new dataset of 77 recordings led to identification of four vocalizations not previously reported in the literature, including the simultaneous production of a hiss and tonal. We find syrinx morphology largely consistent across ontogeny and in male and female adults. Both are capable of producing long duration tonal calls, but these may be more frequent in male birds. Closed-mouth boom calls remain unique to males. A detailed understanding of diversity in parts of early diverging clades is pivotal in attempting to estimate features of the ancestral syrinx in birds and how avian vocalization evolved.

Functional constraints on the number and shape of flight feathers

As a fundamental ecological aspect of most organisms, locomotor function significantly constrains morphology. At the same time, the evolution of novel locomotor abilities has produced dramatic morphological transformations, initiating some of the most significant diversifications in life history. Despite significant new fossil evidence, it remains unclear whether volant locomotion had a single or multiple origins in pennaraptoran dinosaurs and the volant abilities of individual taxa are controversial. The evolution of powered flight in modern birds involved exaptation of feathered surfaces extending off the limbs and tail yet most studies concerning flight potential in pennaraptorans do not account for the structure and morphology of the wing feathers themselves. Analysis of the number and shape of remex and rectrix feathers across a large dataset of extant birds indicates that the number of remiges and rectrices and the degree of primary vane asymmetry strongly correlate with locomotor ability revealing important functional constraints. Among these traits, phenotypic flexibility varies reflected by the different rates at which morphological changes evolve, such that some traits reflect the ancestral condition, whereas others reflect current locomotor function. While Mesozoic birds and Microraptor have remex morphologies consistent with extant volant birds, that of anchiornithines deviate significantly providing strong evidence this clade was not volant. The results of these analyses support a single origin of dinosaurian flight and indicate the early stages of feathered wing evolution are not sampled by the currently available fossil record.

Description of natal down of the ostrich (Struthio camelus) and comparison with common quail (Coturnix coturnix): Developmental and evolutionary implications

Natal down is a feather stage that differs in both form and function from the definitive feathers of adult birds. It has a simpler structure that has been speculated to be similar to the body coverings of non-avian dinosaurs. However, inference of the evolution of natal down has been limited by our understanding of its structural variation in extant birds. Most descriptive work has focused on neognathous birds, limiting our knowledge of the full diversity of feathers in extant taxa. Here, we describe the natal down of a post-hatch ostrich (Struthio camelus) and compare it to that of a post-hatch quail (Coturnix coturnix). We confirm the presence of featherless spaces (apteria) in S. camelus and the lack of barbules on the tips of natal down in both species. We also find differences between dorsal and ventral natal down structures, such as barbule density in S. camelus and the extent of the bare portion of the barb in both species. Surprisingly, we do not find that the neoptiles of either species follow the ideal morphologies for increasing insulation. Finally, we hypothesize that the different barb types present in S. camelus natal down result from a large addition of new barb ridges during development, which is not known except in feathers with a rachis. These results have implications for our understanding of how structure informs function and development in understudied feather types, such as those shared by non-avian dinosaurs.

3D atlas of tinamou (Neornithes: Tinamidae) pectoral morphology: Implications for reconstructing the ancestral neornithine flight apparatus

Palaeognathae, the extant avian clade comprising the flightless ratites and flight-capable tinamous (Tinamidae), is the sister group to all other living birds, and recent phylogenetic studies illustrate that tinamous are phylogenetically nested within a paraphyletic assemblage of ratites. As the only extant palaeognaths that have retained the ability to fly, tinamous may provide key information on the nature of the flight apparatus of ancestral crown palaeognaths-and, in turn, crown birds-as well as insight into convergent modifications to the wing apparatus among extant ratite lineages. To reveal new information about the musculoskeletal anatomy of tinamous and facilitate development of computational biomechanical models of tinamou wing function, we generated a three-dimensional musculoskeletal model of the flight apparatus of the extant Andean tinamou (Nothoprocta pentlandii) using diffusible iodine-based contrast-enhanced computed tomography (diceCT). Origins and insertions of the pectoral flight musculature of N. pentlandii are generally consistent with those of other extant volant birds specialized for burst flight, and the entire suite of presumed ancestral neornithine flight muscles are present in N. pentlandii with the exception of the biceps slip. The pectoralis and supracoracoideus muscles are robust, similar to the condition in other extant burst-flying birds such as many extant Galliformes. Contrary to the condition in most extant Neognathae (the sister clade to Palaeognathae), the insertion of the pronator superficialis has a greater distal extent than the pronator profundus, although most other anatomical observations are broadly consistent with the conditions observed in extant neognaths. This work will help form a basis for future comparative studies of the avian musculoskeletal system, with implications for reconstructing the flight apparatus of ancestral crown birds and clarifying musculoskeletal modifications underlying the convergent origins of ratite flightlessness.

Feather function and the evolution of birds

The ability of feathers to perform many functions either simultaneously or at different times throughout the year or life of a bird is integral to the evolutionary history of birds. Many studies focus on single functions of feathers, but any given feather performs many functions over its lifetime. These functions necessarily interact with each other throughout the evolution and development of birds, so our knowledge of avian evolution is incomplete without understanding the multifunctionality of feathers, and how different functions may act synergistically or antagonistically during natural selection. Here, we review how feather functions interact with avian evolution, with a focus on recent technological and discovery-based advances. By synthesising research into feather functions over hierarchical scales (pattern, arrangement, macrostructure, microstructure, nanostructure, molecules), we aim to provide a broad context for how the adaptability and multifunctionality of feathers have allowed birds to diversify into an astounding array of environments and life-history strategies. We suggest that future research into avian evolution involving feather function should consider multiple aspects of a feather, including multiple functions, seasonal wear and renewal, and ecological or mechanical interactions. 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.

Microstructural and crystallographic evolution of palaeognath (Aves) eggshells

The avian palaeognath phylogeny has been recently revised significantly due to the advancement of genome-wide comparative analyses and provides the opportunity to trace the evolution of the microstructure and crystallography of modern dinosaur eggshells. Here, eggshells of all major clades of Palaeognathae (including extinct taxa) and selected eggshells of Neognathae and non-avian dinosaurs are analysed with electron backscatter diffraction. Our results show the detailed microstructures and crystallographies of (previously) loosely categorized ostrich-, rhea-, and tinamou-style morphotypes of palaeognath eggshells. All rhea-style eggshell appears homologous, while respective ostrich-style and tinamou-style morphotypes are best interpreted as homoplastic morphologies (independently acquired). Ancestral state reconstruction and parsimony analysis additionally show that rhea-style eggshell represents the ancestral state of palaeognath eggshells both in microstructure and crystallography. The ornithological and palaeontological implications of the current study are not only helpful for the understanding of evolution of modern and extinct dinosaur eggshells, but also aid other disciplines where palaeognath eggshells provide useful archive for comparative contrasts (e.g. palaeoenvironmental reconstructions, geochronology, and zooarchaeology).

