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Assessing the Cretaceous superordinal divergence times within birds and placental mammals by using whole mitochondrial protein sequences and an extended statistical framework.

Using the set of all vertebrate mtDNA protein sequences published as of May 1998, plus unpublished examples for elephant and birds, we examined divergence times in Placentalia and Aves. Using a parsimony-based test, we identified a subset of slower evolutionary rate placental sequences that do not appear to violate the clock assumption. Analyzing just these sequences decreases support for Marsupionta and the carnivore + perissodactyl group but increases support for armadillo diverging earlier than rabbit (which may represent the whole Glires group). A major theme of the paper is to use more comprehensive estimates of divergence time standard error (SE). From the well-studied horse/rhino split, estimated to be 55 million years before present (mybp), the splitting time within carnivores is confidently shown to be older than 50 million years. Some of our estimates of divergence times within placentals are relatively old, at up to 169 million years, but are within 2 SE of other published estimates. The whale/cow split at 65 mybp may be older than commonly assumed. All the sampled splits between the main groups of fereuungulates (the clade of carnivores, cetartiodactyls, perissodactyls, and pholidotes) seem to be distinctly before the Cretaceous/Tertiary boundary. Analyses suggest a close relationship between elephants (representing Afrotheria) and armadillos (Xenarthra), and our timing of this splitting is coincident with the opening of the South Atlantic, a major vicariant event. Recalibrating with this event (at 100 mybp), we obtain younger estimates for the earliest splits among placentals. Divergence times within birds are also assessed by using previously unpublished sequences. We fail to reject a clock for all bird taxa available. Unfortunately, available deep calibration points for birds are questionable, so a new calibration based on the age of the Anseriform stem lineage is estimated. The divergence time of rhea and ostrich may be much more recent than commonly assumed, while that of passerines may be older. Our major concern is the rooting point of the bird subtree, as the nearest outgroup (alligator) is very distant.

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Interordinal relationships of birds and other reptiles based on whole mitochondrial genomes.

Several different groups of birds have been proposed as being the oldest or earliest diverging extant lineage within the avian phylogenetic tree, particularly ratites (Struthioniformes), waterfowl (Anseriformes), and shorebirds (Charadriiformes). Difficulty in resolving this issue stems from several factors, including the relatively rapid radiation of primary (ordinal) bird lineages and the lack of characters from an extant outgroup for birds that is closely related to them by measure of time. To help resolve this question, we have sequenced entire mitochondrial genomes for five birds (a rhea, a duck, a falcon, and two perching birds), one crocodilian, and one turtle. Maximum parsimony and maximum likelihood analyses of these new sequences together with published sequences (18 taxa total) yield the same optimal tree topology, in which a perching bird (Passeriformes) is sister to all the other bird taxa. A basal position for waterfowl among the bird study taxa is rejected by maximum likelihood analyses. However, neither the conventional view, in which ratites (including rhea) are basal to other birds, nor tree topologies with falcon or chicken basal among birds could be rejected in the same manner. In likelihood analyses of a subset of seven birds, alligator, and turtle (9 taxa total), we find that increasing the number of parameters in the model shifts the optimal topology from one with a perching bird basal among birds to the conventional view with ratites diverging basally; moreover, likelihood scores for the two trees are not significantly different. Thus, although our largest set of taxa and characters supports a tree with perching birds diverging basally among birds, the position of this earliest divergence among birds appears unstable. Our analyses indicate a sister relationship between a waterfowl/chicken clade and ratites, relative to perching birds and falcon. We find support for a sister relationship between turtles and a bird/crocodilian clade, and for rejecting both the Haemothermia hypothesis (birds and mammals as sister taxa) and the placement of turtles as basal within the phylogenetic tree for amniote animals.

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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.

Amino Acid Sequence↗

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.

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Scratching an ancient itch: an Eocene bird louse fossil.

