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.     

Birds in a bush: five genes indicate explosive evolution of avian orders

All recent studies of bird phylogeny have produced poorly resolved relationships among the orders of Neoaves, the lineage that includes most modern birds. This "bush" result suggests the possibility of an explosive and potentially unresolvable evolutionary radiation. However, simultaneous radiations of multiple lineages are thought to be rare or nonexistent in nature and difficult to corroborate empirically because lack of phylogenetic resolution can also be caused by analytical artifacts. Here we examine the predictions of the explosive radiation hypothesis for five independent genetic datasets for Neoaves. We propose a methodology for testing for polytomies of evolutionary lineages, perform likelihood-ratio tests to compare trees with zero-length branches to more resolved trees, compare topologies between independent gene trees, and propose a power test for the SOWH test. The evidence of (1) extremely short (in some cases zero-length) branches for interordinal relationships across independent gene trees and (2) topological incongruence among gene trees suggests that the bird tree includes essentially simultaneous radiation of multiple lineages. This result explains why a robust phylogeny of birds has not been produced despite much effort on the part of avian systematists.     

Two new avian mitochondrial genomes (penguin and goose) and a summary of bird and reptile mitogenomic features

We report complete mitochondrial (mt) genomes for a penguin (little blue, Eudyptula minor) and a goose (greater white-fronted, Anser albifrons). A revised annotation of avian and reptile mt genomes has been carried out, which improves consistency of labeling gene start and stop positions. In conjunction with this, a summary of mt gene features is presented and a number of conserved patterns and interesting differences identified. The protein-coding genes from the two new genomes were analysed together with those from 17 other birds plus outgroup (reptile) taxa. The unrooted amino acid tree from 19 avian genomes was locally stable with many high bootstrap values using several maximum likelihood methods. In particular, Anseriformes (goose and duck) grouped strongly with Galliformes (chicken) to form Gallianseres, while the penguin paired firmly with the stork. The position where the outgroup joined the avian tree varied with the combination of outgroup taxa used. The three best supported positions of the root were passerine, but the traditional rooting position between paleognaths and neognaths could not be excluded.     

Competition, predation and nest niche shifts among tropical cavity nesters: phylogeny and natural history evolution of parrots (Psittaciformes) and trogons (Trogoniformes)

Nest site selection by birds is a critically important life history trait as competition for suitable sites can be intense, and because birds are at their most vulnerable to predators during nesting. Previous studies show that the clutch size and nestling period evolve in response to competition for nest sites and nest predation, respectively. This provides the opportunity to study the relative contribution of competition and predation to the evolution of nesting niche. Using previously published phylogenies for parrots and trogons, I found evidence for at least 13 independent evolutionary transitions from tree cavities to alternative nesting niches (including termitaria, cliffs, and burrows). I analyzed variations in clutch size, incubation period and nestling period for 16 phylogenetically controlled pairs of species to test the relative roles of competition for tree cavities and nest predation, in favoring evolutionary switches to alternative nest sites. Tree cavity nesting species did not have larger clutch sizes as predicted if competition for tree cavities leads birds to invest heavily in nesting once they obtain a nest site (the limited breeding opportunities hypothesis). Instead I found that shifts to alternative nesting niches were accompanied by an increase in nestling period. As nestling period is a surrogate measure for long-term nest predation rates, this finding suggests that nest predation has been more important than competition in niche diversification among cavity nesting parrots and trogons. The timing of events in South America suggests that the explosive radiation of mammalian nest predators during the Upper-Oligocene, Lower-Miocene (20–30 million years ago) corresponded with the radiation of parrot and trogon taxa that exploit novel nesting niches.     

