Evolution of terrestrial birds in three continents: biogeography and parallel radiations

Aim To reconstruct the biogeographical history of a large clade of mainly terrestrially adapted birds (coraciiform and piciform birds, owls, diurnal raptors, New World vultures, trogons, mousebirds, cuckoo‐rollers, seriemas, parrots and passerines) to test the hypothesis of its Gondwanan origin. Location Global. Methods The phylogenetic tree used in the analysis was a family‐level tree estimated from previously published nuclear DNA sequence data. Each family for which a thorough and taxonomically well‐sampled phylogenetic analysis exists was subject to an initial dispersal–vicariance analysis in order to reconstruct ancestral areas for its two most basal lineages. Both basal lineages were then used to represent the family in the subsequent reconstruction of ancestral distributions for the entire radiation. Results The analysis showed that three reciprocally monophyletic groups of terrestrial birds have diversified in the Gondwanan land areas of Australia, South America and Africa, respectively. Although each of these three groups may also have originally included other groups, the only survivors today from the Australian radiation are the passerines and parrots, while the falcons and seriemas have survived from the South American radiation. The group of survivors from the African radiation is considerably more taxonomically diverse and includes all coraciiform and piciform birds, owls, diurnal raptors (except falcons), New World vultures, trogons, mousebirds and cuckoo‐rollers. Main conclusions The outlined evolutionary scenario with three geographically isolated clades of terrestrial birds is consistent with the available estimates of Late Cretaceous to early Palaeogene dates for these radiations. The diversifications and ecological adaptations within each of the three groups most likely took place in isolation on the different continents. Many cases of convergently evolved adaptations may be revealed through the increased understanding of the phylogenetic relationships of terrestrial birds.     

On the phylogenetic relationships of trogons (Aves, Trogonidae)

Although trogons (Aves, Trogonidae) are well characterized by the possession of heterodactyl feet, their phylogenetic relationships to other extant birds still are only poorly understood. Molecular studies did not show conclusive results and there are amazingly few comparative studies of the anatomy of trogons. Virtually the only hypothesis on trogon relationships that was supported with derived morphological characters is a sister group relationship to alcediniform birds (bee-eaters, kingfishers, and allies), which share a derived morphology of the columella (ear-ossicle) with trogons. However, in this study a very similar columella is reported for the oilbird (Steatornithidae) and additional previously unrecognized derived osteological characters are presented, which are shared by trogons and oilbirds. A numerical cladistic analysis of 28 morphological characters also resulted in monophyly of Trogonidae and Steatornithidae, although the corresponding node was not retained in a bootstrap analysis.     

Phylogenetic relationships within the turacos (Musophagidae)

Cytochrome b sequences were used to investigate both the systematic position of the Musophagidae and the species relationships within the family. Phylogenetic analyses (neighbour-joining, maximum likelihood and maximum parsimony) supported the hypothesis that the Musophagidae are more closely related to the cuckoos, parrots and the Hoatzin than the gamebirds. Within the family, three major clades are evident that correspond to the three subfamilies generally recognized. The 'grey turacos' and the turacin-bearing turacos form two separate monophyletic groups. Corythaixoides leucogaster appears to be basal within the subfamily Criniferinae (the 'grey turacos'). This analysis yields a hypothesis for the controversy surrounding the position of Gallirex porphyreolophus and Tauraco johnstoni, which appear to be closely related and basal to the other turacin-bearing turacos. The Musophaga species are placed within the Tauraco clade and appear to be specialized forms of typical turacos. The superspecies persa forms a monophyletic group, within which T. hartlaubi falls. This is an association that has not been suggested previously.     

