An Unbiased Molecular Approach Using 3'-UTRs Resolves the Avian Family-Level Tree of Life

Accurate, scalable, and fully automated inference of species trees from raw genome assemblies using ROADIES

Current genome sequencing initiatives across a wide range of life forms offer significant potential to enhance our understanding of evolutionary relationships and support transformative biological and medical applications. Species trees play a central role in many of these applications; however, despite the widespread availability of genome assemblies, accurate inference of species trees remains challenging due to the limited automation, substantial domain expertise, and computational resources required by conventional methods. To address this limitation, we present ROADIES, a fully automated pipeline to infer species trees starting from raw genome assemblies. In contrast to the prominent approach, ROADIES incorporates a unique strategy of randomly sampling segments of the input genomes to generate gene trees. This eliminates the need for predefining a set of loci, limiting the analyses to a fixed number of genes, and performing the cumbersome gene annotation and/or whole genome alignment steps. ROADIES also eliminates the need to infer orthology by leveraging existing discordance-aware methods that allow multicopy genes. Using the genomic datasets from large-scale sequencing efforts across four diverse life forms (placental mammals, pomace flies, birds, and budding yeasts), we show that ROADIES infers species trees that are comparable in quality to the state-of-the-art studies but in a fraction of the time and effort, including on challenging datasets with rampant gene tree discordance and complex polyploidy. With its speed, accuracy, and automation, ROADIES has the potential to vastly simplify species tree inference, making it accessible to a broader range of scientists and applications.

Flesh and bone: The musculature and cervical movements of pterosaurs

The osteological variations present in the cervical vertebrae of pterosaurs represent changes in the soft tissues of the neck and reflect their function. Here, we infer the presence, volume, and capacity of the cervical musculature of pterosaurs. We performed our analyses on three-dimensionally preserved cervical series of Anhanguera sp. (AMNH 22555), Anhanguera piscator (NSM-PV 19892), Azhdarcho lancicollis (ZIN PH and CCMGE, several specimens), and Rhamphorhynchus muensteri (MGUH 1891.738), the last three of which were digitally modeled for muscle reconstruction. We identified osteological correlates from structures observed in extant archosaur vertebrae and skulls and supported by Extant Phylogenetic Bracket (EPB) criteria. We estimated the muscular capacity using the "Maximal Force Production" formula. According to our analyses, at least thirteen muscles were present in the neck of pterosaurs, only one of which does not correspond to an EPB level I inference. The muscles that performed skull and neck pitching were more robust and stronger to execute the movements. Muscles that showed extremely low potential had a more cervical stabilization function. Specializations we identified in the muscles are compatible with the foraging habits previously inferred for these pterosaurs, namely surface fishing by Rhamphorhynchus and Anhanguera and capture of small terrestrial prey by Azhdarcho.

Nearly complete late Eocene skull from the North Pacific elucidates the cranial morphology and affinities of the penguin-like Plotopteridae

The extinct Plotopteridae were penguin-like, wing-propelled diving birds of the North Pacific. Recently, the oldest and most complete plotopterid skull has been discovered in the late Eocene lower part of the Lincoln Creek Formation, southern Olympic Peninsula (Washington State, USA), and informs the poorly known cranial morphology of these birds. This skull is somewhat larger than previously described partial skulls from the Oligocene Pysht Formation of the northern Olympic Peninsula, from which it also differs in the shape of the nostrils. It may represent the genus Klallamornis, but a definitive taxonomic assignment is not yet possible. The specimen corroborates a sister group relationship of plotopterids to the suliform Suloidea and exhibits a notable character mosaic. Whereas the long rostrum most closely resembles that of the Fregatidae and some Phalacrocoracidae, the neurocranium is more similar to that of the Sulidae. An arcuate rostral ridge of the basicranium is otherwise only known from the Sphenisciformes, and a pair of prominent longitudinal ridges along the ventral surface of the rostrum is an autapomorphy of plotopterids. The small nostrils are situated at the caudal ends of conspicuous sulci, which are interpreted as vestiges of long, slit-like nostrils and are much less pronounced in extant Suliformes. Long, slit-like nostrils occur in stem group Sphenisciformes and may also have been present in stem group Fregatidae, in which case the nostrils were reduced twice within Suliformes, presumably to prevent salt water influx into the nasal cavity.

Plio-Pleistocene Environmental Changes Drove the Settlement of Aotearoa New Zealand by Australian Open-Habitat Bird Lineages

In a changing environment, vacant niches can be filled either by adaptation of local taxa or range-expanding invading species. The relative tempo of these patterns is of key interest in the modern age of climate change. Aotearoa New Zealand has been a hotspot of biogeographic research for decades due to its long-term isolation and dramatic geological history. An island with high levels of faunal endemicity, it is a system well suited to studying the relative effects of in situ evolution versus dispersal in determining faunal assemblages, while its turbulent climate and geological history provide valuable insights into the evolutionary impacts of environmental changes. Such investigations are of urgent importance given predicted climate change and human impacts rapidly affecting environments globally. Here, we analyse the divergence dates of nearly all endemic Aotearoa New Zealand bird species from their overseas relatives to assess the role of environmental changes in driving speciation and colonisation, with special regard to cooling climate during the Pliocene and Pleistocene. We uncover a wave of colonisation events by Australian open-habitat adapted species since the Pliocene that peaked at the beginning of the Pleistocene. Furthermore, we highlight an even distribution of divergence dates in forest-adapted taxa through time, consistent with millions of years of extensive forest cover. Finally, we note parallels to the modern-day establishment of new bird populations from Australia and suggest this is largely influenced by anthropogenic land-use patterns. This research contributes to the growing body of work recognising the long-lasting impacts of Pleistocene climate change on Aotearoa New Zealand's avifauna, and reinforces biological invasions as a key evolutionary response to changing environmental conditions.

Cretaceous Antarctic bird skull elucidates early avian ecological diversity

Fossils representing Cretaceous lineages of crown clade birds (Aves) are exceptionally rare but are crucial to elucidating major ecological shifts across early avian divergences. Among the earliest known putative crown birds is Vegavis iaai1-5, a foot-propelled diver from the latest Cretaceous (69.2-68.4 million years ago)6 of Antarctica with controversial phylogenetic affinities2,7-10. Initially recovered by phylogenetic analyses as a stem anatid (ducks and closely related species)1,2,11, Vegavis has since been recovered as a stem member of Anseriformes (waterfowl)7-9, or outside Aves altogether10. Here we report a new, nearly complete skull of Vegavis that provides new insight into its feeding ecology and exhibits morphologies that support placement among waterfowl within crown-group birds. Vegavis has an avian beak (absence of teeth and reduced maxilla) and brain shape (hyperinflated cerebrum and ventrally shifted optic lobes). The temporal fossa is well excavated and expansive, indicating that this bird had hypertrophied jaw musculature. The beak is narrow and pointed, and the mandible lacks retroarticular processes. Together, these features comprise a feeding apparatus unlike that of any other known anseriform but like that of other extant birds that capture prey underwater (for example, grebes and loons). The Cretaceous occurrence of Vegavis, with a feeding ecology unique among known Galloanserae (waterfowl and landfowl), is further indication that the earliest anseriform divergences were marked by evolutionary experiments unrepresented in the extant diversity3,11-13.

[Meaning and Mechanisms of Birdsong: Inspiration for Pneumology]

In contrast to humans, the location where sound is produced in birds is not the larynx, but rather the so-called "vocal box" (scientific term "Syrinx"). In some species the syrinx is located at the bifurcation point of the trachea into the two main bronchi (tracheal vocal head), while in some in the main bronchi (bronchial vocal head). During inspiration, part of the air flows into the lungs, and the part needed for singing flows into the air sacs adjacent to the lungs. During expiration, air leaves the air sacs and flows through the syrinx, where the song is created. When birds sing in two voices at the same time, individual sequences are formed simultaneously in the right and left parts of the syrinx.The song analysis is based on spectrograms (so-called sonagrams), which graphically represent the frequency spectrum of bird song.The song consists of one or more verses, which in turn consist of the variable or constant sequence of motives or syllables. Some songbirds have an enormous repertoire of syllables and verses (max. up to 7000 verses per day). In addition to singing, most bird species also have much simpler begging, contact, threatening, flight, alarm and copulation calls.Male birds sing primarily for two reasons: 1. They use song to woo a potential partner. This song provides the females with important information about the applicant's performance and health. 2. Singing serves to defend the territory.In around 40 % of songbird species, females also sing. Pairs of some species sing in perfect synchronization.A number of songbirds imitate both the voices of other songbirds and ambient noises, and many songbirds have regional dialects.Song development depends on genetics and other factors such as the environment, metabolism and hormonal influences. It proceeds step by step and initially includes relatively primitive sequences (so-called "subsongs"), then leads through more complex intermediate forms ("plastic songs") and finally to the completed singing pattern ("full songs").Young birds learn the song of their species at a time when they are not yet singing themselves, often as nestlings aged 10 to 50 days from older members of the species, usually from their fathers.The song of young birds develops, based on the template of adult song, in a network of sensory-motor neurons in the forebrain.Songbirds, especially the zebra finch, currently offer the best model for the neural basis of human language learning. In birds, the so-called "High Vocal Center" orchestrates all brain regions relevant to songs, with the neural control of song being sensitive to sex hormones.