Bird evolution in the Eocene: climate change in Europe and a Danish fossil fauna

The pattern of the evolutionary radiation of modern birds (Neornithes) has been debated for more than 10 years. However, the early fossil record of birds from the Paleogene, in particular, the Lower Eocene, has only recently begun to be used in a phylogenetic context to address the dynamics of this major vertebrate radiation. The Cretaceous-Paleogene (K-P) extinction event dominates our understanding of early modern bird evolution, but climate change throughout the Eocene is known to have also played a major role. The Paleocene and Lower Eocene was a time of avian diversification as a result of favourable global climatic conditions. Deteriorations in climate beginning in the Middle Eocene appear to be responsible for the demise of previously widespread avian lineages like Lithornithiformes and Gastornithidae. Other groups, such as Galliformes display replacement of some lineages by others, probably related to adaptations to a drier climate. Finally, the combination of slowly deteriorating climatic conditions from the Middle Eocene onwards, appears to have slowed the evolutionary rate in Europe, as avian faunas did not differentiate markedly until the Oligocene. Taking biotic factors in tandem with the known Paleogene fossil record of Neornithes has recently begun to illuminate this evolutionary event. Well-preserved fossil taxa are required in combination with ever-improving phylogenetic hypotheses for the inter-relationships of modern birds founded on morphological characters. One key avifauna of this age, synthesised for the first time herein, is the Lower Eocene Fur Formation of Denmark. The Fur birds represent some of the best preserved (often in three dimensions and with soft tissues) known fossil records for major clades of modern birds. Clear phylogenetic assessment of these fossils will prove critical for future calibration of the neornithine evolutionary timescale. Some early diverging clades were clearly present in the Paleocene as evidenced directly by new fossil material alongside the phylogenetically constrained Lower Eocene taxa. A later Oligocene radiation of clades other than Passeriformes is not supported by available fossil data.     

Sex identification of parrots,toucans, and curassows by PCR: Perspectives for wild and captive population studies

Methods for the identification of the sex of bird species without external sexual dimorphism are specially important in field studies and for captive breeding of endangered taxa. We confirmed the accuracy of a polymerase chain reaction (PCR)-based method to identify the sex in three disparate avian orders that included 31 species of parrot, two species of toucan, and eight species of curassow, for which many individuals were previously sexed. In each case, two DNA fragments were amplified in females and one in males with the use of a single set of primers. This method was also tested on unsexed birds of 13 other species of parrot and five species of toucan. The same kind of polymorphism was detected in each. The PCR products of parrots and toucans could be separated in simple agarose gels, while the curassows' products could only be distinguished in acrylamide gels. An advantage of this DNA test is that samples of blood or feathers can be easily collected and stored at room temperature, which is of particular importance for studies of wild birds. Zoo Biol 17:415–423, 1998. © 1998 Wiley-Liss, Inc.     

Different contributions of birds and mammals to seed dispersal of a fleshy-fruited tree

Birds and mammals are important seed dispersers of fleshy-fruited plants. Although their behaviors are different, they frequently consume the same species. Thus to understand the dispersal of fleshy-fruited plants, the contribution of birds and mammals to seed dispersal has to be evaluated. Besides, within birds or mammals, some species may functionally different from others. In this study, we examined seed dispersal of the fleshy-fruited tree Swida controversa focusing on the difference between two frugivore groups (birds and mammals), and differences between species within groups. Collected seeds and S. controversa trees were identified using simple sequence repeat (SSR) genotyping, thus enabling to determine the distance between mother tree and dispersed seeds. The avian species were identified by DNA barcoding of feces, whereas the mammalian species were identified by the shape and smell of feces. Most seeds that fell near or under the maternal trees were dispersed by birds, resulting in short seed dispersal distances (average, 13 m). DNA barcoding detected five taxa of avian dispersers. No differences were detected in seed dispersal distance by different avian taxa (i.e., the distance between dispersed seeds and their maternal trees within the research plot); however the rate of seed immigration from outside the research plot by some avian taxa varied significantly. The seed dispersal distance by mammals was significantly further (127 m; min > 50 m) than that by birds. Additionally, immigrated seeds accounted for approximately two-thirds of mammal-dispersed seeds, indicating that these seeds were from outside the research plot, and that mammals significantly contributed to the long-distance seed dispersal of S. controversa. No differences in seed dispersal distance were detected between different mammalian taxa. Overall, this study revealed that birds and mammals show clearly different seed dispersal patterns, and thus, they play different roles in the regeneration of S. controversa.     

鸟类线粒体DNA研究概述

线粒体DNA作为理想的分子标记已被广泛用于鸟类种群遗传学和进化遗传学的研究,并取得了许多有意义的结果。本文介绍鸟类线粒体DNA的组成、结构特点及多态性的研究,综述近年来有关鸟类分子进化研究的进展情况,对今后的发展进行了初步的探讨。 Abstract:Mitochondrial DNA as a genetic marker has been successfully applied to the study of molecular evolution of birds.The apparently maternal inheritance of mitochondrial DNA and its fast evolution in primary sequence has made it attractive in population and evolutionary genetics.Mitochondrial DNA of birds displays two characteristics not seen in other vertebrates mtDNA,that is,a novel gene order and the absence of an equivalent to the light-strand replication origin.The research on polymorphism of mtDNA can resolve phylogenies of birds both at lower and higher taxonomic levels.Here we review progress on avian molecular evolution in recent years,and make preliminary studies of the development in this field.     