Out of the 30 extant orders of insects, all but one, the parasitic lice (Insecta: Phthiraptera), have a confirmed fossil record. Here, we report the discovery of what appears to be the first bird louse fossil: an exceptionally well-preserved specimen collected from the crater of the Eckfeld maar near Manderscheid, Germany. The 44-million-year-old specimen shows close phylogenetic affinities with modern feather louse ectoparasites of aquatic birds. Preservation of feather remnants in the specimen's foregut confirms its association as a bird ectoparasite. Based on a phylogenetic analysis of the specimen and palaeoecological data, we suggest that this louse was the parasite of a large ancestor to modern Anseriformes (swans, geese and ducks) or Charadriiformes (shorebirds). The crown group position of this fossil in the phylogeny of lice confirms the group's long coevolutionary history with birds and points to an early origin for lice, perhaps inherited from early-feathered theropod dinosaurs.

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Avian evolution, Gondwana biogeography and the Cretaceous-Tertiary mass extinction event.

The fossil record has been used to support the origin and radiation of modern birds (Neornithes) in Laurasia after the Cretaceous-Tertiary mass extinction event, whereas molecular clocks have suggested a Cretaceous origin for most avian orders. These alternative views of neornithine evolution are examined using an independent set of evidence, namely phylogenetic relationships and historical biogeography. Pylogenetic relationships of basal lineages of neornithines, including ratite birds and their allies (Palaleocognathae), galliforms and anseriforms (Galloanserae), as well as lineages of the more advanced Neoves (Gruiformes, (Capimulgiformes, Passeriformes and others) demonstrate pervasive trans-Antarctic distribution patterns. The temporal history of the neornithines can be inferred from fossil taxa and the ages of vicariance events, and along with their biogeographical patterns, leads to the conclusion that neornithines arose in Gondwana prior to the Cretaceous Tertiary extinction event.

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No simple answers for ecological immunology: relationships among immune indices at the individual level break down at the species level in waterfowl.

Understanding immune function in the context of other life-history traits is crucial to understand the evolution of life histories, at both the individual and species levels. As the interest in assessing immune function for these comparative purposes grows, an important question remains unanswered: can immune function be broadly characterized using one or two simple measures? Often, interpretation of individual assays is ambiguous and relationships among different measures of immune function remain poorly understood. Thus, we employed five protocols to measure 13 variables of immune function in ten species of waterfowl (Anseriformes). All assays were based on a single blood sample subdivided into leukocyte (blood smear) and plasma (frozen until analysis) components. All assays were run using samples from every individual, and a nested analysis was used to partition variation/covariation at the levels of species and individuals within species. We detected positive correlations between functionally related measures of immunity within species, but these were absent from comparisons between species. A canonical correlation analysis revealed no significant relationships between the plasma and leukocyte assays at the levels of both individual and species, suggesting that these measures of immunity are neither competitive nor synergistic. We conclude that one measure of each assay type may be required to maximally characterize immune function in studies of a single species, while the same is not true in studies among species.

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An allometric study of pulmonary morphometric parameters in birds, with mammalian comparisons.