Toward resolving deep neoaves phylogeny: data, signal enhancement, and priors

We report three developments toward resolving the challenge of the apparent basal polytomy of neoavian birds. First, we describe improved conditional down-weighting techniques to reduce noise relative to signal for deeper divergences and find increased agreement between data sets. Second, we present formulae for calculating the probabilities of finding predefined groupings in the optimal tree. Finally, we report a significant increase in data: nine new mitochondrial (mt) genomes (the dollarbird, New Zealand kingfisher, great potoo, Australian owlet-nightjar, white-tailed trogon, barn owl, a roadrunner [a ground cuckoo], New Zealand long-tailed cuckoo, and the peach-faced lovebird) and together they provide data for each of the six main groups of Neoaves proposed by Cracraft J (2001). We use his six main groups of modern birds as priors for evaluation of results. These include passerines, cuckoos, parrots, and three other groups termed "WoodKing" (woodpeckers/rollers/kingfishers), "SCA" (owls/potoos/owlet-nightjars/hummingbirds/swifts), and "Conglomerati." In general, the support is highly significant with just two exceptions, the owls move from the "SCA" group to the raptors, particularly accipitrids (buzzards/eagles) and the osprey, and the shorebirds may be an independent group from the rest of the "Conglomerati". Molecular dating mt genomes support a major diversification of at least 12 neoavian lineages in the Late Cretaceous. Our results form a basis for further testing with both nuclear-coding sequences and rare genomic changes.     

A re-evaluation of basal phylogenetic relationships within trogons (Aves: Trogonidae) based on nuclear DNA sequences

The avian clade Trogonidae (trogons) consists of approximately 40 species distributed pantropically in the Neotropical, Afrotropical and Indomalayan zoogeographical regions. In this study, we evaluate the basal phylogenetic relationships within the trogons based on DNA sequences from three nuclear introns [myoglobin intron 2, β -fibrinogen intron 7 and glyceraldehydes-3-phosphodehydrogenase (G3PDH) intron 11]. In addition, previously published cytochrome b and 12S sequences were re-analysed and combined with the nuclear data set. The analysis of the three nuclear genes combined suggests a sister group relationship between the Afrotropical ( Apaloderma ) and Indomalayan ( Harpactes ) clades, whereas the Neotropical taxa ( Trogon , Pharomachrus , and Priotelus ) form an unresolved polytomy basal to these two groups. In addition, two of the three individual gene trees also support a sister group relationship between the Afrotropical and Indomalayan trogons. This is at odds with previously published studies based on mitochondrial sequence data and DNA–DNA hybridization. The third nuclear intron (G3PDH), however, suggests that the Afrotropical trogons are basal relative the other trogons. This was also suggested by the mitochondrial data set, as well as the analysis of the combined nuclear and mitochondrial data. Both of these conflicting hypotheses are supported by high posterior probabilities. An insertion in β -fibrinogen further supports a basal position of the Afrotropical clade. Analyses of the myoglobin intron with additional outgroups place the root differently and strongly support monophyly of each of the zoogeographical regions (including the Neotropics), and these three clades form a basal trichotomy. This suggests that that rooting is a serious problem in resolving basal phylogenetic relationships among the trogons.     

Structure and Evolution of the Mitochondrial DNA Complete Control Region in the Lizard <Emphasis Type="Italic">Lacerta dugesii</Emphasis> (Lacertidae,Sauria)

We sequenced the complete control region (CR) and adjacent tRNAs, partial 12S rRNA, and cytochrome b (over 3100 bp) from eight individuals of Madeiran wall lizards, Lacerta dugesii, from four distinct island populations. The tRNAs exhibit a high degree of intraspecific polymorphisms compared to other vertebrates. All CR sequences include a minisatellite that varies in length between populations but is apparently fixed within them. Variation in minisatellite length appears between populations separated by apparently very short evolutionary time spans. Many motifs identified in the CR of other vertebrates are not highly conserved, although conserved blocks are identifiable between the few published reptile CR sequences. Overall there are extensive differences in the internal organization of the reptile CR compared to the more widely studied mammals and birds. Variability in the CR is lower than in cytochrome b, but higher than in 12S rRNA. Phylogenetic analysis of these sequences produces a well-resolved estimate of relationships between populations.     

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.     

