Molecular phylogeny and evolutionary history of the tit-tyrants (Aves: Tyrannidae)

Tit-tyrants of the genus Anairetes presently consist of six species; five inhabit various regions along the Andean cordillera of South America and one is endemic to the Juan Fernandez Islands off the coast of Chile. Data from mtDNA ND2 and Cyt b sequences were used to construct a phylogeny for all Anairetes species as well as Uromyias agilis, a closely related genus, and Stigmatura as an outgroup, to determine their relationships and history of radiation in South America. Results strongly supported the following paired relationships: A. nigrocristatus-A. reguloides, A. flavirostris-A. alpinus, and A. parulus-A. fernandezianus. This dataset, however, could not resolve basal nodes; therefore relationships among these pairs remains obscure. Moreover the genus Uromyias, controversially separated on morphological criteria from Anairetes, fell within the Anairetes clade, although its exact position could not be ascertained with confidence. The molecular data indicate that this group probably radiated within the past 2 million years, concomitant with highly accentuated cycles of global climatic change. Certain high altitude areas within the Andes may have been stable during global climatic changes and may have served as refugia during the Plio-Pleistocene.     

Enigmatic phylogeny of skuas (Aves:Stercorariidae)

Multiple sources of evidence show that the skuas (Aves:Stercorariidae) are a monophyletic group, closely related to gulls (Laridae. On morphological and behavioural evidence the Stercorariidae are divided into two widely divergent genera, Catharacta and Stercorarius, consistent with observed levels of nuclear and mitochondrial gene divergence. Catharacta skuas are large-bodied and with one exception breed in the Southern Hemisphere. Stercorarius skuas otherwise known as jaegers) are smaller bodied and breed exclusively in the Northern Hemisphere. Evidence from both mitochondrial and nuclear genomes and from ectoparasitic lice (Insecta:Phthiraptera) shows that the Pomarine skua, S. pomarinus, which has been recognized as being somewhat intermediate in certain morphological and behavioural characteristics, is much more closely related to species in the genus Catharacta, especially to the Northern Hemisphere-breeding Great skua, C. skua, than it is to the other two Stercorarius skuas, the Arctic skua, S. parasiticus and the Longtailed skua, S. longicaudus. Three possible explanations that might account for this discordant aspect of skua phylogeny are explored. These involve (i) the segregation of ancestral polymorphism, (ii) convergent evolution of morphology and behaviour or (iii) inter-generic hybridization. The available evidence from both nuclear and mitochondrial genomes does not exclude any of these hypotheses. Thus, resolution of this enigma of skua phylogeny awaits further work.     

Non-monophyly of the avian genus Seicercus (Aves: Sylviidae) revealed by mitochondrial DNA

The phylogeny of all species and nearly all subspecies of Seicercus and representatives of all subgenera in Phylloscopus was estimated based on two mitochondrial genes. According to the gene tree, and supported by non-molecular data, Seicercus belongs in three separate clades. Two of these include only taxa currently classified as Seicercus , while the third comprises S. xanthoschistos and P. occipitalis . These results suggest that both Seicercus and Phylloscopus are paraphyletic. The gene tree suggests two more cases of non-monophyly: (1) the ' S. burkii complex' is separated into two different clades, one of which also includes S. affinis and S. poliogenys ; (2) two populations of S. affinis intermedius are more closely related to S. affinis ocularis than to a third population of intermedius . A recent proposal to split the ' S. burkii complex' into six species is corroborated, as is the recognition of the taxon cognitus as a colour morph of S. affinis intermedius . Our study also revealed unexpectedly large genetic divergences between three different populations of the monotypic S. poliogenys , indicating the presence of cryptic species. Our results underscore the importance of dense sampling at the specific and infraspecific levels in intrageneric phylogenetic studies.     