Recurrent erosion of COA1/MITRAC15 exemplifies conditional gene dispensability in oxidative phosphorylation

Skeletal muscle fibers rely upon either oxidative phosphorylation or the glycolytic pathway with much less reliance on oxidative phosphorylation to achieve muscular contractions that power mechanical movements. Species with energy-intensive adaptive traits that require sudden bursts of energy have a greater dependency on glycolytic fibers. Glycolytic fibers have decreased reliance on OXPHOS and lower mitochondrial content compared to oxidative fibers. Hence, we hypothesized that gene loss might have occurred within the OXPHOS pathway in lineages that largely depend on glycolytic fibers. The protein encoded by the COA1/MITRAC15 gene with conserved orthologs found in budding yeast to humans promotes mitochondrial translation. We show that gene disrupting mutations have accumulated within the COA1 gene in the cheetah, several species of galliform birds, and rodents. The genomic region containing COA1 is a well-established evolutionary breakpoint region in mammals. Careful inspection of genome assemblies of closely related species of rodents and marsupials suggests two independent COA1 gene loss events co-occurring with chromosomal rearrangements. Besides recurrent gene loss events, we document changes in COA1 exon structure in primates and felids. The detailed evolutionary history presented in this study reveals the intricate link between skeletal muscle fiber composition and the occasional dispensability of the chaperone-like role of the COA1 gene.

Gene-tree misrooting drives conflicts in phylogenomic coalescent analyses of palaeognath birds

Phylogenomic analyses of ancient rapid radiations can produce conflicting results that are driven by differential sampling of taxa and characters as well as the limitations of alternative analytical methods. We re-examine basal relationships of palaeognath birds (ratites and tinamous) using recently published datasets of nucleotide characters from 20,850 loci as well as 4301 retroelement insertions. The original studies attributed conflicting resolutions of rheas in their inferred coalescent and concatenation trees to concatenation failing in the anomaly zone. By contrast, we find that the coalescent-based resolution of rheas is premised upon extensive gene-tree estimation errors. Furthermore, retroelement insertions contain much more conflict than originally reported and multiple insertion loci support the basal position of rheas found in concatenation trees, while none were reported in the original publication. We demonstrate how even remarkable congruence in phylogenomic studies may be driven by long-branch misplacement of a divergent outgroup, highly incongruent gene trees, differential taxon sampling that can result in gene-tree misrooting errors that bias species-tree inference, and gross homology errors. What was previously interpreted as broad, robustly supported corroboration for a single resolution in coalescent analyses may instead indicate a common bias that taints phylogenomic results across multiple genome-scale datasets. The updated retroelement dataset now supports a species tree with branch lengths that suggest an ancient anomaly zone, and both concatenation and coalescent analyses of the huge nucleotide datasets fail to yield coherent, reliable results in this challenging phylogenetic context.

Dispersal, not vicariance, explains the biogeographic origin of iguanas on Madagascar

Lizards of the clade Iguanidae (sensu lato) are primarily a New World group. Thus, the remarkable presence of an endemic lineage of iguanas (family Opluridae) on the isolated Indian Ocean island of Madagascar has long been considered a biogeographic anomaly. Previous work attributed this disjunct extant distribution to: (1) vicariance at about 140-165 Ma, caused by the breakup of Gondwana and the separation of South America, Africa, and Madagascar (with subsequent extinction of iguanas on Africa, and potentially other Gondwanan landmasses), (2) vicariance at about 80-90 Ma, caused by the sundering of hypothesized land-bridge connections between South America, Antarctica, India, and Madagascar, or (3) long-distance overwater dispersal from South America to Madagascar. Each hypothesis has been supported with molecular divergence dating analyses, and thus the biogeographic origin of the Opluridae is not yet well resolved. Here we utilize genetic sequences of ultraconserved elements for all Iguania families and the majority of Iguanidae (s.l.) genera, and morphological data for extant and fossil taxa (used for divergence dating analyses), to produce the most comprehensive dataset applied to date to test these origin hypotheses. We find strong support for a sister relationship between the Opluridae (Madagascar) and Leiosauridae (South America). Divergence of the Opluridae from Leiosauridae is dated to between the late Cretaceous and mid-Paleogene, at a time when Madagascar was already an island and was isolated from all other Gondwanan landmasses. Consequently, our results support a hypothesis of long-distance overwater dispersal of the Opluridae lineage, either directly from South America to Madagascar or potentially via Antarctica or Africa, leading to this radiation of iguanas in the Indian Ocean.

(Non)Parallel developmental mechanisms in vertebrate appendage reduction and loss

Appendages have been reduced or lost hundreds of times during vertebrate evolution. This phenotypic convergence may be underlain by shared or different molecular mechanisms in distantly related vertebrate clades. To investigate, we reviewed the developmental and evolutionary literature of appendage reduction and loss in more than a dozen vertebrate genera from fish to mammals. We found that appendage reduction and loss was nearly always driven by modified gene expression as opposed to changes in coding sequences. Moreover, expression of the same genes was repeatedly modified across vertebrate taxa. However, the specific mechanisms by which expression was modified were rarely shared. The multiple routes to appendage reduction and loss suggest that adaptive loss of function phenotypes might arise routinely through changes in expression of key developmental genes.

The evolution of tinamous (Palaeognathae: Tinamidae) in light of molecular and combined analyses

The Neotropical tinamous are of particular interest in our efforts to understand the evolution of modern birds. They inhabit both forested and open environments and, although volant, have limited flight capabilities. Numerous studies have recognized the monophyly of tinamous and their relationships either as sister to the flightless ratites (ostriches, emus and their relatives) or within the ratites themselves. Despite the numerous bird phylogenies published recently, modern investigations of relationships within the tinamous themselves have been limited. Here, we present the first detailed phylogenetic analysis and divergence-date estimation including a significant number of tinamou species, both extant and fossil. The monophyly of most currently recognized polytypic genera is recovered with high support, with the exception of the paraphyletic Nothura and Nothoprocta. The traditional subdivision between those tinamous inhabiting open areas (Nothurinae) and forest environments (Tinaminae) is also confirmed. A temporal calibration of the resultant phylogeny estimates that the basal divergence of crown Tinamidae took place between 31 and 40 Mya.