Explosive radiations and the reliability of molecular clocks: island endemic radiations as a test case

The reliability of molecular clocks has been questioned for several key evolutionary radiations on the basis that the clock might run fast in explosive radiations. Molecular date estimates for the radiations of metazoan phyla (the Cambrian explosion) and modern orders of mammals and birds are in many cases twice as old as the palaeontological evidence would suggest. Could some aspect of explosive radiations speed the molecular clock, making molecular date estimates too old? Here we use 19 independent instances of recent explosive radiations of island endemic taxa as a model system for testing the proposed influence of rapid adaptive radiation on the rate of molecular evolution. These radiations are often characterized by many of the potential mechanisms for fast rates in explosive radiations--such as small population size, elevated speciation rate, rapid rate of morphological change, release from previous ecological constraints, and adaptation to new niches--and represent a wide variety of species, islands, and genes. However, we find no evidence of a consistent increase in rates in island taxa compared to their mainland relatives, and therefore find no support for the hypothesis that the molecular clock runs fast in explosive radiations.     

The quality of the fossil record of Mesozoic birds

The Mesozoic fossil record has proved critical for understanding the early evolution and subsequent radiation of birds. Little is known, however, about its relative completeness: just how 'good' is the fossil record of birds from the Mesozoic? This question has come to prominence recently in the debate over differences in estimated dates of origin of major clades of birds from molecular and palaeontological data. Using a dataset comprising all known fossil taxa, we present analyses that go some way towards answering this question. Whereas avian diversity remains poorly represented in the Mesozoic, many relatively complete bird specimens have been discovered. New taxa have been added to the phylogenetic tree of basal birds, but its overall shape remains constant, suggesting that the broad outlines of early avian evolution are consistently represented: no stage in the Mesozoic is characterized by an overabundance of scrappy fossils compared with more complete specimens. Examples of Neornithes (modern orders) are known from later stages in the Cretaceous, but their fossils are rarer and scrappier than those of basal bird groups, which we suggest is a biological, rather than a geological, signal.     

The complete mitochondrial genomes of sixteen ardeid birds revealing the evolutionary process of the gene rearrangements

Background

The animal mitochondrial genome is generally considered to be under selection for both compactness and gene order conservation. As more mitochondrial genomes are sequenced, mitochondrial duplications and gene rearrangements have been frequently identified among diverse animal groups. Although several mechanisms of gene rearrangement have been proposed thus far, more observational evidence from major taxa is needed to validate specific mechanisms. In the current study, the complete mitochondrial DNA of sixteen bird species from the family Ardeidae was sequenced and the evolution of mitochondrial gene rearrangements was investigated. The mitochondrial genomes were then used to review the phylogenies of these ardeid birds.

Results

The complete mitochondrial genome sequences of the sixteen ardeid birds exhibited four distinct mitochondrial gene orders in which two of them, named as “duplicate tRNA^Glu–CR” and “duplicate tRNA^Thr–tRNA^Pro and CR”, were newly discovered. These gene rearrangements arose from an evolutionary process consistent with the tandem duplication - random loss model (TDRL). Additionally, duplications in these gene orders were near identical in nucleotide sequences within each individual, suggesting that they evolved in concert. Phylogenetic analyses of the sixteen ardeid species supported the idea that Ardea ibis, Ardea modesta and Ardea intermedia should be classified as genus Ardea, and Ixobrychus flavicollis as genus Ixobrychus, and indicated that within the subfamily Ardeinae, Nycticorax nycticorax is closely related to genus Egretta and that Ardeola bacchus and Butorides striatus are closely related to the genus Ardea.

Conclusions

The duplicate tRNAThr–CR gene order is found in most ardeid lineages, suggesting this gene order is the ancestral pattern within these birds and persisted in most lineages via concerted evolution. In two independent lineages, when the concerted evolution stopped in some subsections due to the accumulation of numerous substitutions and deletions, the duplicate tRNAThr–CR gene order was transformed into three other gene orders. The phylogenetic trees produced from concatenated rRNA and protein coding genes have high support values in most nodes, indicating that the mitochondrial genome sequences are promising markers for resolving the phylogenetic issues of ardeid birds when more taxa are added.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-573) contains supplementary material, which is available to authorized users.     