Comprehensive pulmonary morphometric data from 42 species of birds representing ten orders were compared with those of other vertebrates, especially mammals, relating the comparisons to the varying biological needs of these avian taxa. The total lung volume was strongly correlated with body mass. The volume density of the exchange tissue was lowest in the charadriiform and anseriform species and highest in the piciform, cuculiform and passeriform species. The surface area of the blood-gas (tissue) barrier, the volume of the pulmonary capillary blood and the total morphometric pulmonary diffusing capacity were all strongly correlated with body mass. The harmonic mean thickness of both the blood-gas (tissue) barrier and the plasma layer were weakly correlated with body mass. The mass-specific surface area of the blood-gas (tissue) barrier (surface area per gram body mass) and the surface density of the blood-gas (tissue) barrier (i.e. its surface area per unit volume of exchange tissue) were inversely correlated (though weakly) with body mass. The passeriform species exhibited outstanding pulmonary morphometric adaptations leading to a high specific total diffusing capacity per gram body mass, consistent with the comparatively small size and energetic mode of life which typify passeriform birds. The relatively inactive, ground-dwelling domestic fowl (Gallus gallus) had the lowest pulmonary diffusing capacity per gram body mass. The specific total lung volume is about 27% smaller in birds than in mammals but the specific surface area of the blood-gas (tissue) barrier is about 15% greater in birds. The ratio of the surface area of the tissue barrier to the volume of the exchange tissue was also much greater in the birds (170-305%). The harmonic mean thickness of the tissue barrier was 56-67% less in the birds, but that of the plasma layer was about 66% greater in the birds. The pulmonary capillary blood volume was also greater (22%) in the birds. Except for the thickness of the plasma layer, these morphometric parameters all favour the gas exchange capacity of birds. Consequently, the total specific mean morphometric pulmonary diffusing capacity for oxygen was estimated to be about 22% greater in birds than in mammals of similar body mass. This estimate was obtained by employing oxygen permeation constants for mammalian tissue, plasma and erythrocytes, as avian constants were not then available.(ABSTRACT TRUNCATED AT 400 WORDS)

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Serotyping of European isolates of Chlamydia psittaci from poultry and other birds.

A panel of five serovar-specific monoclonal antibodies which distinguish the five known avian serovars of Chlamydia psittaci was used to serotype 45 European avian Chlamydia psittaci isolates. Chlamydial antigen was grown in Buffalo green monkey (BGM) cells or in embryonated chicken eggs and was then inoculated into BGM cells. Serotyping was performed in an indirect immunofluorescence test. The 45 European isolates included 22 isolates from the order Psittaciformes, 9 isolates from the order Columbiformes, 6 isolates from the order Galliformes, 5 isolates from the order Passeriformes, and 3 isolates from the order Anseriformes. All of these were successfully serotyped. No additional serovars were found. One isolate from a duck and two isolates from psittacine birds gave positive immunofluorescences with two monoclonal antibodies considered to be specific for two different serovars. These three isolates were cloned by an agar overlay method. Serotyping of the clones demonstrated that the duck and one psittacine bird each were infected with two different serovars. After cloning, one isolate from a psittacine bird reacted only with serovar A. From these results it was concluded that this serotyping system allows the classification of all isolates tested so far. The results show that similar serovars are prevalent in avian species in Europe and the United States. The results also indicate that birds from a certain order are more susceptible to a distinct serovar. The use of a panel of serovar-specific monoclonal antibodies in the immunofluorescence test provides a reliable method for serotyping avian isolates. Monoclonal antibodies to new avian isolate serovars can easily be added to the panel, which makes the system useful for epidemiological studies.

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The interspersed DNA repeat conserved in water birds' genomes.

A putative old and ubiquitous interspersed DNA repeat family was identified from TaqI restriction, M13 cloning, and sequencing of the genomic DNA of a Mallard (Anas platyrhynchos), a Muscovy Duck (Cairina moschata), a Toulouse Goose (Anser anser), and a Black Swan (Cygnus atratus). A 425-bp consensus core sequence was obtained for the interspersed family. The 425-bp unit was about 2% of the avian genome and was found to be conserved in at least four genera of the order Anseriforme: Anas, Anser, Cairina, and Cygnus.

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Unilateral eye closure and interhemispheric EEG asymmetry during sleep in the pigeon (Columba livia).