Molecular analysis off the phylogeny off 11 genera off the Corvidae

Phylogenetic analysis of 11 genera of Corvidae has been undertaken using a sequence of 925 bp of the cytochrome b gene of the mtDNA. Both maximum-parsimony and maximum-likelihood analyses were performed, and different weighting schemes have been used according to the saturation observed in the data (mostly at the third codon position). The cytochrome b data provide good evidence for the monophyly of the Corvidae, including the Piapiac Ptilostomus afer in spite of its aberrant morphology. In all analyses, the choughs are the first lineage emerging in the family; this result conflicts with the traditional chough-crow group, as well as the hypothesis of the ancestral position of the jays. The monophyly of the American jays is well supported by the molecular data, unlike the Palearctic jays, which are not closely related. The other intergeneric relationships are not strongly supported by bootstrap proportions, and are not congruent in all different weightings and methods, except for groups of species of the same or very closely related genera.     

Molecular phylogeny of short-tailed shrews, Blarina (Insectivora: Soricidae)

Phylogenetic relationships among the three described species of short-tailed shrews (genus Blarina) were inferred based on mitochondrial DNA sequences of 16S rRNA (506 bp) and cytochrome b (1137 bp) from 38 specimens representing B. brevicauda, B. hylophaga, and B. carolinensis, from across their range in North America. Phylogenetic analyses of both data sets combined followed tests showing lack of incongruence between these fragments. Analysis of substitution patterns indicated saturation of transitions at third codon positions in cytochrome b when Blarina sequences were compared to those of Sorex and Cryptotis, used as outgroups. Maximum-likelihood and weighted parsimony supported the monophyly of the genus and placed B. hylophaga as its basal branch, sister to B. brevicauda + B. carolinensis. Phylogeographic analysis revealed a significant partition between eastern and western populations of B. carolinensis and B. brevicauda, on either side of the Mississippi basin. These results are discussed in relation to cytogenetic, morphological, and fossil data.     

Molecular phylogeny of cuckoos supports a polyphyletic origin of brood parasitism

We constructed a molecular phylogeny of 15 species of cuckoos using mitochondrial DNA sequences spanning 553 nucleotide bases of the cytochrome b gene and 298 nucleotide bases of the ND2 gene. A parallel analysis for the cytochrome b gene including published sequences in the Genbank database was performed. Phylogenetic analyses of the sequences were done using parsimony, a sequence distance method (Fitch-Margoliash), and a character-state method which uses probabilities (maximum likelihood). Phenograms support the monophyly of three major clades: Cuculinae, Phaenicophaeinae and Neomorphinae-Crotophaginae. Clamator, a strictly parasitic genus traditionally included within the Cuculinae, groups together with Coccyzus (a nonobligate parasite) and some nesting cuckoos. Tapera and Dromococcyx, the parasitic cuckoos from the New World, appear as sister genera, close to New World cuckoos: Neomorphinae and Crotophaginae. Based on the results, and being conscious that a more strict resolution of the relationships among the three major clades is required, we postulate that brood parasitism has a polyphyletic origin in the Cuculiformes, with parasite species being found within the three defined clades. Evidence suggests that species within each clade share a common parasitic ancestor, but some show partial or total loss of brood parasitic behaviour.     

Among-site rate variation and phylogenetic analysis of 12S rRNA in sigmodontine rodents

We analyze sequences from two mitochondrial genes, cytochrome b (cyt b) and 12S rRNA (12S), for a group of sigmodontine rodents among which phylogenetic relationships are well understood based on concordance of morphological, chromosomal, allozyme, and other DNA data sets. Because these two genes are physically linked on the nonrecombining mitochondrial genome, they necessarily share the same history. Phylogenetic analysis of the cyt b gene recovers the well-corroborated relationships, generally with strong support. None of the methods that we employed, including variously weighted parsimony, neighbor joining on both single-rate and gamma-corrected distances, and maximum likelihood, were able to recover these relationships for the 12S gene. Parsimony analyses of the 12S data resulted in a relatively strongly supported placement of Peromyscus eremicus that conflicts with that suggested by cyt b and all other data. There is extreme among-site rate variation in the 12S sequences and moderate levels in the cyt b sequences. This highly skewed distribution of rates in the 12S gene makes phylogenetic analyses of these sequences particularly susceptible to the misleading effects of nonindependence and other nonrandom noise, suggesting that phylogenetic analyses of data sets that contain a great deal of among-site rate variation be interpreted with caution.      

