Descriptions and phylogenetic relationships of a new genus and two new species of Oligo‐Miocene cormorants (Aves: Phalacrocoracidae) from Australia

Tertiary cormorant fossils (Aves: Phalacrocoracidae) from Late Oligocene deposits in Australia are described. They derive from the Late Oligocene – Early Miocene (26–24 Mya) Etadunna and Namba Formations in the Lake Eyre and Lake Frome Basins, South Australia, respectively. A new genus, Nambashag gen. nov. , with two new species ( Nambashag billerooensis sp. nov. , 30 specimens; Nambashag microglaucus sp. nov. , 14 specimens), has been established. Phylogenetic analyses based on 113 morphological and two integumentary characters indicated that Nambashag is the sister taxon to the Early Miocene Nectornis miocaenus of Europe and all extant phalacrocoracids. As Nambashag, Nectornis, and extant phalacrocoracids constitute a strongly supported clade sister to Anhinga species, the fossil taxa have been referred to Phalacrocoracidae. Sulids and Fregata were successive sister taxa to the Phalacrocoracoidea, i.e. phalacrocoracids + Anhinga. As phalacrocoracids lived in both Europe and Australia during the Late Oligocene and no older phalacrocoracid taxa are known, the biogeographical origin of cormorants remains unanswered. The phylogenetic relationships of extant taxa were not wholly resolved, but contrary to previous morphological analyses, considerable concordance was found with relationships recovered by recent molecular analyses. Microcarbo is sister to all other extant phalacrocoracids, and all Leucocarbo species form a well‐supported clade. © 2011 The Linnean Society of London, Zoological Journal of the Linnean Society, 2011, 163 , 277–314.     

Multiple cenozoic invasions of Africa by penguins (Aves, Sphenisciformes)

Africa hosts a single breeding species of penguin today, yet the fossil record indicates that a diverse array of now-extinct taxa once inhabited southern African coastlines. Here, we show that the African penguin fauna had a complex history involving multiple dispersals and extinctions. Phylogenetic analyses and biogeographic reconstructions incorporating new fossil material indicate that, contrary to previous hypotheses, the four Early Pliocene African penguin species do not represent an endemic radiation or direct ancestors of the living Spheniscus demersus (blackfooted penguin). A minimum of three dispersals to Africa, probably assisted by the eastward-flowing Antarctic Circumpolar and South Atlantic currents, occurred during the Late Cenozoic. As regional sea-level fall eliminated islands and reduced offshore breeding areas during the Pliocene, all but one penguin lineage ended in extinction, resulting in today's depleted fauna.     

Crossvallia unienwillia, a new Spheniscidae (Sphenisciformes, Aves) from the Late Paleocene of Antarctica

Modern penguins are typically small to medium-sized birds, and nearly all known modern specimens are smaller than the most archaic Paleogene relatives. Here we report an incomplete humerus, associated femur and tibiatarsus of a new spheniscid, Crossvallia unienwillia nov. gen. and sp., from the Late Paleocene (~55 million years, Myr) of Antarctica, extending the record of spheniscids by about 15 Myr. Its large size (length ~140 cm) supports the idea that large body size in penguins was acquired independently at different times (Late Paleocene and Late Eocene) under dramatically different environmental conditions. Comparison of its osteological anatomy suggests that the new taxon is closely related to the extinct Anthropornithinae rather than to other penguin lineages.     

A reconsideration of Gallicolumba (Aves: Columbidae) relationships using fresh source material reveals pseudogenes,chimeras, and a novel phylogenetic hypothesis

Phylogenetic analyses of nuclear and mitochondrial DNA sequences were used to test a recent phylogenetic hypothesis for the avian genus Gallicolumba that relied heavily on preserved museum study skins for DNA samples. Our comparisons show that several published gene sequences represent pseudogenes or chimeras of multiple taxa, and these sequences had an adverse influence on phylogeny estimation. A new phylogenetic hypothesis strongly supports the monophyly of Philippine bleeding-hearts, the monophyly of Gallicolumba sensu stricto, and places Leucosarcia as part of an Australasian radiation rather than sister to Alopecoenas. These findings clarify Gallicolumba biogeography and also highlight the need for greater caution in the use of suboptimal source material in molecular systematic studies.     