Aquatic mammals (i.e., Cetaceans, eared seals and manatees) and birds show interhemispheric asymmetries (IA) in slow-wave sleep-related electroencephalographic (EEG) activity, suggesting that the depth of sleep differs between hemispheres. In birds, an association between unilateral eye closure and IA has been reported in five species from three orders (i.e., Galliformes, Charadriiformes, and Anseriformes). Moreover, unilateral eye closure has been observed during behaviorally defined sleep in 29 species from 13 avian orders, suggesting that birds in general display IA during sleep. Despite the apparent prevalence of unilateral eye closure and IA in birds, previous work did not detect IA in the pigeon, thereby challenging the conclusion that this is a general feature of birds. Using digital period amplitude analysis, an objective method for quantifying EEG power (a measure of wave amplitude) across different frequencies, we demonstrate that pigeons do, in fact, display an association between unilateral eye closure and IA. For a given hemisphere, standardized 2-4 Hz EEG power was greater when the contralateral eye was closed when compared to open. We also found that pigeons used the open eye during IA to monitor their environment. In addition, individual pigeons showed a bias for keeping one eye open more than the other. The direction (left vs. right) of this bias differed across birds, and appeared to be influenced by the structure of the surrounding environment. Finally, with the addition of pigeons (order Columbiformes), IA associated with unilateral eye closure has been recorded in four avian orders, suggesting that this form of sleep is widespread in birds.

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Comparative distribution of 2[125I]iodomelatonin binding in the brains of diurnal birds: outgroup analysis with turtles.

The roles that the pineal gland and its hormone melatonin play in the regulation of circadian rhythmicity and photoperiodism vary among vertebrate species. Recently, putative sites of melatonin action have been elucidated in several avian and mammalian species by application of in vitro binding of a radioiodinated melatonin agonist, 2[125I]iodomelatonin (IMEL) and autoradioradiography. These studies in mammals, birds and reptiles have indicated profound differences in the distribution of IMEL binding between these diverse groups, suggesting that these large differences in binding may reflect differences in melatonin function. The present study was performed to determine systematically whether the variance in IMEL binding among avian species corresponds to changes in circadian organization and/or phylogenetic relationships. The distribution of specific IMEL binding was determined in the brains from birds belonging to 14 different species in 5 Orders (Psittaciformes, Passeriformes, Columbiformes, Galliformes and Anseriformes) using in vitro binding, autoradiography and computer-assisted image analysis. The distribution was compared to a similar study in 3 species of turtles as an outgroup. The data indicated IMEL binding in retinorecipient structures of the circadian, tectofugal, thalamofugal and accessory optic visual pathways in all avian species. Relay nuclei and integrative structures of the tectofugal, thalamofugal, accessory optic, and limbic systems, however, bound the hormone to varying degrees. In turtles, binding was observed in retinorecipient structures of the thalamofugal visual pathway and in retinorecipient and integrative areas of the tectofugal visual pathway. No binding was observed in the pineal gland, tuberal hypothalamus or adenohypophysis in any avian or testudine species. This distribution is drastically different from that observed in mammals, where binding predominates in the pars tuberalis of the adenohypophysis and in the suprachiasmatic nucleus, suggesting that the circadian system may influence a wide array of sensory and integrative functions in birds and reptiles through the circadian secretion of melatonin, but that this capacity has been lost in mammals.

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Improvement in plaquing methods for the enumeration of anatid herpesvirus (duck plague virus).

The Holland strain of anatid herpesvirus (AHV) was 2-to 10-fold more efficiently plaqued under liquid medium or semisolid medium containing methylcellulose than in media containing agar, agarose, or Nobel agar. Virus adsorption was complete in 45 min, with the maximum virus titers obtained under liquid medium at 48 h postinfection. The AHV dose-response curve was linear. Pekin duck embryo cultures were more efficient than CCL-141 in plaque response and gave the maximum virus yield per cell. Virus titers were independent of avian cell passage number (to 6), fetal or newborn calf sera (to 10% v/v), and the presence of polyions during adsorption. The host range included cells from several species of Anseriformes and Galliformes.

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Lift-based paddling in diving grebe.

