Phylogeny and biogeography of Oriolidae (Aves: Passeriformes)

Understanding oscine passerine dispersal patterns out of their Australian area of origin is hampered by a paucity of robust phylogenies. We constructed a molecular phylogeny of the oscine family, Oriolidae, which is distributed from Australia through to the Old World. We used the phylogeny to assess direction and timing of dispersal and whether dispersal can be linked with the well‐documented movements of geological terranes in the Indonesian Archipelago. We sampled 29 of 33 species of Oriolidae from fresh tissue and from toe pads from museum specimens, and examined two nuclear introns and two mitochondrial genes. Model‐based phylogenetic analyses yielded strong support for clades that generally mirrored classical systematics. Biogeographical analyses and divergence time estimates demonstrated that the family originated in the Australo‐Papuan region from where it dispersed first to Asia and then onwards to Africa and the Philippines before back‐colonising Asia and the Indonesian archipelago. Thus, contrary to several other avian families in the region, Oriolidae represents a sequential dispersal pattern from Australia to Africa via Asia. However, it is noteworthy that the Pacific islands and archipelagos remain uncolonised and that members inhabiting Wallacea are recent colonisers suggesting that Oriolidae are poorly adapted to island life.     

Systematic relationships and biogeography of the tracheophone suboscines (Aves: Passeriformes)

Based on their highly specialized "tracheophone" syrinx, the avian families Furnariidae (ovenbirds), Dendrocolaptidae (woodcreepers), Formicariidae (ground antbirds), Thamnophilidae (typical antbirds), Rhinocryptidae (tapaculos), and Conopophagidae (gnateaters) have long been recognized to constitute a monophyletic group of suboscine passerines. However, the monophyly of these families have been contested and their interrelationships are poorly understood, and this constrains the possibilities for interpreting adaptive tendencies in this very diverse group. In this study we present a higher-level phylogeny and classification for the tracheophone birds based on phylogenetic analyses of sequence data obtained from 32 ingroup taxa. Both mitochondrial (cytochrome b) and nuclear genes (c-myc, RAG-1, and myoglobin) have been sequenced, and more than 3000 bp were subjected to parsimony and maximum-likelihood analyses. The phylogenetic signals in the mitochondrial and nuclear genes were compared and found to be very similar. The results from the analysis of the combined dataset (all genes, but with transitions at third codon positions in the cytochrome b excluded) partly corroborate previous phylogenetic hypotheses, but several novel arrangements were also suggested. Especially interesting is the result that the genus Melanopareia represents a basal branch within the tracheophone group, positioned in the phylogenetic tree well away from the typical tapaculos with which it has been supposed to group. Other novel results include the observation that the ground antbirds are paraphyletic and that Sclerurus is the sister taxon to an ovenbird-woodcreeper clade. Patterns of generic richness within each clade suggest that the early differentiation of feeble-winged forest groups took place south of the Amazon Basin, while the more recent diversification was near the equator and (in tapaculos and ovenbirds) in the south of the continent.     

Phylogeny and biogeography of the core babblers (Aves: Timaliidae)

The avian family Timaliidae is a species rich and morphologically diverse component of African and Asian tropical forests. The morphological diversity within the family has attracted interest from ecologists and evolutionary biologists, but systematists have long suspected that this diversity might also mislead taxonomy, and recent molecular phylogenetic work has supported this hypothesis. We produced and analyzed a data set of 6 genes and almost 300 individuals to assess the evolutionary history of the family. Although phylogenetic analysis required extensive adjustment of program settings, we ultimately produced a well-resolved phylogeny for the family. The resulting phylogeny provided strong support for major subclades within the family but extensive paraphyly of genera. Only 3 genera represented by more than 3 species were monophyletic. Biogeographic reconstruction indicated a mainland Asian origin for the family and most major clades. Colonization of Africa, Sundaland, and the Philippines occurred relatively late in the family's history and was mostly unidirectional. Several putative babbler genera, such as Robsonius, Malia, Leonardina, and Micromacronus are only distantly related to the Timaliidae.     

