The parrots (Aves: Psittaciformes) from the Middle Miocene of Sansan (Gers,Southern France)

The occurrence of Archaeopsittacus sp. (Psittaciformes) in the fossil deposits of Sansan (France) is reported, testifying to a survival of this genus in the Middle Miocene, as Archaeopsittacus verreauxi was described from the Early Miocene of Saint-Gérand-le-Puy (France) and was recorded only from its type locality. The data discussed here indicate the presence of two parrot species from Sansan, as it is the type locality of another parrot species, Pararallus dispar, only known from this locality. The differences between the humeri of these two taxa are described in detail, together with the differences from the other European fossil parrot species. The presence of more than one species of parrot in the same locality is not rare, but in Europe it is recorded in Sansan for the second time. Evidence for parrots also confirms the paleoenvironmental reconstruction of Sansan, as parrots are primarily arboreal species. Archaeopsittacus also represents one of the few common elements between the Early and Middle Miocene European bird assemblages.     

Chromosome studies of 8 species of parrots of the families Cacatuidae and Psittacidae (Aves: Psittaciformes)

The karyotypes of 7 species of Psittaciformes new to cytology are described: Cacatua galerita, Calyptorhynchus magnificus and Probosciger aterrimus of the Cacatuidae, and Ara macao, A. ararauna, Amazona viridigenalis and Psittrichas fulgidens of the Psittacidae. For reasons of comparison the karyotype of Melopsittacus undulatus is also described. These karyotypes are compared to 8 psittaciform karyotypes previously recorded. There is a remarkable heterogeneity of karyotypes in the Psittaciformes. Nevertheless, it seems possible to recognize Cacatua, Calyptorhynchus and probably also Probosciger (Cacatuidae) by their karyotypes as a clearly related group. The karyotypes of these cacatuids also bear some resemblance to that of Loriculus (Psittacidae). The psittacid genera Amazona, Ara, Nestor, Melopsittacus, Psittacula, Psittacus and Psittrichas are karyologically heterogeneous, but their karyotypes show certain relationships. The karyotype of Brotogeris is very different from those of other psittacids.     

Out of the Bassian province: historical biogeography of the Australasian platycercine parrots (Aves,Psittaciformes)

Schweizer, M., Güntert, M. & Hertwig, S. T. (2012). Out of the Bassian province: historical biogeography of the Australasian platycercine parrots (Aves, Psittaciformes). —Zoologica Scripta, 42, 13–27. Aridification from mid‐Miocene onwards led to a fragmentation of mesic biomes in Australia and an expansion of arid habitats. This influenced the diversification of terrestrial organisms, and the general direction of their radiations is supposed to have been from mesic into drier habitats. We tested this hypothesis in the platycercine parrots that occur in different habitats in Australia and also colonized Pacific islands. We inferred their temporal and spatial diversification patterns using a Bayesian relaxed molecular clock approach based on three nuclear and two mitochondrial genes and model‐based biogeographic reconstructions. The Bassian biota was found to be the centre of origin of platycercine parrots and diversification within two of their three clades coincided with the beginning of aridification of Australia. The associated habitat changes may have catalysed their radiation through adaptation to arid environments and vicariance because of the fragmentation of non‐arid habitats. The small oceanic islands of Melanesia contributed as stepping stones for the colonization of New Zealand from Australia.     

New feather mites of the family Pterolichidae (Acari: Pterolichoidea) from parrots (Aves: Psittaciformes) in Australia

Abstract Seven new feather mite species of the family Pterolichidae are described from various Australian parrots: Apexolichus lathami sp. n. from the swift parrot, Lathamus discolor (Shaw); Titanolichus platycerci sp. n. and Rhytidelasma punctata sp. n. from the pale-headed rosella, Platycercus adscitus (Latham); R. striata sp. n. from the Australian king-parrot, Alisterus scapularis (Lichtenstein); Lorilichus stenolobus sp. n. and Lorilichus curvilobus sp. n. from the rainbow lorikeet, Trichoglossus haematodus (Linnaeus); Psittophagus galahi sp. n. from the galah, Eolophus roseicapillus (Vieillot). We give a brief overview of taxonomic studies of pterolichid mites living on Psittaciformes, and discuss the main diagnostic characters of different generic groups of these mites.     

