Phylogeography of the Alcippe morrisonia (Aves: Timaliidae): long population history beyond late Pleistocene glaciations

Background  

The role of Pleistocene glacial oscillations in current biodiversity and distribution patterns varies with latitude, physical topology and population life history and has long been a topic of discussion. However, there had been little phylogeographical research in south China, where the geophysical complexity is associated with great biodiversity. A bird endemic in Southeast Asia, the Grey-cheeked Fulvetta, Alcippe morrisonia, has been reported to show deep genetic divergences among its seven subspecies. In the present study, we investigated the phylogeography of A. morrisonia to explore its population structure and evolutionary history, in order to gain insight into the effect of geological events on the speciation and diversity of birds endemic in south China.     

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.     

Isolation and characterization of microsatellite markers from reed parrotbill, Paradoxornis heudei (Aves: Timaliidae)

Eleven microsatellite markers were obtained from reed parrotbill, Paradoxornis heudei, using the fast isolation by AFLP of sequences containing repeats (FIASCO) method as part of an effort to compare levels of genetic diversity in different populations of China. Polymorphism levels ranged form 5 to 11 alleles (mean = 9.27) using 32 reed parrotbills, with the observed heterozygosity ranging from 0.037 to 0.80. Six loci were significant deviated from HWE and nine loci showed linkage equilibrium. The utility of these loci on two other Passeriformes species, vinous-throated parrotbill (P. webbianus) and oriental great reed warbler (Acrocephalus orientalis), were also tested.     

Comparative Phyloclimatic Analysis and Evolution of Ecological Niches in the Scimitar Babblers (Aves: Timaliidae: Pomatorhinus)

We present the first extensive and integrative analysis of niche evolution based on climatic variables and a dated molecular phylogeny of a heterogeneous avian group of Southeast Asian scimitar babblers of the genus Pomatorhinus. The four main clades of scimitar babblers have species that co-occur in similar areas across southern Asia but some have diverged at different timeframes, with the most recently evolved clade harboring the highest number of species. Ecological niche models and analysis of contributing variables within a phylogenetic framework indicate instances of convergent evolution of members of different clades onto similar ecological parameter space, as well as divergent evolution of members from within clades. Pomatorhinus species from different clades occupying Himalayan foothills show convergence towards similar climatic tolerances, whereas within a clade, allopatric sister-species occurring in the Himalayas have diverged to occupy different climatic parameter spaces. Comparisons of climatic tolerances of Himalayan foothills taxa with species distributed further south in Assam/Burma and Burma/Thailand indicate convergence towards similar parameter spaces in several climatic variables. Niche overlap was observed to be lower among species of the youngest clade (ruficollis) and higher among species of older clades (ferruginosus). Analysis of accumulation of ecological disparity through time indicates rapid divergence within recent time frames. As a result, Himalayan taxa originating at different temporal scales within the four main scimitar babbler clades have differentiated ecologically only in recently diverged taxa. Our study suggests that the repeated orogenic and climatic fluctuations of the Pliocene and Pleistocene within mainland Southeast Asia served as an important ecological speciation driver within scimitar babblers, by providing opportunities for rapid geographic expansion and filling of novel environmental niches.     

Morphotypes or distinct species? A multilocus assessment of two East Asian scimitar babblers (Aves,Timaliidae)

In birds, widespread species complexes often exhibit dramatic plumage differences across their distribution, which can give rise to discordance between morphotypes and phylogroups. Accurate identification of species diversity may require an integrated approach in which multilocus genetic data are used for inference and further corroborated by ecological, morphometric or behavioural data. Pomatorhinus gravivox and P. swinhoei, which were formerly considered component races of P. erythrogenys, were recently split using a delimitation system that mainly relied on the quantification of differences in phenotypic traits. We therefore carried out a reassessment of this taxonomic recommendation by conducting phylogenetic and population genetic analyses with multilocus genetic data. A deep mitochondrial split with a Kimura 2-parameter distance of 0.061 was observed, mainly corresponding to the two morphologically defined species. However, one individual from P. swinhoei harboured a haplotype of P. gravivox. Individual-based analyses of nuclear loci identified two distinct clusters that were exactly congruent with the two species. BPP delimitation also provided support for the separation. These congruencies support the notion that these two taxa are best regarded as two separate species. The presence of the P. gravivox mitochondrial haplotype in P. swinhoei was most likely a result of hybridization, due to the clear separation of nuclear loci. The speciation might be attributed to paleoclimatic changes but requires further evaluation due to the likelihood of ecological speciation. This study was in accordance with the results inferred from the quantitative system but highlighted the importance of sampling various data, especially in contact zones, in the study of taxonomy and speciation history.     