Karyotype evolution of suliformes and description of a ♂Z1Z1Z2Z2/♀Z1Z2W multiple sex chromosome system in boobies (Sula spp.)

Our comprehension of avian karyotypes still needs to be improved, especially for Suliform birds. To enhance understanding of chromosomal evolution in this order, we conducted conventional and molecular cytogenetic analysis in five species, named Sula dactylatra, Sula leucogaster, Sula sula (Sulidae), Fregata magnificens (Fregatidae), and Nannopterum brasilianum (Phalacrocoracidae). The diploid chromosome number for S. dactylatra and S. leucogaster was established as 2n = 76 in males, and 2n = 75 in females, but S. sula displayed a karyotype of 2n = 76 chromosomes in males. The disparity in diploid chromosome numbers between male and female Sula is due to a multiple sex chromosome system of the Z1Z1Z2Z2/Z1Z2W type. We propose that the emergence of this multiple-sex chromosome system resulted from a Robertsonian translocation involving the W chromosome and the smallest microchromosome. Fregata magnificens exhibited a diploid number 76 (2n = 76), while N. brasilianum displayed a diploid number of 74 (2n = 74) in both sexes. The ribosomal cluster was located in one microchromosome pair in S. dactylatra, S. leucogaster, S. sula, and F. magnificens and in four pairs in N. brasilianum. Our findings provide evidence of a conserved multiple-sex chromosome system within the Sula genus, shedding light on the high karyotype diversity in Suliformes.

Automatic imitation of intransitive actions in macaws

Automatic imitation is the involuntary tendency of humans to copy others' actions even when counterproductive. We examined the automatic imitation of intransitive actions in blue-throated macaws (Ara glaucogularis), employing a stimulus-response-compatibility task. After training seven macaws to perform two different actions with legs and wings upon specific hand commands, the subjects were divided into a compatible and incompatible group. We rewarded the subjects for performing the same action as the conspecific model in the compatible group and the opposite action in the incompatible group. Involuntarily imitating the demonstrated actions, the incompatible group made more errors than the compatible group and took longer to eventually respond correctly. The study provides evidence for the automatic imitation of intransitive actions in non-human animals- parrots, suggesting that arbitrary action imitation facilitated by a mirror-neuron system in parrot brain may be adaptive in the ever-changing complex social environment of parrots and possibly drive cultural evolution.

The Expression of Proteases and the Oligopeptide Transporter PepT1 in the Yolk Sac Membrane, Proventriculus, and Small Intestine During the Development of Anas platyrhynchos domestica Embryo

The role of the yolk sac membrane (YSM) and digestive tract in the processing of egg yolk proteins during embryogenesis is unexplored in the duck Anas platyrhynchos domestica. Here, we investigated in the duck embryo the function of the YSM, proventriculus, and small intestine in protein digestion and uptake. We tested the expression of aminopeptidase N (APN) and the oligopeptide transporter PepT1 as well as the expression of cathepsin B (CTSB) and cathepsin D (CTSD) lysosomal genes in the YSM during incubation days 12, 14, 16-18, 20, 22, 24, 26, and 28 (the day of hatch). Also, we examined embryonic duck pepsinogen (EDPg) expression in the proventriculus and APN and PepT1 expression in the small intestine. In the YSM, CTSD expression was weak compared to that of CTSB, and the expression of CTSB, APN, and PepT1 reached its maximum on day 24 and decreased afterwards. In the proventriculus, EDPg expression peaked on days 17 to 20 and decreased thereafter. The APN and PepT1 expression levels were highest in the jejunum and ileum and reached their maximum on day 28. Our results suggest that the YSM plays a role in the degradation and uptake of the peptides that are digested by the activated yolk proteases, and it also functions in the lysosomal digestion of yolk lipoproteins. Furthermore, the proventriculus is possibly involved in the digestion of yolk proteins. Finally, the jejunum and ileum appear to be the primary sites for peptide digestion and absorption at the end of the incubation.

Insights into avian molecular cytogenetics-with reptilian comparisons

In last 100 years or so, much information has been accumulated on avian karyology, genetics, physiology, biochemistry and evolution. The chicken genome project generated genomic resources used in comparative studies, elucidating fundamental evolutionary processes, much of it funded by the economic importance of domestic fowl (which are also excellent model species in many areas). Studying karyotypes and whole genome sequences revealed population processes, evolutionary biology, and genome function, uncovering the role of repetitive sequences, transposable elements and gene family expansion. Knowledge of the function of many genes and non-expressed or identified regulatory components is however still lacking. Birds (Aves) are diverse, have striking adaptations for flight, migration and survival and inhabit all continents most islands. They also have a unique karyotype with ~ 10 macrochromosomes and ~ 30 microchromosomes that are smaller than other reptiles. Classified into Palaeognathae and Neognathae they are evolutionarily close, and a subset of reptiles. Here we overview avian molecular cytogenetics with reptilian comparisons, shedding light on their karyotypes and genome structure features. We consider avian evolution, then avian (followed by reptilian) karyotypes and genomic features. We consider synteny disruptions, centromere repositioning, and repetitive elements before turning to comparative avian and reptilian genomics. In this context, we review comparative cytogenetics and genome mapping in birds as well as Z- and W-chromosomes and sex determination. Finally, we give examples of pivotal research areas in avian and reptilian cytogenomics, particularly physical mapping and map integration of sex chromosomal genes, comparative genomics of chicken, turkey and zebra finch, California condor cytogenomics as well as some peculiar cytogenetic and evolutionary examples. We conclude that comparative molecular studies and improving resources continually contribute to new approaches in population biology, developmental biology, physiology, disease ecology, systematics, evolution and phylogenetic systematics orientation. This also produces genetic mapping information for chromosomes active in rearrangements during the course of evolution. Further insights into mutation, selection and adaptation of vertebrate genomes will benefit from these studies including physical and online resources for the further elaboration of comparative genomics approaches for many fundamental biological questions.

A Large Marine Bird (Aves: Procellariiformes) from the Eocene of Western Siberia

The article describes the first find of a bird from the Paleogene of Siberia. A fragment of tibiotarsus from the Eocene Tavda Formation of the Tyumen Region (Western Siberia) is assigned to Procellariiformes. The bird is morphologically closer to Procellariidae, but comparable in size to albatrosses (Diomedeidae) and is assumed to represent the stem members of the family. The find indicated for the first time that either stem albatrosses or similar large Procellariiformes could have had a worldwide distribution as early as the Eocene.

Cervical anatomy and its relation to foraging habits in aquatic birds (Aves: Neornithes: Neoaves)

Birds have extremely flexible necks, which help in their search for food. However, studies on the variation in bird cervical anatomy and its relationship with foraging are rare, despite the different habits presented between species. Here, we analyze the anatomy of the neck of aquatic birds and relate it to their foraging strategies. We dissected specimens representing four species of Charadriiformes, 11 species of Phaethoquornithes, and two specimens belonging to the outgroup Telluraves. We chose to emphasize Charadriiformes and Phaethoquornithes because they present several strategies that require cervical mobility and stability. We note that vertebral anatomy and dimensions vary, which affects the shape and size of the soft tissues attached throughout the neck. The synovial cartilage present in the articulatio intercorporalis represents an additional length in the neck, however, this is not longer than that observed in animals with intervertebral discs. Our analysis indicates that birds have a prevalence of dorsoventral movements in the middle of the neck and lateral and rotational movements near the base of the neck, while the region near the head presents a wide range of movement in all directions. Cervical ligaments and muscles throughout the neck provide stability in all segments, although the robustness of the soft tissues indicates that the most caudal portion of the neck is the most stable. The vertebral and soft tissue anatomy is consistent with the extensive mobility in pitching, yaw, and roll movements performed mainly by the head and first segment of the neck during the different foraging of the analyzed birds. Furthermore, the muscles closer to the skull are robust and allow the execution of a variety of habits to capture food in different species. The subsequent cervical segments present differences that explain their reduction in mobility, but they are equally stable.