Molecular phylogenetic perspective on the evolution of the deep-sea fish genusCyclothone (Stomiiformes: Gonostomatidae)

A portion of mitochondrially encoded 12S and 16S ribosomal RNA genes were sequenced from 13 currently recognized species of the midwater deep-sea fish genusCyclothone (Stomiiformes: Gonostomatidae) and three gonostomatid outgroup taxa. Phylogenetic analyses using maximum parsimony and maximum likelihood methods were performed on unambiguously aligned, combined sequences (803 bp) of the two genes. The resultant tree topologies from the two methods were congruent, being robust and supported by various tree statistics, enabling the evolutionary history ofCyclothone to be described in detail. The molecular phylogeny demonstrated striking inconsistencies with previously proposed “natural groups”, although the latter could be confidently refuted by the molecular data. The most significant characteristic of the evolutionary history ofCyclothone was the independent acquisition of an apomorphic depth habitat from the relatively ancestral, lower mesopelagic habitat, by each of three major distinct lineages that had diverged earlier in their evolution. Moreover, such macroevolutionary habitat shifts had been necessarily accompanied by morphological and ecological novelties, presumably originating from paedomorphosis. Repeated evolution of such changes strongly suggests ontogenetic plasticity inCyclothone which could enable these fishes to acquire larval-like, simple organization of body structure. Such a body plan could help them subsist in food-poor surroundings and regulate reproductive variables that take advantage of increasing larval survival toward shallower depths. Recent speciation events, on the contrary, have produced contemporary sister species of allopatric (or microallopatric) distributions, but few morphological and ecological differences. Even if remarkable miniaturization has occurred, such as in the Mediterranean endemicC. pygmaea, it had to have been a simple truncation of ancestral species' ontogeny without attendance of any discernible paedomorphic features. On the basis of the fossil record, geological history of the Mediterranean region, and ectotherm molecular divergence rate, it was estimated thatCyclothone radiation had already started in the early-middle Miocene (17–20 million years ago).     

On the head morphology of Phyllium and the phylogenetic relationships of Phasmatodea (Insecta)

Friedemann K., Wipfler B., Bradler S. and Beutel R.G. 2011 . On the head morphology of Phyllium and the phylogenetic relationships of Phasmatodea (Insecta). —Acta Zoologica (Stockholm) 00 : 1–16. External and internal head structures of Phyllium siccifolium are described in detail. The findings are compared with conditions found in other phasmatodeans and members of other neopteran lineages. The compiled 125 characters were analysed cladistically. A clade Eukinolabia (Phasmatodea + Embioptera) was confirmed. Synapomorphies of these two taxa are the shift of the origin of M. tentorioparaglossalis to the hind margin of the prementum, the presence of M. tentorioscapalis medialis, and antennal muscles that originate exclusively on the anterior tentorial arms. Within Eukinolabia, the position of Timema remains somewhat ambiguous because of missing anatomical data. However, it was confirmed as sister group of Euphasmatodea in a monophyletic Phasmatodea. Apomorphic groundplan features of Euphasmatodea are salivary ducts with separate external openings, apically rounded glossae, the presence of the galealobulus, and the reduction of the antennifer. The monophyly of Neophasmatidae was confirmed. Autapomorphies are the loss of M. frontobuccalis posterior, the anteriorly or dorsally directed maxillary palps, and the reduction of the mandibular incisivi. The analysis of characters of the head yielded three new autapomorphies of Phylliinae, the presence of a protuberance on the attachment site of the dorsal tentorial arms, dorsoventrally flattened maxillary‐ and labial palps, and possibly the narrow and U‐shaped field of trichomes on the apical part of the galea.     

On the phylogenetic relationships of trogons (Aves, Trogonidae)

Although trogons (Aves, Trogonidae) are well characterized by the possession of heterodactyl feet, their phylogenetic relationships to other extant birds still are only poorly understood. Molecular studies did not show conclusive results and there are amazingly few comparative studies of the anatomy of trogons. Virtually the only hypothesis on trogon relationships that was supported with derived morphological characters is a sister group relationship to alcediniform birds (bee-eaters, kingfishers, and allies), which share a derived morphology of the columella (ear-ossicle) with trogons. However, in this study a very similar columella is reported for the oilbird (Steatornithidae) and additional previously unrecognized derived osteological characters are presented, which are shared by trogons and oilbirds. A numerical cladistic analysis of 28 morphological characters also resulted in monophyly of Trogonidae and Steatornithidae, although the corresponding node was not retained in a bootstrap analysis.     

