Enigmatic phylogeny of skuas (Aves:Stercorariidae)

Multiple sources of evidence show that the skuas (Aves:Stercorariidae) are a monophyletic group, closely related to gulls (Laridae. On morphological and behavioural evidence the Stercorariidae are divided into two widely divergent genera, Catharacta and Stercorarius, consistent with observed levels of nuclear and mitochondrial gene divergence. Catharacta skuas are large-bodied and with one exception breed in the Southern Hemisphere. Stercorarius skuas otherwise known as jaegers) are smaller bodied and breed exclusively in the Northern Hemisphere. Evidence from both mitochondrial and nuclear genomes and from ectoparasitic lice (Insecta:Phthiraptera) shows that the Pomarine skua, S. pomarinus, which has been recognized as being somewhat intermediate in certain morphological and behavioural characteristics, is much more closely related to species in the genus Catharacta, especially to the Northern Hemisphere-breeding Great skua, C. skua, than it is to the other two Stercorarius skuas, the Arctic skua, S. parasiticus and the Longtailed skua, S. longicaudus. Three possible explanations that might account for this discordant aspect of skua phylogeny are explored. These involve (i) the segregation of ancestral polymorphism, (ii) convergent evolution of morphology and behaviour or (iii) inter-generic hybridization. The available evidence from both nuclear and mitochondrial genomes does not exclude any of these hypotheses. Thus, resolution of this enigma of skua phylogeny awaits further work.     

Multilocus perspectives on the monophyly and phylogeny of the order Charadriiformes (Aves)

Background  

The phylogeny of shorebirds (Aves: Charadriiformes) and their putative sister groups was reconstructed using approximately 5 kilobases of data from three nuclear loci and two mitochondrial genes, and compared to that based on two other nuclear loci.     

Skeletal adaptations and phylogeny of the oldest mole Eotalpa (Talpidae,Lipotyphla, Mammalia) from the UK Eocene: the beginning of fossoriality in moles

The oldest talpid, Eotalpa, was previously known only from isolated cheek teeth from the European late Middle Eocene to earliest Oligocene. Screenwashing of Late Eocene sediments of the Hampshire Basin, UK, has yielded cranial and postcranial elements: maxilla, dentary, ulna, metacarpals, distal tibia, astragalus, calcaneum, metatarsals and phalanges. In addition to M_1–2 myotodonty, typical talpid features are as follows: ulna with long medially curved olecranon and deep abductor fossa and astragalar body with lateral process. However, Eotalpa retains certain soricid‐like primitive states (M¹ preparacrista, P⁴ with prominent mesiolingual protocone lobe, strongly angled astragalar neck and calcaneum with no space for a cuboid medial process) not found in modern talpids. Eotalpa is more derived than the most primitive living talpid Uropsilus in having lost the M^1–2 talon shelf, developed a convex radial facet on the ulna, an incipient proximal olecranon crest, relatively shorter metapodials and depressed manual unguals. Its astragalus with medial trochlear ridge taller than the lateral one and massive medial plantar process is typical of the Lipotyphla. Eotalpa lacks synostosis of tibia and fibula, found in other Talpidae, Soricidae and Erinaceidae, suggesting that synostosis in these groups has been independently acquired. Cladistic analysis places Eotalpa as stem member of the Talpidae and shows that much homoplasy arose during the early evolution of the family. Ground dwelling in Eotalpa is indicated by the following: astragalus with a medially dipping head, curved in a single plane; calcaneum with distal peroneal process and strongly overlapping ectal and sustentacular facets; and matching sized ectal and sustentacular facets on calcaneum and astragalus. These features would have restricted ankle mobility. Ungual and metatarsal shape and ulnar structure suggest a primitive stage in fossorial evolution and argue against a semiaquatic precursor stage in talpid fossoriality. Shrew‐moles may represent a reversal to surface foraging rather than an intermediate stage in fossoriality.     

