Avian coronavirus in wild aquatic birds

We detected a high prevalence (12.5%) of novel avian coronaviruses in aquatic wild birds. Phylogenetic analyses of these coronaviruses suggest that there is a diversity of gammacoronaviruses and deltacoronaviruses circulating in birds. Gammacoronaviruses were found predominantly in Anseriformes birds, whereas deltacoronaviruses could be detected in Ciconiiformes, Pelecaniformes, and Anseriformes birds in this study. We observed that there are frequent interspecies transmissions of gammacoronaviruses between duck species. In contrast, deltacoronaviruses may have more stringent host specificities. Our analysis of these avian viral and host mitochondrial DNA sequences also suggests that some, but not all, coronaviruses may have coevolved with birds from the same order.     

Comparison of fatty acid compositions in birds feeding in aquatic and terrestrial ecosystems

Fatty acid (FA) contents and compositions in the pectoral muscles of 18 bird species from Novosibirsk, Volgograd, and Yaroslavl oblasts were studied. Three groups of birds that had significantly different FA compositions were distinguished based on a multivariate statistical analysis: Passeriformes, Columbiformes, and a group of waterfowl and waterbird species (Charadriiformes, Anseriformes, Podicipediformes, and Ciconiiformes). The highest content of physiologically important docosahexaenoic acid (22:6n-3, DHA), which is considered a marker of aquatic food, was surprisingly found in the biomass of Passeriformes, which are terrestrial feeders, rather than in the biomass of waterfowls and waterbirds. It was suggested that Passeriformes species had the ability to synthesize large quantities of DHA from short-chain omega-3 FAs, which is rare among animals.     

Evolution of preproinsulin gene in birds

The coding region of the preproinsulin gene has been cloned and partly sequenced in a variety of marine and terrestrial birds (28 species). All genes showed the "ancestral" structure with a large intron-2. The size of intron-2 changed considerably during the evolution of birds (2.4-4.2kb). The hydrophobicity of signal peptides was conserved. Bird C-peptides were predicted to be 28 amino acids long, but circulating C-peptides would be only 26 amino acids long, with Passer as a possible exception. Bird C-peptides were found to lack the sequences identified in mammals as responsible for peptide bioactivity and the structure of the central part. In contrast, predicted insulin sequences were highly conserved. Only two types of analog were identified: the hypoactive form (GluA8), present only in Anseriformes and the hyperactive form (His A8), present in all other species. Based on 3'-nucleotide sequence analysis (extending into intron-2), birds appeared to be monophyletic. Five groups were clearly identified: Paleognathae, Galliformes, Anseriformes, Passeriformes, and Charadriiformes. Paleognathae were suggested as the basal group, supporting the traditional view of avian evolution. Subsequent branching identified a gallo-anserae group and a group containing all other Neognathae. Surprisingly, Columba livia (Columbiforme order) clustered with Galliformes. With represented species, Procellariiformes and possibly Ciconiiformes, and Pelicaniformes were suggested as paraphyletic, in agreement with conclusions from some studies based on mitochondrial DNA sequences.     

Size and structure of the bird genome--I. DNA content of 48 species of Neognathae

The nuclear DNA content was evaluated in 48 species of Neognathae birds belonging to 13 orders, namely Anseriformes, Charadriiformes, Columbiformes, Ciconiiformes, Falconiformes, Galliformes, Gruiformes, Passeriformes, Pelicaniformes, Phoenicopteriformes, Piciformes, Psittaciformes and Strigiformes. The DNA content, expressed in pg/nucleus, ranges from 2.81 to 4.97. The genome size variability within and among families is discussed on the basis of the Hinegardner's (1976) model of genome evolution.     

A phylogenetic analysis of basal Anseriformes, the fossil Presbyornis, and the interordinal relationships of waterfowl