Differential Conservation and Loss of Chicken Repeat 1 (CR1) Retrotransposons in Squamates Reveal Lineage-Specific Genome Dynamics Across Reptiles

Transposable elements (TEs) are repetitive DNA sequences which create mutations and generate genetic diversity across the tree of life. In amniote vertebrates, TEs have been mainly studied in mammals and birds, whose genomes generally display low TE diversity. Squamates (Order Squamata; including ∼11,000 extant species of lizards and snakes) show as much variation in TE abundance and activity as they do in species and phenotypes. Despite this high TE activity, squamate genomes are remarkably uniform in size. We hypothesize that novel, lineage-specific genome dynamics have evolved over the course of squamate evolution. To understand the interplay between TEs and host genomes, we analyzed the evolutionary history of the chicken repeat 1 (CR1) retrotransposon, a TE family found in most tetrapod genomes which is the dominant TE in most reptiles. We compared 113 squamate genomes to the genomes of turtles, crocodilians, and birds and used ancestral state reconstruction to identify shifts in the rate of CR1 copy number evolution across reptiles. We analyzed the repeat landscapes of CR1 in squamate genomes and determined that shifts in the rate of CR1 copy number evolution are associated with lineage-specific variation in CR1 activity. We then used phylogenetic reconstruction of CR1 subfamilies across amniotes to reveal both recent and ancient CR1 subclades across the squamate tree of life. The patterns of CR1 evolution in squamates contrast other amniotes, suggesting key differences in how TEs interact with different host genomes and at different points across evolutionary history.

Genome and life-history evolution link bird diversification to the end-Cretaceous mass extinction

Complex patterns of genome evolution associated with the end-Cretaceous [Cretaceous-Paleogene (K-Pg)] mass extinction limit our understanding of the early evolutionary history of modern birds. Here, we analyzed patterns of avian molecular evolution and identified distinct macroevolutionary regimes across exons, introns, untranslated regions, and mitochondrial genomes. Bird clades originating near the K-Pg boundary exhibited numerous shifts in the mode of molecular evolution, suggesting a burst of genomic heterogeneity at this point in Earth's history. These inferred shifts in substitution patterns were closely related to evolutionary shifts in developmental mode, adult body mass, and patterns of metabolic scaling. Our results suggest that the end-Cretaceous mass extinction triggered integrated patterns of evolution across avian genomes, physiology, and life history near the dawn of the modern bird radiation.

Multi-genome comparisons reveal gain-and-loss evolution of anti-Mullerian hormone receptor type 2 as a candidate master sex-determining gene in Percidae

BACKGROUND

The Percidae family comprises many fish species of major importance for aquaculture and fisheries. Based on three new chromosome-scale assemblies in Perca fluviatilis, Perca schrenkii, and Sander vitreus along with additional percid fish reference genomes, we provide an evolutionary and comparative genomic analysis of their sex-determination systems.

RESULTS

We explored the fate of a duplicated anti-Mullerian hormone receptor type-2 gene (amhr2bY), previously suggested to be the master sex-determining (MSD) gene in P. flavescens. Phylogenetically related and structurally similar amhr2 duplicates (amhr2b) were found in P. schrenkii and Sander lucioperca, potentially dating this duplication event to their last common ancestor around 19-27 Mya. In P. fluviatilis and S. vitreus, this amhr2b duplicate has been likely lost while it was subject to amplification in S. lucioperca. Analyses of the amhr2b locus in P. schrenkii suggest that this duplication could be also male-specific as it is in P. flavescens. In P. fluviatilis, a relatively small (100 kb) non-recombinant sex-determining region (SDR) was characterized on chromosome 18 using population-genomics approaches. This SDR is characterized by many male-specific single-nucleotide variations (SNVs) and no large duplication/insertion event, suggesting that P. fluviatilis has a male heterogametic sex-determination system (XX/XY), generated by allelic diversification. This SDR contains six annotated genes, including three (c18h1orf198, hsdl1, tbc1d32) with higher expression in the testis than in the ovary.

CONCLUSIONS

Together, our results provide a new example of the highly dynamic sex chromosome turnover in teleosts and provide new genomic resources for Percidae, including sex-genotyping tools for all three known Perca species.

Synergistic innovations enabled the radiation of anglerfishes in the deep open ocean

Major ecological transitions are thought to fuel diversification, but whether they are contingent on the evolution of certain traits called key innovations1 is unclear. Key innovations are routinely invoked to explain how lineages rapidly exploit new ecological opportunities.1,2,3 However, investigations of key innovations often focus on single traits rather than considering trait combinations that collectively produce effects of interest.4 Here, we investigate the evolution of synergistic trait interactions in anglerfishes, which include one of the most species-rich vertebrate clades in the bathypelagic, or "midnight," zone of the deep sea: Ceratioidea.5 Ceratioids are the only vertebrates that possess sexual parasitism, wherein males temporarily attach or permanently fuse to females to mate.6,7 We show that the rapid transition of ancestrally benthic anglerfishes into pelagic habitats occurred during a period of major global warming 50-35 million years ago.8,9 This transition coincided with the origins of sexual parasitism, which is thought to increase the probability of successful reproduction once a mate is found in the midnight zone, Earth's largest habitat.5,6,7 Our reconstruction of the evolutionary history of anglerfishes and the loss of immune genes support that permanently fusing clades have convergently degenerated their adaptive immunity. We find that degenerate adaptive immune genes and sexual body size dimorphism, both variably present in anglerfishes outside the ceratioid radiation, likely promoted their transition into the bathypelagic zone. These results show how traits from separate physiological, morphological, and reproductive systems can interact synergistically to drive major transitions and subsequent diversification in novel environments.

Accurate, scalable, and fully automated inference of species trees from raw genome assemblies using ROADIES

Inference of species trees plays a crucial role in advancing our understanding of evolutionary relationships and has immense significance for diverse biological and medical applications. Extensive genome sequencing efforts are currently in progress across a broad spectrum of life forms, holding the potential to unravel the intricate branching patterns within the tree of life. However, estimating species trees starting from raw genome sequences is quite challenging, and the current cutting-edge methodologies require a series of error-prone steps that are neither entirely automated nor standardized. In this paper, we present ROADIES, a novel pipeline for species tree inference from raw genome assemblies that is fully automated, easy to use, scalable, free from reference bias, and provides flexibility to adjust the tradeoff between accuracy and runtime. The ROADIES pipeline eliminates the need to align whole genomes, choose a single reference species, or pre-select loci such as functional genes found using cumbersome annotation steps. Moreover, it leverages recent advances in phylogenetic inference to allow multi-copy genes, eliminating the need to detect orthology. Using the genomic datasets released from large-scale sequencing consortia across three diverse life forms (placental mammals, pomace flies, and birds), we show that ROADIES infers species trees that are comparable in quality with the state-of-the-art approaches but in a fraction of the time. By incorporating optimal approaches and automating all steps from assembled genomes to species and gene trees, ROADIES is poised to improve the accuracy, scalability, and reproducibility of phylogenomic analyses.

Comparative morphology of the avian bony columella

In birds, the columella is the only bony element of the sound conducting apparatus, conveying vibrations of the cartilaginous extracolumella to the fluid of the inner ear. Although avian columellar morphology has attracted some attention over the past century, it nonetheless remains poorly described in the literature. The few existing studies mostly focus on morphological descriptions in relatively few taxa, with no taxonomically broad surveys yet published. Here we use observations of columellae from 401 extant bird species to provide a comprehensive survey of columellar morphology in a phylogenetic context. We describe the columellae of several taxa for the first time and identify derived morphologies characterizing higher-level clades based on current phylogenies. In particular, we identify a derived columellar morphology diagnosing a major subclade of Accipitridae. Within Suliformes, we find that Fregatidae, Sulidae, and Phalacrocoracidae share a derived morphology that is absent in Anhingidae, suggesting a secondary reversal. Phylogenetically informed comparisons allow recognition of instances of homoplasy, including the distinctive bulbous columellae in suboscine passerines and taxa belonging to Eucavitaves, and bulging footplates that appear to have evolved at least twice independently in Strigiformes. We consider phylogenetic and functional factors influencing avian columellar morphology, finding that aquatic birds possess small footplates relative to columellar length, possibly related to hearing function in aquatic habitats. By contrast, the functional significance of the distinctive bulbous basal ends of the columellae of certain arboreal landbird taxa remains elusive.