Phylogeny and biogeography of the parrot genus Prioniturus (Aves: Psittaciformes)

The parrot genus Prioniturus occurs in the oceanic Philippines, Palawan and Wallacea, a geologically dynamic region with a complex history of land and sea. The described taxa of Prioniturus have been variously placed in different assemblages, and different numbers of species have been recognized. However, a phylogenetic framework is so far lacking. This would be the prerequisite to reconstructing dispersal and colonization patterns of Prioniturus across and within Wallacea and the Philippines. Following our robustly supported phylogenetic hypothesis based on two mitochondrial genes, we propose to treat Prioniturus mindorensis comb. nov. as well as Prioniturus montanus and Prioniturus waterstradti as separate species. In Prioniturus discurus discurus and Prioniturus discurus whiteheadi, further studies using additional data and specimens are necessary to clarify their taxonomic status. This result is congruent with other studies demonstrating that alpha diversity of the Philippine avifauna is strongly underestimated. According to our biogeographic reconstruction, Prioniturus has diversified by a complex combination of colonization of islands and subsequent divergence in allopatry among and within island groups. Dispersal between Sulawesi/Wallacea and the Philippines occurred twice and documents a rare case of faunal exchange between these two regions.     

Phylogeny of babblers (Aves, Passeriformes): major lineages, family limits and classification

Babblers, family Timaliidae, have long been subject to debate on systematic position, family limits and internal taxonomy. In this study, we use five molecular regions to estimate the relationships among a large proportion of genera traditionally placed in Timaliidae. We find good support for five main clades within this radiation, and propose a new classification, dividing the babblers into the families Sylviidae and Timaliidae. Within the latter family, four subfamilies are recognized: Zosteropinae, Timaliinae, Pellorneinae and Leiothrichinae. Several taxa, previously not studied with molecular data, are phylogenetically placed within Sylviidae or Timaliidae. This is, however, not the case for the genus Pnoepyga , for which we propose the family name Pnoepygidae fam. n.     

Phylogeny and biogeography of the genus Illadopsis (Passeriformes: Timaliidae) reveal the complexity of diversification of some African taxa

African jungle babblers or illadopsises, genus Illadopsis Heine, 1859, are small shy babblers which occupy the undergrowth of African humid forest habitats. The taxonomy of Illadopsis as well as its biogeography are currently poorly known because the morphological differentiation is rather subtle and no phylogenetic analysis has been undertaken. To investigate these issues, we sequenced four loci (mitochondrial ND2 and ND3, and nuclear myoglobin intron 2 and β-fibrinogen intron 5) for the seven species of Illadopsis . Our analyses retrieve the monophyly of Illadopsis and suggest that I. albipectus and I. cleaveri , I. puveli and I. rufescens , some individuals of I. rufipennis and I. pyrrhoptera are sister taxa respectively. I. fulvescens appears to be an isolated taxon and our data reveal several cases of "incipient speciation" among its populations. Our dating analyses, using a Bayesian relaxed-clock method, reveal that most splits in Illadopsis occurred synchronously around the Plio-Pleistocene transition, suggesting that some diversification events in African forest taxa took place before the onset of the large-amplitude climatic cycles of the Pleistocene epoch. Thus, the diversification of African taxa in time and space to be more complex than the Pleistocene time frame traditionally associated with the diversification of African forest taxa. Instead we observe a process of differentiation which roughly corresponds to the broadly hypothesised lowland refugia of upper Guinea, eastern and western Guinea-Congolia, although the time frame of this divergence well predates the Pleistocene epoch. Our results also suggest that deep genetic divergences do exist among species complexes of African birds which differ only slightly in morphological characters. As such, molecular analyses are powerful and essential tools if we are to construct the evolutionary history of such lineages in a meaningful manner.     