Embryonic Development of the Avian Sternum and Its Morphological Adaptations for Optimizing Locomotion

The sternum is part of the forelimb appendicular skeleton found in most terrestrial vertebrates and has become adapted across tetrapods for distinctive modes of locomotion. We review the regulatory mechanisms underlying sternum and forelimb development and discuss the possible gene expression modulation that could be responsible for the sternal adaptations and associated reduction in the forelimb programme found in flightless birds. In three phylogenetically divergent vertebrate lineages that all undertake powered flight, a ventral extension of the sternum, named the keel, has evolved independently, most strikingly in volant birds. In flightless birds, however, the sternal keel is absent, and the sternum is flattened. We review studies in a variety of species that have analysed adaptations in sterna morphology that are related to the animal’s mode of locomotion on land, in the sky and in water.

Phylogeny and sex chromosome evolution of palaeognathae

Many paleognaths (ratites and tinamous) have a pair of homomorphic ZW sex chromosomes in contrast to the highly differentiated sex chromosomes of most other birds. To understand the evolutionary causes for the different tempos of sex chromosome evolution, we produced female genomes of 12 paleognathous species and reconstructed the phylogeny and the evolutionary history of paleognathous sex chromosomes. We uncovered that Palaeognathae sex chromosomes had undergone stepwise recombination suppression and formed a pattern of "evolutionary strata". Nine of the 15 studied species' sex chromosomes have maintained homologous recombination in their long pseudoautosomal regions extending more than half of the entire chromosome length. We found that in older strata, the W chromosome suffered more serious functional gene loss. Their homologous Z-linked regions, compared with other genomic regions, have produced an excess of species-specific autosomal duplicated genes that evolved female-specific expression, in contrast to their broadly expressed progenitors. We speculate the "defeminization" of Z chromosome with underrepresentation of female-biased genes and slow divergence of sex chromosomes of paleognaths might be related to their distinctive mode of sexual selection targeting females that evolved in their common ancestors.

Regulation of vertebrate forelimb development and wing reduction in the flightless emu

The vertebrate limb is a dynamic structure which has evolved into many diverse forms to facilitate complex behavioral adaptations. The principle molecular and cellular processes that underlie development of the vertebrate limb are well characterized. However, how these processes are altered to drive differential limb development between vertebrates is less well understood. Several vertebrate models are being utilized to determine the developmental basis of differential limb morphogenesis, though these typically focus on later patterning of the established limb bud and may not represent the complete developmental trajectory. Particularly, heterochronic limb development can occur prior to limb outgrowth and patterning but receives little attention. This review summarizes the genetic regulation of vertebrate forelimb diversity, with particular focus on wing reduction in the flightless emu as a model for examining limb heterochrony. These studies highlight that wing reduction is complex, with heterochronic cellular and genetic events influencing the major stages of limb development. Together, these studies provide a broader picture of how different limb morphologies may be established during development.

Psychological and Physiological Stress in Hens With Bone Damage

Abnormalities in bone development in humans and non-humans can lead to impaired physical and psychological health; however, evidence is lacking regarding the role of individual psychosocial factors in the development of poor bone conditions. Addressing this lack of knowledge, we used low-productive laying hens (n = 93) and assessed behavioral responses to an open-field test [at 17, 18, 29, 33 weeks of age (wa)], an aerial predator test (at 39 wa), and a social reinstatement test (at 42 wa). Bone condition was assessed using a palpation technique on five occasions (at 16, 29, 33, 45, 58 wa), with half of the hens experiencing damage (deviations, fractures, or both) at 29 wa and all hens by 58 wa. Corticosterone (CORT) concentration in feathers (at 16, 33, 58 wa) and body weight (at 23, 47, 58 wa) were also investigated. We hypothesized that lighter birds (at 23 wa) with higher CORT (at 16 wa) and open field-induced fear collected before the onset of lay (at 17 and 18 wa) are associated with a worse bone condition when in lay. We also hypothesized that those birds with more damage at the peak of laying (at 29 wa) would be lighter at 47 and 58 wa and more fearful by showing higher open field-induced (at 29 and 33 wa) and predator-induced fear responses, however, acting less socially toward conspecifics. These hens were also expected to have higher CORT (at 33 and 58 wa). Our results show no association between open-field fear level and fear behavior, CORT concentration, or body weight on the one hand (all measured before starting to lay) and bone damage at 29 wa on the other. When in lay, bone damage was associated with more pecking and less crossing zones when faced with an open-field situation at 29 wa and improved sociality at 42 wa. This study provides the first evidence of a relationship of bone health with fear, sociality, and stress response. When in poor bone condition, our hens had enhanced psychological stress measured by fear behavior reactivity but not physiological stress measured as feather CORT concentration.

Cretaceous origins of the vibrotactile bill-tip organ in birds

Some probe-foraging birds locate their buried prey by detecting mechanical vibrations in the substrate using a specialized tactile bill-tip organ comprising mechanoreceptors embedded in densely clustered pits in the bone at the tip of their beak. This remarkable sensory modality is known as 'remote touch', and the associated bill-tip organ is found in probe-foraging taxa belonging to both the palaeognathous (in kiwi) and neognathous (in ibises and shorebirds) clades of modern birds. Intriguingly, a structurally similar bill-tip organ is also present in the beaks of extant, non-probing palaeognathous birds (e.g. emu and ostriches) that do not use remote touch. By comparison with our comprehensive sample representing all orders of extant modern birds (Neornithes), we provide evidence that the lithornithids (the most basal known palaeognathous birds which evolved in the Cretaceous period) had the ability to use remote touch. This finding suggests that the occurrence of the vestigial bony bill-tip organ in all modern non-probing palaeognathous birds represents a plesiomorphic condition. Furthermore, our results show that remote-touch probe foraging evolved very early among the Neornithes and it may even have predated the palaeognathous-neognathous divergence. We postulate that the tactile bony bill-tip organ in Neornithes may have originated from other snout tactile specializations of their non-avian theropod ancestors.