Molecular phylogeny of the genus Buteo (Aves: Accipitridae) based on mitochondrial marker sequences

DNA sequences of the mitochondrial nd6 gene and the non-repetitive part of the pseudo-control region (PsiCR) were isolated from 101 individuals to analyze the phylogenetic relationships among all buzzards of the genus Buteo and other buteonine genera. Comparisons of the two marker sequences indicate that the PsiCR evolved two times faster than the nd6 gene. The PsiCR proved to be an efficient, neutral genetic marker sequence for phylogenetic analyses at the intrageneric level, especially suitable for analyses based on old tissues, where only short fragments can be obtained. The molecular data set implies a neotropical origin of the genus Buteo. Monophyly of the genus Buteo as currently defined is contradicted due to the positions of Asturina nitida, Geranoaetus melanoleucus, Buteo magnirostris, and Buteo leucorrhous. These findings suggest several taxonomic consequences. A. nitida and G. melanoleucus should be included into the genus Buteo. Moreover, B. leucorrhous should be transferred into the genus Percnohierax (which clusters with Parabuteo), and B. magnirostris into the genus Rupornis. According to this classification of the genus Buteo, the basal lineage of the genus is formed by a clade containing Buteo polyosoma, Buteo poecilochrous, and Buteo melanoleucus. The "woodland buteos" form a paraphyletic assemblage with B. magnirostris as a clearly separated lineage basal to the genus Buteo.     

Molecular Systematics of the Malagasy Babblers (Passeriformes: Timaliidae) and Warblers (Passeriformes: Sylviidae), Based on Cytochrome b and 16S rRNA Sequences

The phylogenetic relationships of the Timaliidae (babblers) and Sylviidae (warblers) have long challenged ornithologists. We focus here on three Malagasy genera currently assigned to the Timaliidae, Mystacornis, Oxylabes, and Neomixis, and on their relationships with other babblers and warblers using the sequences of two mitochondrial genes (cytochrome b and 16S rRNA). Maximum parsimony analyses show that the Malagasy “babblers” are not related to any of the other African and Asian babblers. The genus Mystacornis is neither a babbler nor a warbler. The other Malagasy “babblers” are members of warbler groups (the monophyly of the Sylviidae is not demonstrated). Oxylabes madagascariensis and Hartertula flavoviridis (we recognize Hartertula as a genus for the species flavoviridis, previously Neomixis flavoviridis) constitute, with two presumed sylviine taxa, Thamnornis chloropetoides and Cryptosylvicola randrianasoloi, a warbler radiation endemic to the island of Madagascar. The other Neomixis species (tenella, striatigula, and viridis) belong to another warbler group comprising cisticoline taxa. These results show that the Timaliidae did not disperse to Madagascar. Rather, the island has been colonized, independently, by at least two clades of warblers, probably originating from Africa, where the Sylviidae radiation has been the most extensive.     

Foods of the Dartford warbler Sylvia undata on southern English heathland (Aves: Sylviidae)

This paper describes the invertebrates of Callunetum and gorse on lowland heaths in Dorset and relates how these were exploited by the Dartford warbler Sylvia undata , a scarce bird of interest to nature conservation and one of the small number of wholly insectivorous resident passerines in Britain. Gorse had a denser invertebrate fauna than Callunetum and was used for feeding at a frequency out of proportion to its abundance. Diets of adult birds closely reflected the taxonomic composition of the gorse and Callunetum faunas exploited in the observed proportions, though some noxious taxa were avoided and below a certain limit, creatures of above average size were selected. Major foods were beetles, spiders, lepidopteran larvae and bugs. Nestling birds received a diet differing in taxonomic composition and size from that of the adults, and variations between habitats were found which accorded with observations on the habitat preferences of the Dartford warbler. An experimental investigation showed the importance of gorse as a source of food for young and the adults flew considerable distances ignoring extensive deep stands of heather nearer to the nest. The possible influence of competing insectivorous vertebrates on Dartford warblers is discussed. Various mammals and reptiles appeared to be the major vertebrate predators in Callunetum, but little competition was anticipated in gorse. Scarcity of gorse on the heaths and low densities of invertebrates in heather explained the low densities at which Dartford warblers occur.     