Structure and Evolution of the Mitochondrial DNA Complete Control Region in the Lizard Lacerta dugesii (Lacertidae, Sauria)

Abstract We sequenced the complete control region (CR) and adjacent tRNAs, partial 12S rRNA, and cytochrome b (over 3100 bp) from eight individuals of Madeiran wall lizards, Lacerta dugesii, from four distinct island populations. The tRNAs exhibit a high degree of intraspecific polymorphisms compared to other vertebrates. All CR sequences include a minisatellite that varies in length between populations but is apparently fixed within them. Variation in minisatellite length appears between populations separated by apparently very short evolutionary time spans. Many motifs identified in the CR of other vertebrates are not highly conserved, although conserved blocks are identifiable between the few published reptile CR sequences. Overall there are extensive differences in the internal organization of the reptile CR compared to the more widely studied mammals and birds. Variability in the CR is lower than in cytochrome b, but higher than in 12S rRNA. Phylogenetic analysis of these sequences produces a well-resolved estimate of relationships between populations.     

Testing hypotheses about the sister group of the passeriformes using an independent 30-locus data set

Although many phylogenetic studies have focused on developing hypotheses about relationships, advances in data collection and computation have increased the feasibility of collecting large independent data sets to rigorously test controversial hypotheses or carefully assess artifacts that may be misleading. One such relationship in need of independent evaluation is the position of Passeriformes (perching birds) in avian phylogeny. This order comprises more than half of all extant birds, and it includes one of the most important avian model systems (the zebra finch). Recent large-scale studies using morphology, mitochondrial, and nuclear sequence data have generated very different hypotheses about the sister group of Passeriformes, and all conflict with an older hypothesis generated using DNA-DNA hybridization. We used novel data from 30 nuclear loci, primarily introns, for 28 taxa to evaluate five major a priori hypotheses regarding the phylogenetic position of Passeriformes. Although previous studies have suggested that nuclear introns are ideal for the resolution of ancient avian relationships, introns have also been criticized because of the potential for alignment ambiguities and the loss of signal due to saturation. To examine these issues, we generated multiple alignments using several alignment programs, varying alignment parameters, and using guide trees that reflected the different a priori hypotheses. Although different alignments and analyses yielded slightly different results, our analyses excluded all but one of the five a priori hypotheses. In many cases, the passerines were sister to the Psittaciformes (parrots), and taxa were members of a larger clade that includes Falconidae (falcons) and Cariamidae (seriemas). However, the position of Coliiformes (mousebirds) was highly unstable in our analyses of 30 loci, and this represented the primary source of incongruence among analyses. Mousebirds were united with passerines or parrots in some analyses, suggesting an additional hypothesis that needs to be considered in future studies. There was no clear evidence that base-compositional convergence, saturation, or long-branch attraction affected our conclusions. These results provide independent evidence excluding four major hypotheses about the position of passerines, allowing the extensive studies on this group to be placed in a more rigorous evolutionary framework.     

Phylogeny of the genus Apodemus with a special emphasis on the subgenus Sylvaemus using the nuclear IRBP gene and two mitochondrial markers: cytochrome b and 12S rRNA

Phylogenetic relationships among 17 extant species of Murinae, with special reference to the genus Apodemus, were investigated using sequence data from the nuclear protein-coding gene IRBP (15 species) and the two mitochondrial genes cytochrome b and 12S rRNA (17 species). The analysis of the three genes does not resolve the relationships between Mus, Apodemus, and Rattus but separates Micromys from these three genera. The analysis of the two mitochondrial regions supported an association between Apodemus and Tokudaia and indicated that these two genera are more closely related to Mus than to Rattus or Micromys. Within Apodemus, the mitochondrial data sets indicated that 8 of the 9 species analyzed can be sorted into two main groups: an Apodemus group, with A. agrarius, semotus, and peninsulae, and a Sylvaemus group, with uralensis, flavicollis, alpicola, sylvaticus, and hermonensis. The position of Apodemus mystacinus is ambiguous and might be either included in Sylvaemus or considered a distinct subgenus, Karstomys, more closely related to Sylvaemus than to Apodemus. Estimation of the divergence time for these taxa suggests a separation between 7 and 8 My ago for the three groups (mystacinus and the two subgenera Apodemus and Sylvaemus). Within each subgenus, divergence times are between 5.4 and 6 My for Apodemus and between 2.2 and 3.5 My for Sylvaemus and mystacinus.     