Phylogeny of Passerida (Aves: Passeriformes) based on nuclear and mitochondrial sequence data

Passerida is a monophyletic group of oscine passerines that includes almost 3500 species (about 36%) of all bird species in the world. The current understanding of higher-level relationships within Passerida is based on DNA-DNA hybridizations [C.G. Sibley, J.E. Ahlquist, Phylogeny and Classification of Birds, 1990, Yale University Press, New Haven, CT]. Our results are based on analyses of 3130 aligned nucleotide sequence data obtained from 48 ingroup and 13 outgroup genera. Three nuclear genes were sequenced: c-myc (498-510 bp), RAG-1 (930 bp), and myoglobin (693-722 bp), as well one mitochondrial gene; cytochrome b (879 bp). The data were analysed by parsimony, maximum-likelihood, and Bayesian inference. The African rockfowl and rockjumper are found to constitute the deepest branch within Passerida, but relationships among the other taxa are poorly resolved--only four major clades receive statistical support. One clade corresponds to Passeroidea of [C.G. Sibley, B.L. Monroe, Distribution and Taxonomy of Birds of the World, 1990, Yale University Press, New Haven, CT] and includes, e.g., flowerpeckers, sunbirds, accentors, weavers, estrilds, wagtails, finches, and sparrows. Starlings, mockingbirds, thrushes, Old World flycatchers, and dippers also group together in a clade corresponding to Muscicapoidea of Sibley and Monroe [op. cit.]. Monophyly of their Sylvioidea could not be corroborated--these taxa falls either into a clade with wrens, gnatcatchers, and nuthatches, or one with, e.g., warblers, bulbuls, babblers, and white-eyes. The tits, penduline tits, and waxwings belong to Passerida but have no close relatives among the taxa studied herein.     

Phylogeny, biogeography and a new taxonomy for the Gecarcinucoidea Rathbun, 1904 (Decapoda: Brachyura)

Phylogenetic relationships of gecarcinucoid freshwater crabs were investigated, based on morphology of the male second gonopod. In addition, a comparison of sequences from the mitochondrial large subunit rRNA gene helped to resolve the phylogeny of this group and relationships to other Old World freshwater crabs. As a result, we recognise two sister groups within the Gecarcinucoidea, the African Deckeniidae and the Asian Gecarcinucidae. Deckeniidae includes three monophyletic clades, the Deckeniinae in East Africa and on the Seychelles, the West African Globonautinae and the Malagasy Hydrothelphusinae. Gecarcinucidae comprises two sister groups, the Gecarcinucinae with representatives in Sri Lanka, India and southeast Asia, and the Parathelphusinae in India, southeast Asia, the Sundaic Islands and Australia. Interpretation of our phylogenetic results leads us to propose a new biogeographic hypothesis for the Gecarcinucoidea. Most likely, the gecarcinucoid freshwater crabs have an African origin; their distribution can be explained by successive events of dispersal. This model can be correlated with palaeogeographical and palaeoclimatological data for the Cenozoic, suggesting a gecarcinucoid dispersal to Asia via the “Lemurian Stepping-Stones”, a chain of islands in the West-Indian Ocean that were emergent in times of low sea levels during the Oligocene.     

Multi-locus phylogeny of the family Acrocephalidae (Aves: Passeriformes) – The traditional taxonomy overthrown

We present the first study of the warbler family Acrocephalidae based on one mitochondrial and three nuclear DNA loci, in total 2900 bp, including most or all of the species in three (Acrocephalus, Hippolais and Chloropeta) of the four genera and one species in the fourth genus (Nesillas) in this family. All three genera were suggested to be non-monophyletic, although the non-monophyly of Acrocephalus is not fully convincingly demonstrated. Six major clades were found, which agreed largely with the results from two earlier mitochondrial studies, and for which the names Hippolais, Iduna, Acrocephalus, Calamocichla, Notiocichla and Calamodus have been used. However, the results also revealed some new constellations, due to better resolution of deeper nodes and the inclusion of more taxa. The taxonomic implications are discussed.     

