Genome of an iconic Australian bird: High‐quality assembly and linkage map of the superb fairy‐wren (Malurus cyaneus)

The superb fairy‐wren, Malurus cyaneus, is one of the most iconic Australian passerine species. This species belongs to an endemic Australasian clade, Meliphagides, which diversified early in the evolution of the oscine passerines. Today, the oscine passerines comprise almost half of all avian species diversity. Despite the rapid increase of available bird genome assemblies, this part of the avian tree has not yet been represented by a high‐quality reference. To rectify that, we present the first high‐quality genome assembly of a Meliphagides representative: the superb fairy‐wren. We combined Illumina shotgun and mate‐pair sequences, PacBio long‐reads, and a genetic linkage map from an intensively sampled pedigree of a wild population to generate this genome assembly. Of the final assembled 1.07‐Gb genome, 975 Mb (90.4%) was anchored onto 25 pseudochromosomes resulting in a final superscaffold N50 of 68.11 Mb. This high‐quality bird genome assembly is one of only a handful which is also accompanied by a genetic map and recombination landscape. In comparison to other pedigree‐based bird genetic maps, we find that the fairy‐wren genetic map more closely resembles those of Taeniopygia guttata and Parus major maps, unlike the Ficedula albicollis map which more closely resembles that of Gallus gallus. Lastly, we also provide a predictive gene and repeat annotation of the genome assembly. This new high‐quality, annotated genome assembly will be an invaluable resource not only regarding the superb fairy‐wren species and relatives but also broadly across the avian tree by providing a novel reference point for comparative genomic analyses.     

Early Cretaceous (Berriasian) birds and pterosaurs from the Cornet bauxite mine,Romania

Abstract: We revisit a small but extremely significant collection of bird and pterosaur bones from the Lower Cretaceous (Berriasian) of western Romania. These fossils were collected in the late 1970s and early 1980s from a Lower Cretaceous (Berriasian) conglomerate lens deep in a bauxite mine at Cornet, close to the city of Oradea, Romania, and they caused a sensation when first described. Some fossils were initially ascribed to the early bird genus Archaeopteryx as well as to the modern clade Neornithes, an astonishing avian assemblage if correct. Described pterosaurs include dsungaripterids and a cervical vertebra that is likely the oldest azhdarchid pterosaur known from Europe and perhaps the world. Not only does the Cornet azhdarchid support an Eurasian origin for this clade, it is also significant because of its size: it is one of the smallest representatives of this pterosaur clade yet reported. Aside from their phylogenetic affinities, these unique Romanian fossils are also important because of their age; in particular, very few birds are known globally from the earliest Cretaceous. Re‐examination of collections in Oradea confirms the presence of both birds and pterosaurs in the Cornet bauxite: although the fragmentary bird remains are mostly indeterminate, one record of a hesperornithiform is confirmed. There is no evidence for Archaeopteryx at the Cornet site while the two supposed neornithines (Palaeocursornis biharicus Kessler and Jurcsák and Eurolimnornis corneti Kessler and Jurcsák) are based on undiagnostic remains and are here regarded as nomina dubia.     

Sequence determination of a new parrot bornavirus‐5 strain in Japan: implications of clade‐specific sequence diversity in the regions interacting with host factors

In this study, the genome sequence of a new parrot bornavirus‐5 (PaBV‐5) detected in Eclectus roratus was determined. Phylogenetic analysis showed that the genus Bornavirus is divided into three major clades and that PaBV‐5 belongs to clade 2, which contains avian viruses that exhibit infectivity to mammalian cells. Sequence comparisons of the regions known to interact with host factors indicated that the clade 2 avian viruses possess sequences intermediate between the clade 1 mammalian viruses and the clade 3 avian viruses, suggesting that the identified regions might contribute to the differences in virological properties between the three clades.     

Combined phylogenetic analysis of a new North American fossil species confirms widespread Eocene distribution for stem rollers (Aves,Coracii)

We report a nearly complete skeleton of a new species of stem roller (Aves, Coracii) from the early Eocene Green River Formation of North America. The new species is most closely related to two species‐depauperate lineages, Coraciidae (rollers) and Brachypteraciidae (ground rollers), that form a monophyletic crown clade (Coracioidea) with an exclusively Old World extant distribution. Phylogenetic analysis utilizing a matrix of 133 morphological characters and sequence data from three genes (RAG‐1, c‐myc, and ND2) identifies the new species as a stem member of the Coracii more closely related to the crown clade than the only previously identified New World taxon, Primobucco mcgrewi. The phylogenetic placement of the new species and Primobucco mcgrewiindicates a widespread northern hemisphere distribution in the Eocene with subsequent restriction to Africa, Madagascar, Australia, and temperate to tropical parts of Europe and Asia. It provides evidence of further ecological diversity in early stem Coracii and convergence on crown morphologies. The new species contributes to mounting evidence that extant distributions for major avian subclades may be of comparatively recent origin. Further late Palaeogene sampling is needed to elucidate potential drivers for shifting avian distributions and disappearance of Coracii from North America. © 2009 The Linnean Society of London, Zoological Journal of the Linnean Society, 2009, 157 , 586–611.     