New view on the organization and evolution of Palaeognathae mitogenomes poses the question on the ancestral gene rearrangement in Aves

BACKGROUND

Bird mitogenomes differ from other vertebrates in gene rearrangement. The most common avian gene order, identified first in Gallus gallus, is considered ancestral for all Aves. However, other rearrangements including a duplicated control region and neighboring genes have been reported in many representatives of avian orders. The repeated regions can be easily overlooked due to inappropriate DNA amplification or genome sequencing. This raises a question about the actual prevalence of mitogenomic duplications and the validity of the current view on the avian mitogenome evolution. In this context, Palaeognathae is especially interesting because is sister to all other living birds, i.e. Neognathae. So far, a unique duplicated region has been found in one palaeognath mitogenome, that of Eudromia elegans.

RESULTS

Therefore, we applied an appropriate PCR strategy to look for omitted duplications in other palaeognaths. The analyses revealed the duplicated control regions with adjacent genes in Crypturellus, Rhea and Struthio as well as ND6 pseudogene in three moas. The copies are very similar and were subjected to concerted evolution. Mapping the presence and absence of duplication onto the Palaeognathae phylogeny indicates that the duplication was an ancestral state for this avian group. This feature was inherited by early diverged lineages and lost two times in others. Comparison of incongruent phylogenetic trees based on mitochondrial and nuclear sequences showed that two variants of mitogenomes could exist in the evolution of palaeognaths. Data collected for other avian mitogenomes revealed that the last common ancestor of all birds and early diverging lineages of Neoaves could also possess the mitogenomic duplication.

CONCLUSIONS

The duplicated control regions with adjacent genes are more common in avian mitochondrial genomes than it was previously thought. These two regions could increase effectiveness of replication and transcription as well as the number of replicating mitogenomes per organelle. In consequence, energy production by mitochondria may be also more efficient. However, further physiological and molecular analyses are necessary to assess the potential selective advantages of the mitogenome duplications.

Convergent morphological responses to loss of flight in rails (Aves: Rallidae)

The physiological demands of flight exert strong selection pressure on avian morphology and so it is to be expected that the evolutionary loss of flight capacity would involve profound changes in traits. Here, we investigate morphological consequences of flightlessness in a bird family where the condition has evolved repeatedly. The Rallidae include more than 130 recognized species of which over 30 are flightless. Morphological and molecular phylogenetic data were used here to compare species with and without the ability to fly in order to determine major phenotypic effects of the transition from flighted to flightless. We find statistical support for similar morphological response among unrelated flightless lineages, characterized by a shift in energy allocation from the forelimbs to the hindlimbs. Indeed, flightless birds exhibit smaller sterna and wings than flighted taxa in the same family along with wider pelves and more robust femora. Phylogenetic signal tests demonstrate that those differences are independent of phylogeny and instead demonstrate convergent morphological adaptation associated with a walking ecology. We found too that morphological variation was greater among flightless rails than flighted ones, suggesting that relaxation of physiological demands during the transition to flightlessness frees morphological traits to evolve in response to more varied ecological opportunities.

Genetic factors for short life span associated with evolution of the loss of flight ability

Acquisition or loss of flying ability is evolutionarily linked with maximum life span (MLS) in mammals and birds. Although ecological factors, such as extrinsic mortality, may lead to either shortened or extended life spans through natural selection, MLS is influenced by complex molecular and metabolic processes, and the genetic changes associated with flying ability that have led to either a longer or shorter MLS are unknown. Here, we examine the parallel evolution of flight in mammals and birds and investigate positively selected genes at branches where either the acquisition (in little brown bats and large flying foxes) or loss (in Adélie penguins, emperor penguins, common ostriches, emus, great spotted kiwis, little spotted kiwis, okarito brown kiwis, greater rheas, lesser rheas, and cassowaries) of flight abilities occurred. Although we found no shared genes under selection among all the branches of interest, 7 genes were found to be positively selected in 2 of the branches. Among the 7 genes, only IGF2BP2 is known to affect both life span and energy expenditure. The positively selected mutations detected in IGF2BP2 likely affected the functionality of the encoded protein. IGF2BP2, which has been reported to simultaneously prolong life span and increase energy expenditure, could be responsible for the evolution of shortened MLS associated with the loss of flying ability.

Evolutionary Dynamics of Sex Chromosomes of Paleognathous Birds

Standard models of sex chromosome evolution propose that recombination suppression leads to the degeneration of the heterogametic chromosome, as is seen for the Y chromosome in mammals and the W chromosome in most birds. Unlike other birds, paleognaths (ratites and tinamous) possess large nondegenerate regions on their sex chromosomes (PARs or pseudoautosomal regions). It remains unclear why these large PARs are retained over >100 Myr, and how this retention impacts the evolution of sex chromosomes within this system. To address this puzzle, we analyzed Z chromosome evolution and gene expression across 12 paleognaths, several of whose genomes have recently been sequenced. We confirm at the genomic level that most paleognaths retain large PARs. As in other birds, we find that all paleognaths have incomplete dosage compensation on the regions of the Z chromosome homologous to degenerated portions of the W (differentiated regions), but we find no evidence for enrichments of male-biased genes in PARs. We find limited evidence for increased evolutionary rates (faster-Z) either across the chromosome or in differentiated regions for most paleognaths with large PARs, but do recover signals of faster-Z evolution in tinamou species with mostly degenerated W chromosomes, similar to the pattern seen in neognaths. Unexpectedly, in some species, PAR-linked genes evolve faster on average than genes on autosomes, suggested by diverse genomic features to be due to reduced efficacy of selection in paleognath PARs. Our analysis shows that paleognath Z chromosomes are atypical at the genomic level, but the evolutionary forces maintaining largely homomorphic sex chromosomes in these species remain elusive.

The phylogenetic significance of the morphology of the syrinx, hyoid and larynx, of the southern cassowary, Casuarius casuarius (Aves, Palaeognathae)

BACKGROUND

Palaeognathae is a basal clade within Aves and include the large and flightless ratites and the smaller, volant tinamous. Although much research has been conducted on various aspects of palaeognath morphology, ecology, and evolutionary history, there are still areas which require investigation. This study aimed to fill gaps in our knowledge of the Southern Cassowary, Casuarius casuarius, for which information on the skeletal systems of the syrinx, hyoid and larynx is lacking - despite these structures having been recognised as performing key functional roles associated with vocalisation, respiration and feeding. Previous research into the syrinx and hyoid have also indicated these structures to be valuable for determining evolutionary relationships among neognath taxa, and thus suggest they would also be informative for palaeognath phylogenetic analyses, which still exhibits strong conflict between morphological and molecular trees.