A phylogenetic analysis of 123 morphological characters of basal waterfowl (Aves: Anseriformes) and other selected avian orders confirmed that the screamers (Anhimae: Anhitn-idae) are the sister-group of other waterfowl (Anseres), and that the magpie goose (Anseranatidae: Anseranas semipalmata) is the sister group of other modern waterfowl exclusive of screamers (Anatidae sensu stricto). The analysis also supports the traditional hypothesis of the gallinaceous birds (Galliformes) as the sister group of the Anseriformes. Presbyornis, a fossil from the early Eocene of Wyoming and averred by Olson & Feduccia as showing that the Anseriformes were derived from shorebirds (Charadriiformes), was found to represent the sister group of the Anatidae. Associated hypotheses by Olson & Feduccia concerning the implications of Presbyornis for the phylogenetic relationships of flamingos (Phoenicopteriformes), the position of the Anhimidae within the waterfowl, relationships among modern Anatidae, and a plausible evolutionary scenario for waterfowl also are rejected. Analyses revealed that cranial characters were critical to the establishment of the Galliformes as the sister group of the Anseriformes; exclusion of the Anhimidae, especially in combination with Anseranas, also undermined the support for this inference. Placement of Presbyornis as the sister group of the Anatidae casts doubt on the role suggested by Feduccia of ‘transitional shorebirds' in the origin of modern avian orders, and calls into question the concept of ‘fossil mosaics’. The phylogenetic hypothesis is used to reconstruct an evolutionary scenario for selected ecomorphological characters in the galliform-anseriform transition, to predict the most parsimonious states of these characters for Presbyornis, and to propose a phylogenetic classification of the higher-order taxa of waterfowl. This re-examination of Presbyornis also is used to exemplify the fundamental methodological shortcomings of the intuitive approach to the reconstruction of phylogenetic relationships.     

An updated list and some comments on the occurrence of intraspecific nest parasitism in birds

This paper presents a list, compiled from the literature, of bird species in which intraspecific nest parasitism (INP) occurs. INP was reported in 234 species: one Struthioniformes, two Tinamiformes, two Procellariiformes, six Podicipediiformes, five Ciconiiformes, one Phoenicopteriformes, 74 Anseriformes, one Falconiformes, 32 Galliformes, eight Gruiformes, 19 Charadriiformes, nine Columbiformes, five Cuculiformes, two Apodiformes, one Coraciiformes and 66 Passeriformes. Hence, INP is very common among precocial species, and less so among altricials. Irrespective of this, most INP birds are colonial.     

Relationship between osteology and aquatic locomotion in birds: determining modes of locomotion in extinct Ornithurae

The evolutionary history of aquatic invasion in birds would be incomplete without incorporation of extinct species. We show that aquatic affinities in fossil birds can be inferred by multivariate analysis of skeletal features and locomotion of 245 species of extant birds. Regularized discriminant analyses revealed that measurements of appendicular skeletons successfully separated diving birds from surface swimmers and flyers, while also discriminating among different underwater modes of swimming. The high accuracy of this method allows detection of skeletal characteristics that are indicative of aquatic locomotion and inference of such locomotion in bird species with insufficient behavioural information. Statistical predictions based on the analyses confirm qualitative assessments for both foot‐propelled (Hesperornithiformes) and wing‐propelled (Copepteryx) underwater locomotion in fossil birds. This is the first quantitative inference of underwater modes of swimming in fossil birds, enabling future studies of locomotion in extinct birds and evolutionary transitions among locomotor modes in avian lineage.     

A phylogenetic study of bird karyotypes

Karyotypes were compared in 48 species, including 6 subspecies, of birds from 12 orders: Casuariiformes, Rheiformes, Sphenisciformes, Pelecaniformes, Ciconiiformes, Anseriformes, Phoenicopteriformes, Gruiformes, Galliformes, Columbiformes, Falconiformes and Strigiformes. — With the exception of the family Accipitridae, all the species studied are characterized by typical bird karyotypes with several pairs of macrochromosomes and a number of microchromosomes, though the boundary between the two is not necessarily sharp. The comparative study of complements revealed that a karyotype with 3 morphologically distinct pairs of chromosomes is frequently encountered in all orders except the Strigiformes. Those 3 pairs, submetacentric nos. 1 and 2, and a subtelocentric or telocentric no. 3, are not only morphologically alike but also have conspicuous homology revealed by the G-banding patterns. Furthermore, G-banding analysis provided evidence for the derivation of the owl karyotype from a typical bird karyotype.—The above cytogenetic features led to the assumption that the 3 pairs of marker chromosomes had been incorporated into an ancestral bird karyotype. It seems probable that those chromosomes have been transmitted without much structural changes from a common ancestor of birds and turtles, since the presence of the same marker chromosomes in the fresh water turtle Geoclemys reevesii is ascertained by G-banding patterns. — A profile of a primitive bird karyotype emerged through the present findings. Hence, it has become possible to elucidate mechanisms involved in certain structural changes of macrochromosomes observed in birds. It was concluded that a major role had been played by centric fission as well as fusion, translocation, and pericentric inversion.     

