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.     

Deep ecomorphological and genetic divergence in Steller's Jays (Cyanocitta stelleri,Aves: Corvidae)

The relationship between ecology and morphology is a cornerstone of evolutionary biology, and quantifying variation across environments can shed light on processes that give rise to biodiversity. Three morphotypes of the Steller''s Jay (Cyanocitta stelleri) occupy different ecoregions in western North America, which vary in climate and landcover. These morphotypes (Coastal, Interior, Rocky Mountain) differ in size, plumage coloration, and head pattern. We sampled 1080 Steller''s Jays from 68 populations (plus 11 outgroups) to address three main questions using data on morphology, plumage, genetics (mtDNA, microsatellites), and ecological niches: (1) How do phenotypic and genetic traits vary within and among populations, morphotypes, and ecoregions? (2) How do population‐level differences in Steller''s Jays compare with other sister species pairs of North American birds? (3) What can we infer about the population history of Steller''s Jays in relation to past climates, paleoecology, and niche evolution? We found substantial morphological, genetic, and ecological differentiation among morphotypes. The greatest genetic divergence separated Coastal and Interior morphotypes from the Rocky Mountain morphotype, which was associated with warmer, drier, and more open habitats. Microsatellites revealed additional structure between Coastal and Interior groups. The deep mtDNA split between Coastal/Interior and Rocky Mountain lineages of Steller''s Jay (ND2 ~ 7.8%) is older than most North American avian sister species and dates to approximately 4.3 mya. Interior and Rocky Mountain morphotypes contact across a narrow zone with steep clines in traits and reduced gene flow. The distribution of the three morphotypes coincides with divergent varieties of ponderosa pine and Douglas fir. Species distribution models support multiple glacial refugia for Steller''s Jays. Our integrative dataset combined with extensive geographic sampling provides compelling evidence for recognizing at least two species of Steller''s Jay.     

Morphological variation versus genetic divergence: a taxonomic implication for Mogannia species (Cicadidae: Cicadinae)

Species showing intraspecific morphological variation tend to be very difficult to identify using morphological characters. One such example is the cicada genus Mogannia where some species show considerable intraspecific variation mainly exhibited by wing pattern and body colouration. Thirty-one variants covering different putative species of Mogannia were recognized and illustrated in the present paper. Molecular data of mitochondrial COI and Cytb sequences were employed to test the level of variation and phylogeny of them. The existence of a ‘barcoding gap’ between intraspecific and interspecific genetic divergences and the reciprocally monophyletic clades indicate that all the closely related variants represent a single species, and that all these variants correspond to six species, respectively. However, the evolutionary relationships of intraspecific variants are not resolved possibly due to insufficient genetic variation among them. Our results indicated that some morphological characters, especially the wing pattern and body colouration, and even the number of apical processes of the aedeagus in a couple of related species, must be used with great caution in delimiting Mogannia species and their relatives. The factors responsible for intraspecific morphological variation and phylogeny of Mogannia spp. are preliminarily discussed.     

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.     

Phylogenetic divergence in leatherside chub (Gila copei) inferred from mitochondrial cytochrome b sequences

We examined intra-specific phylogenetic relationships in leatherside chub, Gila copei. The complete mitochondrial (mt) cytochrome b gene (1140 bp) was sequenced for 30 individuals from 10 populations that span the geographical distribution of this species. Traditional phylogenetic analyses revealed two deeply divergent and evolutionarily distinct mtDNA clades that are geographically separated in northern and southern drainage basins. Interpopulation sequence variation between clades ranged from 7.7 to 8.1%. The northern clade was genetically more similar and phylogenetically more closely related to the selected out-group Lepidomeda m. mollispinus than to the southern clade, suggesting that the taxonomy of this species may require revision. Sequence variation among populations within clades ranged from 0 to 0.3% in the north and from 0 to 0.7% in the south. Statistical parsimony was used to construct phylogenetic networks of haplotypes within clades. Nested clade analysis revealed that geographical fragmentation has played an important role in genetic structuring within northern and southern clades.     

Species delimitation based on multiple criteria: the Spotted Bush Warbler Bradypterus thoracicus complex (Aves: Megaluridae)

We demonstrate the importance of using multiple criteria in species delimitations, whatever the conceptual base for species delimitation. We do this by studying plumage, biometrics, egg coloration, song, mitochondrial DNA and habitat/altitudinal distribution in the Spotted Bush Warbler Bradypterus thoracicus (Blyth) complex, and by conducting playback experiments. Taxa that we suggest are best treated as separate species [B. thoracicus (Blyth), B. davidi (La Touche) and B. kashmirensis (Sushkin)] differ in most or all of these aspects, particularly in song and mitochondrial DNA, while those that we treat as subspecies (suschkini) or synonyms (przevalskii) differ slightly and only in morphology. © 2008 The Linnean Society of London, Zoological Journal of the Linnean Society, 2008, 154 , 291–307.     