The evolution of the Indian Ocean parrots (Psittaciformes): extinction, adaptive radiation and eustacy

Parrots are among the most recognisable and widely distributed of all bird groups occupying major parts of the tropics. The evolution of the genera that are found in and around the Indian Ocean region is particularly interesting as they show a high degree of heterogeneity in distribution and levels of speciation. Here we present a molecular phylogenetic analysis of Indian Ocean parrots, identifying the possible geological and geographical factors that influenced their evolution. We hypothesise that the Indian Ocean islands acted as stepping stones in the radiation of the Old-World parrots, and that sea-level changes may have been an important determinant of current distributions and differences in speciation. A multi-locus phylogeny showing the evolutionary relationships among genera highlights the interesting position of the monotypic Psittrichas, which shares a common ancestor with the geographically distant Coracopsis. An extensive species-level molecular phylogeny indicates a complex pattern of radiation including evidence for colonisation of Africa, Asia and the Indian Ocean islands from Australasia via multiple routes, and of island populations ‘seeding’ continents. Moreover, comparison of estimated divergence dates and sea-level changes points to the latter as a factor in parrot speciation. This is the first study to include the extinct parrot taxa, Mascarinus mascarinus and Psittacula wardi which, respectively, appear closely related to Coracopsis nigra and Psittacula eupatria.     

Molecular systematics and species limits in the Philippine fantails (Aves: Rhipidura)

Islands have long-attracted scientists because of their relatively simple biotas and stark geographic boundaries. However, for many islands and archipelagos, this simplicity may be overstated because of methodological and conceptual limitations when these biotas were described. One archipelago that has received relatively little recent attention is the Philippine islands. Although much of its biota was documented long ago, taxonomic revision and evolutionary study has been surprisingly scarce, and only a few molecular phylogenetic studies are beginning to appear. We present a molecular phylogeny and taxonomic revision for the Philippine fantails (Aves: Rhipidura) using nuclear and mitochondrial DNA sequences. Our results suggest that current taxonomy underestimates diversity in the group. Some morphologically distinct subspecies warrant species status, whereas one was indistinguishable genetically and morphologically and should not be retained. A few taxa require additional sampling for thorough taxonomic assessment. Patterns of diversity within Philippine Rhipidura mostly corroborate predictions of the Pleistocene aggregate island complex (PAIC) hypothesis, in which diversity is expected to be partitioned by deep water channels separating Pleistocene aggregate islands rather than by current islands. Substantial structure within PAIC clades indicates that additional drivers of diversification should be considered.     

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.     

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.     

A species tree for the Australo-Papuan Fairy-wrens and allies (Aves: Maluridae)

We explored the efficacy of species tree methods at the family level in birds, using the Australo-Papuan Fairy-wrens (Passeriformes: Maluridae) as a model system. Fairy-wrens of the genus Malurus are known for high intensities of sexual selection, resulting in some cases in rapid speciation. This history suggests that incomplete lineage sorting (ILS) of neutrally evolving loci could be substantial, a situation that could compromise traditional methods of combining loci in phylogenetic analysis. Using 18 molecular markers (5 anonymous loci, 7 exons, 5 introns, and 1 mitochondrial DNA locus), we show that gene tree monophyly across species could be rejected for 16 of 18 loci, suggesting substantial ILS at the family level in these birds. Using the software Concaterpillar, we also detect three statistically distinct clusters of gene trees among the 18 loci. Despite substantial variation in gene trees, species trees constructed using four different species tree estimation methods (BEST, BUCKy, and STAR) were generally well supported and similar to each other and to the concatenation tree, with a few mild discordances at nodes that could be explained by rapid and recent speciation events. By contrast, minimizing deep coalescences produced a species tree that was topologically more divergent from those of the other methods as measured by multidimensional scaling of trees. Additionally, gene and species trees were topologically more similar in the BEST analysis, presumably because of the species tree prior employed in BEST which appropriately assumes that gene trees are correlated with each other and with the species tree. Among the 18 loci, we also discovered 102 independent indel markers, which also proved phylogenetically informative, primarily among genera, and displayed a ～4-fold bias towards deletions. As suggested in earlier work, the grasswrens (Amytornis) are sister to the rest of the family and the emu-wrens (Stipiturus) are sister to fairy-wrens (Malurus, Clytomyias). Our study shows that ILS is common at the family level in birds yet, despite this, species tree methods converge on broadly similar results for this family.     