Molecular phylogeny of songbirds (Aves: Passeriformes) and the relative utility of common nuclear marker loci

While the monophyly of the largest avian order Passeriformes as well as its suborders suboscines (Tyranni) and oscines (Passeri) is well established, lower phylogenetic relationships of this fast radiated taxon have been a continuous matter of debate, especially within the suborder oscines. Many studies analyzing phylogenetic relationships of the Passeriformes using molecular markers have been published, which led to a better resolved phylogeny. Conflicting hypotheses and still remaining uncertainties, especially within the Passerida, have repeatedly stimulated further research with additional new markers. In the present study we used a combination of established molecular markers (RAG‐1, RAG‐2, c‐myc) and the recently introduced ZENK. We accomplished phylogenetic analyses using maximum parsimony, maximum likelihood and Bayesian inference, both separately for all genes and simultaneously. To assess the phylogenetic utility of the different genes in avian systematics we analyzed the influence of each data partition on the phylogenetic tree yielded by the combined approach using partitioned Bremer support. Compared with the other single gene analyses, the ZENK trees exhibited by far the best resolution and showed the lowest amount of homoplasy. Our data indicate that this gene is—at least in passerines—suitable for inference of even old taxonomic splits. Our combined analysis yields well‐supported phylogenetic hypotheses for passerine phylogeny and apart from corroborating recently proposed hypotheses on phylogenetic relationships in the Passeriformes we provide evidence for some new hypotheses. The subdivision of the Passerida into three superfamilies, Sylvioidea, Passeroidea and Muscicapoidea, the first as sister to the two latter groups is strongly supported. We found evidence for a split between Paridae and the remaining Sylvioidea. © The Willi Hennig Society 2007.     

Molecular phylogeny and the historical biogeography of the warblers of the genus Sylvia (Aves)

A molecular phylogeny based on DNA/DNA hybridization revealed that the Sylvia-Parisoma complex is monophyletic and includes three main groups of species, the “mid-European” warblers, the genus Parisoma, and the “eu-Mediterranean” Sylvia species sensu stricto. The latter can be assigned to three main clusters, a “West-Mediterranean” group, a “Central-Mediterranean group”, and an “East-Mediterranean” group. The radiation of the whole complex is much more ancient than formerly believed. It started ca 12–13 Ma ago and the ancestors of the main extant groups differentiated during the Pliocene. Only speciation events within the “eu-Mediterranean” lineages occurred during the Pleistocene. The paleoclimatical and paleoecological history of the Mediterranean region is too complicated to provide any evidence for direct relationships between past events and evolutionary steps of these taxa which did not leave any reliable fossil record. However, some major speciation events may be related to well documented climatical crises as well as paleobotanical data. The largely man-induced extension of matorrals over several millenia presumably extended the range of several species that were formerly much more restricted, which complicates reconstruction of the spatio-temporal course of speciation.     

A multilocus phylogeny of the Sulidae (Aves: Pelecaniformes)

Gene trees will often differ from the true species history, the species tree, as a result of processes such as incomplete lineage sorting. New methods such as Bayesian Estimation of the Species Tree (BEST) use the multispecies coalescent to model lineage sorting, and directly infer the species tree from multilocus DNA sequence data. The Sulidae (Aves: Pelecaniformes) is a family of ten booby and gannet species with a global distribution. We sequenced five nuclear intron loci and one mitochondrial locus to estimate a species tree for the Sulidae using both BEST and by concatenating nuclear loci. We also used fossil calibrated strict and relaxed molecular clocks in BEAST to estimate divergence times for major nodes in the sulid phylogeny. Individual gene trees showed little phylogenetic conflict but varied in resolution. With the exception of the mitochondrial gene tree, no gene tree was completely resolved. On the other hand, both the BEST and concatenated species trees were highly resolved, strongly supported, and topologically consistent with each other. The three sulid genera (Morus, Sula, Papasula) were monophyletic and the relationships within genera were mostly consistent with both a previously estimated mtDNA gene tree and the mtDNA gene tree estimated here. However, our species trees conflicted with the mtDNA gene trees in the relationships among the three genera. Most notably, we find that the endemic and endangered Abbott's booby (Papasula abbotti) is likely basal to all other members of the Sulidae and diverged from them approximately 22 million years ago.     