Complexity of avian evolution revealed by family-level genomes

Despite tremendous efforts in the past decades, relationships among main avian lineages remain heavily debated without a clear resolution. Discrepancies have been attributed to diversity of species sampled, phylogenetic method and the choice of genomic regions1-3. Here we address these issues by analysing the genomes of 363 bird species4 (218 taxonomic families, 92% of total). Using intergenic regions and coalescent methods, we present a well-supported tree but also a marked degree of discordance. The tree confirms that Neoaves experienced rapid radiation at or near the Cretaceous-Palaeogene boundary. Sufficient loci rather than extensive taxon sampling were more effective in resolving difficult nodes. Remaining recalcitrant nodes involve species that are a challenge to model due to either extreme DNA composition, variable substitution rates, incomplete lineage sorting or complex evolutionary events such as ancient hybridization. Assessment of the effects of different genomic partitions showed high heterogeneity across the genome. We discovered sharp increases in effective population size, substitution rates and relative brain size following the Cretaceous-Palaeogene extinction event, supporting the hypothesis that emerging ecological opportunities catalysed the diversification of modern birds. The resulting phylogenetic estimate offers fresh insights into the rapid radiation of modern birds and provides a taxon-rich backbone tree for future comparative studies.

Synthetic analysis of trophic diversity and evolution in Enantiornithes with new insights from Bohaiornithidae

Enantiornithines were the dominant birds of the Mesozoic, but understanding of their diet is still tenuous. We introduce new data on the enantiornithine family Bohaiornithidae, famous for their large size and powerfully built teeth and claws. In tandem with previously published data, we comment on the breadth of enantiornithine ecology and potential patterns in which it evolved. Body mass, jaw mechanical advantage, finite element analysis of the jaw, and traditional morphometrics of the claws and skull are compared between bohaiornithids and living birds. We find bohaiornithids to be more ecologically diverse than any other enantiornithine family: Bohaiornis and Parabohaiornis are similar to living plant-eating birds; Longusunguis resembles raptorial carnivores; Zhouornis is similar to both fruit-eating birds and generalist feeders; and Shenqiornis and Sulcavis plausibly ate fish, plants, or a mix of both. We predict the ancestral enantiornithine bird to have been a generalist which ate a wide variety of foods. However, more quantitative data from across the enantiornithine tree is needed to refine this prediction. By the Early Cretaceous, enantiornithine birds had diversified into a variety of ecological niches like crown birds after the K-Pg extinction, adding to the evidence that traits unique to crown birds cannot completely explain their ecological success.

A region of suppressed recombination misleads neoavian phylogenomics

Genomes are typically mosaics of regions with different evolutionary histories. When speciation events are closely spaced in time, recombination makes the regions sharing the same history small, and the evolutionary history changes rapidly as we move along the genome. When examining rapid radiations such as the early diversification of Neoaves 66 Mya, typically no consistent history is observed across segments exceeding kilobases of the genome. Here, we report an exception. We found that a 21-Mb region in avian genomes, mapped to chicken chromosome 4, shows an extremely strong and discordance-free signal for a history different from that of the inferred species tree. Such a strong discordance-free signal, indicative of suppressed recombination across many millions of base pairs, is not observed elsewhere in the genome for any deep avian relationships. Although long regions with suppressed recombination have been documented in recently diverged species, our results pertain to relationships dating circa 65 Mya. We provide evidence that this strong signal may be due to an ancient rearrangement that blocked recombination and remained polymorphic for several million years prior to fixation. We show that the presence of this region has misled previous phylogenomic efforts with lower taxon sampling, showing the interplay between taxon and locus sampling. We predict that similar ancient rearrangements may confound phylogenetic analyses in other clades, pointing to a need for new analytical models that incorporate the possibility of such events.

Unraveling the evolutionary origin of the complex Nuclear Receptor Element (cNRE), a cis-regulatory module required for preferential expression in the atrial chamber

Cardiac function requires appropriate proteins in each chamber. Atria requires slow myosin to act as reservoirs, while ventricles demand fast myosin for swift pumping. Myosins are thus under chamber-biased cis-regulation, with myosin gene expression imbalances leading to congenital heart dysfunction. To identify regulatory inputs leading to cardiac chamber-biased expression, we computationally and molecularly dissected the quail Slow Myosin Heavy Chain III (SMyHC III) promoter that drives preferential expression to the atria. We show that SMyHC III gene states are orchestrated by a complex Nuclear Receptor Element (cNRE) of 32 base pairs. Using transgenesis in zebrafish and mice, we demonstrate that preferential atrial expression is achieved by a combinatorial regulatory input composed of atrial activation motifs and ventricular repression motifs. Using comparative genomics, we show that the cNRE might have emerged from an endogenous viral element through infection of an ancestral host germline, revealing an evolutionary pathway to cardiac chamber-specific expression.

Differences in vocal brain areas and astrocytes between the house wren and the rufous-tailed hummingbird

The house wren shows complex song, and the rufous-tailed hummingbird has a simple song. The location of vocal brain areas supports the song's complexity; however, these still need to be studied. The astrocytic population in songbirds appears to be associated with change in vocal control nuclei; however, astrocytic distribution and morphology have not been described in these species. Consequently, we compared the distribution and volume of the vocal brain areas: HVC, RA, Area X, and LMAN, cell density, and the morphology of astrocytes in the house wren and the rufous-tailed hummingbird. Individuals of the two species were collected, and their brains were analyzed using serial Nissl- NeuN- and MAP2-stained tissue scanner imaging, followed by 3D reconstructions of the vocal areas; and GFAP and S100β astrocytes were analyzed in both species. We found that vocal areas were located close to the cerebral midline in the house wren and a more lateralized position in the rufous-tailed hummingbird. The LMAN occupied a larger volume in the rufous-tailed hummingbird, while the RA and HVC were larger in the house wren. While Area X showed higher cell density in the house wren than the rufous-tailed hummingbird, the LMAN showed a higher density in the rufous-tailed hummingbird. In the house wren, GFAP astrocytes in the same bregma where the vocal areas were located were observed at the laminar edge of the pallium (LEP) and in the vascular region, as well as in vocal motor relay regions in the pallidum and mesencephalon. In contrast, GFAP astrocytes were found in LEP, but not in the pallidum and mesencephalon in hummingbirds. Finally, when comparing GFAP astrocytes in the LEP region of both species, house wren astrocytes exhibited significantly more complex morphology than those of the rufous-tailed hummingbird. These findings suggest a difference in the location and cellular density of vocal circuits, as well as morphology of GFAP astrocytes between the house wren and the rufous-tailed hummingbird.

Arthrological reconstructions of the pterosaur neck and their implications for the cervical position at rest

The lack of any pterosaur living descendants creates gaps in the knowledge of the biology of this group, including its cervical biomechanics, which makes it difficult to understand their posture and life habits. To mitigate part of this issue, we reconstructed the cervical osteology and arthrology of three pterosaurs, allowing us to make inferences about the position of the neck of these animals at rest. We used scans of three-dimensionally preserved cervical series of Anhanguera piscator, Azhdarcho lancicollis and Rhamphorhynchus muensteri for the reconstructions, thus representing different lineages. For the recognition of ligaments, joint cartilages, and levels of overlapping of the zygapophyses, we applied the Extant Phylogenetic Bracket method, based on various extant birds and on Caiman latirostris. We inferred that pterosaur intervertebral joints were probably covered by a thin layer of synovial cartilage whose thickness varied along the neck, being thicker in the posterior region. Ignoring this cartilage can affect reconstructions. According to the vertebral angulation, their neck was slightly sinuous when in rest position. Our analyses also indicate that pterosaurs had segmented and supra-segmented articular cervical ligaments, which could confer stabilization, execute passive forces on the neck and store elastic energy.