Seroepizootiology of selected infectious disease agents in free-living birds of prey in Germany

Four hundred forty-eight blood plasma samples from free-living birds of prey from Berlin and the Brandenburg area in eastern Germany were tested for antibodies against Newcastle disease virus (NDV), falcon herpesvirus (FHV), owl herpesvirus (OHV), and Chlamydia psittaci. Antibodies to NDV were detected in 6 (2%) of 346 tested diurnal birds of prey, whereas none of the owls (n = 55) was positive. The positive samples originated from two common buzzards (Buteo buteo), three ospreys (Pandion haliactus) and one marsh harrier (Circus aeruginosus). Titers varied between 1:8 and 1:32. Of 253 birds of prey one osprey (<1%) tested positive for antibodies to FHV with low titer of 1:6. This is the first detection of antibodies against FHV in an osprey. Furthermore, antibodies against OHV could be found in one tawny owl (Strix aluco) and one common buzzard (2 of 253, 1%) with low titers of 1:6. Of 422 birds of prey 267 (63%) tested positive for antibodies to Chlamydia psittaci with titers varying between 1:5 and 1:256 which reflects the ubiquitous occurrence of Chlamydia psittaci in these birds of prey.     

Three fundamental contributions of molecular genetics to avian ecology and evolution

Studies in molecular genetics are having revisionary impact in at least three broad areas of avian ecology and evolution: mating systems, geographic population structure and gene flow, and phylogenetic relationships among species and higher taxa. With regard to mating systems, genetic analyses of maternity and paternity have revealed unexpectedly high frequencies of extra-pair fertilization and intraspecific brood parasitism in numerous avian species (including those thought to be socially monogamous), and these discoveries are prompting a fundamental reshaping of mating system theory for birds. With regard to genetic structure, molecular markers have uncovered a great variety of depths and patterns in the phylogeographic histories of conspecific populations, and these findings provide novel perspectives on historical gene flow regimes and species concepts. With regard to evolutionary relationships among higher avian taxa, molecular findings have suggested several phylogenetic realignments, thus prompting renewed interest in the cross-comparative aspects of molecular and morphological evolution as well as of alternative procedures for molecular analysis.     

Three fundamental contributions of molecular genetics to avian ecology and evolution

Studies in molecular genetics are having revisionary impact in at least three broad areas of avian ecology and evolution: mating systems, geographic population structure and gene flow, and phylogenetic relationships among species and higher taxa. With regard to mating systems, genetic analyses of maternity and paternity have revealed unexpectedly high frequencies of extra-pair fertilization and intraspecific brood parasitism in numerous avian species (including those thought to be socially monogamous), and these discoveries are prompting a fundamental reshaping of mating system theory for birds. With regard to genetic structure, molecular markers have uncovered a great variety of depths and patterns in the phylogeographic histories of conspecific populations, and these findings provide novel perspectives on historical gene flow regimes and species concepts. With regard to evolutionary relationships among higher avian taxa, molecular findings have suggested several phylogenetic realignments, thus prompting renewed interest in the cross-comparative aspects of molecular and morphological evolution as well as of alternative procedures for molecular analysis.     

The roles of speciation and divergence time in the loss of duplicate gene expression

In 50 million years the tetraploid catostomid fishes have lost the expression of approximately half of their duplicate genes, with species rich taxa having lost more than species poor taxa. We have constructed a phylogenetic tree of the catostomids based primarily on morphological data, and have estimated the divergence times from the fossil record and genetic distances. The losses of duplicate gene expression were then analyzed conditionally given this tree. Three probabilistic models were generated to describe the process of loss of gene expression: gene dysfunction depends on (1) time alone, (2) the number of speciation events alone, or (3) a combination of speciation and time. A maximum likelihood analysis revealed that the two component model fits the data better than the other models. The loss of duplicate gene expression is mediated by null mutations at structural and/or regulatory genes, and the rate of fixation of these nulls might have been enhanced by any reductions in population size accompanying speciation events. This reduction may explain the lower number of duplicate genes expressed in the more speciose taxa.     

Mitochondrial resolution of a deep branch in the genealogical tree for perching birds.