Insight into glycan diversity and evolutionary lineage based on comparative Avio-N-glycomics and sialic acid analysis of 88 egg whites of Galloanserae

A large set of glycome information was obtained from egg white proteins of 88 samples from Galloanserae (63 Anseriformes and 25 Galliformes). The data were obtained on whole N-glycan structures and types of sialic acids of these egg whites by glycoblotting-based high-throughput and quantitative glycomics. The results revealed clear trends and complexity patterns as well as diversity among taxonomic groups. It is well-known that chicken, a representative domesticated poultry involved in Galliformes, can become an influenza host. However, our data demonstrate that duck, wild goose, and swan of Anseriformes are representative migratory birds that are known as natural hosts of the influenza virus. Hierarchical clustering analysis of the expression pattern of N-glycome (total of 61 N-glycan peaks) revealed that the members of Galloanserae can be classified into two major groups and five submajor clusters (clusters 1-5) on the basis of simple m/z values obtained by MALDI-TOF MS. It is clear that expression patterns of N-glycomes in the five clusters are influenced significantly by the features such as the body size of the birds, rather than by the difference of the family. On the other hand, quantitative analysis showed that the total amounts of sialic acids in egg whites of Galliformes were distinctly larger than those of Anseriformes. However, it was also revealed in Anseriformes that Neu5Gc and KDN, in addition to common Neu5Ac, were expressed significantly in both N- and O-glycans of glycoproteins and glycosphingolipids, suggesting the influence of their lifestyles and diet. This is the first report that KDN exists in egg white. These results and the environmental factors are discussed preliminarily with respect to their evolutionary lineage.     

Interim Response of Wading Birds (Pelecaniformes and Ciconiiformes) and Waterfowl (Anseriformes) to the Kissimmee River Restoration Project,Florida, U.S.A

Success of the Kissimmee River Restoration Project will be evaluated in part by monitoring populations of wading birds (Pelecaniformes and Ciconiiformes) and waterfowl (Anseriformes). These two waterbird guilds were integral components of the pre‐channelization river–floodplain ecosystem, and both declined substantially following channelization. Restoration is expected to attract wading birds and waterfowl by reintroducing naturally fluctuating water levels, seasonal hydroperiods, and historic vegetation communities. Post‐construction aerial surveys (November 2001 to May 2008) within the Phase I restoration area indicate that the abundance and species richness of both wading birds and waterfowl have shown a positive restoration response thus far. Dry season abundance of aquatic wading birds and waterfowl has exceeded restoration expectations (≥30.6 birds/km² and ≥3.9 birds/km², respectively) each year since the completion of restoration Phase I in 2001. While there has been a significant positive restoration effect on waterfowl abundance, waterfowl species richness (n = 6) has not yet reached the restoration expectation of ≥13 species. Abundance of the terrestrial cattle egret (Bubulcus ibis), which increased dramatically after the majority of floodplain wetlands were converted to cattle pastures in the channelized system, has shown a significant negative response to restoration. It is anticipated that completion of the remaining phases of restoration (II/III), and implementation of the Kissimmee River Headwaters Revitalization water regulation schedule by 2019, will further increase and improve habitat for wading birds and waterfowl by reestablishing floodplain hydrology that more closely mimics historical conditions.     

Multiple and independent cessation of recombination between avian sex chromosomes

Birds are characterized by female heterogamety; females carry the Z and W sex chromosomes, while males have two copies of the Z chromosome. We suggest here that full differentiation of the Z and W sex chromosomes of birds did not take place until after the split of major contemporary lineages, in the late Cretaceous. The ATP synthase alpha-subunit gene is now present in one copy each on the nonrecombining part of the W chromosome (ATP5A1W) and on the Z chromosome (ATP5A1Z). This gene seems to have evolved on several independent occasions, in different lineages, from a state of free recombination into two sex-specific and nonrecombining variants. ATP5A1W and ATP5A1Z are thus more similar within orders, relative to what W (or Z) are between orders. Moreover, this cessation of recombination apparently took place at different times in different lineages (estimated at 13, 40, and 65 million years ago in Ciconiiformes, Galliformes, and Anseriformes, respectively). We argue that these observations are the result of recent and traceable steps in the process where sex chromosomes gradually cease to recombine and become differentiated. Our data demonstrate that this process, once initiated, may occur independently in parallel in sister lineages.     

Melanin Concentration Gradients in Modern and Fossil Feathers

In birds and feathered non-avian dinosaurs, within-feather pigmentation patterns range from discrete spots and stripes to more subtle patterns, but the latter remain largely unstudied. A ∼55 million year old fossil contour feather with a dark distal tip grading into a lighter base was recovered from the Fur Formation in Denmark. SEM and synchrotron-based trace metal mapping confirmed that this gradient was caused by differential concentration of melanin. To assess the potential ecological and phylogenetic prevalence of this pattern, we evaluated 321 modern samples from 18 orders within Aves. We observed that the pattern was found most frequently in distantly related groups that share aquatic ecologies (e.g. waterfowl Anseriformes, penguins Sphenisciformes), suggesting a potential adaptive function with ancient origins.     