Differential Conservation and Loss of CR1 Retrotransposons in Squamates Reveals Lineage-Specific Genome Dynamics across Reptiles

Transposable elements (TEs) are repetitive DNA sequences which create mutations and generate genetic diversity across the tree of life. In amniotic vertebrates, TEs have been mainly studied in mammals and birds, whose genomes generally display low TE diversity. Squamates (Order Squamata; ~11,000 extant species of lizards and snakes) show as much variation in TE abundance and activity as they do in species and phenotypes. Despite this high TE activity, squamate genomes are remarkably uniform in size. We hypothesize that novel, lineage-specific dynamics have evolved over the course of squamate evolution to constrain genome size across the order. Thus, squamates may represent a prime model for investigations into TE diversity and evolution. To understand the interplay between TEs and host genomes, we analyzed the evolutionary history of the CR1 retrotransposon, a TE family found in most tetrapod genomes. We compared 113 squamate genomes to the genomes of turtles, crocodilians, and birds, and used ancestral state reconstruction to identify shifts in the rate of CR1 copy number evolution across reptiles. We analyzed the repeat landscapes of CR1 in squamate genomes and determined that shifts in the rate of CR1 copy number evolution are associated with lineage-specific variation in CR1 activity. We then used phylogenetic reconstruction of CR1 subfamilies across amniotes to reveal both recent and ancient CR1 subclades across the squamate tree of life. The patterns of CR1 evolution in squamates contrast other amniotes, suggesting key differences in how TEs interact with different host genomes and at different points across evolutionary history.

A juvenile bird with possible crown-group affinities from a dinosaur-rich Cretaceous ecosystem in North America

BACKGROUND

Living birds comprise the most speciose and anatomically diverse clade of flying vertebrates, but their poor early fossil record and the lack of resolution around the relationships of the major clades have greatly obscured extant avian origins.

RESULTS

Here, I describe a Late Cretaceous bird from North America based on a fragmentary skeleton that includes cranial material and portions of the forelimb, hindlimb, and foot and is identified as a juvenile based on bone surface texture. Several features unite this specimen with crown Aves, but its juvenile status precludes the recognition of a distinct taxon. The North American provenance of the specimen supports a cosmopolitan distribution of early crown birds, clashes with the hypothesized southern hemisphere origins of living birds, and demonstrates that crown birds and their closest relatives coexisted with non-avian dinosaurs that independently converged on avian skeletal anatomy, such as the alvarezsaurids and dromaeosaurids.

CONCLUSIONS

By revealing the ecological and biogeographic context of Cretaceous birds within or near the crown clade, the Lance Formation specimen provides new insights into the contingent nature of crown avian survival through the Cretaceous-Paleogene mass extinction and the subsequent origins of living bird diversity.

Entopallium Lost GFAP Immunoreactivity during Avian Evolution: Is GFAP a "Condition Sine Qua Non"?

INTRODUCTION

The present study demonstrates that in the same brain area the astroglia can express GFAP (the main cytoskeletal protein of astroglia) in some species but not in the others of the same vertebrate class. It contrasts the former opinions that the distribution of GFAP found in a species is characteristic of the entire class. The present study investigated birds in different phylogenetic positions: duck (Cairina moschata domestica), chicken (Gallus gallus domesticus), and quails (Coturnix japonica and Excalfactoria chinensis) of Galloanserae; pigeon (Columba livia domestica) of a group of Neoaves, in comparison with representatives of other Neoaves lineages, which emerged more recently in evolution: finches (Taeniopygia guttata and Erythrura gouldiae), magpie (Pica pica), and parrots (Melopsittacus undulatus and Nymphicus hollandicus).

METHODS

Following a perfusion with 4% buffered paraformaldehyde, immunoperoxidase reactions were performed with two types of anti-GFAP: monoclonal and polyclonal, on floating sections.

RESULTS

The entopallium (formerly "ectostriatum," a telencephalic area in birds) was GFAP-immunopositive in pigeon and in the representatives of Galloanserae but not in songbirds and parrots, which emerged more recently in evolution. The lack of GFAP expression of a brain area, however, does not mean the lack of astroglia. Lesions induced GFAP expression in the territory of GFAP-immunonegative entopallia. It proved that the GFAP immunonegativity is not due to the lack of capability, but rather the suppression of GFAP production of the astrocytes in this territory. In the other areas investigated besides the entopallium (optic tectum and cerebellum), no considerable interspecific differences of GFAP immunopositivity were found. It proved that the immunonegativity of entopallium is due to neither the general lack of GFAP expression nor the incapability of our reagents to detect GFAP in these species.

CONCLUSION

The data are congruent with our proposal that a lack of GFAP expression has evolved in different brain areas in vertebrate evolution, typically in lineages that emerged more recently. Comparative studies on GFAP-immunopositive and GFAP-immunonegative entopallia may promote understanding the role of GFAP in neural networks.

Comparative chromosome painting in three Pelecaniformes species (Aves): Exploring the role of macro and microchromosome fusions in karyotypic evolution

Pelecaniformes is an order of waterbirds that exhibit diverse and distinct morphologies. Ibis, heron, pelican, hammerkop, and shoebill are included within the order. Despite their fascinating features, the phylogenetic relationships among the families within Pelecaniformes remain uncertain and pose challenges due to their complex evolutionary history. Their karyotypic evolution is another little-known aspect. Therefore, to shed light on the chromosomal rearrangements that have occurred during the evolution of Pelecaniformes, we have used whole macrochromosome probes from Gallus gallus (GGA) to show homologies on three species with different diploid numbers, namely Cochlearius cochlearius (2n = 74), Eudocimus ruber (2n = 66), and Syrigma sibilatrix (2n = 62). A fusion between GGA6 and GGA7 was found in C. cochlearius and S. sibilatrix. In S. sibilatrix the GGA8, GGA9 and GGA10 hybridized to the long arms of biarmed macrochromosomes, indicating fusions with microchromosomes. In E. ruber the GGA7 and GGA8 hybridized to the same chromosome pair. After comparing our painting results with previously published data, we show that distinct chromosomal rearrangements have occurred in different Pelecaniformes lineages. Our study provides new insight into the evolutionary history of Pelecaniformes and the chromosomal changes involving their macrochromosomes and microchromosomes that have taken place in different species within this order.

Multi-genome comparisons reveal gain-and-loss evolution of the anti-Mullerian hormone receptor type 2 gene, an old master sex determining gene, in Percidae

The Percidae family comprises many fish species of major importance for aquaculture and fisheries. Based on three new chromosome-scale assemblies in Perca fluviatilis, Perca schrenkii and Sander vitreus along with additional percid fish reference genomes, we provide an evolutionary and comparative genomic analysis of their sex-determination systems. We explored the fate of a duplicated anti-Mullerian hormone receptor type-2 gene (amhr2bY), previously suggested to be the master sex determining (MSD) gene in P. flavescens. Phylogenetically related and structurally similar amhr2 duplications (amhr2b) were found in P. schrenkii and Sander lucioperca, potentially dating this duplication event to their last common ancestor around 19-27 Mya. In P. fluviatilis and S. vitreus, this amhr2b duplicate has been lost while it was subject to amplification in S. lucioperca. Analyses of the amhr2b locus in P. schrenkii suggest that this duplication could be also male-specific as it is in P. flavescens. In P. fluviatilis, a relatively small (100 kb) non-recombinant sex-determining region (SDR) was characterized on chromosome-18 using population-genomics approaches. This SDR is characterized by many male-specific single-nucleotide variants (SNVs) and no large duplication/insertion event, suggesting that P. fluviatilis has a male heterogametic sex determination system (XX/XY), generated by allelic diversification. This SDR contains six annotated genes, including three (c18h1orf198, hsdl1, tbc1d32) with higher expression in testis than ovary. Together, our results provide a new example of the highly dynamic sex chromosome turnover in teleosts and provide new genomic resources for Percidae, including sex-genotyping tools for all three known Perca species.

Stem albatrosses wandered far: a new species of Plotornis (Aves, Pan-Diomedeidae) from the earliest Miocene of New Zealand

Albatrosses are among the most intensely studied groups of living birds, yet their fossil record remains sparse. Despite modern albatrosses being more abundant and widespread in the Southern Hemisphere, the vast majority of fossil albatrosses identified to date come from Northern Hemisphere localities. Here, we describe Plotornis archaeonautes sp. nov., a new albatross species from the earliest Miocene that represents the earliest record of Procellariiformes in New Zealand and the earliest uncontroversial record of the clade Pan-Diomedeidae from the Southern Hemisphere. Phylogenetic analyses support the placement of Plotornis outside of the clade uniting all extant albatrosses. The new fossil reveals that stem lineage albatrosses were widespread by the onset of the Neogene. Although the humerus of Plotornis archaeonautes exhibits a short processus supracondylaris dorsalis, this early species may have possessed at least one of the unique ossifications associated with the patagial bracing system present in modern albatrosses.

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.