Molecular systematics and diversification of the Asian scimitar babblers (Timaliidae, Aves) based on mitochondrial and nuclear DNA sequences

The Asian scimitar babblers, including the genus Pomatorhinus and Xiphirhynchus, are a small group of babblers characterized by long down-curved bills and a distribution throughout East and Southeast Asia. To infer the molecular phylogeny of this group and their divergence time, we examined sequences of multiple fragments including two entire mitochondrial genes and four nuclear introns (4352 bp in total) from multiple samples of eight of the nine recognized species of Asian scimitar babblers. The phylogeny resulting from the concatenated multi-locus dataset suggests that Pomatorhinus is paraphyletic. Due to its paraphyly, we propose dividing the traditional genus Pomatorhinus into two morphologically and genetically diagnosable genera: Pomatorhinus and Erythrogenys. Results of the molecular dating based on the conventional mitochondrial DNA divergence rate indicates that the diversification of these babblers is likely congruent with the historical climatic events. Our findings shed light on the diversification of avian species in southern Asia, a poorly studied biodiversity hotspot.     

Genetic divergence and population demography of the Hainan endemic Black-throated Laughingthrush (Aves: Timaliidae, Garrulax chinensis monachus) and adjacent mainland subspecies

Geographic variation in the Black-throated Laughingthrush (Garrulax chinensis) is examined to infer the influence of Pleistocene glacial oscillations on the genetic diversity of its subspecies. Mitochondrial evidence suggests that the endemic Hainan Island taxon, G. c. monachus, is monophyletic, whereas its closest continental relatives, G. c. chinensis and G. c. lochmius, are not. Multilocus coalescent analysis based on two mitochondrial and two nuclear intron loci indicates inter-subspecific genetic differentiation during the Pleistocene and substantial post-divergence genetic introgression from G. c. chinensis into G. c. lochmius. In contrast, G. c. monachus experienced no post-divergence gene flow despite occasional land-bridge contact with its continental relatives, suggesting its isolation may have been imposed by ecology as well as geography. It is probably reproductively isolated and should be treated as a distinct species.     

Towards resolving and redefining Amphipyrinae (Lepidoptera,Noctuoidea, Noctuidae): a massively polyphyletic taxon

Amphipyrinae have long been a catchall taxon for Noctuidae, with most members lacking discernible morphological synapomorphies that would allow their assignment to one of the many readily diagnosable noctuid subfamilies. Here data from seven gene regions (> 5500 bp) for more than 120 noctuid genera are used to infer a phylogeny for Amphipyrinae and related subfamilies. Sequence data for 57 amphipyrine genera – most represented by the type species of the genus – are examined. We present here the first large‐scale molecular phylogenetic study of Amphipyrinae and the largest molecular phylogeny of Noctuidae to date; several proposed nomenclatural changes for well‐supported results; and the identification of areas of noctuid phylogeny where greater taxon sampling and/or genomic‐scale data are needed. Adult and larval morphology, along with life‐history traits, for taxonomic groupings most relevant to the results are discussed. Amphipyrinae are significantly redefined; many former amphipyrines, excluded as a result of these analyses, are reassigned to other noctuid subfamily‐level taxa. Four genera, Chamaeclea Grote, Heminocloa Barnes & Benjamin, Hemioslaria Barnes & Benjamin and Thurberiphaga Dyar, are transferred to the tribe Chamaecleini Keegan & Wagner tribe n. in Acontiinae. Stiriina is elevated to Stiriinae rev. stat. , Grotellina is elevated to Grotellinae rev. stat. and Annaphilina is elevated to Annaphilini rev. stat. Acopa Harvey is transferred to Bryophilinae, Aleptina Dyar is transferred to Condicinae, Leucocnemis Hampson and Oxycnemis gracillinea (Grote) are transferred to Oncocnemidinae, Nacopa Barnes & Benjamin is transferred to Noctuinae and Narthecophora Smith is transferred to Stiriinae. Azenia Grote (and its subtribe Azeniina), Cropia Walker, Metaponpneumata Möschler, Sexserrata Barnes & Benjamin and Tristyla Smith are transferred to Noctuidae incertae sedis. Hemigrotella Barnes & McDunnough (formerly in subtribe Grotellina) is retained in Amphipyrinae. Argentostiria Poole and Bistica Dyar are retained in Stiriini but removed from incertae sedis position. This published work has been registered on ZooBank: http://zoobank.org/urn:lsid:zoobank.org:pub:4A140782‐31BA‐445A‐B7BA‐6EAB98ED43FA .     