鸟类迁徙与滨海旅游项目关系——以碧海银沙为例

2018年7月-2019年5月,采用样线法和样点法对启东长江口(北支)自然保护区恒大海上威尼斯碧海银沙海水浴场内鸟类多样性进行了调查,共记录到鸟类9目23科51种,其中鸻形目、雁形目、鹳形目、鸊鷉目等水鸟为鸟类群落的构成主体。不同季节鸟类多样性指数(H)依次为秋季迁徙期>春季迁徙期>夏季繁殖期>越冬期,鸟种由多至少依次为越冬期>秋季迁徙期>春季迁徙期>夏季繁殖期,鸟类数量由多至少依次为越冬期>春季迁徙期>秋季迁徙期>夏季繁殖期。从客流季节集中指数R值来看,碧海银沙旅游区客流量受季节影响变动明显,春、秋、冬三季客流量占比过低。对客流量与鸟类多样性相关指标进行相关性分析,发现二者整体呈负相关,月客流量与鸟类种数相关性较高。本研究探讨了滨海旅游与鸟类迁徙之间的关系,为滨海旅游景区在协调旅游与鸟类迁徙的时空错峰管理提供决策依据。     

Calibration of avian molecular clocks

Molecular clocks can be calibrated using fossils within the group under study (internal calibration) or outside of the group (external calibration). Both types of calibration have their advantages and disadvantages. An internal calibration may reduce extrapolation error but may not be from the best fossil record, raising the issue of nonindependence. An external calibration may be more independent but also may have a greater extrapolation error. Here, we used the advantages of both methods by applying a sequential calibration to avian molecular clocks. We estimated a basal divergence within birds, the split between fowl (Galliformes) and ducks (Anseriformes), to be 89.8 +/- 6.97 MYA using an external calibration and 12 rate-constant nuclear genes. In turn, this time estimate was used as an internal calibration for three species-rich avian molecular data sets: mtDNA, DNA-DNA hybridization, and transferrin immunological distances. The resulting time estimates indicate that many major clades of modern birds had their origins within the Cretaceous. This supports earlier studies that identified large gaps in the avian fossil record and suggests that modern birds may have coexisted with other avian lineages for an extended period during the Cretaceous. The new time estimates are concordant with a continental breakup model for the origin of ratites.     

Indices of Anseriform body shape based on the relative size of major skeletal elements and their relationship to reproductive effort

To assess whether relative clutch mass (RCM) in Anseriformes (wildfowl or waterfowl) is constrained by body shape, principal components (PCs) of size‐adjusted measurements of five major skeletal elements of adult males and females of 60 species of Anseriformes provided indices of body shape. PC1 accounted for 69.8% of the variance and contrasted anterior elements (cranium and sternum) to posterior elements (synsacrum, femur and tibiotarsus). PC1 scores were high in species with a ‘duck‐like’ body shape and low in those with a ‘goose‐like’ body shape. Over the phylogeny of Anseriformes, decreased PC1 scores were associated with feeding on land. PC2 accounted for 18.6% of the variance and contrasted core elements (sternum and synsacrum) with peripheral elements (cranium, femur and tibiotarsus). High PC2 scores were associated with dependence on animal food, particularly in diving species. PC3 accounted for 7.7% of the variance and reflected mainly the relative size of the femur, which was low in diving species. Controlling statistically for phylogenetically independent contrasts in female body shape, there was a significant positive partial correlation between RCM and PC1, suggesting that independent of body size, body shape imposes constraints on reproductive effort in Anseriformes. The results suggest that models of the evolution of reproductive effort in this order, and perhaps in other orders, of birds should control for the effects of body shape.     

An explanation of the relationships between mass, metabolic rate and characteristic skeletal length for birds and mammals

A theory explaining the relationships between metabolic rate and body mass for birds and mammals is developed in terms of the mitochondrion theory of aerobic metabolism, the sliding filament theory of muscle contraction, simple models of vertebrate anatomy and activity, and other propositions. Both body mass and metabolic rates are shown to result from a homogeneous vertebrate design quantitatively expressed in terms of a set of nearly invariant parameters with five degrees of freedom: propulsion technique, mitochondrion capability, non-skeletal muscle mass exponent, characteristic skeletal length, and sturdiness factor. The first three of the degrees of freedom are phylogenetic group specific. The last two vary considerably even within a single species. The theory is shown to agree satisfactorily with placental mammal, marsupial mammal, passerine bird and nonpasserine bird data. Algorithms for determining metabolic rates and body mass as functions of skeletal characteristic length are developed and quantitative estimates of the constants occurring in the algorithms are given.     