Systematic relationships of the palaeogene family Presbyornithidae (Aves: Anseriformes)

The early Tertiary (Paleocene and Eocene) family Presbyornithidae is one of the most completely known group of fossil birds. Essentially all parts of the skeleton are represented in the fossil record, allowing a thorough analysis of the phylogenetic position of the family. Forty-two families of nonpasserine birds representing the orders Ciconiiformes, Anseriformes, Galliformes, Gruiformes and Charadriiformes, were included in a cladistic analysis of 71 skeletal characters. The previously suggested anseriform affinity of the Presbyornithidae was confirmed. Furthermore, the family proved to be closer to the Anatidae than to the Anhimidae or Anseranatidae. The many postcranial similarities with certain charadriiform birds as the Burhinidae, obviously are plesiomorphies. By this observation, a better undestanding of character evolution in nonpasserine skeletal morphology is gained. The often suggested close relationship of anseriform and galliform birds is not confirmed by osteology. Instead, the Anseriformes and the Phoenicopteridae form a monophyletic clade that is the sister to the remaining ciconiiform birds. This result renders the Ciconiiformes sensu Wetmore (1960) polyphyletic.     

Morphology and phylogeny of Dicellophilus,a centipede genus with a highly disjunct distribution (Chilopoda: Mecistocephalidae)

The centipede genus Dicellophilus Cook, 1896 (Chilopoda: Geophilomorpha: Mecistocephalidae) has been revised by means of a comparative examination of representative specimens of all the species: morphological variation has been documented by means of both light and scanning electronic microscopy, the geographical distribution has been reassessed and updated based on published and new records, and the phyletic relations between the species have been analysed based on morphological evidence. Dicellophilus is confirmed as a highly distinct lineage, supported by synapomorphies in the labrum and in the pattern of coxal organs. Four species are morphologically recognized, each of them occurring in one of three limited, highly disjunct areas in a restricted boreal temperate belt: Dicellophilus carniolensis (C.L. Koch, 1847) is limited to central Europe (central–eastern Alps, Dinarids, Carpathians, and Dobrogea), Dicellophilus pulcher (Kishida, 1928) occurs in Japan (Honshu), and Dicellophilus anomalus (Chamberlin, 1904) and Dicellophilus limatus (Wood, 1862) both occur in the south‐western part of North America (California and Oregon). High support has been found for the following phyletic relationships: (D. carniolensis (D. pulcher (D. anomalus + D. limatus))). Dicellophilus carniolensis is strongly distinct in some autapomorphic traits, including enlarged clypeus and fewer mandibular lamellae, whereas the sister species D. anomalus and D. limatus share some derived features, including an elongated head and associated appendages, longer antennal setae, and stronger forcipular tubercles. The peculiar geographical distribution of Dicellophilus and the historical scenario suggested by the phylogeny are very unusual in respect to the biogeographical patterns known in all other major groups of terrestrial animals. © 2010 The Linnean Society of London, Zoological Journal of the Linnean Society, 2010, 158 , 501–532.     

A phylogeny of extant penguins (Aves: Sphenisciformes) combining morphology and mitochondrial sequences

The phylogenetic relationships among the penguins have received little attention, despite their well‐known anatomy and the conspicuous nature of the group. Previous attempts have included datasets limited to few, mostly osteological characters, and one study was based on integumentary and breeding characters. We developed a morphological matrix comprising 159 morphological characters of osteology (70 characters), myology (15), digestive tract (1), integument (66), and breeding (7 characters), scored in 18 extant forms (all currently recognized species plus one distinct subspecies). A gaviiform was placed at the root, and 11 species of representative procellariiform groups completed the outgroup. A heuristic parsimony analysis under equal weights was performed. We also compiled DNA sequences available in GenBank for the mitochondrial genes 12S rDNA and cytochrome b. We included the two data partitions in a combined analysis under direct optimization. Both analyses recovered the monophyly of Sphenisciformes and all the traditional polytypic genera. Morphological characters performed optimally at the ordinal and generic nodes, also providing resolution and varying degrees of support at supra‐ and intrageneric nodes. The comparison of molecular and morphological results indicated that the most significant problem in the phylogeny of extant penguins is rooting the ingroup. The mutual interaction of molecular and morphological data decreases the ambiguity regarding the placement of the root, and provides a resolved, relatively well‐supported phylogeny of extant penguins. Biogeographical patterns based on breeding ranges and derived from the combined analysis show that the major intercontinental vicariance events detected are consistent with cold marine current patterns of the Southern Hemisphere. © The Willi Hennig Society 2005.     