Morphological evidence for sister group relationship between flamingos (Aves: Phoenicopteridae) and grebes (Podicipedidae)

A recent molecular analysis strongly supported sister group relationship between flamingos (Phoenicopteridae) and grebes (Podicipedidae), a hypothesis which has not been suggested before. Flamingos are long-legged filter-feeders whereas grebes are morphologically quite divergent foot-propelled diving birds, and sister group relationship between these two taxa would thus provide an interesting example of evolution of different feeding strategies in birds. To test monophyly of a clade including grebes and flamingos, I performed a cladistic analysis of 70 morphological characters which were scored for 17 taxa. Parsimony analysis of these data supported monophyly of the taxon (Podicipedidae + Phoenicopteridae) and the clade received high bootstrap support. Previously overlooked morphological, oological and parasitological evidence is recorded which supports this hypothesis, and which makes the taxon (Podicipedidae + Phoenicopteridae) one of the best supported higher-level clades within modern birds. The phylogenetic significance of some fossil flamingo-like birds is discussed. The Middle Eocene taxon Juncitarsus is most likely the sister taxon of the clade (Podicipedidae + (Palaelodidae + Phoenicopteridae)) although resolution of its exact systematic position awaits revision of the fossil material. Contrary to previous assumptions, it is more parsimonious to assume that flamingos evolved from a highly aquatic ancestor than from a shorebird-like ancestor.  © 2004 The Linnean Society of London, Zoological Journal of the Linnean Society , 2004, 140 , 157–169.     

The molecular phylogeny of Alpinia (Zingiberaceae): a complex and polyphyletic genus of gingers

Alpinia is the largest, most widespread, and most taxonomically complex genus in the Zingiberaceae with 230 species occurring throughout tropical and subtropical Asia. Species of Alpinia often predominate in the understory of forests, while others are important ornamentals and medicinals. Investigations of the evolutionary relationships of a subset of species of Alpinia using DNA sequence-based methods specifically test the monophyly of the genus and the validity of the previous classifications. Seventy-two species of Alpinia, 27 non-Alpinia species in the subfamily Alpinioideae, eight species in the subfamily Zingiberoideae, one species in the subfamily Tamijioideae, and three species in the outgroup genus Siphonochilus (Siphonochiloideae) were sequenced for the plastid matK region and the nuclear internal transcribed spacer (ITS) loci. Parsimony analyses of both individual and combined data sets identified six polyphyletic clades containing species of Alpinia distributed across the tribe Alpinieae. These results were supported by a Bayesian analysis of the combined data set. Except in a few specific cases, these monophyletic groupings of species do not correspond with either Schumann's (1904) or Smith's (1990) classification of the genus. Here we build on previous molecular analyses of the Alpinioideae and propose the next steps necessary to recognize new generic boundaries in the Alpinieae.     

The karyotype of the osprey,Pandion haliaetus (Aves: Falconiformes)

The karyotype of the osprey consists of 74 chromosomes. There are no large macrochromosomes and no typical microchromosomes. Autosome No. 2 has a prominent secondary constriction in the long arm. The Z chromosome is similar in size and shape to the largest autosome, the W is a small metacentric. Among the Falconiformes, the osprey karyotype mainly resembles the karyotypes of some accipitrid species. However, certain characteristic features of the karyotype, a unique secondary constriction chromosome and absence of microchromosomes, speak in favour of maintaining the osprey in a family of its own, Pandionidae.     

The polyphyletic origin of the "Cheilostomata" (Bryszoa)

The relative appearance of the parietal muscles in the development of the zooids has been studied in several ctenostomatous and “cheilostomatous” species. A comparison of the different on-togenetical sequences demonstrated that a “cheilostomatous” type of organization of the zooids with a great probability has been achieved in minimum three times independentl and originated from different ctenostomatous sub-grous: the Membranidea from plesiomorgic victorelloids (ancestors of Bulbella with not yet developed peristomial tube), the Inoviceiata (Aetea) from advanced forms of victorelloids with reduced primary parietal muscles (perhaps stcies related to Pottsiella), and Penetrantia from arachnidioid or vesicularioid ancestors (?). Therefore, the classical orders ^α“Ctenostomata” and “Cheilostomata” represent only “stage groups” but no monohyletic systematical units. Because of the new concept and interpretation I propose a new name for the united group: Cteno-Cheilostomata, supra-ord. nov.     

The Phthiraptera (Insecta) parasitic on flamingoes (Phoenicopteridae: Aves)

The phthirapteran parasites occurring on the flamingoes are listed and their distribution discussed. New species of Anaticola and Anatoecus are described.     

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.     