RESULTS

The morphology of the syrinx, hyoid and larynx of C. casuarius is described from CT scans. The syrinx is of the simple tracheo-bronchial syrinx type, lacking specialised elements such as the pessulus; the hyoid is relatively short with longer ceratobranchials compared to epibranchials; and the larynx is comprised of entirely cartilaginous, standard avian anatomical elements including a concave, basin-like cricoid and fused cricoid wings. As in the larynx, both the syrinx and hyoid lack ossification and all three structures were most similar to Dromaius. We documented substantial variation across palaeognaths in the skeletal character states of the syrinx, hyoid, and larynx, using both the literature and novel observations (e.g. of C. casuarius). Notably, new synapomorphies linking Dinornithiformes and Tinamidae are identified, consistent with the molecular evidence for this clade. These shared morphological character traits include the ossification of the cricoid and arytenoid cartilages, and an additional cranial character, the articulation between the maxillary process of the nasal and the maxilla.

CONCLUSION

Syrinx, hyoid and larynx characters of palaeognaths display greater concordance with molecular trees than do other morphological traits. These structures might therefore be less prone to homoplasy related to flightlessness and gigantism, compared to typical morphological traits emphasised in previous phylogenetic studies.

Whole-Genome Analyses Resolve the Phylogeny of Flightless Birds (Palaeognathae) in the Presence of an Empirical Anomaly Zone

Palaeognathae represent one of the two basal lineages in modern birds, and comprise the volant (flighted) tinamous and the flightless ratites. Resolving palaeognath phylogenetic relationships has historically proved difficult, and short internal branches separating major palaeognath lineages in previous molecular phylogenies suggest that extensive incomplete lineage sorting (ILS) might have accompanied a rapid ancient divergence. Here, we investigate palaeognath relationships using genome-wide data sets of three types of noncoding nuclear markers, together totaling 20,850 loci and over 41 million base pairs of aligned sequence data. We recover a fully resolved topology placing rheas as the sister to kiwi and emu + cassowary that is congruent across marker types for two species tree methods (MP-EST and ASTRAL-II). This topology is corroborated by patterns of insertions for 4274 CR1 retroelements identified from multispecies whole-genome screening, and is robustly supported by phylogenomic subsampling analyses, with MP-EST demonstrating particularly consistent performance across subsampling replicates as compared to ASTRAL. In contrast, analyses of concatenated data supermatrices recover rheas as the sister to all other nonostrich palaeognaths, an alternative that lacks retroelement support and shows inconsistent behavior under subsampling approaches. While statistically supporting the species tree topology, conflicting patterns of retroelement insertions also occur and imply high amounts of ILS across short successive internal branches, consistent with observed patterns of gene tree heterogeneity. Coalescent simulations and topology tests indicate that the majority of observed topological incongruence among gene trees is consistent with coalescent variation rather than arising from gene tree estimation error alone, and estimated branch lengths for short successive internodes in the inferred species tree fall within the theoretical range encompassing the anomaly zone. Distributions of empirical gene trees confirm that the most common gene tree topology for each marker type differs from the species tree, signifying the existence of an empirical anomaly zone in palaeognaths.

Symmetry breaking in the embryonic skin triggers directional and sequential plumage patterning

The development of an organism involves the formation of patterns from initially homogeneous surfaces in a reproducible manner. Simulations of various theoretical models recapitulate final states of natural patterns, yet drawing testable hypotheses from those often remains difficult. Consequently, little is known about pattern-forming events. Here, we surveyed plumage patterns and their emergence in Galliformes, ratites, passerines, and penguins, together representing the three major taxa of the avian phylogeny, and built a unified model that not only reproduces final patterns but also intrinsically generates shared and varying directionality, sequence, and duration of patterning. We used in vivo and ex vivo experiments to test its parameter-based predictions. We showed that directional and sequential pattern progression depends on a species-specific prepattern: an initial break in surface symmetry launches a travelling front of sharply defined, oriented domains with self-organising capacity. This front propagates through the timely transfer of increased cell density mediated by cell proliferation, which controls overall patterning duration. These results show that universal mechanisms combining prepatterning and self-organisation govern the timely emergence of the plumage pattern in birds.

A survey of plumage patterns and their emergence in Galliformes, ratites, passerines, and penguins shows that their formation depends on a species-specific prepattern in the embryo and demonstrates that universal mechanisms govern the timely emergence of natural patterns in birds.

The effects of growth rate and biomechanical loading on bone laminarity within the emu skeleton

The orientation of vascular canals in primary bone may reflect differences in growth rate and/or adaptation to biomechanical loads. Previous studies link specific canal orientations to bone growth rates, but results between different taxa are contradictory. Circumferential vascular canals (forming laminar bone) have been hypothesized to reflect either (or both) rapid growth rate or locomotion-induced torsional loading. Previous work on the hindlimb biomechanics in the emu shows that the femur and tibiotarsus experience large shear strains, likely resulting from torsional loads that increase through ontogeny. Here, we test how growth rate and biomechanical loading affect bone laminarity in wing and hindlimb elements from growing emu (2–60 wks). If laminar bone is an adaptation to torsion-induced shear strains, it should increase from juveniles to adults. Alternatively, if bone laminarity reflects rapid growth, as has been shown previously in emu, it should be abundant in fast-growing juveniles and decrease with age. Transverse mid-shaft histological sections from the limb bones (femur, tibiotarsus, humerus, ulna, and radius) were prepared and imaged. Growth rates were measured using fluorescent bone labels. Vascular canal orientation was quantified using laminarity index (proportion of circumferential canals). Principal components analysis was performed to convert highly correlated variables (i.e., mass, age, growth rate, and shear strain) into principal components. Random-intercept beta regression modeling determined which principal components best explained laminarity. The fastest growth rates were found in young individuals for all five skeletal elements. Maximum growth rate did not coincide with peak laminarity. Instead, in the femur and tibiotarsus, elevated laminarity is strongly correlated with adult features such as large size, old age, and modest growth rate. This result is contrary to predictions made based on a previous study of emu but is consistent with results observed in some other avian species (penguin, chicken). Shear strain in the caudal octant of the femur and tibiotarsus is positively correlated with laminarity but has a weaker effect on laminarity relative to mass, age, and growth rate. Laminarity in the wing elements is variable and does not correlate with ontogenetic factors (including mass, age, and growth rate). Its presence may relate to relaxed developmental canalization or a retained ancestral feature. In conclusion, ontogeny (including growth rate) is the dominant influence on vascular canal orientation at least in the hindlimb of the emu.