To examine the hydrodynamic propulsion mechanism of a diving great crested grebe (Podiceps cristatus), the three-dimensional kinematics was determined by digital analysis of sequential video images of dorsal and lateral views. During the acceleration phase of this foot-propelled bird, the feet move through an arc in a plane nearly normal to the bird's line of motion through the water, i.e. the toes move dorsally and medially but not caudally relative to the water. The kinematics of the grebe's lobed feet is different from that in anseriforms, whose feet move in a plane mostly parallel to the bird's line of progress through the water. Our results suggest that the foot-propelled locomotor mechanism of grebes is based primarily on a lift-producing leg and foot stroke, in contrast to the drag-based locomotion assumed previously. We suggest that the lift-based paddling of grebes considerably increases both maximum swimming speed and energetic efficiency over drag-based propulsion. Furthermore, the results implicate a new interpretation of the functional morphology of these birds, with the toes serving as a self-stabilizing multi-slotted hydrofoil during the power phase.

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Digeneans and cestodes parasitic in the white-faced ibis Plegadis chihi (Aves: Threskiornithidae) from Argentina.

Some digeneans and cestodes parasitic in a population of the white-faced ibis Plegadis chihi (Vieillot) from Buenos Aires province, Argentina, are presented. The digeneans Dietziella egregia (Dietz, 1909), Patagifer bilobus (Rudolphi, 1819), Ascocotyle (Leighia) hadra Ostrowski de Nuñez, 1992 and Posthodiplostomum nanum Dubois, 1937 from the intestine; Prosthogonimus ovatus (Rudolphi, 1803) from the cloaca; Athesmia heterolecithodes (Braun, 1899) from the bile ducts and the cestode Hymenolepis megalops (Nitzsch in Creplin, 1829) from the cloaca, were recorded. The discovery of D. egregia, P. ovatus, A. heterolecithodes and P. nanum constitute new host and/or new geographical records. Adults of A. (L.) hadra, previously described in experimental definitive hosts, are first reported from a naturally infected bird. Hymenolepis megalops, a cestode of Anseriformes is first reported from Ciconiiformes.

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Phorcotabanus cinereus (Wiedemann, 1821) (Diptera, Tabanidae), an ornithophilic species of Tabanid in Central Amazon, Brazil.

In Central Amazon, Brazil, the tabanid Phorcotabanus cinereus (Wiedemann) was recorded attacking the native duck Cairina moschata (Linnaeus) (Anseriformes, Anatidae). The flight and behavior of the tabanid during the attacks and the host's defenses were videotaped and analyzed in slow motion. The tabanid was recorded flying rapidly around the heads of the ducks before landing. Landing always took place on the beak, and then the tabanid walked to the fleshy caruncle on the basal part of the beak to bite and feed. Firstly the duck defends itself through lateral harsh head movements, and then, when it is being bitten, it defends itself by rubbing its head on the body, or dipping the head into water, when swimming. If disturbed, the fly resumed the same pattern of flight as before and would generally try to land again on the same host and bite in the same place. This feeding activity was observed predominantly between 9:30 am and 4:30 pm and always in open areas, near aquatic environments, from June 1996 to January 1997, the dry season in Central Amazon. To test the attractiveness of other animals to P. cinereus, mammals, caimans and domestic and wild birds were placed in suitable habitat and the response of P. cinereus observed. P. cinereus did not attack these animals, suggesting that this species has a preference for ducks, which are plentiful in the region.

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Molecular cloning of the cDNAs for pituitary glycoprotein hormone alpha subunits of two species of duck and their gene regulation.