No Signs of Adaptations for High Flight Intensity in the Mitochondrial Genome of Birds

Mitochondrial genomes are expected to show adaptations for optimizing aerobic respiration in birds that make intense use of flight. However, there is limited empirical evidence of such a relationship. We here examine correlates of several mitochondrial genome characteristics and flight use across a diverse sample of 597 bird species. We developed an index of flight use intensity that ranged from 0 in flightless species to 9 in migratory hummingbirds and examined its association with nucleobase composition, amino acid class composition, and amino acid site allelic variation using phylogenetic comparative methods. We found no evidence of mitochondrial genome adaptations to flight intensity. Neither nucleotide composition nor amino acid properties showed consistent patterns related to flight use. While specific sites in mitochondrial genes exhibited variation associated with flight intensity, there was limited association between specific amino acid residues and flight intensity levels. Our findings suggest a complex genetic architecture for aerobic performance traits, where multiple genes in both mitochondria and the nucleus may contribute to overall performance. Other factors, such as gene expression regulation and anatomical adaptations, may play a more significant role in influencing flight performance than changes in mitochondrial genes. These findings highlight the need for comprehensive genomic analyses to unravel the intricate relationship between genetic variants and aerobic performance in birds.

A New Species of Sandgrouse (Aves: Pteroclidae) from the Early Pleistocene of the Crimea

Sandgrouse (Pteroclidae, Pterocliformes) are specialized ground birds of open arid landscapes with a very poorly studied evolutionary history. In the late Pliocene-early Pleistocene, Pteroclidae are known only from few localities in Southern Europe. The article describes a relatively large fossil sandgrouse from the early Pleistocene of the Taurida cave in the Crimea. This is the first record of Pteroclidae in the ancient faunas of the Black Sea region and Eastern Europe. The unusual structure of the tibiotarsus makes it possible to describe the fossil form from Taurida Cave as a new species, Pterocles bosporanus sp. nov.

A high-quality genome assembly highlights the evolutionary history of the great bustard (Otis tarda, Otidiformes)

Conservation genomics often relies on non-invasive methods to obtain DNA fragments which limit the power of multi-omic analyses for threatened species. Here, we report multi-omic analyses based on a well-preserved great bustard individual (Otis tarda, Otidiformes) that was found dead in the mountainous region in Gansu, China. We generate a near-complete genome assembly containing only 18 gaps scattering in 8 out of the 40 assembled chromosomes. We characterize the DNA methylation landscape which is correlated with GC content and gene expression. Our phylogenomic analysis suggests Otidiformes and Musophagiformes are sister groups that diverged from each other 46.3 million years ago. The genetic diversity of great bustard is found the lowest among the four available Otidiformes genomes, possibly due to population declines during past glacial periods. As one of the heaviest migratory birds, great bustard possesses several expanded gene families related to cardiac contraction, actin contraction, calcium ion signaling transduction, as well as positively selected genes enriched for metabolism. Finally, we identify an extremely young evolutionary stratum on the sex chromosome, a rare case among birds. Together, our study provides insights into the conservation genomics, adaption and chromosome evolution of the great bustard.

Insights into the Biology of Leucocytozoon Species (Haemosporida, Leucocytozoidae): Why Is There Slow Research Progress on Agents of Leucocytozoonosis?

Blood parasites of the genus Leucocytozoon (Leucocytozoidae) only inhabit birds and represent a readily distinct evolutionary branch of the haemosporidians (Haemosporida, Apicomplexa). Some species cause pathology and even severe leucocytozoonosis in avian hosts, including poultry. The diversity of Leucocytozoon pathogens is remarkable, with over 1400 genetic lineages detected, most of which, however, have not been identified to the species level. At most, approximately 45 morphologically distinct species of Leucocytozoon have been described, but only a few have associated molecular data. This is unfortunate because basic information about named and morphologically recognized Leucocytozoon species is essential for a better understanding of phylogenetically closely related leucocytozoids that are known only by DNA sequence. Despite much research on haemosporidian parasites during the past 30 years, there has not been much progress in taxonomy, vectors, patterns of transmission, pathogenicity, and other aspects of the biology of these cosmopolitan bird pathogens. This study reviewed the available basic information on avian Leucocytozoon species, with particular attention to some obstacles that prevent progress to better understanding the biology of leucocytozoids. Major gaps in current Leucocytozoon species research are discussed, and possible approaches are suggested to resolve some issues that have limited practical parasitological studies of these pathogens.

Genomic phylogeography illuminates deep cyto-nuclear discordances in midwife toads (Alytes)

The advent of genomic methods allows us to revisit the evolutionary history of organismal groups for which robust phylogenies are still lacking, particularly in species complexes that frequently hybridize. In this study, we conduct RAD-sequencing (RAD-seq) analyses of midwife toads (genus Alytes), an iconic group of western Mediterranean amphibians famous for their parental care behavior, but equally infamous for the difficulties to reconstruct their evolutionary history. Through admixture and phylogenetic analyses of thousands of loci, we provide the most comprehensive phylogeographic framework for the A. obstetricans complex to date, as well as the first fully resolved phylogeny for the entire genus. As part of this effort, we carefully explore the influence of different sampling schemes and data filtering thresholds on tree reconstruction, showing that several, slightly different, yet robust topologies may be retrieved with small datasets obtained by stringent SNP calling parameters, especially when admixed individuals are included. In contrast, analyses of incomplete but larger datasets converged on the same phylogeny, irrespective of the reconstruction method used or the proportion of missing data. The Alytes tree features three Miocene-diverged clades corresponding to the proposed subgenera Ammoryctis (A. cisternasii), Baleaphryne (A. maurus, A. dickhilleni and A. muletensis), and Alytes (A. obstetricans complex). The latter consists of six evolutionary lineages, grouped into three clades of Pliocene origin, and currently delimited as two species: (1) A. almogavarii almogavarii and A. a. inigoi; (2) A. obstetricans obstetricans and A. o. pertinax; (3) A. o. boscai and an undescribed taxon (A. o. cf. boscai). These results contradict the mitochondrial tree, due to past mitochondrial captures in A. a. almogavarii (central Pyrenees) and A. o. boscai (central Iberia) by A. obstetricans ancestors during the Pleistocene. Patterns of admixture between subspecies appear far more extensive than previously assumed from microsatellites, causing nomenclatural uncertainties, and even underlying the reticulate evolution of one taxon (A. o. pertinax). All Ammoryctis and Baleaphryne species form shallow clades, so their taxonomy should remain stable. Amid the prevalence of cyto-nuclear discordance among terrestrial vertebrates and the usual lack of resolution of conventional nuclear markers, our study advocates for phylogeography based on next-generation sequencing, but also encourages properly exploring parameter space and sampling schemes when building and analyzing genomic datasets.

LTR Retroelements and Bird Adaptation to Arid Environments

TEs are known to be among the main drivers in genome evolution, leading to the generation of evolutionary advantages that favor the success of organisms. The aim of this work was to investigate the TE landscape in bird genomes to look for a possible relationship between the amount of specific TE types and environmental changes that characterized the Oligocene era in Australia. Therefore, the mobilome of 29 bird species, belonging to a total of 11 orders, was analyzed. Our results confirmed that LINE retroelements are not predominant in all species of this evolutionary lineage and highlighted an LTR retroelement dominance in species with an Australian-related evolutionary history. The bird LTR retroelement expansion might have happened in response to the Earth’s dramatic climate changes that occurred about 30 Mya, followed by a progressive aridification across most of Australian landmasses. Therefore, in birds, LTR retroelement burst might have represented an evolutionary advantage in the adaptation to arid/drought environments.

Coloniality and development impact intraclutch consistency of avian eggs: a comparative analysis of the individual repeatability of eggshell size and shape metrics

In oviparous animals, egg morphology is considered an aspect of the extended phenotype of the laying mother and, thus, can be directly assessed for consistency both within and between individual females. Despite a recently renewed interest in the evolution and mechanics of avian eggshell morphology, we still lack a large-scale, comparative understanding of which egg traits are individually plastic and whether individual consistency is shaped by ecological and life history traits at the species level. Here, we aimed to understand whether intraclutch repeatability per se of different eggshell metrics is an evolving trait that responds to selection pressures from socio-ecological contexts across a diverse group of avian species for which clutch-level eggshell morphology data were available to us. Coloniality, ontogeny, and incubation period had significant impacts on the comparative patterns of relative individual repeatability among two egg metrics (i.e., size and shape), whereas other life history traits (including adult size, clutch size, nest type, migration, breeding latitude, host status of brood parasitism) did not have statistical impacts. Our results also demonstrate that individual consistency has a more widespread phylogenetic distribution than expected by evolutionary contingency across avian diversity. Future analyses should also incorporate the effects of intra- and interspecific covariation in other morphological and physiological traits on the evolution of individual consistency, especially those relevant to egg recognition, including eggshell color and maculation.