The osteohistological variability in the evolution of basal avialans

Basal avialans have been the focus of numerous histological studies in the past decade, from which different osteohistological patterns have been described. In this review, we look at the osteohistology in selected specimens from the four major avian groups: the long-tailed Avialae (Archaeopteryx and Jeholornithiformes), basal Pygostylia, Enantiornithes and Euornithes. Developmental and evolutionary changes in the three major bone layers are observed throughout the bone cortex of the limbs, may it be interspecific or intraspecific. Most noteworthy is the adaptive change from the overall lamellar/parallel-fibered bone tissue to a fibrolamellar complex in the mid-cortex as of the basal Pygostylia, potentially even as of the Jeholornithiformes. This change is generally associated with an increase in the density and complexity of the neurovascular network. Another evolutionary-developmental feature is the progressive loss of post-natal growth marks as of the non-ornithurine Euornithes, indicative of uninterrupted bone growth as observed in extant Neornithes. Our comparisons of the osteohistological patterns allow us to better determine how and when specific features typical observed in the avian crown group developed, associated with external and internal factors, and how they lead to what is commonly observed in extant Neornithes.     

Rethinking Avian Response to Tamarix on the Lower Colorado River: A Threshold Hypothesis

Many of the world’s large river systems have been greatly altered in the past century due to river regulation, agriculture, and invasion of introduced Tamarix spp. (saltcedar, tamarisk). These riverine ecosystems are known to provide important habitat for avian communities, but information on responses of birds to differing levels of Tamarix is not known. Past research on birds along the Colorado River has shown that avian abundance in general is greater in native than in non‐native habitat. In this article, we address habitat restoration on the lower Colorado River by comparing abundance and diversity of avian communities at a matrix of different amounts of native and non‐native habitats at National Wildlife Refuges in Arizona. Two major patterns emerged from this study: (1) Not all bird species responded to Tamarix in a similar fashion, and for many bird species, abundance was highest at intermediate Tamarix levels (40–60%), suggesting a response threshold. (2) In Tamarix‐dominated habitats, the greatest increase in bird abundance occurred when small amounts of native vegetation were present as a component of that habitat. In fact, Tamarix was the best vegetation predictor of avian abundance when compared to vegetation density and canopy cover. Our results suggest that to positively benefit avian abundance and diversity, one cost‐effective way to rehabilitate larger monoculture Tamarix stands would be to add relatively low levels of native vegetation (～20–40%) within homogenous Tamarix habitat. In addition, this could be much more cost effective and feasible than attempting to replace all Tamarix with native vegetation.     

A small stem-galliform bird (Aves: Paraortygidae) from the Eocene of Uzbekistan

Landfowl (order Galliformes) are among the most characteristic birds of the modern avian faunas, but their early evolutionary history is insufficiently known. The diversity of previously described Eocene galliforms implies a great role of Eocene diversification in the early evolution of this group. However, almost nothing is known about the Eocene diversity of galliforms in Asia, even though this large continent with a variety of habitats might have played a significant role in their early evolution. Here we describe a partial coracoid from the Lutetian–Bartonian of Uzbekistan, which is the oldest diagnosable galliform bird in Asia, and is further the first landbird known from this geographical area. The specimen displays a unique morphology with few autapomorphies and an unexpected combination of similarities with the African genus Scopelortyx and Eurasian Paraortyx, and hence is described as a new taxon, Xorazmortyx turkestanensis gen. et sp. nov., within the extinct family Paraortygidae, being the first Asian representative of this clade. Similarities with the African genus Scopelortyx indicate a connection of land bird faunas between northern Africa/Arabia and Asia in the middle Eocene. Better dispersal abilities of the early galliforms Paraortygidae are inferred from the osteology of their pectoral girdle and the humerus, which do not show adaptations to the powerful burst take off (escape flight), characteristic of most modern Phasianidae.     