A nuclear DNA phylogeny and proposed taxonomic revision of African greenbuls (Aves, Passeriformes, Pycnonotidae)

The Pycnonotidae (bulbuls and greenbuls) comprise approximately 130 species and are widely distributed across Africa and Asia, mainly in evergreen thickets and forest. Recent molecular findings suggest a basal split between the African and the Asian species, although the three African Pycnonotus species are part of the Asian radiation and represent a relative recent immigration to Africa. In this study we investigate the phylogenetic relationships within the African clade, which with the exclusion of Pycnonotus contains approximately 50 species, of which the majority are placed in three large genera Andropadus , Phyllastrephus and Chlorocichla . We use three nuclear markers (myoglobin intron 2, ODC introns 6 and 7 along with intervening exon 7, and β-fibrinogen intron 5), together encompassing 2072 aligned positions, to infer the relationships within the African clade. The resulting tree is generally well supported and indicates that none of the three largest currently recognized genera are monophyletic. For instance, the species included in Andropadus represent three different clades that are not each other's closest relatives. The montane species currently placed in that genus form a strongly supported clade, which is sister to Ixonotus , Thescelocichla, Baeopogon and Chlorocichla , although within this clade the genus Chlorocichla is polyphyletic. The remaining Andropadus species fall into two groups, one of these with A . importunus and A . gracilirostris , which along with Calyptocichla serina form a basal branch in the African greenbul radiation. In support of some previous studies the Leaf-love ( Pyrrhurus scandens ) is placed within Phyllastrephus . We also propose a new classification that reflects the phylogenetic relationships among African greenbuls.     

Historical biogeography of tits (Aves: Paridae, Remizidae)

Tits (Aves: Paroidea) are distributed all over the northern hemisphere and tropical Africa, with highest species numbers in China and the Afrotropic. In order to find out if these areas are also the centers of origin, ancestral areas were reconstructed based on a molecular phylogeny. The Bayesian phylogenetic reconstruction was based on sequences for three mitochondrial genes and one nuclear gene. This phylogeny confirmed most of the results of previous studies, but also indicated that the Remizidae are not monophyletic and that, in particular, Cephalopyrus flammiceps is sister to the Paridae. Four approaches, parsimony- and likelihood-based ones, were applied to derive the areas occupied by ancestors of 75?% of the extant species for which sequence data were available. The common ancestor of the Paridae and the Remizidae inhabited tropical Africa and China. The Paridae, as well as most of its (sub)genera, originated in China, but Baeolophus originated in the Nearctic and Cyanistes in the Western Palearctic. Almost all biogeographic reconstruction methods produced similar results, but those which consider the likelihood of the transition from one area to another should be preferred.     

Extreme Endemic Radiation of the Malagasy Vangas (Aves: Passeriformes)

Phylogenetic relationships of the family Vangidae and representatives of several other passeriform families were inferred from 882 base positions of mitochondrial DNA sequences of 12S and 16S rRNA genes. Results indicated the monophyly of the Vangidae, which includes the genus Tylas, hitherto often placed in the family Pycnonotidae. Our results also revealed the Malagasy endemic Newtonia, a genus never previously assigned to the Vangidae, to be a member of this family. These results suggest the occurrence of an extensive in situ radiation of this family within Madagascar, and that the extant high diversity of this family is not the result of multiple colonizations from outside. The extremely high morphological and ecological diversification of the family seems to have been enhanced through the use and ultimate occupancy of vacant niches in this island. Received: 8 September 2000 / Accepted: 13 February 2001     

Regulation of numbers in the Great tit (Aves: Passeriformes)

The census data of the Great tit collected by Perrins (1965) and others in Marley Wood near Oxford are analysed for density-dependence. Clutch size and hatching success are density-dependent and sufficiently so to regulate the population at the observed level (assuming that there is in addition a fairly large density-independent mortality). There may also be some weak density-dependent mortality outside the breeding season. The density-dependent variations in clutch size are probably in the main due to shortage of available food and density-dependent hatching failure is caused by predation. Territorial behaviour has been shown experimentally to determine breeding density, and may produce a density-dependent effect outside the breeding season. These three factors are responsible for regulation of the Great tit population in Marley Wood.     