Systematics and evolution of the Pan‐Alcidae (Aves,Charadriiformes)

Puffins, auks and their allies in the wing‐propelled diving seabird clade Pan‐Alcidae (Charadriiformes) have been proposed to be key pelagic indicators of faunal shifts in Northern Hemisphere oceans. However, most previous phylogenetic analyses of the clade have focused only on the 23 extant alcid species. Here we undertake a combined phylogenetic analysis of all previously published molecular sequence data (～ 12 kb) and morphological data (n = 353 characters) with dense species level sampling that also includes 28 extinct taxa. We present a new estimate of the patterns of diversification in the clade based on divergence time estimates that include a previously vetted set of twelve fossil calibrations. The resultant time trees are also used in the evaluation of previously hypothesized paleoclimatic drivers of pan‐alcid evolution. Our divergence dating results estimate the split of Alcidae from its sister taxon Stercorariidae during the late Eocene (～ 35 Ma), an evolutionary hypothesis for clade origination that agrees with the fossil record and that does not require the inference of extensive ghost lineages. The extant dovekie Alle alle is identified as the sole extant member of a clade including four extinct Miocene species. Furthermore, whereas an Uria + Alle clade has been previously recovered from molecular analyses, the extinct diversity of closely related Miocepphus species yields morphological support for this clade. Our results suggest that extant alcid diversity is a function of Miocene diversification and differential extinction at the Pliocene–Pleistocene boundary. The relative timing of the Middle Miocene climatic optimum and the Pliocene–Pleistocene climatic transition and major diversification and extinction events in Pan‐Alcidae, respectively, are consistent with a potential link between major paleoclimatic events and pan‐alcid cladogenesis.     

The phylogeny of the Praomys complex (Rodentia: Muridae) and its phylogeographic implications

Among the African Murinae (Rodentia, Muridae), the Praomys complex, whose systematics has been studied by different approaches, has raised numerous taxonomic problems. Different taxa, namely Praomys, Mastomys , Myomys and Hylomyscus have been considered either as separate genera or subgenera of Praomys . In order to understand the relationships within the Praomys complex and to test the monophyly of the genus Praomys , a cladistic analysis was conducted, based on morpho-anatomical factors involving different species of Praomys , Mastomys , Myomys and Hylomyscus. The results indicate that the Praomys complex is monophyletic, as are the genera Hylomyscus , Mastomys and Myomys , whereas the genus Praomys appears paraphyletic. Indeed, a group of species including Praomys jacksoni was found to be more closely related to the genera Mastomys and Myomys than to a Praomys tullbergi -group. The biotopes and the distribution areas of the species were mapped on the phylogeny. It appears that the different clades each present a relative ecological cohesion and are arranged according to a gradient from closed to open habitats. From there, an evolutionary scenario is proposed for the emergence of the different clades and species of the genus Praomys sensu stricto.     

Egg size, composition and offspring quality in some Alcidae (Aves: Charadriiformes)

The composition of fresh and fully developed (pipping) eggs of four alcids, Razorbill, Common guillemot, Brünnich's guillemot and Atlantic puffin was examined. There were no differences in egg composition between the semi-precocial Atlantic puffin and the three species with "intermediate" developmental patterns. The absolute amount of yolk increased with egg size in fresh eggs, and the relative amount remained constant with egg size for Common guillemot and Razorbill, but decreased in the Atlantic puffin. In fully developed eggs chick weight and egg weight were closely correlated, and this was due mainly to larger eggs producing chicks with larger yolk reserves. Under some conditions chicks from larger eggs do better than those from smaller eggs. Several factors influence egg size; a comparison of first and replacement eggs laid by the same females showed that a maternal effect accounted for 60–90% of the variance in egg-size and that laying date accounted for most of the remaining variance.     

The old wasp and the tree: fossils, phylogeny and biogeography in the Orussidae (Insecta, Hymenoptera)

The phylogenetic relationships of the fossil orussid taxa Mesorussus taimyrensis and Minyorussus luzzi are examined by analysing them together with a large data set compiled previously for the extant Orussidae. The fossils are placed in an unresolved trichotomy with the extant Orussidae. The phylogeny is used for evaluating the hypothesis that the ancestors of the family had reduced body size; the results of this analysis are inconclusive. The biogeographical history of the Orussidae is explored. The common ancestor of the family was probably widespread, the initial splitting events taking place prior to or coinciding with the separation of Laurasia from Gondwana. Later putative vicariance events can be correlated with the gradual breakup of Gondwana. However, the biogeographical history of the Orussidae is dominated by speciation within regions and dispersal. The minimum age of the common ancestor of the Orussidae is >180 Myr when estimated from the biogeographical pattern, >95 Myr when estimated from the phylogenetic position of the fossils; the earlier date is considered to be the most likely.  © 2004 The Linnean Society of London , Biological Journal of the Linnean Society , 2004, 82 , 139–160.     