Bird evolution: testing the Metaves clade with six new mitochondrial genomes

Background  

Evolutionary biologists are often misled by convergence of morphology and this has been common in the study of bird evolution. However, the use of molecular data sets have their own problems and phylogenies based on short DNA sequences have the potential to mislead us too. The relationships among clades and timing of the evolution of modern birds (Neoaves) has not yet been well resolved. Evidence of convergence of morphology remain controversial. With six new bird mitochondrial genomes (hummingbird, swift, kagu, rail, flamingo and grebe) we test the proposed Metaves/Coronaves division within Neoaves and the parallel radiations in this primary avian clade.     

Mesozoic birds of China—a synoptic review

A synoptic review of the discoveries and studies of Chinese Mesozoic birds is provided in this paper. ⁴⁰Ar/³⁹Ar dating of several bird-bearing deposits in the Jehol Group has established a geochronological framework for the study of the early avian radiation. Chinese Mesozoic birds had lasted for at least 11 Ma during about 131 Ma and 120 Ma (Barremian to Aptian) of the middle and late Early Cretaceous, respectively. In order to further evaluate the change of the avian diversity in the Jehol Biota, six new orders and families are erected based on known genera and species, which brings the total number of orders of Chinese Mesozoic birds to 15 and highlights a remarkable radiation ever since the first appearance of birds in the Late Jurassic. Chinese Early Cretaceous birds had experienced a significant differentiation in morphology, flight, diet and habitat. Further examination of the foot of Jeholornis suggests this bird might not have possessed a fully reversed hallux. However, the attachment of metatarsal I to the medial side of metatarsal II does not preclude trunk climbing, a pre-adaptation for well developed perching life of early birds. Arboreality had proved to be a key adaptation in the origin and early evolution of bird flight, and the adaptation to lakeshore environment had played an equally important role in the origin of ornithurine birds and their near-modern flight skill. Many Chinese Early Cretaceous birds had preserved the direct evidence of their diet, showing that the most primitive birds were probably mainly insectivorous and that specialized herbivorous or carnivorous (e.g., piscivorous) dietary adaptation had appeared only in later advanced forms. The only known Early Cretaceous bird embryo fossil has shown that precocial birds had occurred prior to altricial birds in avian history, and the size of the embryo and other analysis indicate it probably had a short incubation period. Leg feathers probably have a wide range of distribution in early birds, further suggesting that leg feathers had played a key role in the beginning stage of the flight of birds. Finally, the Early Cretaceous avian radiation can be better understood against the background of their unique ecosystem. The advantage of birds in the competitions with other vertebrate groups such as pterosaurs had probably not only resulted in the rapid differentiation and radiation of birds but also the worldwide spreading of pterosaurs and other vertebrates from East Asia in the Early Cretaceous. Selected from Vertebrata PalAsiatica 2006, 44 (1): 74–98     

Congruent Avian Phylogenies Inferred from Mitochondrial and Nuclear DNA Sequences

Recent molecular studies addressing the phylogenetic relationships of avian orders have had conflicting results. While studies using nuclear DNA sequences tend to support traditional taxonomic views, also supported by morphological data [(paleognaths (galloanseres (all other birds)))], with songbirds forming a clade within Neoaves (all other birds), analyses with complete mtDNA genomes have resulted in topologies that place songbirds as one of the earliest-diverging avian lineages. Considering that over half of the extant bird species are songbirds, these different results have very different implications for our understanding of avian evolution. We analyzed data sets comprising nearly 4 kb of mitochondrial DNA (mtDNA) (complete 12S, ND1, ND2, and cytochrome b) plus 600 bp of the nuclear gene c-mos for 15 birds that were chosen to represent all major avian clades and to minimize potential long-branch attraction problems; we used a partition-specific maximum likelihood approach. Our results show congruence with respect to the ingroup among phylogenies obtained with mtDNA and the nuclear gene c-mos, separately or combined. The data sets support a traditional avian taxonomy, with paleognaths (ratites and tinamous) occupying a basal position and with songbirds more derived and forming a monophyletic group. We also show that, for mtDNA studies, turtles may be a better outgroup for birds than crocodilians because of their slower rate of sequence evolution.     

