Systematic affinities of the lyrebirds (Passeriformes: Menura), with a novel classification of the major groups of passerine birds

Phylogenetic relationships of the lyrebirds are investigated using DNA sequence data. The aligned data matrix consists of 4027 bp obtained from three nuclear genes (c-myc, RAG-1 and myoglobin intron II) and two mitochondrial genes (cytochrome b and ND2). Both maximum-likelihood and parsimony analyses show that the lyrebirds unambiguously belong to the oscine radiation, and that they are the sister taxon to all other oscines. The results do not support the suggestion based on DNA-DNA hybridization data (Sibley and Ahlquist, 1990) that the treecreepers and bowerbirds are part of the lyrebird clade. Nevertheless, treecreepers and bowerbirds are sister taxa to all other oscines (except the lyrebirds) and may constitute a monophyletic group, although bootstrap support values for this clade are low. A major disagreement between the present analysis and that based on DNA-DNA hybridization data is that the Corvida (sensu Sibley and Ahlquist, 1990) and Passerida are not reciprocally monophyletic, as we find the latter group be nested within the Corvida. Also, the superfamilies Meliphagoidea and Corvoidea sensu, are not recovered as monophyletic in the present study. Within the oscine radiation, all taxa belonging to the earliest splits are confined to the Australo-Papuan region. This suggests strongly that the origins and early radiation of the oscines occurred in the southern supercontinent Gondwana. A new classification of the major groups of passerines is presented following from the results presented in the present study, as well as those published recently on analyses of sequence data from the nuclear c-myc and RAG-1 genes (Ericson et al., 2002; Irestedt et al., 2001).     

Inter-familial relationships of the shorebirds (Aves: Charadriiformes) based on nuclear DNA sequence data

Background  

Phylogenetic hypotheses of higher-level relationships in the order Charadriiformes based on morphological data, partly disagree with those based on DNA-DNA hybridisation data. So far, these relationships have not been tested by analysis of DNA sequence data. Herein we utilize 1692 bp of aligned, nuclear DNA sequences obtained from 23 charadriiform species, representing 15 families. We also test earlier suggestions that bustards and sandgrouses may be nested with the charadriiforms. The data is analysed with methods based on the parsimony and maximum-likelihood criteria.     

Nuclear DNA from old collections of avian study skins reveals the evolutionary history of the Old World suboscines (Aves, Passeriformes)

Museum study skins represent an invaluable source of DNA for phylogenetics, phylogeography and population genetics. This becomes evident by comparing the number of study skins of birds housed in museums worldwide ( c . 10 million) with the corresponding number of tissue samples (probably fewer than 500 000). While the laboratory techniques used hitherto have primarily allowed PCR-based studies of mitochondrial genes from museum skins, we present here the first avian phylogeny based on a large number of nuclear sequences. The targeted fragment sizes and the properties of the primers used are important contributory factors to obtain good amplification results. In this study we routinely amplified fragments of c. 350 bp nuclear DNA. This advance in methodology opens up a new avenue for the use of avian museum skins, as nuclear DNA is especially useful when studying ancient patterns of diversification. The phylogenetic hypothesis of the Old World suboscines (Eurylaimides) presented herein strongly supports a monophyletic origin of the pittas (Pittidae). The phylogeny further suggests that pittas could be divided into three major groups, in agreement with the external morphological variation found in this group. The broadbills (Eurylaimidae) as currently defined are, on the other hand, found to be a paraphyletic family, as both Sapayoa aenigma and the asities (Philepittidae) are nested among them. Based on the phylogenetic results we suggest a revised classification of the Old World suboscines (Eurylaimides).     

Phylogeny of major lineages of suboscines (Passeriformes) analysed by nuclear DNA sequence data

Phylogenetic relationships among major groups of passeriform birds were studied by analyses of nucleotide sequence data from two nuclear genes, c- myc and RAG-1. The results corroborated both the monophyly of the order Passeriformes, and the major dichotomy into oscine and suboscine passerines previously suggested based on syringeal morphology and DNA-DNA hybridizations. The representatives of the Old World suboscines (families Eurylaimidae, Philepittidae and Pittidae) formed a monophyletic clade. The New World suboscines clustered into two clades. The first contained Conopophaga (Conopophagidae), Furnarius (Furnariidae), Lepidocolaptes (Dendrocolaptidae), Thamnophilus (Formicariidae), and Rhinocrypta (Rhinocryptidae). Previously, the monophyly of this group has been inferred from their possession of a unique, "tracheophone" syrinx, and from DNA-DNA hybridisation data. The second clade of New World suboscines includes Gubernetes and Muscivora (Tyrannidae), Phytotoma (Phytotomidae), Tityra (Cotingidae) and Pipra (Pipridae). This group of families have been considered monophyletic based on morphology (although ambiguously) and DNA-DNA hybridisation. The sister group relationship of Tityra and Phytotoma supports the previously supposed cotingid affinity of Phytotoma . Nuclear DNA data also unambiguously group the lyrebirds Menura with the oscines.
The presented results from the analysis of nuclear DNA agree well with morphology and DNA-DNA hybridisation data. The precise age of the divergences studied herein are unknown but based on interpretations of the fossil record of passerine birds many of them might date back to the early Tertiary. The agreement between data from the nuclear DNA and other sources, along with the fact that neither of the studied genes showed sign of saturation, indicate the great potential of these two nuclear genes to resolve very old divergences in birds.     