青藏高原裸裂尻属鱼类两个疑难种的分子系统学

裸裂尻鱼属[Schizopygopsis（Steindachner）]鱼类广泛分布于青藏高原各河流上游干支流及其湖泊之中,由于其广泛的分布域和特殊的生态环境而被生物学家视为青藏高原隆升过程中淡水鱼类物种起源、进化的模式物种。然而,该属鱼类种间具有非常相似的形态特征,致使大渡软刺裸裂尻鱼（Sp．malacanthus chengi）和前腹裸裂尻鱼（Sp．anteroventris）的分类学地位一直存在争议。本文采用聚合酶链式反应（PCR）和直接测序的方法,获得了裸裂尻鱼属两个分类疑难种和5个指名种（n=17）以及5个近缘种（n=5）共23个个体的细胞色素b（Cytb）基因的全序列（1140bp）,并以同亚科的齐口裂腹鱼（Schizothorax cprenanti）作为外群构建了ML、MP和Bayesian进化树。序列差异和分子系统学分析表明,Sp．malacanthus schengi和软刺裸裂尻鱼（Sp．malacanthus）间存在较大的差异（2．06％）,两者并不聚在同一枝上;Sp．anteroventris独立成一枝,与其它指名裸裂尻鱼间显示出较大差异（4．38％-5．53％）,综合其它形态差异共同提示,Sp．mnlacanthus chengi应提升为独立种,沿用Sp．chengi的种名,而Sp．anteroventris应该是裸裂尻鱼属的一个独立种。     

Molecular systematics ofCardamine and allied genera (Brassicaceae): Its and non-coding chloroplast DNA

Representatives of the generaCardamine, Dentaria, Nasturtium, Rorippa andArmoracia (Brassicaceae) were analyzed to elucidate their phylogenetic relationships based on nuclear (ITS) and non-coding chloroplast (cp) DNA sequences.Dentaria seems to be polyphyletic. The two studiedDentaria species group with differentCardamine clades, and it is argued thatD. bulbifera is an allopolyploid originating from a hybridization between aCardamine and aDentaria species. In the ITS tree,Nasturtium andRorippa form well supported clades but their relationship toCardamine andArmoracia remains unresolved. In the cpDNA tree,Nasturtium groups together withCardamine. Hybridization events apparently played a role in the evolution ofNasturtium. TheCardamine/Nasturtium clade is separated from a clade placingRorippa andArmoracia together.Armoracia is closely related toRorippa. Analyses of the 19Cardamine species studied revealed three main groupings, a northern hemispheric and two southern hemispheric groups. Within the northern hemisphere taxa theC. pratensis complex forms a well supported clade which seems to be closely related toC. amara, C. raphanifolia andC. flexuosa. The positions ofC. hirsuta andC. impatiens are uncertain. The two southern hemisphere clades consist of New Guinean species and south-eastern Australian/Tasmanian and subantarctic species, respectively. They may reflect migration routes from the northern to the southern hemisphere, but further studies are necessary to fully understand the evolution of the bihemispheric distribution pattern ofCardamine.     

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.     

Electromyographic studies of the syrinx in parrots (Aves,Psittacidae)

Summary The vocal organ (syrinx) of a bird may contain either extrinsic muscles alone or both extrinsic and intrinsic muscles. The former arise and insert on the trachea and affect the syrinx only indirectly; the latter also arise on the trachea but insert directly on syringeal elements. It is widely supposed that syringeal muscles can affect modulations of the sounds the birds make, and further, that the intrinsic muscles are closely associated with such a function. However, the exact roles of the two groups of muscles have not been directly observed.The psittacid syrinx, which has one (for practical purposes) pair of extrinsic and two pairs of intrinsic muscles, is about as simple as one can find in birds capable of uttering a wide variety of sounds. We have taken electromyograms from the syringeal muscles of five species of parrots. In all of these, the extrinsic sternotrachealis showed the simple activation pattern activity previously described from several non-passerine species that possess only extrinsic muscles. The intrinsic muscles, however, showed a variety of activity patterns. The relatively simple call of Cyanoliseus patagonus again showed the simple activation pattern. In Myiopsitta monachus, the muscles showed a string of pulses that matched to pulses of sound in a strongly amplitude modulated call. Agapornis roseicollis used at least two distinct patterns, each associated with a different call.The results are consistent with an hypothesis that, because of their indirect attachment of the syrinx, extrinsic muscles are poorly suited to the production of precise, rapid changes in syringeal action, but rather will function in an on-off switch capacity. Intrinsic muscles are so situated that, given proper neurological stimulus, they can effect a variety of alterations in the sound pattern. Hence, intrinsic muscles are necessary for the evolution of large vocabularies and variable vocal behavior.     

Multi-locus phylogeny clarifies the systematics of the Australo-Papuan robins (Family Petroicidae, Passeriformes)