The cDNAs encoding pituitary glycoprotein hormone alpha subunits (PGHalphas) of two species of duck (Muscovy duck, Cairina moschata and Pekin duck, Anas platyrhynchos domesticus) were cloned and sequenced to better understand the phylogenic diversity and evolution of PGHalpha molecules in vertebrates. Oligonucleotide primers were designed and used for reverse transcription PCR (RT-PCR) amplification of PGHalpha cDNA fragments from total cellular RNA of pituitary glands. The remaining sequences were completed by rapid amplification of the cDNA ends. The nucleotide sequence of isolated PGHalpha cDNA of both ducks are identical, including 81 bp of 5' untranslated region (UTR), 360 bp of coding region, and 272 bp of 3'-UTR followed by a 13 bp poly(A)(+) tract. The total number of amino acids deduced from the cDNA of the duck PGHalpha is 120 with a signal peptide of 24 amino acids and a mature protein of 96 amino acids. PGHalphas of the ducks (order Anseriformes) share 96% homology of amino acid sequence in signal peptide, and 100% homology in mature proteins with chicken, quail and turkey (order Galliformes). Our data thus demonstrate identical inter-order homology of PGHalpha mature protein in birds. Ten cysteine residues, presumably forming five disulfide bonds within the alpha subunit, and four proline residues, presumably responsible for folding of the molecule, are conserved in the alpha subunit of ducks. Northern blot analysis revealed that PGHalpha mRNA is expressed only in the pituitary. In order to study factors regulating the gene expression of PGHalpha mRNA, duck pituitary fragments were incubated with GnRH, TRH, testosterone, or triiodothyronine (T(3)). GnRH and TRH increased, while testosterone and T(3) decreased, PGHalpha mRNA levels. This is the first report in birds of TRH up-regulation and down-regulation by testosterone and T(3) under in vitro conditions. The present study demonstrates both ducks have the same cDNA nucleotide and deduced amino acid sequences in the PGHalpha subunit, exhibiting identical inter-genus homology within the family of Anatidae. The findings from mRNA expression work suggest that hypothalamic GnRH and TRH up-regulate, while testosterone and T(3) down-regulate, PGHalpha gene expression in ducks.

Amino Acid Sequence↗

First surveillance study of avian orthoavulavirus type 1 in wild birds in Morocco: Insights and implications for future monitoring.

BACKGROUND: Wild birds, particularly migratory species, can act as natural reservoirs and vectors of avian orthoavulavirus type 1 (AOAV-1) or Newcastle disease virus (NDV), contributing to its spread across regions and potentially threatening domestic poultry populations. AOAV-1, also known as NDV, is a major pathogen affecting avian species and poses a global threat to poultry production. It belongs to the Paramyxoviridae family and is an RNA virus encoding six key proteins, including the fusion (F) protein, which determines pathogenicity. AOAV-1 is classified into three pathotypes based on virulence: velogenic (highly pathogenic), mesogenic (moderately pathogenic), and lentogenic (mild or asymptomatic). In Morocco, AOAV-1 is endemic in poultry production systems, as evidenced by recent studies reporting a 52.1% seroprevalence and active viral RNA detection in backyard chickens in the Khemisset and Skhirat-Temara provinces; however, effective vaccination strategies have contributed to controlling the clinical signs and widespread dissemination of the virus. AIM: The main objective of this study was to investigate the presence of AOAV-1 in wild bird populations across Morocco, providing insights into possible transmission of infection affecting domestic poultry. METHODS: From November 2016 to April 2022, a total of 1984 samples were collected from 840 individual birds, encompassing 79 species, 25 families, and 12 orders. The majority of the samples belonged to Charadriiformes, Anseriformes, Pelecaniformes, and Passeriformes. Sampling was conducted at 17 wetlands and six additional locations throughout Morocco. Viral detection was performed using real-time reverse transcriptase PCR (RT-qPCR) targeting Matrix (M) and RNA polymerase (L) genes to confirm the presence of AOAV-1. RESULTS: Although the study spanned 6 years and included a large number of samples from bird orders considered primary AOAV-1 reservoirs, all samples tested negative for NDV RNA using both M and L gene targets. CONCLUSION: This study represents the first effort in Morocco to monitor wild birds for AOAV-1. The samples analyzed were initially collected for avian influenza surveillance, which shares epidemiological similarities with Newcastle's disease. However, to improve future surveillance efforts, sample collection should be optimized to target scenarios with the highest probability of virus detection.

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