A molecular phylogeny of the cotingas (Aves: Cotingidae)

The phylogenetic relationships of members of Cotingidae were investigated using >2100 bp of sequence data from two nuclear introns (myoglobin intron 2 and G3PDH intron 11) and one protein-coding mitochondrial gene (cytochrome b). Strong support was found for a monophyletic clade including 23 traditional cotingid genera, corresponding to the Cotingidae sensu [Remsen, J.V. Jr., Jaramillo, A., Nores, M., Pacheco, J.F., Robbins, M.B., Schulenberg, T.S., Stiles, F.G., da Silva, J.M.C., Stotz, D.F., Zimmer, K.J., 2005. Version 2005-11-15. A classification of the bird species of South America. American Ornithologists' Union. ]. Neither Oxyruncus nor any of the genera in Tityrinae sensu [Prum, R.O, Lanyon, W.E., 1989. Monophyly and phylogeny of the Schiffornis group (Tyrannoidea). Condor 91, 444-461.] are members of Cotingidae. Within Cotingidae a polytomy of four well-supported clades was recovered: (1) the fruiteaters Pipreola and Ampelioides; (2) the Ampelion group, including Phytotoma; (3) Rupicola and Phoenicircus; and (4) the 'core cotingas' consisting of the remainder of the Cotingas (e.g. fruitcrows, Cotinga, Procnias, Lipaugus, and Carpodectes), with Snowornis in a basal position. The separation of Snowornis from Lipaugus [Prum, R.O, Lanyon, W.E., 1989. Monophyly and phylogeny of the Schiffornis group (Tyrannoidea). Condor 91, 444-461.] was strongly supported, as were the close relationships between Gymnoderus and Conioptilon, and between Tijuca and Lipaugus. However, basal relationships among 'core cotinga' clades were not resolved.     

Molecular phylogeny and systematics of Neotropical toucanets in the genus Aulacorhynchus (Aves,Ramphastidae)

Bonaccorso, E., Guayasamin, J. M., Peterson, A. T. & Navarro‐Sigüenza, A. G. (2011). Molecular phylogeny and systematics of Neotropical toucanets in the genus Aulacorhynchus (Aves, Ramphastidae). —Zoologica Scripta, 40, 336–349. We studied the phylogenetic relationships in the genus Aulacorhynchus, an assemblage of Neotropical toucanets distributed from Mexico south to Bolivia. Based on mitochondrial and nuclear DNA characters, we obtained a robust hypothesis of relationships for all recognized species, including good representation of distinct geographic populations. Our results support the monophyly of the genus Aulacorhynchus, but contradict previous taxonomic arrangements. The genus is made up of three major clades: the Aulacorhynchus prasinus complex, Aulacorhynchus huallagae + Aulacorhynchus coeruleicinctis, and Aulacorhynchus haematopygus + Aulacorhynchus sulcatus + Aulacorhynchus derbianus. Andean populations of A. derbianus are more closely related to A. sulcatus than to Pantepuian populations of A. derbianus, rendering A. derbianus paraphyletic. Based on the molecular phylogeny, and information on geographic distributions and morphological and behavioural characters, we review the specific status of these taxa and propose a new taxonomic arrangement within Aulacorhynchus.     

Isolation and characterization of microsatellite markers in Ijima's leaf warbler,Phylloscopus ijimae (Aves: Sylviidae)

Microsatellite markers were isolated from Ijima's leaf warbler, Phylloscopus ijimae. From an enriched genomic library and using the fast isolation by AFLP of sequences containing repeats (FIASCO) method, 10 polymorphic loci were obtained. Four to 12 alleles were identified in an analysis of 23 Ijima's leaf warblers, with the degree of heterozygosity ranging from 0.35 to 0.87. The markers were tested in four species of Phylloscopus and two other non‐Phylloscopus species of Sylviidae. Some loci were successfully amplified and showed polymorphism in Phylloscopus species, whereas amplification in the non‐Phylloscopus species was less successful.     

Ultraconserved elements resolve the phylogeny of potoos (Aves: Nyctibiidae)

In this study, we apply a genome‐scale set of molecular markers, ultraconserved elements, to fully resolve the phylogeny of a family of secretive, nocturnal birds, the potoos (Nyctibiidae). This dataset provides an opportunity to explore some challenges of phylogenetic analyses of genome‐scale datasets, which we address in several ways. We generate data matrices ranging between 2610–4175 loci (1 477 319–3 848 295 aligned base pairs) that represent versions of the data differing in whether or not alignments were trimmed prior to concatenation, and whether 100 or 75% of all taxa were required to be represented by data for inclusion of a given locus. These matrices are analyzed with both maximum likelihood and coalescent algorithms, to check for artifacts of concatenation. Then, we subsample our data matrix by locus into randomly‐selected replicates of 125–1000 loci, and compare the topologies and statistical support of the resulting trees to look for evidence of systematic error. In analyses of complete matrices, we find strong statistical support for all ingroup nodes of the tree with no evidence for systematic error introduced by alignment trimming, missing data, or concatenation. We find further support for that topology in our subsampling analyses and statistical topology tests. The earliest branch of the tree separates Nyctibius bracteatus from the rest of the potoos, followed successively by N. grandis and N. aethereus. Two pairs of species, N. jamaicensis plus N. griseus, and N. leucopterus plus N. aethereus comprise the distal tips of the tree. Finally, we compare our strongly supported topology to those of previous studies, and use the phylogeny to examine the evolutionary history of potoos.     