The Australo-Papuan family Petroicidae (Aves: Passeriformes) has been the focus of much systematic debate about its relationships with other passerine families, as well as relationships within the family. Mostly conservative morphology within the group limits the effectiveness of traditional taxonomic analyses and has contributed to ongoing systematic debate. To assess relationships within the family, we sampled 47 individuals from 26 species, representing the majority of genera and species, for four loci: 528 base pairs (bp) of C-myc, 501 bp of BA20454 and 336 bp of BA23989 from nuclear DNA and 1005 bp of the mitochondrial ND2 gene. There was consensus between individual loci and overall support for major lineages was strong. Partitioned Bayesian analyses of all four loci produced a fully resolved and very well-supported phylogeny that addresses many of the previous systematic debates in this group. The Eopsaltriinae as construed is monophyletic with the exception of Eopsaltria flaviventris, which is nested within Microeca as an unremarkable member of that genus. This relationship is corroborated by morphology and egg color and pattern. Petroicinae as currently construed was not monophyletic and comprised two lineages that are paraphyletic with respect to each other. The third subfamily, Drymodinae, remains incertae sedis. The mangrove robin, Peneonanthe pulverulenta, of tropical Australia and New Guinea is nested within a clade that also contained the sampled species of Peneothello and Melanodryas, a novel relationship. Preliminary biogeographic and divergence time estimates from these results are discussed and a new subfamily arrangement proposed.     

Molecular systematics of dormice (Rodentia: Gliridae) and the radiation of Graphiurus in Africa

The phylogenetic relationships among the Gliridae (order Rodentia) were assessed using 3430 nucleotides derived from three nuclear fragments (beta-spectrin non-erythrocytic 1, thyrotropin and lecithin cholesterol acyl transferase) and one mitochondrial gene (12S rRNA). We included 14 glirid species, representative of seven genera of the three recognized subfamilies (Graphiurinae, Glirinae and Leithiinae) in our analysis. The molecular data identified three evolutionary lineages that broadly correspond to the three extant subfamilies. However, the data suggest that the genus Muscardinus, previously regarded as falling within the Glirinae, should be included in the Leithiinae. Molecular dating using local molecular clocks and partitioned datasets allowed an estimate of the timing of cladogenesis within the glirids. Graphiurus probably diverged early in the group's evolution (40-50 Myr ago) and the three subfamilies diverged contemporaneously, probably in Europe. The radiation within Graphiurus is more recent, with the colonization of Africa by this lineage estimated at ca. 8-10 Myr ago.     

A multilocus molecular phylogeny of the parrots (Psittaciformes): support for a Gondwanan origin during the cretaceous

The question of when modern birds (Neornithes) first diversified has generated much debate among avian systematists. Fossil evidence generally supports a Tertiary diversification, whereas estimates based on molecular dating favor an earlier diversification in the Cretaceous period. In this study, we used an alternate approach, the inference of historical biogeographic patterns, to test the hypothesis that the initial radiation of the Order Psittaciformes (the parrots and cockatoos) originated on the Gondwana supercontinent during the Cretaceous. We utilized broad taxonomic sampling (representatives of 69 of the 82 extant genera and 8 outgroup taxa) and multilocus molecular character sampling (3,941 bp from mitochondrial DNA (mtDNA) genes cytochrome oxidase I and NADH dehydrogenase 2 and nuclear introns of rhodopsin intron 1, tropomyosin alpha-subunit intron 5, and transforming growth factor ss-2) to generate phylogenetic hypotheses for the Psittaciformes. Analyses of the combined character partitions using maximum parsimony, maximum likelihood, and Bayesian criteria produced well-resolved and topologically similar trees in which the New Zealand taxa Strigops and Nestor (Psittacidae) were sister to all other psittaciforms and the cockatoo clade (Cacatuidae) was sister to a clade containing all remaining parrots (Psittacidae). Within this large clade of Psittacidae, some traditionally recognized tribes and subfamilies were monophyletic (e.g., Arini, Psittacini, and Loriinae), whereas several others were polyphyletic (e.g., Cyclopsittacini, Platycercini, Psittaculini, and Psittacinae). Ancestral area reconstructions using our Bayesian phylogenetic hypothesis and current distributions of genera supported the hypothesis of an Australasian origin for the Psittaciformes. Separate analyses of the timing of parrot diversification constructed with both Bayesian relaxed-clock and penalized likelihood approaches showed better agreement between geologic and diversification events in the chronograms based on a Cretaceous dating of the basal split within parrots than the chronograms based on a Tertiary dating of this split, although these data are more equivocal. Taken together, our results support a Cretaceous origin of Psittaciformes in Gondwana after the separation of Africa and the India/Madagascar block with subsequent diversification through both vicariance and dispersal. These well-resolved molecular phylogenies will be of value for comparative studies of behavior, ecology, and life history in parrots.     

Phylogenetic analysis of some Neogene phasianid genera (Aves: Phasianidae)

Phylogenetic analysis based on osteological characters of some Neogene and Recent phasianids is performed. Phylogenetic tree shows close relationships of Plioperdix with Ammoperdix and Tologuica with Excalfactoria. Chauvireria is at the base of the clade (Alectoris + (Coturnix + (Excalfactoria + Tologuica))). Palaeoperdix is relatively close to the lineage of large pheasants.