Fossil grebes from the Truckee Formation (Miocene) of Nevada and a new phylogenetic analysis of Podicipediformes (Aves)

Podicipediformes is a cosmopolitan clade of foot‐propelled diving birds that, despite inhabiting marine and lacustrine environments, have a poor fossil record. In this contribution, we describe three new grebe fossils from the diatomite beds of the Late Miocene Truckee Formation (10.2 ± 0.2 Ma) of Nevada (USA). Two postcranial skeletons and an associated set of wing elements indicate that at least two distinct grebe species occupied the large, shallow Lake Truckee during the Miocene. Phylogenetic analysis of morphological data supports a basal divergence between a clade uniting the dabchicks (Tachybaptus, Limnodytes, Poliocephalus) and a clade uniting Podilymbus, Rollandia, Podiceps and Aechmophorus. Missing data, combined with a paucity of informative skeletal characters, make it difficult to place the Truckee grebes within either of these major clades. Given the weak projection of the cnemial crests compared with extant grebes, it also remains plausible that these specimens represent stem lineage grebes. Although more material is needed to resolve the phylogenetic position of the Truckee grebes, our analysis offers insight into the tempo of grebe evolution by placing the Miocene taxon Thiornis sociata within the dabchick clade. Thiornis sociata provides a minimum age calibration of 8.7 Ma for the basal divergence among dabchicks. Based on the recovery of a nonmonophyletic Tachybaptus and placement of the Western Hemisphere ‘Tachybaptus’ dominicus as the basal member of the otherwise exclusively Eastern Hemisphere dabchick clade, we resurrect the genus Limnodytes for this extant species (Limnodytes dominicus). Our results also nest the large, long‐necked Aechmophorus grebes within the genus Podiceps, as the sister taxon to Podiceps major.     

Combined phylogenetic analysis of a new North American fossil species confirms widespread Eocene distribution for stem rollers (Aves,Coracii)

We report a nearly complete skeleton of a new species of stem roller (Aves, Coracii) from the early Eocene Green River Formation of North America. The new species is most closely related to two species‐depauperate lineages, Coraciidae (rollers) and Brachypteraciidae (ground rollers), that form a monophyletic crown clade (Coracioidea) with an exclusively Old World extant distribution. Phylogenetic analysis utilizing a matrix of 133 morphological characters and sequence data from three genes (RAG‐1, c‐myc, and ND2) identifies the new species as a stem member of the Coracii more closely related to the crown clade than the only previously identified New World taxon, Primobucco mcgrewi. The phylogenetic placement of the new species and Primobucco mcgrewiindicates a widespread northern hemisphere distribution in the Eocene with subsequent restriction to Africa, Madagascar, Australia, and temperate to tropical parts of Europe and Asia. It provides evidence of further ecological diversity in early stem Coracii and convergence on crown morphologies. The new species contributes to mounting evidence that extant distributions for major avian subclades may be of comparatively recent origin. Further late Palaeogene sampling is needed to elucidate potential drivers for shifting avian distributions and disappearance of Coracii from North America. © 2009 The Linnean Society of London, Zoological Journal of the Linnean Society, 2009, 157 , 586–611.     