Clades within the ‘higher land birds’, evaluated by nuclear DNA sequences

In this study we investigated the phylogenetic relationships within the ‘higher land birds’ by parsimony analysis of nucleotide DNA sequences obtained from the two nuclear, protein-coding genes, c- myc and RAG-1. Nuclear genes have not previously been used to address this phylogenetic question. The results include high jackknife support for a monophyletic Apodiformes (including the Trochilidae). This arrangement was further supported by the observation of an insertion of four amino acids in the c- myc gene in all apodiform taxa. Monophyly was also inferred for each of the two piciform groups Galbulae and Pici. Within Pici, the Capitonidae was found to be paraphyletic, with the New World barbets more closely related to the Ramphastidae than to the Old World barbets. Another clade with high jackknife support consists of the Upupidae, Phoeniculidae and Bucerotidae. The families Momotidae and Todidae, and Coraciidae and Brachypteraciidae, respectively, also form well supported monophyletic clades. The results are inconclusive regarding the monophyly of the orders Coraciiformes and Piciformes, respectively.     

Sillem's Mountain Finch Leucosticte sillemi is a valid species of rosefinch (Carpodacus,Fringillidae)

Sillem's Mountain Finch Leucosticte sillemi was described in 1992 on the basis of an adult and an immature specimen collected in western Tibet in September 1929, but its taxonomic validity and phylogenetic position have been unclear. Based on phylogenetic analysis of mitochondrial DNA from the holotype, we show that L. sillemi is not a colour morph of Brandt's Mountain Finch Leucosticte brandti but represents a valid, previously overlooked species of rosefinch (Carpodacus) that has secondarily acquired a pale plumage convergent on that of Leucosticte. Sillem's Mountain Finch is one of the least known species of bird and represents the only known species of rosefinch in which males have no reddish plumage coloration. This species and its sister taxon, the Tibetan Rosefinch Carpodacus roborowskii, are likely to be the world's highest‐altitude sister‐species pair of birds.     

Complete taxon sampling of the avian genus Pica (magpies) reveals ancient relictual populations and synchronous Late‐Pleistocene demographic expansion across the Northern Hemisphere

Previous studies have suggested that bird populations in east Asia were less affected by Pleistocene climatic fluctuations than those in Europe and North America. However, this is mainly based on comparisons among species. It would be more relevant to analyse geographical populations of widespread species or species complexes. We analyzed two mitochondrial genes and two nuclear introns for all taxa of Pica to investigate 1) which Earth history factors have shaped the lineage divergence, and 2) whether different geographical populations were differently affected by the Pleistocene climatic changes. Our mitochondrial tree recovered three widespread lineages, 1) in east Asia, 2) across north Eurasia, and 3) in North America, respectively, with three isolated lineages in northwest Africa, Arabia and the Qinghai‐Tibet Plateau, respectively. Divergences among lineages took place 1.4–3.1 million yr ago. The northwest African population was sister to the others, which formed two main clades. In one of these, Arabia was sister to Qinghai‐Tibet, and these formed the sister clade to the east Asia clade. The other main clade comprised the North American and north Eurasian clades. There was no or very slight structure within these six geographical clades, including a lack of differentiation between the two North American species black‐billed magpie P. hudsonia and yellow‐billed magpie P. nutalli. Demographic expansion was recorded in the three most widespread lineages after 0.06 Ma. Asymmetric gene flow was recorded in the north Eurasian clade from southwestern Europe eastward, whereas the east Asian clade was rooted in south central China. Our results indicate that the fragmentation of the six clades of Pica was related to climatic cooling and aridification during periods of the Pliocene–Pleistocene. Populations on both sides of the Eurasian continent were similarly influenced by the Pleistocene climate changes and expanded concomitantly with the expansion of steppes. Based on results we also propose a revised taxonomy recognising seven species of Pica.     

Parallel evolution of lichen growth forms in the family Roccellaceae (Arthoniales, Ascomycota)

The phylogenetic relationships within the family Roccellaceae (lichen fungi) were investigated. Seventy‐two nucleotide sequences of the nuclear large subunit ribosomal RNA gene (LSU) and the second largest RNA polymerase subunit (RPB2) were newly obtained from 48 taxa. The family Roccellaceae was highly supported as monophyletic. The fruticose growth habit has evolved or been lost multiple times in the family and several times even within genera. In Roccellina with 31 species it has evolved three times and in Pentagenella with three species it has been lost once. The genera Roccella and Roccellina were found paraphyletic as two Roccella species nested with Roccellina. The non‐fruticose genus Roccellina was emended to include these two fruticose species as well as the monotypic, fruticose genus Roccellaria. As a result of the phylogenetic analyses six new nomenclatural combinations were made: Pentagenella corallina (Follm. and Peine) Tehler, Pentagenella ligulata (Peine and Follm.) Tehler, Roccellina cumingiana (Gay) Tehler, Roccellina hypomecha (Ach.) Tehler, Roccellina mollis (Hampe) Tehler, Roccellina portentosa (Mont. ex Gay) Tehler. Roccella is mainly distributed on the northern hemisphere while Roccellina is mainly distributed on the southern hemisphere. The Roccella species present on the Galapagos Islands are related to those in California and the northern hemisphere not, as was generally believed, to those in Chile and the southern hemisphere. The present data set may indicate that Bayesian analysis can give misleading topologies and overestimated posterior support values when insufficiently sampled taxa are included in an otherwise well sampled data set. © The Willi Hennig Society 2007.