Phylogeny and evolution of the Australo-Papuan honeyeaters (Passeriformes, Meliphagidae)

We analyzed nucleotide variation at four loci for 75 species to produce a phylogenetic hypothesis for the Meliphagidae, and to examine the evolution and biogeographic history of the Meliphagidae. Both maximum parsimony and Bayesian methods of phylogenetic analysis were employed. The family was found to be monophyletic, though the genera Certhionyx, Anthochaera, and Phylidonyris were not. Four major clades were recovered and the spinebills (Acanthorhynchus) formed the sister clade to the remainder of the family in most analyses. The Australian endemic arid-adapted chats (Epthianura, Ashbyia) were found to be nested deeply within the family Meliphagidae. No evidence was found to support the hypothesis of separate New Guinean and Australian endemic radiations, nor of a close phylogenetic relationship between taxa from the New Guinea highlands and those from Australian northern rainforests.     

Phylogeny, taxonomy, and biogeography of the oriental pitvipers of the genus trimeresurus (reptilia: viperidae: crotalinae): a molecular perspective

Based on sequence variation in 806 bp of the mitochondrial 12S rRNA gene, phylogenetic relationships were inferred for 14 species of Trimeresurus (sensu lato) including all East Asian members. Samples analyzed also included representatives of all assemblages of species that are frequently treated as separate genera except for T. mangshanensis, a type species of the recently described monotypic genus Ermia. Results support some previous accounts chiefly from morphological studies, such as distinct divergence of T. wagleri from the remainder, and monophyly of T. mucrosquamatus, T. flavoviridis, T. jerdonii, T. elegans and T. tokarensis. On the other hand, our results negated a putative close affinity of T. monticola and T. okinavensis, and indicated the sister relationship of the latter with T. gracilis. Phylogenetic relationships revealed in this study suggested that the genus Trimeresurus dispersed into the Ryukyu region at least three times, and that T. flavoviridis and T. tokarensis from the central Ryukyus constitute a relict clade.     

Molecular phylogenetics and diversification of the genus Sporophila (Aves: Passeriformes)

The evolutionary affinities within and among many groups of nine-primaried oscines remain unresolved. One such group is Sporophila, a large genus of New World tanager-finches. Our study focused particularly on clarifying the relationship between this genus and a closely related one, Oryzoborus, and on examining the phylogenetic affinities of the "capuchinos," a group of 11 Sporophila species that share a similar male plumage coloration pattern. Our phylogenetic analyses, based on 498 bp of mitochondrial DNA sequence, indicated that: (1) Oryzoborus is embedded within a well-supported clade containing all Sporophila species, which strongly suggests that both genera should be merged, (2) the species of capuchinos comprise a monophyletic group, implying that the plumage patterns common to all probably arose only once, and (3) the capuchinos clade is comprised of two sub-clades, one including two species that are distributed in northern South America and the other one containing eight species that are present south of the Amazon River. Mean sequence divergence among the southern capuchinos species was extremely low, suggesting a rapid radiation within the last half-million years that may be related to the high level of sexual selection present in the genus and might have been promoted by marine ingressions and egressions that occurred in some southern coastal regions of South America in the Late Pleistocene.     

Molecular taxonomy of Brazilian tyrant-flycatchers (Passeriformes: Tyrannidae)