The first record of Anomoepus tracks from the Middle Jurassic of Henan Province,Central China

Small, gracile mostly tridactyl tracks from the Middle Jurassic of Henan Province represent the first example of the ichnogenus Anomoepus from this region. They represent a growing number of reports (at least eight) of this ichnogenus from the Jurassic of China. In conjunction with Changpeipus and Eubrontes, they appear characteristic of known global footprint biochrons. Anomoepus indicates the presence of ornithischian dinosaurs that are often scarce or unknown from skeletal remains in coeval deposits. When first discovered, these tracks were informally referred to as bird tracks. This interpretation reflects convergence between small Jurassic Anomoepus and avian theropod tracks that are hitherto known only from the Cretaceous and the Cenozoic. However, most Anomoepus are larger and more robust than any hitherto known Mesozoic avian tracks.     

Implications of Plasmodium parasite infected mosquitoes on an insular avifauna: the case of Socorro Island,México

Avian malaria (Plasmodium spp.) has been implicated in the decline of avian populations in the Hawaiian Islands and it is generally agreed that geographically isolated and immunologically naïve bird populations are particularly vulnerable to the pathogenic effects of invasive malaria parasites. In order to assess the potential disease risk of malaria to the avifauna of Socorro Island, México, we surveyed for Plasmodium isolates from 1,300 resident field‐caught mosquitoes. Most of them were identified as Aedes (Ochlerotatus) taeniorhynchus (Wiedemann, 1821), which were abundant in the salt marshes. We also collected Culex quinquefasciatus Say, 1823 close to human dwellings. Mitochondrial ND5 and COII gene sequences of Ae. taeniorhynchus were analyzed and compared to corresponding sequences of mosquitoes of the Galápagos Islands, Latin America, and the North American mainland. Aedes lineages from Socorro Island clustered most closely with a lineage from the continental U.S. Plasmodium spp. DNA was isolated from both species of mosquitoes. From 38 positive pools, we isolated 11 distinct mitochondrial Cytb lineages of Plasmodium spp. Seven of the Plasmodium lineages represent previously documented avian infective strains while four were new lineages. Our results confirm a potential risk for the spread of avian malaria and underscore the need to monitor both the mosquito and avian populations as a necessary conservation measure to protect endangered bird species on Socorro Island.     

Interannual patterns of avian diseases in wild New Zealand avifauna near conservation areas

The past few years have seen a noticeable increase in the emergence of infectious diseases in wildlife, especially vector-borne diseases, presenting a challenge for the conservation of endangered species. One such vector-borne disease, avian malaria (Plasmodium spp.) is on the rise in New Zealand avifauna, threatening bird populations that are among the most extinction-prone in the world. Furthermore, recent reports have outlined an increase in deaths of native iconic bird species specifically due to this disease. In order to help manage breakouts of this pathogen at a local scale, we need a better understanding of potential drivers of the emergence of avian malaria in wild New Zealand avifauna. Here, we set to test the role of climatic drivers in synchronizing contacts between avian hosts and vectors, assess the temporal stability of transmission dynamics between years, and determine the role of introduced species in causing spill-over of this pathogen towards native species. Our study focused on three sites that were sampled regularly during two consecutive years in the austral summer, each site being adjacent to a breeding colony of Yellow-eyed penguins (Megadyptes antipodes). Our results reveal an overall temporal stability of avian malaria incidence patterns, with a decrease in infection throughout the austral summer for both sampled years. Moreover, we highlight a phylogenetic signal among sampled bird species, with introduced species being more heavily infected by avian malaria than their native counterparts. In contrast, we found no effect of the two climatic drivers investigated, temperature and rainfall, on mosquito abundance. Our results suggest a strong effect of alien species acting as reservoirs for diseases spilling-over towards immunologically naïve species, and provide conservation managers with a critical timeframe to control avian malaria breakouts.     

First record of a tarsometatarsus of Tonsala hildegardae (Plotopteridae) and other avian remains from the late Eocene/early Oligocene of Washington State (USA)

New bird fossils from the late Eocene/early Oligocene Makah Formation and the Oligocene Pysht Formation on the Olympic Peninsula (Washington State, USA) are described. A partial skeleton from the Pysht Formation includes the first reported tarsometatarsus of Tonsala hildegardae Olson, 1980, a wing-propelled diving bird of the taxon Plotopteridae. It shows that Tonsala had a tarsometatarsus that was morphologically intermediate between that of the late Eocene Phocavis and more derived plotopterids. We introduce the new taxon Tonsalinae nov. subfam. for a clade including all named plotopterids except Phocavis, Plotopterum, and the recently described Stemec. We furthermore describe a partial plotopterid pelvis and a sternum from the Makah Formation. The sternum shows a close resemblance to that of extant Phalacrocoracoidea (cormorants and darters) and may be the earliest North American record of this taxon.     