Skeletal Correlates for Body Mass Estimation in Modern and Fossil Flying Birds

Scaling relationships between skeletal dimensions and body mass in extant birds are often used to estimate body mass in fossil crown-group birds, as well as in stem-group avialans. However, useful statistical measurements for constraining the precision and accuracy of fossil mass estimates are rarely provided, which prevents the quantification of robust upper and lower bound body mass estimates for fossils. Here, we generate thirteen body mass correlations and associated measures of statistical robustness using a sample of 863 extant flying birds. By providing robust body mass regressions with upper- and lower-bound prediction intervals for individual skeletal elements, we address the longstanding problem of body mass estimation for highly fragmentary fossil birds. We demonstrate that the most precise proxy for estimating body mass in the overall dataset, measured both as coefficient determination of ordinary least squares regression and percent prediction error, is the maximum diameter of the coracoid’s humeral articulation facet (the glenoid). We further demonstrate that this result is consistent among the majority of investigated avian orders (10 out of 18). As a result, we suggest that, in the majority of cases, this proxy may provide the most accurate estimates of body mass for volant fossil birds. Additionally, by presenting statistical measurements of body mass prediction error for thirteen different body mass regressions, this study provides a much-needed quantitative framework for the accurate estimation of body mass and associated ecological correlates in fossil birds. The application of these regressions will enhance the precision and robustness of many mass-based inferences in future paleornithological studies.     

Parallel radiations in the primary clades of birds

Knowledge of avian phylogeny is prerequisite to understanding the circumstances and timing of the diversification of birds and the evolution of morphological, behavioral, and life-history traits. Recent molecular datasets have helped to elucidate the three most basal clades in the tree of living birds, but relationships among neoavian orders (the vast majority of birds) remain frustratingly vexing. Here, we examine intron 7 of the beta-fibrinogen gene in the most taxonomically inclusive survey of DNA sequences of nonpasserine bird families and orders to date. These data suggest that Neoaves consist of two sister clades with ecological parallelisms comparable to those found between marsupial and placental mammals. Some members of the putative respective clades have long been recognized as examples of convergent evolution, but it was not appreciated that they might be parts of diverse parallel radiations. In contrast, some traditional orders of birds are suggested by these data to be polyphyletic, with representative families in both radiations.     

The middle ear of the skull of birds: the Pelecaniformes and Ciconiiformes

The anatomy of the middle ear region of the skull is described for the families of the Avian orders Pelecaniformes and Ciconiiformes. Emphasis is placed on the foramina and paths of the nerves and blood vessels. The morphology of the basicranium and quadrate is also discussed. Comparative analyses of the characters are used to assess taxonomic conclusions.
Extant Pelecaniformes consist of six families, four of which are monogenic: Phaethontidae, Pelecanidae, Anhingidae and Fregatidae; one is composed of two genera: Sulidae; and the last has three genera: Phalacrocoracidae. Several years ago a relationship was suggested which would ally the Phaethontidae and the Fregatidae. While these families share several non middle ear characters the anatomy of the middle ear is not compatible with any particular relationship. Indeed, several obvious differences are described. The data presented here are consistent with the idea that the Phaethontidae and the Fregatidae each form a separate group of Pelecaniform birds, with the rest of the families forming a third group. Several differences in the middle ear region of the species of Anhingidae suggest that the family may be composed of two genera.
While sharing many Ciconiiform characters the Ciconiidae have been shown not to be as closely related to the Ardeidae as they are to other families of Ciconiiformes. In addition, evidence is presented to support the recent idea that the three species of ibis (I. ibis, I. cinereus and I. leucocephalus ) be united within the genus Mycteria. Also supported is the notion that Balaeniceps is Pelecaniform in character, and not Ciconiiform.     

TWO NEW PARROTS (PSITTACIFORMES) FROM THE LOWER EOCENE FUR FORMATION OF DENMARK

Abstract:  Two new fossil psittaciform birds from the Lower Eocene 'Mo Clay' (Fur Formation) of Denmark ( c . 54 Ma) are described. An unnamed specimen is assigned to the extinct avian family of stem-group parrots, Pseudasturidae (genus and species incertae sedis ), while a second ( Mopsitta tanta gen. et sp. nov.) is the largest fossil parrot yet known. Both specimens are the first fossil records of these birds from Denmark. Although the phylogenetic position of Mopsitta is unclear (it is classified as family incertae sedis ), this form is phylogenetically closer to Recent Pstittacidae than to other known Palaeogene psittaciforms and may, therefore, represent the oldest known crown-group parrot.