Weak phylogenetic effects on ecological niches of Sylvia warblers

To understand the evolution of ecological niches it is important to know whether niche evolution is constrained by phylogeny. We approached this question for Sylvia warblers by testing if closely related species are more similar in 20 ecologically relevant morphological traits than distantly related species. Phylogenetic relatedness was quantified using a molecular phylogeny based on the mitochondrial cytochrome b gene. By Principal Component Analysis (PCA) two major niche axes were extracted. We tested the individual ecomorphological traits and the positions of the species on the PCA axes for phylogenetic effects using Mantel tests. The results demonstrated small but significant phylogenetic effects only for the length of the middle toe, a trait probably correlated with locomotion. In general, however, phylogenetic effects were very weak. This suggests that ecological niches in passerine birds have the potential to evolve rapidly and are not subject to major phylogenetic constraints.     

Molecular phylogenetics of Iberian wall lizards (Podarcis): is Podarcis hispanica a species complex?

Phylogenetic relationships between species and morphotypes of Podarcis wall lizards from the Iberian Peninsula and north Africa were estimated using partial 12S rRNA and cytochrome b mitochondrial DNA sequences. All species except Podarcis hispanica form monophyletic units. P. hispanica is paraphyletic, although all identified morphotypes are monophyletic. These morphotypes represent highly divergent lineages showing 10-15% pairwise sequence divergence with the cytochrome b gene. The data suggest that P. hispanica is a species complex. We recommend using P. hispanica* until additional sampling delimits the number and ranges of species currently referred to P. hispanica. P. carbonelli, which has recently been raised to species status, is confirmed as a genetically distinct form. P. atrata is genetically distinct, but much more closely related to some populations of P. hispanica than previously thought.     

The mtDNA sequence of the ostrich and the divergence between paleognathous and neognathous birds

The complete mitochondrial DNA (mtDNA) molecule of the ostrich, Struthio camelus, was sequenced. The size of the molecule is 16,591 nucleotides. Since the ostrich represents the paleognathous birds, comparison with the mtDNA of the neognathous chicken, the only avian species reported so far in databases, made it possible to identify common and, probably, general avian mtDNA characteristics. Relative to other vertebrates, the avian NADH6 and tRNA-Glu genes are positioned upstream of the control region rather than the cytochrome b gene. The NADH3 gene of the ostrich is terminated by a stop codon at position 207. Thus, the gene is about 140 nucleotides shorter than in other vertebrates. The sequence for L-strand origin of replication is missing in both birds, and four transfer RNA genes of the two avian mtDNAs deviate from common characteristics of tRNAs of vertebrate mtDNAs by having an adenine (and not a thymidine) at position 8. Due to the absence of suitable fossils, most paleontological datings of avian divergences are conjectural. Molecular dating of the divergence between the ostrich and the chicken indicates that these two avian lineages separated 80-90 MYA. Phylogenetic analysis of complete cytochrome b genes of six avian orders showed that Passeriformes represent the earliest divergence among recent birds, contradicting the commonly accepted notion of a basal position of the Palaeognathae among recent birds.      