Estimating Flight Style of Early Eocene Stem Palaeognath Bird Calciavis grandei (Lithornithidae)

Lithornithids are volant stem palaeognaths from the Paleocene-Eocene. Except for these taxa and the extant neotropical tinamous, all other known extinct and extant palaeognaths are flightless. Investigation of properties of the lithornithid wing and its implications for inference of flight style informs understood locomotor diversity within Palaeognathae and may have implications for estimation of ancestral traits in the clade. Qualitative comparisons with their closest extant volant relatives, the burst-flying tinamous, previously revealed skeletal differences suggesting lithornithids were capable of sustained flight, but quantitative work on wing morphology have been lacking. Until comparatively recently, specimens of lithornithids preserving wing feather remains have been limited. Here, we reconstruct the wing of an exceptionally preserved specimen of the Early Eocene lithornithid Calciavis grandei and estimate body mass, wing surface area, and wing span. We then estimate flight parameters and compare our estimates with representatives from across Aves in a statistical framework. We predict that flight in C. grandei was likely marked by continuous flapping, and that lithornithids were capable of sustained flight and migratory behavior. Our results are consistent with previous hypotheses that the ancestor of extant Palaeognathae may also have been capable of sustained flight. Anat Rec, 303:1035-1042, 2020. © 2019 Wiley Periodicals, Inc.

Bayesian Detection of Convergent Rate Changes of Conserved Noncoding Elements on Phylogenetic Trees

Conservation of DNA sequence over evolutionary time is a strong indicator of function, and gain or loss of sequence conservation can be used to infer changes in function across a phylogeny. Changes in evolutionary rates on particular lineages in a phylogeny can indicate shared functional shifts, and thus can be used to detect genomic correlates of phenotypic convergence. However, existing methods do not allow easy detection of patterns of rate variation, which causes challenges for detecting convergent rate shifts or other complex evolutionary scenarios. Here we introduce PhyloAcc, a new Bayesian method to model substitution rate changes in conserved elements across a phylogeny. The method assumes several categories of substitution rate for each branch on the phylogenetic tree, estimates substitution rates per category, and detects changes of substitution rate as the posterior probability of a category switch. Simulations show that PhyloAcc can detect genomic regions with rate shifts in multiple target species better than previous methods and has a higher accuracy of reconstructing complex patterns of substitution rate changes than prevalent Bayesian relaxed clock models. We demonstrate the utility of PhyloAcc in two classic examples of convergent phenotypes: loss of flight in birds and the transition to marine life in mammals. In each case, our approach reveals numerous examples of conserved nonexonic elements with accelerations specific to the phenotypically convergent lineages. Our method is widely applicable to any set of conserved elements where multiple rate changes are expected on a phylogeny.

Convergent genomic signatures of flight loss in birds suggest a switch of main fuel

Flight loss in birds is as characteristic of the class Aves as flight itself. Although morphological and physiological differences are recognized in flight-degenerate bird species, their contributions to recurrent flight degeneration events across modern birds and underlying genetic mechanisms remain unclear. Here, in an analysis of 295 million nucleotides from 48 bird genomes, we identify two convergent sites causing amino acid changes in ATGL^Ser321Gly and ACOT7^Ala197Val in flight-degenerate birds, which to our knowledge have not previously been implicated in loss of flight. Functional assays suggest that Ser321Gly reduces lipid hydrolytic ability of ATGL, and Ala197Val enhances acyl-CoA hydrolytic activity of ACOT7. Modeling simulations suggest a switch of main energy sources from lipids to carbohydrates in flight-degenerate birds. Our results thus suggest that physiological convergence plays an important role in flight degeneration, and anatomical convergence often invoked may not.

Flight loss has occurred numerous times in bird evolution. Here, the authors examine convergent sites in the exonic and intronic sequences of 48 bird genomes, finding amino-acid changes in two genes, ATGL and ACOT7, with potential implications for a change in metabolism rather than anatomy.

Convergent regulatory evolution and loss of flight in paleognathous birds

A core question in evolutionary biology is whether convergent phenotypic evolution is driven by convergent molecular changes in proteins or regulatory regions. We combined phylogenomic, developmental, and epigenomic analysis of 11 new genomes of paleognathous birds, including an extinct moa, to show that convergent evolution of regulatory regions, more so than protein-coding genes, is prevalent among developmental pathways associated with independent losses of flight. A Bayesian analysis of 284,001 conserved noncoding elements, 60,665 of which are corroborated as enhancers by open chromatin states during development, identified 2355 independent accelerations along lineages of flightless paleognaths, with functional consequences for driving gene expression in the developing forelimb. Our results suggest that the genomic landscape associated with morphological convergence in ratites has a substantial shared regulatory component.

Multifactorial processes underlie parallel opsin loss in neotropical bats

The loss of previously adaptive traits is typically linked to relaxation in selection, yet the molecular steps leading to such repeated losses are rarely known. Molecular studies of loss have tended to focus on gene sequences alone, but overlooking other aspects of protein expression might underestimate phenotypic diversity. Insights based almost solely on opsin gene evolution, for instance, have made mammalian color vision a textbook example of phenotypic loss. We address this gap by investigating retention and loss of opsin genes, transcripts, and proteins across ecologically diverse noctilionoid bats. We find multiple, independent losses of short-wave-sensitive opsins. Mismatches between putatively functional DNA sequences, mRNA transcripts, and proteins implicate transcriptional and post-transcriptional processes in the ongoing loss of S-opsins in some noctilionoid bats. Our results provide a snapshot of evolution in progress during phenotypic trait loss, and suggest vertebrate visual phenotypes cannot always be predicted from genotypes alone.

Bats are famous for using their hearing to explore their environments, yet fewer people are aware that these flying mammals have both good night and daylight vision. Some bats can even see in color thanks to two light-sensitive proteins at the back of their eyes: S-opsin which detects blue and ultraviolet light and L-opsin which detects green and red light. Many species of bat, however, are missing one of these proteins and cannot distinguish any colors; in other words, they are completely color-blind.

Some bat species found in Central and South America have independently lost their ability to see blue-ultraviolet light and have thus also lost their color vision. These bats have diverse diets – ranging from insects to fruits and even blood – and being able to distinguish color may offer an advantage in many of their activities, including hunting or foraging. The vision genes in these bats, therefore, give scientists an opportunity to explore how a seemingly important trait can be lost at the molecular level.