Increased taxon and character sampling reveals novel intergeneric relationships in the Cracidae (Aves: Galliformes)

The Cracidae is one of the most endangered bird families in the World. Several studies have been published recently on the evolution and conservation of cracids. Phylogenetic analyses using a fragment of 661 bp of the mitochondrial cytochrome b gene for 39 different species of cracids corroborated most relationships found in previous studies. The present work attempts to refine the former phylogenetic hypothesis by increasing taxon sampling and combining molecular with osteological, integumentary and behavioural characters using Maximum Parsimony (MP) and Bayesian analyses. We present both separate and combined total evidence analyses with our molecular data, 152 osteological and 74 integumentary + behavioural characters. While supporting most aspects of the molecular-based hypotheses, the tree based on the combined matrix suggests several modifications of the generic composition for each of the two subfamilies: Penelopinae and Cracinae, and supports the merging of the genera Pipile with Aburria and Mitu with Pauxi . These results suggest that increased taxon and character sampling from a diversity of sources may be at least as important as increased sampling of only one type. Besides, of a total of 891 characters we had 437 parsimony-informative sites (almost half of the analyzable sites) proving the efficiency of a total-evidence approach.     

Taxonomic and phylogenetic relationships among the genera of the True Citrus Fruit Trees Group (Aurantioideae,Rutaceae) based on AFLP markers

Fifty-nine genotypes representing six genera of the True Citrus Fruit Trees Group (Aurantioideae, Rutaceae) were analyzed using AFLP technique to study their taxonomic and phylogenetic relationships. Fifteen primer combinations (out of 64 screened) were selected based on the polymorphism and quality of the bands produced by the primer and used in the present study. A total of 312 bands were obtained, of which 305 (97.8%) were polymorphic. The UPGMA tree of all genotypes was constructed based on the AFLP data using PAUP* beta version 4.0b8 software. Our AFLP molecular tree clearly confirms that the True Citrus Fruit Trees Group is monophyletic and supports the division of the group into genera mainly based on morphological characters, except that the genus Fortunella was nested within the genus Citrus cluster (as a monophyletic sub-branch). The subdivision of the genus Citrus into subgen. Papeda and subgen. Eucitrus as suggested by W. T. Swingle based on morphological characters and the point of view that C. medica, C. grandis and C. reticulata are the three basic species of the subgen. Eucitrus were also supported by our molecular data. In addition, contrary to the expectation based on morphological data, however, our molecular data demonstrated that C. ichangensis is more closely related to C. junos of the subgen. Eucitrus than to the C. hystrix of the subgen. Papeda. Furthermore, our study provided the first evidence that C. mangshanensis is basal to all the loose-skin citrus types. Finally, the taxonomic and phylogenetic relationships among the six genera and the important genotypes of the genus Citrus were dis-cussed in detail.     

Beyond a morphological paradox: complicated phylogenetic relationships of the parrotbills (Paradoxornithidae, Aves)

The parrotbills (Paradoxornithidae, meaning "birds of paradox," Aves) are a group of Old World passerines with perplexing taxonomic histories due to substantial morphological and ecological variation at various levels. In this study, phylogenetic relationships of the parrotbills were reconstructed based on sequences of two mitochondrial segments and three nuclear coding regions. Three major clades with characteristic body size and plumage coloration were found in both mtDNA and nuclear gene trees. However, mtDNA phylogeny suggested that the Paradoxornithidae is paraphyletic and relationships among three major parrotbill clades were poorly resolved. On the contrary, apparent and well-supported monophyletic relationships among the three major clades of Paradoxornithidae were revealed by concatenated nuclear dataset. Since paraphyly based on mtDNA data has commonly been found within avian taxa, the conflicting phylogenetic signal between mtDNA and nuclear loci revealed in this study indicates that results obtained from mtDNA dataset alone need to be evaluated with caution. Taxonomic implications of our phylogenetic findings are discussed. These phylogenies also point out areas for future investigation regarding the rapid diversification, morphological evolution and environmental adaptation of various parrotbill species or species complexes.     

A re-evaluation of basal phylogenetic relationships within trogons (Aves: Trogonidae) based on nuclear DNA sequences