A comparison of cytochrome b and DNA hybridization data bearing on the phylogeny of swallows (Aves: Hirundinidae)

Cytochrome b sequence data from 17 species representing 16 genera of swallows (Aves: Hirundinidae) were compared with DNA-DNA hybridization data from the same species in a taxonomic congruence assessment of swallow phylogeny. In the process, subsets (partitions) of the cytochrome b sequence data were examined in light of the DNA hybridization distances to assess their potential phylogenetic informativeness. When the sequence data were weighted-with or without reference to the DNA hybridization data-they produced parsimony and maximum likelihood (but not distance) trees that were largely congruent with the DNA hybridization tree. To this extent, the cytochrome b data supported many of the phylogenetic conclusions based on the DNA hybridization tree and vice versa. However, the cytochrome b data produced largely unresolved trees when branch robustness was tested by bootstrapping and other methods. This poor resolution appeared to be caused by a lack of hierarchical structure in the cytochrome b distances, which were confined to a narrow range (between 10-13%), compressed by saturation, and noisy. Partition analysis by codon sites and protein domains yielded typical avian cytochrome b patterns, except for idiosyncrasies attributable to the genetic divergence level of swallows in comparison to other groups of birds whose cytochrome b sequences have been analyzed.     

Molecular systematics of the genus Megoura (Hemiptera: Aphididae) using mitochondrial and nuclear DNA sequences

To construct the molecular systematics of the genus Megoura (Hemiptera: Aphididae), DNA based-identifi-cation was performed using four mitochondrial and three nuclear DNA regions: partial cytochrome c oxidase I (COI), partial tRNA-leucine + cytochrome c oxidase II (tRNA/COII), cytochrome b (CytB), partial 12S rRNA + tRNA-valine + 16S rRNA (12S/16S), elongation factor-1 alpha (EF1 alpha), and the internal transcribed spacers 1 and 2 (ITS1, ITS2). Pairwise sequence divergences between taxa were compared, and phylogenetic analyses were performed based on each DNA region separately, and the combined datasets. COI, CytB, EF1 alpha, ITS1, and ITS2 were relatively effective in determining species and resolving their relationships. By contrast, the sequences of tRNA/COII and 12S/16S were not able to separate the closely related species. CytB and EF1alpha gave better resolution with higher average sequence divergences (4.7% for CytB, 5.2% for EF1 alpha). The sequence divergence of COI (3.0%) was moderate, and those of the two ITS regions (1.8% for ITS1, 2.0% for ITS2) were very low. Phylogenetic trees were constructed by minimum evolution, maximum parsimony, maximum likelihood, and Bayesian phylogenetic analyses. The results indicated that the phylogenetic relationships between Megoura species were associated with their host preferences. Megoura brevipilosa and M. lespedezae living on Lespedeza were closely related, and M. nigra, monophagous on Vicia venosa, was rather different from M. crassicauda, M. litoralis, and M. viciae, which are oligophagous on Lathyrus and Vicia. The three populations of M. crassicauda formed a clade separated from M. litoralis and M. viciae. Nevertheless M. litoralis and M. viciae, which are morphologically similar, were not separated due to negligible sequence divergence. We discuss the phylogenetic relationships of the Megoura, and the usefulness of the seven DNA regions for determining the species level phylogeny of aphids.     

Molecular Phylogeny of Mitochondrial Cytochrome b and 12S rRNA Sequences in the Felidae: Ocelot and Domestic Cat Lineages

Molecular phylogeny of the cat family Felidae is derived using two mitochondrial genes, cytochrome b and 12S rRNA. Phylogenetic methods of weighted maximum parsimony and minimum evolution estimated by neighbor-joining are employed to reconstruct topologies among 20 extant felid species. Sequence analyses of 363 bp of cytochrome b and 376 bp of the 12S rRNA genes yielded average pair-wise similarity values between felids ranging from 94 to 99% and from 85 to 99%, respectively. Phylogenetic reconstruction supports more recent, intralineage associations but fails to completely resolve interlineage relationships. Both genes produce a monophyletic group ofFelisspecies but vary in the placement of the pallas cat. The ocelot lineage represents an early divergence within the Felidae, with strong associations between ocelot and margay, Geoffroy's cat and kodkod, and pampas cat and tigrina. Implications of the relative recency of felid evolution, presence of ancestral polymorphisms, and influence of outgroups in placement of the topological root are discussed.