The evolutionary history of cockatoos (Aves: Psittaciformes: Cacatuidae)

Cockatoos are the distinctive family Cacatuidae, a major lineage of the order of parrots (Psittaciformes) and distributed throughout the Australasian region of the world. However, the evolutionary history of cockatoos is not well understood. We investigated the phylogeny of cockatoos based on three mitochondrial and three nuclear DNA genes obtained from 16 of 21 species of Cacatuidae. In addition, five novel mitochondrial genomes were used to estimate time of divergence and our estimates indicate Cacatuidae diverged from Psittacidae approximately 40.7 million years ago (95% CI 51.6-30.3 Ma) during the Eocene. Our data shows Cacatuidae began to diversify approximately 27.9 Ma (95% CI 38.1-18.3 Ma) during the Oligocene. The early to middle Miocene (20-10 Ma) was a significant period in the evolution of modern Australian environments and vegetation, in which a transformation from mainly mesic to xeric habitats (e.g., fire-adapted sclerophyll vegetation and grasslands) occurred. We hypothesize that this environmental transformation was a driving force behind the diversification of cockatoos. A detailed multi-locus molecular phylogeny enabled us to resolve the phylogenetic placements of the Palm Cockatoo (Probosciger aterrimus), Galah (Eolophus roseicapillus), Gang-gang Cockatoo (Callocephalon fimbriatum) and Cockatiel (Nymphicus hollandicus), which have historically been difficult to place within Cacatuidae. When the molecular evidence is analysed in concert with morphology, it is clear that many of the cockatoo species' diagnostic phenotypic traits such as plumage colour, body size, wing shape and bill morphology have evolved in parallel or convergently across lineages.     

The possible polyphyletic origin of copper tolerance inAgrostis tenuis (Gramineae)

The effect of increased copper concentration in solution on the rooting of seven copper tolerant populations ofAgrostis tenuis has been examined using the regression technique ofFinlay &Wilkinson (1963). Three types of response to increased copper concentration have been detected, and it is suggested that these reflect a different genetic control of copper tolerance in different populations.     

The pterolichoid feather mites (Acarina, Astigmata) of the Megapodiidae (Aves, Galliformes)

The pterolichoid feather mites of megapodes are reviewed. Named taxa are briefly discussed and most are figured. The Pterolichidae (Pterolichinae) are: Ascetohchus Perez & Atyeo, three species; Echinozonus Atyeo & Perez, six species; Pereziella Atyeo, two species; and Phycoferus Atyeo & Perez, two species. New pterolichine taxa, with the type species listed first, include: Botryaspis cordiforma gen. et sp.n. and B. cordata gen. et sp.n.; Cycloprotarsus lineatus gen. et sp.n., C. centralis gen. et sp.n. and C. monacrotrichus gen. et sp.n.; Eurypterolichus gen.n. for Pterolichus navicula comb.n. Trouessart & Neumann and E. coniger gen. et sp.n.; Goniodurus gen.n. for Pterolichus ( Pseudalloptes ) quadratus comb.n. Trouessart and G. bilobatus gen. et sp.n.; Haptepigynus gen.n. for Pterolichus ( Pseudalloptes ) tridentiger comb.n. Trouessart and H. holonotus gen. et sp.n.; Heliaspis ventralis gen. et sp.n.; Leipobius ocellatus gen. et sp.n.; Maleolichus maleo gen. et sp.n.; Mayracarus gen.n. for Pterolichus (P.) tritilobus comb.n. Trouessart; Megapodobius arcuatus gen. et sp.n. and M. striatus gen. et sp.n.; Oxygynurus brevissimus gen. et sp.n., O. longicaulis gen. et sp.n., O. mediocaulis gen. et sp.n. and O. parvicaulis gen. et sp. n.; Prionoturus amembranatus gen. et sp. n.; Talegallobius bidentatus gen. et sp.n.; and Tanysomacarus imperfectus gen. et sp.n. and T. brachymeles gen. et sp.n. A new taxon of the Thoracosathesidae is: Thoracosathes caudiculata sp.n. Keys are provided and host- commensal associations are discussed. All taxa are restricted to the Megapodiidae. Cheylabis fuscina Trouessart is assigned to Pereziella and has as a synonym P. dupilcata Atyeo.     

The Mechanoreceptor Organs of the Lamellirostral Birds (Anseriformes,Aves)

Two types of surface tactile epidermal formations are identified in the bill tip organ of 11 species of lamellirostral birds. Their density arrangement and ratio in the mandible and maxilla are greater in dabbling ducks (filter-feeder species) than in herbivorous and in actively pursuing species. The length and proportions of the connective tissue tubules enclosing the encapsulated mechanoreceptors in filter-feeder species differ significantly from the others. The vibroreceptor endings are significantly more numerous in filter-feeder species and the touch endings in nonfiltering ones. The latter are smaller in the filter-feeder species. Within the walls of the connective tissue tubules, tactile epitheliocytes are registered for the first time. The structure of keratinocytes separating epidermal papillae of the bill tip organ apparently ensures their mobility. The bill tip organ is probably involved in the communication process of waterfowl.