The avian clade Trogonidae (trogons) consists of approximately 40 species distributed pantropically in the Neotropical, Afrotropical and Indomalayan zoogeographical regions. In this study, we evaluate the basal phylogenetic relationships within the trogons based on DNA sequences from three nuclear introns [myoglobin intron 2, β -fibrinogen intron 7 and glyceraldehydes-3-phosphodehydrogenase (G3PDH) intron 11]. In addition, previously published cytochrome b and 12S sequences were re-analysed and combined with the nuclear data set. The analysis of the three nuclear genes combined suggests a sister group relationship between the Afrotropical ( Apaloderma ) and Indomalayan ( Harpactes ) clades, whereas the Neotropical taxa ( Trogon , Pharomachrus , and Priotelus ) form an unresolved polytomy basal to these two groups. In addition, two of the three individual gene trees also support a sister group relationship between the Afrotropical and Indomalayan trogons. This is at odds with previously published studies based on mitochondrial sequence data and DNA–DNA hybridization. The third nuclear intron (G3PDH), however, suggests that the Afrotropical trogons are basal relative the other trogons. This was also suggested by the mitochondrial data set, as well as the analysis of the combined nuclear and mitochondrial data. Both of these conflicting hypotheses are supported by high posterior probabilities. An insertion in β -fibrinogen further supports a basal position of the Afrotropical clade. Analyses of the myoglobin intron with additional outgroups place the root differently and strongly support monophyly of each of the zoogeographical regions (including the Neotropics), and these three clades form a basal trichotomy. This suggests that that rooting is a serious problem in resolving basal phylogenetic relationships among the trogons.     

Evidence for a phylogenetic position of button quails (Turnicidae: Aves) among the Gruiformes

The phylogenetic position of the Turnicidae (Aves) was unresolved. Historically, they were classified as members of the Struthioniformes, Galliformes, Charadriiformes, Columbiformes or the Gruiformes. In these classifications they had taxonomic rank of order 'Turniciformes' or family 'Turnicidae'. However, most of these studies followed phenetic methodology and used morphological similarity of taxa and plesiomorphic characters to classify Turnix . Recent phylogenetic studies on the basis of morphological character analyses or phenetic comparisons based on DNA-DNA hybridization experiments failed to clarify the phylogenetic realtionship of Turnix and suggested a position as 'incerte sedis', either among the Gruiformes or as the parvclass 'Turnicac'as a sistergroup to the 'Neoaves'.
We studied skeletal and myological material of Turnix to resolve its phylogenetic position. Further, we considered all characters that were previously discussed in literature to classify Turnix and tested them for their potential use in phylogenetic analysis. We added several yet unemployed morphological characters of phylogenetic significance to the analysis. The Struthioniformes, 'Galloanseres', and Columbiformes are each characterized by a clear set of autapomorpies. Only one autapomorphy in known for the Gruiformes but this character is of satisfying consistency and can be found in all families of the Gruiformes (Gruidae, Psophiidae, Aramidae. Rallidae) and Turnix. Turnix and the Rallidae share four complex morphological characters implying a close phylogenetic relationship. The data presented in this paper support the hypothesis that Turnix is a member of the Gruiformes with close relationships to the Rallidae. No evidence was found that would support a parvclass 'Turnicae'as sistergroup to the 'Neoaves'.     

Isolation and characterization of macaroni penguin (Eudyptes chrysolophus) microsatellite loci and their utility in other penguin species (Spheniscidae, AVES)

We report the characterization of 25 microsatellite loci isolated from the macaroni penguin (Eudyptes chrysolophus). Thirteen loci were arranged into four multiplex sets for future genetic studies of macaroni penguin populations. All 25 loci were tested separately in each of four other penguin species [Adélie penguin (Pygoscelis adeliae), chinstrap penguin (Pygoscelis antarctica), gentoo penguin (Pygoscelis papua) and king penguin (Aptenodytes patagonicus)]. Between eight and 12 loci were polymorphic per species. These loci are expected to be useful for studies of population genetic structure in a range of penguin species.     

Taxonomic revision and phylogenetic analysis of the flightless Mancallinae (Aves, Pan-Alcidae)

Although flightless alcids from the Miocene and Pliocene of the eastern Pacific Ocean have been known for over 100 years, there is no detailed evaluation of diversity and systematic placement of these taxa. This is the first combined analysis of morphological and molecular data to include all extant alcids, the recently extinct Great Auk Pinguinus impennis, the mancalline auks, and a large outgroup sampling of 29 additional non-alcid charadriiforms. Based on the systematic placement of Mancallinae outside of crown clade Alcidae, the clade name Pan-Alcidae is proposed to include all known alcids. An extensive review of the Mancallinae fossil record resulted in taxonomic revision of the clade, and identification of three new species. In addition to positing the first hypothesis of inter-relationships between Mancallinae species, phylogenetic results support placement of Mancallinae as the sister taxon to all other Alcidae, indicating that flightlessness evolved at least twice in the alcid lineage. Convergent osteological characteristics of Mancallinae, the flightless Great Auk, and Spheniscidae are summarized, and implications of Mancallinae diversity, radiation, and extinction in the context of paleoclimatic changes are discussed.     