Comprehensive phylogeny of the laughingthrushes and allies (Aves,Leiothrichidae) and a proposal for a revised taxonomy

DNA phylogenies have gradually shed light on the phylogenetic relationships of the large babbler group. We focus in this study on the family Leiothrichidae (laughingthrushes and “song babblers”), which represents the largest clade of babblers in terms of species diversity. Our phylogeny includes all genera and 82% of the recognized species, using mitochondrial and nuclear loci. The sister group to Leiothrichidae is composed of the Pellorneidae (“jungle babblers”) plus the genus Alcippe. Within Leiothrichidae, four strongly supported primary clades (A–D) are recovered. Clade A includes Grammatoptila, Laniellus and Cutia. Clade B includes a large group of laughingthrushes, all of them classified in Trochalopteron. In Clade C, the two laughingthrushes endemic to southern India, T. fairbanki and T. cachinnans, which have recently been proposed to be placed in the newly erected genus Montecincla, form a sister clade to the group comprising the “song babblers” (Lioptila, Leiothrix, Heterophasia, Minla, Liocichla, Actinodura, Chrysominla, Siva, and Sibia). Clade D includes the African babblers (Turdoides, Phyllanthus, Kupeornis), Asian relatives (Argya, Acanthoptila, Chatarrhaea) and all remaining laughingthrushes (Garrulax). The time estimates suggest that the early diversification of the Leiothrichidae occurred in the mid‐Miocene, a period that corresponds to the diversification of many passerine groups in Asia. A revised taxonomic classification of the family is proposed in the light of these results.     

Multiple levels of allopatric divergence in the endemic Philippine fruit bat Haplonycteris fischeri (Pteropodidae)

As part of a larger comparative phylogeographical study of Philippine fruit bats, I used fragments of the mitochondrial genes cytochrome  b and ND2 to investigate phylogeography and diversification in Haplonycteris fischeri , a pteropodid bat endemic to the Philippines but widespread within the archipelago. Genetic diversity in H. fischeri was extremely high in these commonly studied genes, with 101 unique haplotypes in 123 sequenced individuals, although small, continuously isolated islands had less diversity than had large island complexes. Seven monophyletic groups and one paraphyletic group were restricted to individual islands, groups of islands, or parts of islands. Each Pleistocene island complex had a single resident monophyletic lineage; these five groups were separated by approximately 6–8% sequence divergence and apparently have been diverging for 4–6 Myr. Within island groups, monophyletic lineages on some individual islands suggest that current ocean channels have also been barriers to gene flow; in some cases, multiple allopatric clades were present on single islands. Basal divergence dates were estimated to be in the early Pliocene, and most diversification was apparently connected to the ongoing geological evolution of the Philippines. Geological history and current geography interact with ecology to cause substantial genetic differentiation within this primary forest-specialist species.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 88 , 329–349.     

Sorting out the Snakebirds: The species status,phylogeny, and biogeography of the Darters (Aves: Anhingidae)

Although the avian family Anhingidae is unequivocally monophyletic, the number and relationships of the component species within the single genus (Anhinga) have long remained unclear. Here, we use extensive mitochondrial and nuclear DNA sequence data (8,878 bp) to show that four species should be recognized. Our fully resolved and well‐supported tree shows that the American Anhinga (Anhinga anhinga) is sister to the three Old World species, with the Oriental (A. melanogaster) and African (A. rufa) Darters sister within the Old World clade, which also includes the Australian Darter (A. novaehollandiae). We estimate that the divergence between the New World and Old World branches occurred 19–22 mya, with the Australian Darter separating from its Old World congeners 14–16 mya and the Oriental and African species splitting ~10 mya. The genus is yet another example of osteological conservatism in the Suliformes, which is comparable to that shown by the cormorants and shags. Nevertheless, the relationships we infer are congruent with recent plumage studies and are biogeographically plausible. We suggest that further investigation of the variation within the African and Australian Darters would be of interest.     