Quantitative investigation of pengornithid enantiornithine diet reveals macrocarnivorous ecology evolved in birds by Early Cretaceous

The diet of Mesozoic birds is poorly known, limiting evolutionary understanding of birds' roles in modern ecosystems. Pengornithidae is one of the best understood families of Mesozoic birds, hypothesized to eat insects or only small amounts of meat. We investigate these hypotheses with four lines of evidence: estimated body mass, claw traditional morphometrics, jaw mechanical advantage, and jaw finite element analysis. Owing to limited data, the diets of Eopengornis and Chiappeavis remain obscure. Pengornis, Parapengornis, and Yuanchuavis show adaptations for vertebrate carnivory. Pengornis also has talons similar to living raptorial birds like caracaras that capture and kill large prey, which represents the earliest known adaptation for macrocarnivory in a bird. This supports the appearance of this ecology ∼35 million years earlier than previously thought. These findings greatly increase the niche breadth known for Early Cretaceous birds, and shift the prevailing view that Mesozoic birds mainly occupied low trophic levels.

Checklist and distribution of Galliform Birds (Order: Galliformes) in Iraq

A total of four genera and four species belong to one family, Phasianidae, Order Galliformes; about 72 specimens deposited in the bird's collection in the Iraq "Natural History Research Center and Museum INHM" were reviewed. In the current study, morphometrics of four species of taxidermy Galliform birds: Chukor Alectoris graeca (Meisner, 1804), Seesee Ammoperdix griseogularis (Brandt, 1843), Quail Coturnix coturnix (Linnaeus, 1758), and Black Partridge Francolinus francolinus (Linnaeus, 1766) were documented. In addition, the distribution ranges throughout Iraq and the Global Conservation Status of each mentioned species were reviewed and comprehensively discussed. The current study concluded that the collection of four species belongs to the Phasinidae Family of Galliformes Order, which deserved in INHM still abundance in the Iraqi environment; that Chukers Alectoris sp. more abundance in mountains and hills areas west and north of Iraq; While, Black partridge Francolinnus francolinus is more abundance in wetlands and Marshes south of Iraq. Global Conservation status listed them as Least Concern (LC). Keywords: Black partridge, Chukar, Galliform birds, Phasianidae, Quail.

Metabolic rate, sleep duration, and body temperature in evolution of mammals and birds: the influence of geological time of principal groups divergence

This study contains an analysis of basal metabolic rate (BMR) in 1817 endothermic species. The aim was to establish how metabolic scaling varies between the main groups of endotherms during evolution. The data for all the considered groups were combined and the common exponent in the allometric relationship between the BMR and body weight was established as b = 0.7248. Reduced to the common slope, the relative metabolic rate forms the following series: Neognathae – Passeriformes – 1.00, Neognathae – Non-Passeriformes – 0.75, Palaeognathae – 0.53, Eutheria – 0.57, Marsupialia – 0.44, and Monotremata – 0.26. The main finding is that the metabolic rate in the six main groups of mammals and birds consistently increases as the geological time of the group’s divergence approaches the present. In parallel, the average body temperature in the group rises, the duration of sleep decreases and the duration of activity increases. BMR in a taxon correlates with its evolutionary age: the later a clade diverged, the higher is its metabolic rate and the longer is its activity period; group exponents decrease as group divergence nears present times while with increase metabolic rate during activity, they not only do not decrease but can increase. Sleep duration in mammals was on average 40% longer than in birds while BMR, in contrast, was 40% higher in birds. The evolution of metabolic scaling, body temperature, sleep duration, and activity during the development of endothermic life forms is demonstrated, allowing for a better understanding of the underlying principles of endothermy formation.

A chromosome-level reference genome and pangenome for barn swallow population genomics

Insights into the evolution of non-model organisms are limited by the lack of reference genomes of high accuracy, completeness, and contiguity. Here, we present a chromosome-level, karyotype-validated reference genome and pangenome for the barn swallow (Hirundo rustica). We complement these resources with a reference-free multialignment of the reference genome with other bird genomes and with the most comprehensive catalog of genetic markers for the barn swallow. We identify potentially conserved and accelerated genes using the multialignment and estimate genome-wide linkage disequilibrium using the catalog. We use the pangenome to infer core and accessory genes and to detect variants using it as a reference. Overall, these resources will foster population genomics studies in the barn swallow, enable detection of candidate genes in comparative genomics studies, and help reduce bias toward a single reference genome.

Exceptional preservation and foot structure reveal ecological transitions and lifestyles of early theropod flyers

Morphology of keratinised toe pads and foot scales, hinging of foot joints and claw shape and size all inform the grasping ability, cursoriality and feeding mode of living birds. Presented here is morphological evidence from the fossil feet of early theropod flyers. Foot soft tissues and joint articulations are qualitatively assessed using laser-stimulated fluorescence. Pedal claw shape and size are quantitatively analysed using traditional morphometrics. We interpret these foot data among existing evidence to better understand the evolutionary ecology of early theropod flyers. Jurassic flyers like Anchiornis and Archaeopteryx show adaptations suggestive of relatively ground-dwelling lifestyles. Early Cretaceous flyers then diversify into more aerial lifestyles, including generalists like Confuciusornis and specialists like the climbing Fortunguavis. Some early birds, like the Late Jurassic Berlin Archaeopteryx and Early Cretaceous Sapeornis, show complex ecologies seemingly unique among sampled modern birds. As a non-bird flyer, finding affinities of Microraptor to a more specialised raptorial lifestyle is unexpected. Its hawk-like characteristics are rare among known theropod flyers of the time suggesting that some non-bird flyers perform specialised roles filled by birds today. We demonstrate diverse ecological profiles among early theropod flyers, changing as flight developed, and some non-bird flyers have more complex ecological roles.

The endocast of the insular and extinct Sylviornis neocaledoniae (Aves, Galliformes), reveals insights into its sensory specializations and its twilight ecology

Sylviornis neocaledoniae (Galliformes, Sylviornithidae), a recently extinct bird of New-Caledonia (Galliformes, Sylviornithidae) is the largest galliform that ever lived and one of the most enigmatic birds in the world. Herein, for the first time, we analyze its neuroanatomy that sheds light on its lifestyle, its brain shape and patterns being correlated to neurological functions. Using morphometric methods, we quantified the endocranial morphology of S. neocaledoniae and compared it with extinct and extant birds in order to obtain ecological and behavioral information about fossil birds. Sylviornis neocaledoniae exhibited reduced optic lobes, a condition also observed in nocturnal taxa endemic to predator-depauperate islands, such as Elephant birds. Functional interpretations suggest that S. neocaledoniae possessed a well-developed somatosensorial system and a good sense of smell in addition to its specialized visual ability for low light conditions, presumably for locating its food. We interpret these results as evidence for a crepuscular lifestyle in S. neocaledoniae.

Epistatic Effects Between Amino Acid Insertions and Substitutions Mediate Toxin resistance of Vertebrate Na+,K+-ATPases

The recurrent evolution of resistance to cardiotonic steroids (CTS) across diverse animals most frequently involves convergent amino acid substitutions in the H1-H2 extracellular loop of Na+,K+-ATPase (NKA). Previous work revealed that hystricognath rodents (e.g., chinchilla) and pterocliform birds (sandgrouse) have convergently evolved amino acid insertions in the H1-H2 loop, but their functional significance was not known. Using protein engineering, we show that these insertions have distinct effects on CTS resistance in homologs of each of the two species that strongly depend on intramolecular interactions with other residues. Removing the insertion in the chinchilla NKA unexpectedly increases CTS resistance and decreases NKA activity. In the sandgrouse NKA, the amino acid insertion and substitution Q111R both contribute to an augmented CTS resistance without compromising ATPase activity levels. Molecular docking simulations provide additional insight into the biophysical mechanisms responsible for the context-specific mutational effects on CTS insensitivity of the enzyme. Our results highlight the diversity of genetic substrates that underlie CTS insensitivity in vertebrate NKA and reveal how amino acid insertions can alter the phenotypic effects of point mutations at key sites in the same protein domain.