Sadier, Davies et al. now report that S-opsin has been lost more than a dozen times during the evolutionary history of these Central and South American bats. The analysis used samples from 55 species, including animals caught from the wild and specimens from museums. As with other proteins, the instructions encoded in the gene sequence for S opsin need to be copied into a molecule of RNA before they can be translated into protein. As expected, S-opsin was lost several times because of changes in the gene sequence that disrupted the formation of the protein. However, at several points in these bats’ evolutionary history, additional changes have taken place that affected the production of the RNA or the protein, without an obvious change to the gene itself. This finding suggests that other studies that rely purely on DNA to understand evolution may underestimate how often traits may be lost. By capturing ‘evolution in action’, these results also provide a more complete picture of the molecular targets of evolution in a diverse set of bats.

Evolution: Flight of the Ratites

The flightless ratite birds are scattered all across the Southern hemisphere, on landmasses that have long been separated from each other. But how did they get there? They flew in from the North.

Why Do Phylogenomic Data Sets Yield Conflicting Trees? Data Type Influences the Avian Tree of Life more than Taxon Sampling

Phylogenomics, the use of large-scale data matrices in phylogenetic analyses, has been viewed as the ultimate solution to the problem of resolving difficult nodes in the tree of life. However, it has become clear that analyses of these large genomic data sets can also result in conflicting estimates of phylogeny. Here, we use the early divergences in Neoaves, the largest clade of extant birds, as a "model system" to understand the basis for incongruence among phylogenomic trees. We were motivated by the observation that trees from two recent avian phylogenomic studies exhibit conflicts. Those studies used different strategies: 1) collecting many characters [$\sim$ 42 mega base pairs (Mbp) of sequence data] from 48 birds, sometimes including only one taxon for each major clade; and 2) collecting fewer characters ($\sim$ 0.4 Mbp) from 198 birds, selected to subdivide long branches. However, the studies also used different data types: the taxon-poor data matrix comprised 68% non-coding sequences whereas coding exons dominated the taxon-rich data matrix. This difference raises the question of whether the primary reason for incongruence is the number of sites, the number of taxa, or the data type. To test among these alternative hypotheses we assembled a novel, large-scale data matrix comprising 90% non-coding sequences from 235 bird species. Although increased taxon sampling appeared to have a positive impact on phylogenetic analyses the most important variable was data type. Indeed, by analyzing different subsets of the taxa in our data matrix we found that increased taxon sampling actually resulted in increased congruence with the tree from the previous taxon-poor study (which had a majority of non-coding data) instead of the taxon-rich study (which largely used coding data). We suggest that the observed differences in the estimates of topology for these studies reflect data-type effects due to violations of the models used in phylogenetic analyses, some of which may be difficult to detect. If incongruence among trees estimated using phylogenomic methods largely reflects problems with model fit developing more "biologically-realistic" models is likely to be critical for efforts to reconstruct the tree of life. [Birds; coding exons; GTR model; model fit; Neoaves; non-coding DNA; phylogenomics; taxon sampling.].

A genetic signature of the evolution of loss of flight in the Galapagos cormorant

We have a limited understanding of the genetic and molecular basis of evolutionary changes in the size and proportion of limbs. We studied wing and pectoral skeleton reduction leading to flightlessness in the Galapagos cormorant (Phalacrocorax harrisi). We sequenced and de novo assembled the genomes of four cormorant species and applied a predictive and comparative genomics approach to find candidate variants that may have contributed to the evolution of flightlessness. These analyses and cross-species experiments in Caenorhabditis elegans and in chondrogenic cell lines implicated variants in genes necessary for transcriptional regulation and function of the primary cilium. Cilia are essential for Hedgehog signaling, and humans affected by skeletal ciliopathies suffer from premature bone growth arrest, mirroring skeletal features associated with loss of flight.

Distinct developmental pathways underlie independent losses of flight in ratites

Recent phylogenetic studies question the monophyly of ratites (large, flightless birds incorporating ostriches, rheas, kiwis, emus and cassowaries), suggesting their paraphyly with respect to flying tinamous (Tinamidae). Flightlessness and large body size have thus likely evolved repeatedly among ratites, and separately in ostriches (Struthio) and emus (Dromaius). Here, we test this hypothesis with data from wing developmental trajectories in ostriches, emus, tinamous and chickens. We find the rate of ostrich embryonic wing growth falls within the range of variation exhibited by flying taxa (tinamous and chickens), but that of emus is extremely slow. These results indicate flightlessness was acquired by different developmental mechanisms in the ancestors of ostriches (peramorphosis) and the emu-cassowary clade (paedomorphosis), and corroborate the hypothesis that flight loss has evolved repeatedly among ratites.

Conserved Nonexonic Elements: A Novel Class of Marker for Phylogenomics

Noncoding markers have a particular appeal as tools for phylogenomic analysis because, at least in vertebrates, they appear less subject to strong variation in GC content among lineages. Thus far, ultraconserved elements (UCEs) and introns have been the most widely used noncoding markers. Here we analyze and study the evolutionary properties of a new type of noncoding marker, conserved nonexonic elements (CNEEs), which consists of noncoding elements that are estimated to evolve slower than the neutral rate across a set of species. Although they often include UCEs, CNEEs are distinct from UCEs because they are not ultraconserved, and, most importantly, the core region alone is analyzed, rather than both the core and its flanking regions. Using a data set of 16 birds plus an alligator outgroup, and ∼3600-∼3800 loci per marker type, we found that although CNEEs were less variable than bioinformatically derived UCEs or introns and in some cases exhibited a slower approach to branch resolution as determined by phylogenomic subsampling, the quality of CNEE alignments was superior to those of the other markers, with fewer gaps and missing species. Phylogenetic resolution using coalescent approaches was comparable among the three marker types, with most nodes being fully and congruently resolved. Comparison of phylogenetic results across the three marker types indicated that one branch, the sister group to the passerine + falcon clade, was resolved differently and with moderate (>70%) bootstrap support between CNEEs and UCEs or introns. Overall, CNEEs appear to be promising as phylogenomic markers, yielding phylogenetic resolution as high as for UCEs and introns but with fewer gaps, less ambiguity in alignments and with patterns of nucleotide substitution more consistent with the assumptions of commonly used methods of phylogenetic analysis.