Quantitative trait and allozyme divergence in the Greenfinch (Carduelis chloris, Aves: Fringillidae)

Quantitative trait divergence and variability among 12 greenfinch populations across continental Europe was examined and compared to divergence in neutral genetic markers (allozymes). The added among locality variance component for 16 skeletal traits was large (mean 28%, range 4–48%) equalling a divergence of up to three SD units. The divergence in quantitative traits (Qst = 0.04-0.48) greatly exceeded that in alloymes (F_ST= 0.01-0.07), indicating the differentiation in quantitative traits to be larger than expected by mutation and drift alone. This conclusion was consistent also with results from the multivariate approach of Rogers & Harpending. However, genetic and morphometric distances between populations were positively correlated, even when controlling for the geographic distance separating pairs of populations. In concordance with Bergmann's rule, most traits were strongly and positively correlated with latitude, indicating latitudinally ordered genetic or/and environmental effects. However, the correlation between lower mandible width and latitude was strongly negative, demonstrating an inverse relationship between beak size and body size across the populations. These results are interpreted to reflect the re-colonization of history of northern Europe (genetic and geographic distances correlated) which has been paralleled by selection acting on quantitative traits (Q_ST>F_ST)- In particular, the counter-gradient variation in beak width, a functionally important trait, is suggestive of an adaptive basis for quantitative trait divergence.     

Cellular and genetic models of H6PDH and 11β‐HSD1 function in skeletal muscle

Glucocorticoids are important for skeletal muscle energy metabolism, regulating glucose utilization, insulin sensitivity, and muscle mass. Nicotinamide adenine dinucleotide phosphate‐dependent 11β‐hydroxysteroid dehydrogenase type 1 (11β‐HSD1)‐mediated glucocorticoid activation in the sarcoplasmic reticulum (SR) is integral to mediating the detrimental effects of glucocorticoid excess in muscle. 11β‐Hydroxysteroid dehydrogenase type 1 activity requires glucose‐6‐phosphate transporter (G6PT)‐mediated G6P transport into the SR for its metabolism by hexose‐6‐phosphate dehydrogenase (H6PDH) for NADPH generation. Here, we examine the G6PT/H6PDH/11β‐HSD1 triad in differentiating myotubes and explore the consequences of muscle‐specific knockout of 11β‐HSD1 and H6PDH. 11β‐Hydroxysteroid dehydrogenase type 1 expression and activity increase with myotube differentiation and in response to glucocorticoids. Hexose‐6‐phosphate dehydrogenase shows some elevation in expression with differentiation and in response to glucocorticoid, while G6PT appears largely unresponsive to these particular conditions. When examining 11β‐HSD1 muscle‐knockout mice, we were unable to detect significant decrements in activity, despite using a well‐validated muscle‐specific Cre transgene and confirming high‐level recombination of the floxed HSD11B1 allele. We propose that the level of recombination at the HSD11B1 locus may be insufficient to negate basal 11β‐HSD1 activity for a protein with a long half‐life. Hexose‐6‐phosphate dehydrogenase was undetectable in H6PDH muscle‐knockout mice, which display the myopathic phenotype seen in global KO mice, validating the importance of SR NADPH generation. We envisage these data and models finding utility when investigating the muscle‐specific functions of the 11β‐HSD1/G6PT/H6PDH triad.     

Systematics of dusky salamanders, Desmognathus (Caudata: Plethodontidae), in the mountain and Piedmont regions of Virginia and North Carolina, USA

We analysed mitochondrial (cytochrome  b ) nucleotide sequences, nuclear allozyme markers, and morphometric characters to investigate species boundaries and phylogenetic relationships among dusky salamanders ( Desmognathus ) in the southern Blue Ridge and adjacent Piedmont Physiographic Provinces of Virginia and North Carolina. Our results revealed four distinct mitochondrial DNA clades that are also characterized by distinct allozyme markers. One clade consists of sequences derived from populations distributed from New England to south-western Virginia that are referable to Desmognathus fuscus Rafinesque, 1820, although there is considerable sequence and allozyme divergence within this clade. A second clade consists of sequences derived from populations referable to Desmognathus planiceps Newman, 1955, a form that we resurrect from its long synonymy under D. fuscus . Desmognathus planiceps and D. fuscus also differ in mandibular tooth shape. Two other cytochrome  b sequences recovered from populations along the Blue Ridge escarpment in southern Virginia are quite divergent from those of the previous two clades, and these populations may represent yet another distinct species. Sequences from a population in the Brushy Mountains in the Piedmont of northern North Carolina are similar to those of Desmognathus carolinensis . Population groupings indicated by allozyme data generally correspond to the cytochrome  b clades. Cryptic diversity in Appalachian desmognathan salamanders clearly requires further study. © 2008 The Linnean Society of London, Zoological Journal of the Linnean Society , 2008, 152 , 115–130.     