Taxonomy and sexual dimorphism of a new species of Loxoconcha (Podocopida: Ostracoda) from the Pleistocene of the Japan Sea

A new ostracod, Loxoconcha kamiyai sp. nov. in the Family Loxoconchidae, is described from the Pleistocene Omma Formation of Japan. Its geological and geographical distributions suggest that this species was once endemic to the Japan Sea, where it would have evolved until the Pliocene. Since the early Pleistocene, this species would have become extinct within this marginal sea during glacial maxima, probably due to its narrower salinity tolerances and geographical distributions than those of extant species inhabiting the euryhaline environments in other seas. The distributional patterns of pore systems in this species strongly suggest its closest phylogenetic affinities to a living species, Loxocorniculum mutsuense . These two species show a unique adult sexual dimorphism in the anterior element of the hingement. Taking the female hingement morphology as a standard, the male hingement can be explained in terms of heterochrony, i.e. paedomorphosis. Sexual hingement dimorphism with paedomorphosis occurs in only one phylogenetic group of the genus Loxoconcha , which is distinguished by the ontogenetic distributional patterns of pore systems. This morphology may represent relict primitive characters of ancient ostracods and could be an important character for evaluating the history of sexual dimorphism in ostracods since the Palaeozoic.  © 2008 The Linnean Society of London, Zoological Journal of the Linnean Society , 2008, 153 , 239–251.     

Descriptions and phylogenetic relationships of two new genera and four new species of Oligo‐Miocene waterfowl (Aves: Anatidae) from Australia

The Tertiary anatid fossils (Aves: Anatidae) from Oligocene and Miocene deposits in Australia are described. Most fossils derive from the Late Oligocene – Early Miocene (26–24 Mya) Etadunna and Namba Formations, respectively, in the Lake Eyre and Lake Frome Basins of South Australia. The local faunas from these two formations contain the same suite of anatid species. Two new genera, the oxyurine Pinpanetta, with three new species (Pi. tedfordi, 18 specimens; Pi. vickersrichae, 15 specimens; Pi. fromensis, 20 specimens), and the tadornine Australotadorna, for a large new species known from eight specimens, are established. Three anatid bones from the Waite Formation (c. 8 Mya) at Alcoota, Northern Territory reveal the presence of a tadornine that is neither Australotadorna nor an extant Tadorna species, and an indeterminate duck about the size of Malacorhynchus. Phylogenetic analyses establish Pinpanetta as a basal member of an oxyurine (stiff‐tailed duck) radiation. Oxyurines are found to include the Recent Stictonetta and Malacorhynchus as basal members, along with the fossil taxa Mionetta, Manuherikia, and Dunstanetta, and the traditionally included Recent Oxyura, Biziura, Thalassornis, and Nomonyx. © 2009 The Linnean Society of London, Zoological Journal of the Linnean Society, 2009, 156 , 411–454.     

Species boundaries,phylogenetic relationships,and ecological differentiation inAnthriscus (Apiaceae)

Species boundaries and phylogenetic relationships of 17 taxa ofAnthriscus (Apiaceae), with special emphasis on the critical sect.Cacosciadium, were explored using morphological data with principal component analysis, phenetics, and phylogenetics. The analyses did not provide satisfactory resolution of taxa from sect.Cacosciadium and only four species were retained. The total number of species was reduced to nine. Sect.Cacosciadium is distinguished by only two synapomorphies while sects.Anthriscus andCaroides are better supported. Present geographic and ecological variation suggests that the radiation ofAnthriscus occurred through divergence of peripheral isolated populations adapting to different habitats: high montane meadows and screes, shady climax forests, and seasonally dry habitats at lower altitudes. The adaptive significance of particular morphological traits is discussed.