The tyrannids are one of the most diverse groups of birds in the world, and the most numerous suboscine family in the Neotropics. Reflecting such diversity, many taxonomic issues arise in this group, mainly due to morphological similarities, even among phylogenetically distant species. Other issues appear at higher taxonomic levels, mostly brought up by genetic studies, making systematics a rather inconclusive issue. This study looks into the use of DNA barcodes method to discriminate and identify Tyrannidae species occurring in the Atlantic Forest and Cerrado biomes of Brazil. We analysed 266 individuals of 71 tyrant‐flycatcher species from different geographical locations by sequencing 542 bp of the mtDNA COI gene. The great majority of the analysed species showed exclusive haplotypes, usually displaying low intraspecific diversity and high interspecific divergence. Only Casiornis fuscus and Casiornis rufus, suggested in some studies to belong to a single species, could not be phylogenetically separated. High intraspecific diversity was observed among Elaenia obscura individuals, which can suggest the existence of cryptic species in this taxon. The same was also observed for Suiriri suiriri, considered by some authors to comprise at least two species, and by others to be divided into three subspecies. Additionally, the use of sequences from voucher specimens allowed us to correct four misidentifications that had happened in the field. Our findings suggest a great power of the COI barcodes to discriminate species of the Tyrannidae family that are found in Brazil.     

Phylogeny and biogeography of the Vitrinidae (Gastropoda: Stylommatophora)

The phylogeny of the Vitrinidae is reconstructed in a cladistic analysis based on characters of the genitalia, the copulation behaviour and the radula. The genera with an atrial stimulator turned out to be the earliest branches of the Vitrinidae, whereas the genera with a glandula amatoria form a monophyletic, taxonomically apomorphic group. The differences between the proposed phylogeny and previous hypotheses are discussed. The ancestral areas of the Vitrinidae and its sister group, the limacoid slugs Boettgerillidae–Limacidae–Agriolimacidae, are estimated using weighted ancestral area analysis. The Vitrinidae and the limacoid slugs might have originated by a vicariance event between Central Europe and the Near East. © 2002 The Linnean Society of London. Zoological Journal of the Linnean Society , 2002, 134 , 347–358.     

An ancient African radiation of corvoid birds (Aves: Passeriformes) detected by mitochondrial and nuclear sequence data

The Malaconotidae, Platysteiridae and Vangidae represent an African and Malagasy assemblage of closely related corvoid taxa with distinctive morphology. Their relationships with their putative Asian closest relatives, and thus their biogeographic history, have not hitherto been thoroughly evaluated. We present evidence that the African and Malagasy groups originated through a single African colonization event c. 37.7 ± 4.6 Myr BP. Three main groups that differ in their foraging behaviour diverged c. 35.8 ± 4.5 Myr BP, suggesting that an African radiation occurred around that time. Several disperal events out of Africa to Madagascar (Vangidae) and Indo-Malaya ( Philentoma , Hemipus and Tephrodornis ) took place about 28.9 ± 4.0 Myr BP (Oligocene), a period when faunistic exchanges between Eurasia and Africa seem to have been common. Our estimation of the colonization of Madagascar by the Vangidae is 28.9 ± 4.0 Myr BP, in congruence with the estimated colonization of Madagascar by several African vertebrate groups (carnivorous mammals, snakes, sylvioid passerines, treefrogs, turtles).     

The preglossale of Passer (Aves: Passeriformes)--a skeletal neomorph

A skeletal neomorph – the preglossale – is described from the tip of the tongue in Passer. This medial unpaired skeletal element is a dorsally open trough articulating with the anterior tips of the paraglossalia and supporting the heavy epidermal pad of the seed-cup. The large paired Mm. hypoglossus anterior originate from the posterior half of the preglossale and insert onto the anterior bodies of the paired paraglossalia; they serve to depress the anterior portion of the preglossale. A regular pattern of dermal papillae is present in the seed-cup; these are arranged in about 20 rows of six to 8 papillae per row. Each papilla contains a series of Merkel cells and associated nerve endings (touch receptors). The seed-cup serves to orient and hold the seed in place while it is being husked; the battery of tactile receptors provides information on the position of the seed on the tongue. The preglossale serves to support the seed-cup and to change its shape – the curvature of the dorsal surface – as it is depressed relative to the paraglossalia. The paraglossale and associated features of the seed-cup in Passer would provide a valuable preparation to study a diversity of problems such as developmental interactions between endomesodermal and ecto-mesenchymal skeletal features, the ontogenetical development of Merkel cells, and the sensory physiology of Merkel cells and their associated nerve endings as tactile corpuscles.