Tertiary plotopterids (Aves, Plotopteridae) and a novel hypothesis on the phylogenetic relationships of penguins (Spheniscidae)

Plotopterids (Aves: Plotopteridae) are extinct wing-propelled diving birds which exhibit a strikingly similar wing morphology to penguins (Spheniscidae), but also share derived characters with 'pelecaniform' birds that are absent in penguins. The similarities between Plotopteridae and Spheniscidae have hitherto been attributed to convergence, and plotopterids were considered to be most closely related to the 'pelecaniform' Phalacrocoracidae (cormorants) and Anhingidae (anhingas). However, here I show that assignment of plotopterids to 'pelecaniform' birds does not necessarily preclude them from being the sister taxon of penguins. Cladistic analysis of 68 morphological characters resulted in sister group relationship between Plotopteridae and Spheniscidae, and the clade (Plotopteridae + Spheniscidae) was shown to be the sister taxon of the Suloidea, i.e. a clade including Sulidae (boobies and gannets), Phalacrocoracidae, and Anhingidae. Derived characters are discussed which support this novel hypothesis. Paedomorphosis probably accounts for the absence of derived characters in penguins that are shared by Plotopteridae and members of the Steganopodes. Plotopterids exemplify the importance of fossil birds for analyzing the phylogenetic relationships of modern taxa that exhibit a highly apomorphic morphology.     

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.     

Morphological and molecular taxonomy of a new Daptonema (Nematoda,Xyalidae) with comments on the systematics of some related taxa

A new species of Daptonema is described based upon morphological characters and 18S rRNA sequence. Daptonema matrona sp. nov. was collected in Pina Basin (north‐eastern Brazil). It differs from all other species of the genus by the presence of reduced cephalic setae and straight spicules. These features require an adaptation of the generic diagnosis. Moreover, the females are characterized by intra‐uterine development of the offspring, considered herein as their major autapomorphic feature. Molecular systematic analyses supported Daptonema matrona sp. nov. as a distinct genetic and evolutionary lineage. The data also indicate hypotheses of taxonomic synonymies amongst some related taxa from Xyalidae as well as the paraphyly of Daptonema. © 2010 The Linnean Society of London, Zoological Journal of the Linnean Society, 2010, 158 , 1–15.     

Molecular phylogeny and divergence of major clades in the Puntius complex (Teleostei: Cypriniformes)

Puntius sensu lato (s.l.) was one of the most speciose genera in the family Cyprinidae. There are around 120 valid species widely distributed in South-East and South Asia, and South China. Puntius has long been known as an artificial assemblage and ‘catch-all’ genus in which a large number of small, unrelated cyprinids have been placed. With new species and genera being described each year, obtaining detailed knowledge of the phylogenetic relationships of this complex is critically important in the assessment of a natural classification. In the present study, two mitochondrial and four nuclear genes were used to examine the inter-specific and inter-generic relationships of the Puntius complex and to test the monophyly of the current genera. Divergence time analysis was performed to explore the origin, evolution, and divergence of major clades in Puntius s.l. Results revealed that the genera Puntius seusu stricto (s.s.), Systomus, Pethia, Haludaria, Desmopuntius and Puntigrus were monophyletic with high support. However, monophyly of Barbodes, Striuntius and Sahyadria was not supported. Dawkinsia and Sahyadria formed a highly supported clade. Puntius semifasciolatus and P. snyderi from South China and Taiwan represent a new lineage. Inferences from divergence time analysis indicated that Puntius s.l. likely dated to early Miocene. Major clades in Puntius s.l. diverged during Miocene as well.     

Morphological and molecular characterization of the small armoured dinoflagellate Heterocapsa minima (Peridiniales,Dinophyceae)

The dinophycean genus Heterocapsa is of considerable interest as it contains a number of bloom-forming and/or harmful species. Fine structure of organic body scales is regarded as the most important morphological feature for species determination but currently is unknown for the species H. minima described by Pomroy 25 years ago. Availability of a culture of H. minima collected in the south-west of Ireland allowed us to provide important information for this species, including cell size, cell organelle location, thecal plate pattern, body scale fine structure and molecular phylogeny. Light microscopy revealed the presence of one reticulate chloroplast, an elongated centrally located nucleus, and the presence of one pyrenoid surrounded by a starch sheath. Scanning electron microscopy (SEM) of the thecal plate pattern indicated that Pomroy erroneously designated the narrow first cingular plate as a sulcal plate. In addition, SEM revealed as yet unreported details of the apical pore complex and uncommon ornamentations of hypothecal plates. Organic body scales of H. minima were about 400 nm in size, roundish, with a small central hole and one central, six peripheral and three radiating spines. They differ from other body scales described within this genus allowing for positive identification of H. minima. Heterocapsa minima shares gross cell morphological features (hyposome smaller than episome, elongated nucleus in the middle of the cell, one pyrenoid located in the episome on its left side) with H. arctica (both subspecies H. arctica subsp. arctica and H. arctica subsp. frigida), H. lanceolata and H. rotundata. These relationships are reflected in the phylogenetic trees based on LSU and ITS rDNA sequence data, which identified H. arctica (both subspecies), H. rotundata and H. lanceolata as close relatives of H. minima.