The evolution of giant flightless birds and novel phylogenetic relationships for extinct fowl (Aves, Galloanseres)

The extinct dromornithids, gastornithids and phorusrhacids are among the most spectacular birds to have ever lived, with some giants exceeding 500 kg. The affinities and evolution of these and other related extinct birds remain contentious, with previous phylogenetic analyses being affected by widespread convergence and limited taxon sampling. We address these problems using both parsimony and tip-dated Bayesian approaches on an expansive taxon set that includes all key extinct flightless and flighted (e.g. Vegavis and lithornithids) forms, an extensive array of extant fowl (Galloanseres), representative Neoaves and palaeognaths. The Paleogene volant Lithornithidae are recovered as stem palaeognaths in the Bayesian analyses. The Galloanseres comprise four clades inferred to have diverged in the Late Cretaceous on Gondwana. In addition to Anseriformes and Galliformes, we recognize a robust new clade (Gastornithiformes) for the giant flightless Dromornithidae (Australia) and Gastornithidae (Eurasia, North America). This clade exhibits parallels to ratite palaeognaths in that flight presumably was lost and giant size attained multiple times. A fourth clade is represented by the Cretaceous Vegavis (Antarctica), which was strongly excluded from Anseriformes; thus, a crucial molecular calibration point needs to be reconsidered. The presbyornithids Wilaru (Australia) and Presbyornis (Northern Hemisphere) are robustly found to be the sister group to Anatoidea (Anseranatidae + Anatidae), a relatively more basal position than hitherto recognized. South America's largest bird, Brontornis, is not a galloansere, but a member of Neoaves related to Cariamiformes; therefore, giant Galloanseres remain unknown from this continent. Trait analyses showed that while gigantism and flightlessness evolved repeatedly in groups, diet is constrained by phylogeny: all giant Galloanseres and palaeognaths are herbivores or mainly herbivorous, and giant neoavians are zoophagous or omnivorous.

Exploratory and descriptive study on nutritional characteristics and quality of eggs from Chilean partridge (Nothoprocta perdicaria)

This work aims to contribute more information on tinamou eggs by performing an exploratory and descriptive study of some of their nutritional and quality characteristics. The chemical composition of tinamou egg showed a high protein content in white (85% dry basis) and high lipid concentration in yolk (52% db). The iron (Fe) content in white was higher than hen egg (0.47 mg/100 g) and this could be associated with the observed pinkish color of the white. As in the hen egg, the major fatty acids in tinamou yolk were: oleic (39%), linoleic (23%) and palmitic (20%). The cholesterol content of tinamou was 21.2 mg/g of yolk, and 100 g of whole egg provides 589 mg of cholesterol. As in the hen egg, tinamou egg white showed high levels of lysine, sulfur-containing amino acids, threonine and valine with respect to the recommended allowance for an adult man. All essential amino acids with the exception of histidine cover the adult requirements. The shell inorganic composition of these eggs is calcium carbonate and the morphology was similar to other avian eggs. Tinamou egg is small and elongated, with a dark brown color. The eggshell is thinner and experiences more deformation but less breaking strength than hen eggshell.

Advances on tinamou phylogeny: an assembled cladistic study of the volant palaeognathous birds

Tinamous are volant terrestrial birds, endemic to the Neotropics. Here, an inclusive phenotype-based phylogenetic study of the interrelationships among all extinct and living species of tinamous is conducted. In this cladistic analysis, results are compared between main character subsets and with previous molecular studies. Special attention is paid to character definition and scoring of integumentary and behavioural characters: transformation costs are applied to analyse egg coloration and plumage characters-on the basis of pigment composition and overlap of pigmentation patterns respectively-in the context of generalized (Sankoff) parsimony. Cladistic analysis recovers the traditional subdivision between those tinamous specialized for open areas (Nothurinae) and those inhabiting forested environments (Tinaminae) and support the monophyly of recognized genera. The present study demonstrates that morphological analysis yields highly congruent results when compared with previous molecular studies; thus, it provides morphological synapomorphies for clades that have been proposed by these molecular analyses. The placement of the fossil species within the open-area (Nothurinae) and the forest-dwelling (Tinaminae) tinamous is also consistent with the palaeoenvironmental conditions inferred from the associated flora and fauna.

Co-option of the cardiac transcription factor Nkx2.5 during development of the emu wing

The ratites are a distinctive clade of flightless birds, typified by the emu and ostrich that have acquired a range of unique anatomical characteristics since diverging from basal Aves at least 100 million years ago. The emu possesses a vestigial wing with a single digit and greatly reduced forelimb musculature. However, the embryological basis of wing reduction and other anatomical changes associated with loss of flight are unclear. Here we report a previously unknown co-option of the cardiac transcription factor Nkx2.5 to the forelimb in the emu embryo, but not in ostrich, or chicken and zebra finch, which have fully developed wings. Nkx2.5 is expressed in emu limb bud mesenchyme and maturing wing muscle, and mis-expression of Nkx2.5 throughout the limb bud in chick results in wing reductions. We propose that Nkx2.5 functions to inhibit early limb bud expansion and later muscle growth during development of the vestigial emu wing.

The transcription factor Nkx2.5 is essential for heart development. Here, the authors identify a previously unknown expression domain for Nkx2.5 in the emu wing and explore its role in diminished wing bud development in the flightless emu, compared with three other birds that have functional wings.

Time to Spread Your Wings: A Review of the Avian Ancient DNA Field

Ancient DNA (aDNA) has the ability to inform the evolutionary history of both extant and extinct taxa; however, the use of aDNA in the study of avian evolution is lacking in comparison to other vertebrates, despite birds being one of the most species-rich vertebrate classes. Here, we review the field of “avian ancient DNA” by summarising the past three decades of literature on this topic. Most studies over this time have used avian aDNA to reconstruct phylogenetic relationships and clarify taxonomy based on the sequencing of a few mitochondrial loci, but recent studies are moving toward using a comparative genomics approach to address developmental and functional questions. Applying aDNA analysis with more practical outcomes in mind (such as managing conservation) is another increasingly popular trend among studies that utilise avian aDNA, but the majority of these have yet to influence management policy. We find that while there have been advances in extracting aDNA from a variety of avian substrates including eggshell, feathers, and coprolites, there is a bias in the temporal focus; the majority of the ca. 150 studies reviewed here obtained aDNA from late Holocene (100–1000 yBP) material, with few studies investigating Pleistocene-aged material. In addition, we identify and discuss several other issues within the field that require future attention. With more than one quarter of Holocene bird extinctions occurring in the last several hundred years, it is more important than ever to understand the mechanisms driving the evolution and extinction of bird species through the use of aDNA.