Complete phylogeny and historical biogeography of true rosefinches (Aves: Carpodacus)

True rosefinches (Aves: Carpodacus) are restricted to Eurasia, and 19 out of 25 species occur in the Sino‐Himalayas, making this the likely centre of origin. To test this hypothesis, suggested species splits had to be evaluated and potential further cryptic diversity unravelled. A taxon‐complete dated molecular phylogeny was reconstructed using maximum‐likelihood and Bayesian methods. Maximum‐parsimony and likelihood approaches were applied to deduce ancestral areas. Rosefinches, including the widespread Carpodacus erythrinus (Pallas, 1770), originated in south‐west China (and the Himalayas) 14 Mya, and gave rise to a smaller clade consisting of C. erythrinus, Haematospiza sipahi (Hodgson, 1836), and Chaunoproctus ferreorostris (Vigors, 1829), and a larger clade with 22 species. The latter split into four major lineages through vicariance during the uplift of the Himalayas. The suggested species splits of dubius from Carpodacus thura Bonaparte & Schlegel, 1850, formosanus from Carpodacus vinaceus Verreaux, 1871, grandis from Carpodacus rhodochlamys Brandt, 1843, verreauxii from Carpodacus rodopeplus (Vigors, 1831) (even polyphyletic) could be supported, whereas the suggested split of severtzovi from Carpodacus rubicilla (Güldenstädt, 1775) appears to be too young, and should be considered intraspecific. On the other hand, the central Asian lineage of Carpodacus synoicus Temminck, 1825 deserves species rank [Carpodacus stolickae (Hume, 1874)]. The Carpodacus eos/pulcherrimus complex consists of four lineages, pulcherrimus/argyrophrys and davidianus [Carpodacus pulcherrimus s.s. (Moore, 1856)], and eos and waltoni [Carpodacus waltoni (Sharpe, 1905)]. © 2013 The Linnean Society of London     

A phylogenetic analysis of the evolution of moult strategies in Western Palearctic warblers (Aves: Sylviidae)

Adult birds replace their flight feathers (moult) at least once per year, either in summer after termination of breeding or (in the case of some long-distance migratory species) in the winter quarters. We reconstructed the evolutionary pathways leading to summer and winter moult using recently published molecular phylogenetic information on the relationships of the Western Palearctic warblers (Aves: Sylviidae). Our phylogenetic analysis indicates that summer moult is the ancestral pattern and that winter moult has evolved 7–10 times in this clade. As taxa increased their migratory distance and colonized northern breeding areas, summer moult disappeared and winter moult evolved. Our data also allows us to trace the historical origins of unusual moult patterns such as the split-moult and biannual moult strategies: the most parsimonous explanations for their origins is that they evolved from ancestral states of summer moult. We briefly discuss our results in the light of recent criticisms against phylogenetic comparative methods and the utility of historical versus functional definitions of adapation.     

Enemy Recognition of Reed Warblers (Acrocephalus scirpaceus): Threats and Reproductive Value Act Independently in Nest Defence Modulation

Organisms should respond more aggressively towards species perceived as a danger to their offspring, but intensity of defence may be gauged by the value of current offspring weighed against the value of future reproductive opportunities. We tested whether defensive responses of nesting reed warblers (Acrocephalus scirpaceus) are the result of an interaction effect between the type of stimulus confronted and the value of the warbler’s nesting attempt. We quantified the ability of reed warblers to discriminate among brood parasites, nestling predators and non‐threatening species at different stages of the breeding cycle. We also determined whether variables that influence the value of offspring, such as time of season, size and age of clutch or brood, and time of day and number of visits to the nest, explain variation in the intensity of defence recorded during the egg and nestling stages. Responses to the three stimuli differed significantly, as reed warblers consistently directed their mobbing calls and attacks towards parasites, whereas they were less conspicuous when confronted with models of predators. Reed warblers modulated their responses towards each stimulus in accordance with the threat each posed at a specific nesting stage, whereas they were not affected by other variables relative to their reproductive potential. The churr call, however, was uttered independently of the stimulus, as it was triggered by the mere presence of nestlings in the nest.     