Animal mitochondrial DNA (mtDNA) is known to contain information about the genealogical relations among closely related species and is shown here to yield information about distant relations as well. Our results also draw attention to the need for caution in using third positions of codons for tree construction. This is evident from comparative studies of the cytochrome b gene in 13 species representing major groups within the order of perching birds (Passeriformes). Sequences of a 924 base-pair segment of this gene were obtained from each of these species via the polymerase chain reaction and a novel set of versatile primers. With a woodpecker sequence as an outgroup, trees that separate songbirds from other perching birds and resolve the ancient branch leading to songbirds were obtained utilizing the conservative first and second positions of codons. Analysis of positions within codons suggests that, for deep branches, the skewed base composition at the fast-changing third positions can result in phylogenetic disinformation, which conflicts with the information retained in the first and second positions. The mitochondrial tree shows broad concordance with that based on hybridization of nuclear DNA; however, parsimony and maximum likelihood methods suggest a close kinship between thrushes and Australian babblers, in agreement with the traditional morphological classification.     

Rates of dinosaur limb evolution provide evidence for exceptional radiation in Mesozoic birds

Birds are the most diverse living tetrapod group and are a model of large-scale adaptive radiation. Neontological studies suggest a radiation within the avian crown group, long after the origin of flight. However, deep time patterns of bird evolution remain obscure because only limited fossil data have been considered. We analyse cladogenesis and limb evolution on the entire tree of Mesozoic theropods, documenting the dinosaur–bird transition and immediate origins of powered flight. Mesozoic birds inherited constraints on forelimb evolution from non-flying ancestors, and species diversification rates did not accelerate in the earliest flying taxa. However, Early Cretaceous short-tailed birds exhibit both phenotypic release of the hindlimb and increased diversification rates, unparalleled in magnitude at any other time in the first 155 Myr of theropod evolution. Thus, a Cretaceous adaptive radiation of stem-group birds was enabled by restructuring of the terrestrial locomotor module, which represents a key innovation. Our results suggest two phases of radiation in Avialae: with the Cretaceous diversification overwritten by extinctions of stem-group birds at the Cretaceous–Palaeogene boundary, and subsequent diversification of the crown group. Our findings illustrate the importance of fossil data for understanding the macroevolutionary processes generating modern biodiversity.     

New nuclear evidence for the oldest divergence among neognath birds: the phylogenetic utility of ZENK (i)

To date, there is little consensus concerning the phylogenetic relationships among neognath orders, which include all extant birds except ratites and tinamous. Different data sets, both molecular and morphologic, have yielded radically different and often unresolved ordinal topologies, especially within the neoaves clade. This lack of resolution and ongoing conflict indicates a need for additional phylogenetic characters to be applied to the question of higher-level avian phylogeny. In this study, sequences of a single-copy nuclear gene, ZENK, were used to reconstruct an ordinal-level phylogeny of neognath birds. Strong support was indicated for the oldest divergence within Neognathae; the chicken- and duck-like birds formed a clade that was sister to all other modern birds. In addition, many families of traditional taxonomic orders clustered together in the ZENK tree, indicating the gene's general phylogenetic reliability. However, within the neoaves clade, there was little support for relationships among orders, which is a result similar to all other recent molecular studies of higher-level avian phylogeny. This similarity among studies suggests the possibility of a rapid radiation of the major neoaves lineages. Despite the ongoing lack of neoaves resolution, ZENK's sequence divergence and base composition patterns indicate its general utility as a new phylogenetic marker for higher-level avian systematics.     

Two spinal cords in birds: novel insights into early avian evolution

Birds can be subdivided into two large superordinal assemblages based on differences in the dorsal horn of the spinal grey matter. Palaeognaths (i.e. ratites and tinamous), along with a few other orders of neognathous birds, exhibit the primitive dorsal horn state characteristic of other amniotes wherein cutaneous nerves form a single map of the body surface across the dorsal horn. In contrast, the vast majority of neognaths exhibit a novel, distinctly bifid dorsal horn wherein cutaneous nerves form not one, but two separate maps of the skin, each lying side-by-side. This unusual dorsal horn organization, which has been highly conserved and represents the derived state in birds, may identify a novel, major avian clade. These findings shed new light on historically problematic taxa and the early evolutionary branching sequence among living birds. Most notably, they reveal that the traditional orders Gruiformes, Columbiformes, Cuculiformes and Piciformes are unnatural assemblages. Further, in addition to palaeognaths, these findings suggest that most gruiforms, including buttonquails and mesites, as well as pigeons, cuckoos, woodpeckers and songbirds, represent ancient lineages whose ancestry predates the majority of ''modern'' birds. The phylogeny of living birds may thus be likened more to a dense bush than the traditional tree, with more than half of all living species arising from a basal side branch.