Ancient proteins resolve controversy over the identity of Genyornis eggshell

The realization that ancient biomolecules are preserved in "fossil" samples has revolutionized archaeological science. Protein sequences survive longer than DNA, but their phylogenetic resolution is inferior; therefore, careful assessment of the research questions is required. Here, we show the potential of ancient proteins preserved in Pleistocene eggshell in addressing a longstanding controversy in human and animal evolution: the identity of the extinct bird that laid large eggs which were exploited by Australia's indigenous people. The eggs had been originally attributed to the iconic extinct flightless bird Genyornis newtoni (†Dromornithidae, Galloanseres) and were subsequently dated to before 50 ± 5 ka by Miller et al. [Nat. Commun. 7, 10496 (2016)]. This was taken to represent the likely extinction date for this endemic megafaunal species and thus implied a role of humans in its demise. A contrasting hypothesis, according to which the eggs were laid by a large mound-builder megapode (Megapodiidae, Galliformes), would therefore acquit humans of their responsibility in the extinction of Genyornis. Ancient protein sequences were reconstructed and used to assess the evolutionary proximity of the undetermined eggshell to extant birds, rejecting the megapode hypothesis. Authentic ancient DNA could not be confirmed from these highly degraded samples, but morphometric data also support the attribution of the eggshell to Genyornis. When used in triangulation to address well-defined hypotheses, paleoproteomics is a powerful tool for reconstructing the evolutionary history in ancient samples. In addition to the clarification of phylogenetic placement, these data provide a more nuanced understanding of the modes of interactions between humans and their environment.

Keys to the avian Haemoproteus parasites (Haemosporida, Haemoproteidae)

BACKGROUND

Haemoproteus is a sister genus to malaria parasites (Plasmodium), which both belong to the order Haemosporida (Apicomplexa). Parasites of both genera are flourishing in birds, however, Haemoproteus species are noticeably less investigated. This is unfortunate because knowledge about close relatives of malaria pathogens is important for better understanding the evolutionary origin and basic biological features of the entire group of haemosporidian infections. Moreover, recent findings show that Haemoproteus species can cause severe damage of various bird organs due to megalomeronts and other exo-erythrocytic stages. These haemosporidians are remarkably diverse, but remain neglected partly due to difficulties in species identification. Hundreds of Haemoproteus genetic lineages have been reported in birds, and numerous new lineages are found each year, but most remain unidentified to the species level. Numerous new Haemoproteus pathogens were described during the past 20 years. However, keys for their identification are absent. Identification of Haemoproteus species remains a difficult task and is an obstacle for better understanding of the distribution and epidemiology of these parasites. This study aimed to develop comprehensive keys for the identification of described avian Haemoproteus species using morphological features of their blood stages (gametocytes).

METHODS

Type and voucher preparations of avian Haemoproteus species were accessed in museums in Europe, Australia and the USA. Gametocytes of most described species were examined, and these data formed a background for this study. The data also were considered from published articles containing parasite species descriptions. The method of dichotomous keys was applied. The most difficult steps in the keys were accompanied with references to the corresponding parasite pictures.

RESULTS

In all, 201 published articles were included in this review. Morphological diagnostic features of gametocytes of all described Haemoproteus species were analysed and compared. Illustrated keys for identification of these parasite species were developed. Available information about the molecular characterization of Haemoproteus parasites was provided.

CONCLUSION

This review shows that 177 described species of avian Haemoproteus can be distinguished and identified in blood films using morphological characters of their gametocytes and host cells. These species were incorporated in the keys. Information about possible morphologically cryptic parasites was provided. Molecular markers are available for only 42% of the described Haemoproteus parasites, calling for researchers to fill this gap.

Comprehensive taxon sampling and vetted fossils help clarify the time tree of shorebirds (Aves, Charadriiformes)

Shorebirds (Charadriiformes) are a globally distributed clade of modern birds and, due to their ecological and morphological disparity, a frequent subject of comparative studies. While molecular phylogenies have been key to establishing the suprafamilial backbone of the charadriiform tree, a number of relationships at both deep and shallow taxonomic levels remain poorly resolved. The timescale of shorebird evolution also remains uncertain as a result of extensive disagreements among the published divergence dating studies, stemming largely from different choices of fossil calibrations. Here, we present the most comprehensive non-supertree phylogeny of shorebirds to date, based on a total-evidence dataset comprising 353 ingroup taxa (90% of all extant or recently extinct species), 27 loci (15 mitochondrial and 12 nuclear), and 69 morphological characters. We further clarify the timeline of charadriiform evolution by time-scaling this phylogeny using a set of 14 up-to-date and thoroughly vetted fossil calibrations. In addition, we assemble a taxonomically restricted 100-locus dataset specifically designed to resolve outstanding problems in higher-level charadriiform phylogeny. In terms of tree topology, our results are largely congruent with previous studies but indicate that some of the conflicts among earlier analyses reflect a genuine signal of pervasive gene tree discordance. Monophyly of the plovers (Charadriidae), the position of the ibisbill (Ibidorhyncha), and the relationships among the five subfamilies of the gulls (Laridae) could not be resolved even with greatly increased locus and taxon sampling. Moreover, several localized regions of uncertainty persist in shallower parts of the tree, including the interrelationships of the true auks (Alcinae) and anarhynchine plovers. Our node-dating and macroevolutionary rate analyses find support for a Paleocene origin of crown-group shorebirds, as well as exceptionally rapid recent radiations of Old World oystercatchers (Haematopodidae) and select genera of gulls. Our study underscores the challenges involved in estimating a comprehensively sampled and carefully calibrated time tree for a diverse avian clade, and highlights areas in need of further research.

Hard ticks (Acari: Ixodidae) associated with birds in Europe: Review of literature data

Hard ticks (Acari: Ixodidae) are considered the most important transmitters of pathogens in the temperate zone that covers most of Europe. In the era of climate change tick-borne diseases are predicted to undergo geographical range expansion toward the north through regions that are connected to southern areas of the continent by bird migration. This alone would justify the importance of synthesized knowledge on the association of tick species with avian hosts, yet birds also represent the most taxonomically and ecologically diverse part of urban vertebrate fauna. Birds frequently occur in gardens and near animal keeping facilities, thus playing a significant role in the dispersal of ticks and tick-borne pathogens in synanthropic environments. The primary aim of this review is to provide a comprehensive reference source (baseline data) for future studies, particularly in the context of discovering new tick-host associations after comparison with already published data. The records on the ixodid tick infestations of birds were assessed from nearly 200 papers published since 1952. In this period, 37 hard tick species were reported from 16 orders of avian hosts in Europe. Here we compile a list of these tick species, followed by the English and Latin name of all reported infested bird species, as well as the tick developmental stage and country of origin whenever this information was available. These data allowed a first-hand analysis of general trends regarding how and at which developmental stage of ticks tend to infest avian hosts. Five tick species that were frequently reported from birds and show a broad geographical distribution in the Western Palearctic (Ixodes arboricola, I. frontalis, I. ricinus, Haemaphysalis concinna and Hyalomma marginatum) were also selected for statistical comparisons. Differences were demonstrated between these tick species regarding their association with bird species that typically feed from the ground and those that rarely occur at the soil level. The ecology of these five bird-infesting tick species is also illustrated here according to avian orders, taking into account the ecology (habitat type) and activity (circadian rhythm and feeding level) of most bird species that represent a certain order.

A 14,000-year-old genome sheds light on the evolution and extinction of a Pleistocene vulture

The New World Vulture [Coragyps] occidentalis (L. Miller, 1909) is one of many species that were extinct by the end of the Pleistocene. To understand its evolutionary history we sequenced the genome of a 14,000 year old [Coragyps] occidentalis found associated with megaherbivores in the Peruvian Andes. occidentalis has been viewed as the ancestor, or possibly sister, to the extant Black Vulture Coragyps atratus, but genomic data shows occidentalis to be deeply nested within the South American clade of atratus. Coragyps atratus inhabits lowlands, but the fossil record indicates that occidentalis mostly occupied high elevations. Our results suggest that occidentalis evolved from a population of atratus in southwestern South America that colonized the High Andes 300 to 400 kya. The morphological and morphometric differences between occidentalis and atratus may thus be explained by ecological diversification following from the natural selection imposed by this new and extreme, high elevation environment. The sudden evolution of a population with significantly larger body size and different anatomical proportions than atratus thus constitutes an example of punctuated evolution.

14,000 year old DNA reveals the evolutionary dynamics and adaptations of South American vultures.