Phylogeny and classification of the Scopulini moths (Lepidoptera: Geometridae, Sterrhinae)

The phylogenetic relationships of the genera in the geometrid tribe Scopulini (Lepidoptera: Sterrhinae) were examined using 141 characters of adult morphology and ecology. The study material included 92 species, representing all previously recognized genera and covering the morphological variation and full geographical range of the tribe. The cladistic analysis resulted in 20 equally parsimonious trees and a strict consensus cladogram based on these was well resolved. A majority of the recovered synapomorphic characters have been used previously in the taxonomy of the tribe. However, many novel characters were found in the sclerotized structures of the thorax. Many previously recognized genera were found to be nonmonophyletic and based on the present revised, synapomorphy-based classification, the number of recovered genera is reduced considerably. Twenty new generic synonyms and 90 new or revived species combinations are proposed. Seven genera are considered valid, with the large genus Scopula Schrank including over 85% of all species in the tribe. The taxonomic history of the tribe is reviewed and the problems of earlier classifications are discussed. A key to the genera is presented, although an informal diagnosis is preferred. All recognized genera are illustrated and a revised world checklist of the Scopulini is presented.  © 2005 The Linnean Society of London, Zoological Journal of the Linnean Society , 2005, 143 , 473−530.     

Phylogenetic relationships within the Laridae (Charadriiformes: Aves) inferred from mitochondrial markers

Gulls (Aves: Laridae) constitute a recent and cosmopolite family of well-studied seabirds for which a robust phylogeny is needed to perform comparative and biogeographical analyses. The present study, the first molecular phylogeny of all Larids species (N=53), is based on a combined segment of mtDNA (partial cytochrome b and control region). We discuss our phylogenetic tree in the light of previous suggestions based on morphological, behavioral, and plumage characters. Although the phylogeny is not fully resolved, it highlights several robust species groups and confirms or identifies for the first time some sister relationships that had never been suggested before. The Dolphin Gull (Leucophaeus scoresbii) for instance, is identified as the sister species of the Grey Gull (Larus modestus) and the Ross's Gull (Rhodostethia rosea) forms a monophyletic group with the Little Gull (Larus minutus). Our results clearly demonstrate that the genus Larus as currently defined is not monophyletic, since current taxonomy of gulls is based on the use of convergent phenotypic characters. We propose a new systematic arrangement that better reflects their evolutionary history.     

The Anatidae and Scolopacidae (Aves: Anseriformes,Charadriiformes) from the late Neogene of Gargano,Italy

The late Neogene (MN13-14) fissure fillings found in the limestone quarries near Apricena (Foggia, Southern Italy) contain a well-diversified fossil bird assemblage. Most of the bird taxa show endemic characteristics following the high degree of insularity of the whole vertebrate assemblage. In addition to the endemic taxa, some non-endemic forms are present, mostly only recently found after the still ongoing revision of the whole bird remains. Here the remains of Anatidae and Scolopacidae are presented. This analysis reveals the occurrence of at least two taxa of Anatidae, Anas velox and Anatidae indet., and two taxa of Scolopacidae, Calidris sp. and an Scolopacidae indet. In addition, some remains are determined as Charadriiformes indet., but they probably represent more than one taxon, even if their bad status of preservation does not allow any further consideration. The detailed study of these remains and their comparison with the other European Neogene taxa already described is carried out.     