Phylogenetic relationships and speciation patterns in an African savanna dwelling bird genus (Myrmecocichla)

Phylogenetic relationships among eight of nine Myrmecocichla chat species were inferred from DNA data. Bayesian posterior probabilities and maximum‐likelihood bootstrap percentages strongly supported most branches in the phylogeny. Based on these results, Myrmecocichla, as currently defined, is not monophyletic. The results indicated that Myrmecocichla albifrons is part of a Cercomela + Oenanthe clade, whereas Oenanthe monticola is shown to be a Myrmecocichla. In addition, Myrmecocichla arnotti is shown to be polyphyletic. Phylogenetic analyses support three Southern versus Eastern or Northern speciation events. The dating of these speciation events suggests that they correspond to periods when the Afrotropical forests were expanded to coastal Kenya, 3–5 Mya. This forest expansion thus served as a vicariant driver of speciation in the genus, a result consistent with speciation patterns in other arid‐adapted African bird genera. Our haplotype analysis within one of the most widespread and habitat diverse Myrmecocichla species (formicivora, a southern African endemic) showed little genetic variation. Along with speciation patterns shown for Myrmecocichla and other avian genera, this lack of standing variation would appear to support large, inter‐regional drivers of speciation as having the largest effect on the diversification of arid‐adapted Africa bird species, which is in stark contrast to other vertebrate lineages whose genetic structure often shows strong intra‐regional effects. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 106 , 180–190.     

First record of a fossil bird from the Early Cretaceous of Thailand

We present the first known occurrence of a Mesozoic fossil bird from Thailand. The new specimen is the distal end of a left humerus, from the Early Cretaceous Sao Khua Formation in the Northeast of the country, and testifies to the presence of a medium-sized avian in these non-marine strata. This is also the first Mesozoic bird known from the whole of Southeast Asia. To cite this article: E. Buffetaut et al., C. R. Palevol 4 (2005).     

A new Lower Cretaceous bird from China and tooth reduction in early avian evolution

A new avian genus and species, Zhongjianornis yangi gen. et sp. nov., is reported from the Lower Cretaceous lacustrine deposits of the Jiufotang Formation in Liaoning, northeast China. The new taxon is characterized by possessing the following combination of features: upper and lower jaws toothless, snout pointed, humerus with large and robust deltopectoral crest, second phalanx of the major manual digit longer than the first phalanx, unguals of the alular and major digits of similar length and significantly shorter than the corresponding penultimate phalanges, tibiotarsus slender and more than twice the length of the tarsometatarsus, and metatarsal IV longer than the other metatarsals. Phylogenetic analysis indicates that Zhongjianornis is phylogenetically basal to Confuciusornis and the dominant Mesozoic avian groups, Enantiornithes and Ornithurae, and therefore provides significant new information regarding the diversification of birds in the Early Cretaceous. It also represents the most basal bird that completely lacks teeth, suggesting that tooth loss was more common than expected in early avian evolution and that the avian beak appeared independently in several avian lineages, most probably as a response to selective pressure for weight reduction. Finally, the presence of a significantly enlarged humeral deltopectoral crest suggests that Zhongjianornis shares with other basal birds such as Jeholornis, Sapeornis and Confuciusornis a distinctive mode of adaptation for flight contrasting with that seen in more advanced birds, which instead possess an elongated sternum and a prominent keel.     

A new basal ornithuromorph bird (Aves: Ornithothoraces) from the Early Cretaceous of China with implication for morphology of early Ornithuromorpha

Ornithuromorpha is the most derived avian group in the Early Cretaceous, advanced members of which encompass all living birds (Neornithes). Here we report on a new basal ornithuromorph bird, Bellulia rectusunguis gen. et sp. nov., represented by a nearly complete skeleton from the Early Cretaceous Jehol Biota in northeastern China. A comprehensive phylogenetic analysis resolved the new taxon in a basal position that is only more derived than Archaeorhynchus and Jianchangornis among ornithuromorphs, increasing the morphological diversity of basal ornithuromorphs. The new specimen has a V‐shaped furcula with a short hypocleidium, a feature otherwise known only in Schizooura among Cretaceous ornithuromorphs. We discuss the implications of the new taxon on the evolution of morphology of primitive ornithuromorphs, particularly of pectoral girdle, sternum and limb proportion pertaining to powered flight. The preserved gastroliths and pedal morphology indicate herbivory and lakeshore adaption for this new species. © 2015 The Linnean Society of London