Skeletal morphology and the phylogeny of skuas (Aves: Charadriiformes,Stercorariidae)

The skuas (Aves: Charadriiformes, Stercorariidae) consist of two assemblages. On the basis of size, plumage, and distributional similarities, each of the two assemblages has long been considered monophyletic, and this traditional hypothesis has commonly been manifested in the recognition of two genera, Stercorarius and Catharacta; conversely, more recently collected molecular and ectoparasite evidence yields an alternative hypothesis, in which one member of Stercorarius, Stercorarius pomarinus, is more closely related to the forms in Catharacta than to the other Stercorarius sp. In this study we used skeletal morphology to test the competing hypotheses of skua phylogeny. Cladistic analysis of 141 osteological characters provided strong support for the molecular/ectoparasite hypothesis. However, those skeletal data did not support a sister‐taxon relationship between S. pomarinus and Catharacta skua, as inferred from mitochondrial DNA sequence data; instead, they resolved pomarinus as the sister of a monophyletic Catharacta. Additionally, our skeletal evidence did not support a sister‐group relationship between skuas and auks, as constraining skua/auk monophyly increased the tree length by nearly 5%. © 2009 The Linnean Society of London, Zoological Journal of the Linnean Society, 2009, 157 , 612–621.     

The radiation of the Seicercus burkii complex and its congeners (Aves: Sylviidae): molecular genetics and bioacoustics

Cryptic species of passerine birds lack notable morphological differentiation and can best be identified by molecular and bioacoustic markers. Here we investigate seven cryptic species of the golden-spectacled warbler (Seicercus burkii complex) with respect to territorial song and cytochrome-b (cyt-b) sequences. Their phylogenetic relations to other Seicercus species and to members of the genus Phylloscopus are inferred by the same methods. Three separate lineages of Seicercus are nested within different branches of the molecular Phylloscopus tree. The S. burkii complex is a monophyletic unit comprising seven species (S. burkii s. str., S. whistleri, S. valentini, S. soror, S. omeiensis, S. tephrocephalus and S. affinis). S. xanthoschistos turned out to be a close relative of Phylloscopus davisoni within the P. reguloides group. Two isolated sister taxa, S. grammiceps and S. castaniceps, also branch together with the P. reguloides group. Within the S. burkii complex the overall haplotype and nucleotide diversity is highest in taxa from the Chinese middle and upper mountain belt (S. valentini, S. omeiensis and S. soror), indicating at least partially restricted gene flow in these species. This is explained by the fragmentation of high-altitude habitats in China while in the Himalayas the vicariant species S. whistleri inhabits a more continuous mountain belt at the same altitude. For the Chinese species from medium and high altitudes, past range expansion is indicated by significantly negative Tajima Ds. According to pairwise genetic distances, most species of the S. burkii complex have diverged 5 myr ago, the most recent split between S. burkii and S. tephrocephalus is dated 2 myr ago. Coalescence times for haplotype lineages of the different species range from 9 up to 12 myr, and between 5 and 6 myr for S. burkii and S. tephrocephalus.

Within Seicercus divergence of song features such as frequency parameters and syntax structures correlate with genetic distances between taxa. The three cyt-b lineages of Seicercus correspond to different clusters in a discriminant analysis by acoustic parameters. Common syntax structures of territorial song in the Phylloscopus/Seicercus assemblage are: (1) an introductory element derived from specific calls and (2) a syntax of trills and repeated element groups or a combination of both. There are clear indications that these song structures have repeatedly emerged, were lost or were altered in different branches of the phylogenetic tree at different times. Absolute differences between taxa in frequency parameters or in an acoustic divergence index increase significantly with growing genetic distances. However, due to multiple parallel evolution phylogenetic information provided by single acoustic traits decreases with increasing numbers of taxa involved in the investigation.