Complete phylogeny and historical biogeography of true rosefinches (Aves: Carpodacus)

True rosefinches (Aves: Carpodacus) are restricted to Eurasia, and 19 out of 25 species occur in the Sino‐Himalayas, making this the likely centre of origin. To test this hypothesis, suggested species splits had to be evaluated and potential further cryptic diversity unravelled. A taxon‐complete dated molecular phylogeny was reconstructed using maximum‐likelihood and Bayesian methods. Maximum‐parsimony and likelihood approaches were applied to deduce ancestral areas. Rosefinches, including the widespread Carpodacus erythrinus (Pallas, 1770), originated in south‐west China (and the Himalayas) 14 Mya, and gave rise to a smaller clade consisting of C. erythrinus, Haematospiza sipahi (Hodgson, 1836), and Chaunoproctus ferreorostris (Vigors, 1829), and a larger clade with 22 species. The latter split into four major lineages through vicariance during the uplift of the Himalayas. The suggested species splits of dubius from Carpodacus thura Bonaparte & Schlegel, 1850, formosanus from Carpodacus vinaceus Verreaux, 1871, grandis from Carpodacus rhodochlamys Brandt, 1843, verreauxii from Carpodacus rodopeplus (Vigors, 1831) (even polyphyletic) could be supported, whereas the suggested split of severtzovi from Carpodacus rubicilla (Güldenstädt, 1775) appears to be too young, and should be considered intraspecific. On the other hand, the central Asian lineage of Carpodacus synoicus Temminck, 1825 deserves species rank [Carpodacus stolickae (Hume, 1874)]. The Carpodacus eos/pulcherrimus complex consists of four lineages, pulcherrimus/argyrophrys and davidianus [Carpodacus pulcherrimus s.s. (Moore, 1856)], and eos and waltoni [Carpodacus waltoni (Sharpe, 1905)]. © 2013 The Linnean Society of London     

Cryptic clades, fruit wall morphology and biology of Andira (Leguminosae: Papilionoideae)

Andira comprises 29 species distributed throughout tropical America, with two subspecies in Africa. Its fruits are unusual for a papilionoid legume because they are drupes. The majority of species have fruits dispersed by bats, but eight species have larger fruits dispersed by-rodents. Some fruits of both dispersal types are secondarily dispersed by water. Cladistic analysis of chloroplast DNA (cpDNA) restriction site characters discovered four well-supported clades of Andira species. None of these 'cryptic' clades had been recognized by previous workers, because they are not apparently marked by any known morphological innovations. This prompted a search for new characters that might support these groupings. An anatomical study of fruit walls of 25 Andira species revealed the presence of three principal endocarp types, dominated by (1) parenchyma, (2) fibres, or (3) stone cells. These features arc best coded as a single unordered multistate character. When incorporated into a simultaneous cladistic analysis of previously gathered molecular and morphological data, states of this endocarp character are shown to be apomorphies for two of the well-supported clades evident in the cpDNA restriction site data. The most likely plesiomorphic state for the endocarp is parenchyma-dominated. Thicker, stronger endocarps of fibres and stone cells may have evolved in response to the need to protect the seed from predators.     

A molecular phylogeny of the cotingas (Aves: Cotingidae)

The phylogenetic relationships of members of Cotingidae were investigated using >2100 bp of sequence data from two nuclear introns (myoglobin intron 2 and G3PDH intron 11) and one protein-coding mitochondrial gene (cytochrome b). Strong support was found for a monophyletic clade including 23 traditional cotingid genera, corresponding to the Cotingidae sensu [Remsen, J.V. Jr., Jaramillo, A., Nores, M., Pacheco, J.F., Robbins, M.B., Schulenberg, T.S., Stiles, F.G., da Silva, J.M.C., Stotz, D.F., Zimmer, K.J., 2005. Version 2005-11-15. A classification of the bird species of South America. American Ornithologists' Union. ]. Neither Oxyruncus nor any of the genera in Tityrinae sensu [Prum, R.O, Lanyon, W.E., 1989. Monophyly and phylogeny of the Schiffornis group (Tyrannoidea). Condor 91, 444-461.] are members of Cotingidae. Within Cotingidae a polytomy of four well-supported clades was recovered: (1) the fruiteaters Pipreola and Ampelioides; (2) the Ampelion group, including Phytotoma; (3) Rupicola and Phoenicircus; and (4) the 'core cotingas' consisting of the remainder of the Cotingas (e.g. fruitcrows, Cotinga, Procnias, Lipaugus, and Carpodectes), with Snowornis in a basal position. The separation of Snowornis from Lipaugus [Prum, R.O, Lanyon, W.E., 1989. Monophyly and phylogeny of the Schiffornis group (Tyrannoidea). Condor 91, 444-461.] was strongly supported, as were the close relationships between Gymnoderus and Conioptilon, and between Tijuca and Lipaugus. However, basal relationships among 'core cotinga' clades were not resolved.