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FIGURE 5 in A morphological and molecular phylogenetic analysis of relationships between genera of the nematode sub-family Cloacininae (Stossich) (Strongyloidea Chabertiidae) parasitic in kangaroos, wallabies and rat-kangaroos (Marsupialia Macropodoidea)

FIGURE 5. Molecular phylogenetic analysis of available representatives of the Cloacininae based on ITS+ sequence data. GenBank registration numbers for sequence data follow each taxon. Numerals represent posterior probabilities.

FIGURE 1 in A morphological and molecular phylogenetic analysis of relationships between genera of the nematode sub-family Cloacininae (Stossich) (Strongyloidea Chabertiidae) parasitic in kangaroos, wallabies and rat-kangaroos (Marsupialia Macropodoidea)

FIGURE 1. Buccal capsules of representative genera of the Cloacininae (lateral views). A. Rugopharynx rosemariae Beveridge & Presidente (Pharyngostrongylinea); B. Cyclostrongylus kartana (Mawson) (Pharyngostrongylinea); C. Thallostonema lichtenfelsi Beveridge (Zoniolaiminea); D. Tethystrongylus coronatus Beveridge (Zoniolaiminea); E. Parazoniolaimus collaris Johnston & Mawson (Labiostrongylinea); F. Labiostrongylus labiostrongylus Yorke & Maplestone (Labiostrongylinea); G. Rugostrongylus labiatus (Davey & Wood) (Pharyngostrongylinea); H. Pharyngostrongylus kappa Mawson (Pharyngostrongylinea); I. Macroponema comani Mawson (Macropostrongylinea); J. Popovastrongylus pearsoni (Johnston & Mawson) (Coronostrongylinea); K. Popovastrongylus macropodis Beveridge (Coronostrongylinea); L. Alocostoma clelandi (Johnston & Mawson) (Macropostrongylinea); M. Cloacina hydriformis Johnston & Mawson (Cloacininea); N. Monilonema ochetocephalum Beveridge (Macropostrongylinea); O. Wallabinema thylogale Beveridge (Zoniolaiminea); P. Woodwardostrongylus petrogale Beveridge (Pharyngostrongylinea); Q. Dorcopsinema simile Smales (Labiostrongylinea); R. Zoniolaimus mawsonae Beveridge (Zoniolaiminea); S. Coronostrongylus coronatus Johnston & Mawson (Coronostrongylinea); T. Papillostrongylus labiatus Johnston & Mawson (Coronostrongylinea). Figures redrawn from: Beveridge, 1982 (A, B, G, H); Beveridge, 1983 (C, D, O, R), Beveridge, 1986a (tribe Macropostrongylinea) (I); Beveridge, 1986b (Popovastrongylus) (J, K); Beveridge, 1986c (Alocostoma) (L); Beveridge, 1986d (Molinonema) (N); Beveridge, 1998a (P); Beveridge, 1998b (M); Beveridge, 2002 (S); Chilton et al., 2002 (T); Huby-Chilton et al., 2002 (R); Smales, 2002 (E), 1994 (F), 1999 (Q).

FIGURE 3 in A morphological and molecular phylogenetic analysis of relationships between genera of the nematode sub-family Cloacininae (Stossich) (Strongyloidea Chabertiidae) parasitic in kangaroos, wallabies and rat-kangaroos (Marsupialia Macropodoidea)

FIGURE 3. Oesophagi of representative genera of the Cloacininae. A. Cloacina metis Beveridge; B. Coronostrongylus coronatus Johnston & Mawson; C. Wallabinema thylogale Beveridge; D. Spirostrongylus spirostrongylus Yorke & Maplestone; E. Pharyngostrongylus kappa Mawson; F. Zoniolaimus mawsonae Beveridge; G. Thallostonema lichtenfelsi Beveridge; H. Labiomultiplex eugenii (Johnston & Mawson) (Labiostrongylinea). Figures redrawn from Beveridge, 1982 (D, E); Beveridge, 1983 (C, G); Beveridge, 1998a (A); Beveridge, 2002 (B); Huby-Chilton et al., 2002 (F); Smales, 1994 (H).

FIGURE 2 in A morphological and molecular phylogenetic analysis of relationships between genera of the nematode sub-family Cloacininae (Stossich) (Strongyloidea Chabertiidae) parasitic in kangaroos, wallabies and rat-kangaroos (Marsupialia Macropodoidea)

FIGURE 2. Features of the oral region of representative genera of the Cloacininae. A. Anterior extremity of buccal capsules of Thallostonema lichtenfelsi Beveridge (Zoniolaiminea); B. Monilonema ochetocephalum Beveridge (Macropostrongylinea); C. Alocostoma propinquum Beveridge (Macropostrongylinea); D. Macroponema comani Mawson (Macropostrongylinea); E. Rugopharynx rosemariae Beveridge & Presidente (Pharyngostrongylinea); Apical views of the mouth opening: F. Cyclostrongylus kartana (Mawson) (Pharyngostrongylinea); G. Woodwardostrongylus petrogale Beveridge (Pharyngostrongylinea); H. Papillostrongylus labiatus Johnston & Mawson, 1939 (Coronostrongylinea); I. Zoniolaimus mawsonae Beveridge (Zoniolaiminea); J. Wallabinema thylogale Beveridge (Zoniolaiminea); K. Pharyngostrongylus kappa Mawson (Pharyngostrongylinea); L. Popovastrongylus pearsoni (Johnston & Mawson) (Coronostrongylinea); M. Dorcopsistrongylus ewini Purwaningsih & Smales (Pharyngostrongylinea); N. Tethystrongylus coronatus Beveridge (Zoniolaiminea); O. Thallostonema lichtenfelsi Beveridge (Zoniolaiminea); P. Labiostrongylus labiostrongylus Yorke & Maplestone (Labiostrongylinea); Q. Dorcopsinema simile Smales (Labiostrongylinea). Figures redrawn from Beveridge, 1982 (E, F, K); Beveridge, 1983 (A, J, N, O); Beveridge, 1986a (D, H); Beveridge, 1986b (L); Beveridge, 1986c (C); Beveridge, 1986d (B); Beveridge, 1998a (G); Huby-Chilton et al., 2002 (I); Purwaningsih & Smales, 2010 (M); Smales, 1994 (P); Smales, 1999 (Q).

opencc-zeroDec 2014View details →

Data from: Inflation of molecular clock rates and dates: molecular phylogenetics, biogeography, and diversification of a global cicada radiation from Australasia (Hemiptera: Cicadidae: Cicadettini)

Dated phylogenetic trees are important for studying mechanisms of diversification, and molecular clocks are important tools for studies of organisms lacking good fossil records. However, studies have begun to identify problems in molecular clock dates caused by uncertainty of the modeled molecular substitution process. Here we explore Bayesian relaxed-clock molecular dating while studying the biogeography of ca. 200 species from the global cicada tribe Cicadettini. Because the available fossils are few and uninformative, we calibrate our trees in part with a cytochrome oxidase I (COI) clock prior encompassing a range of literature estimates for arthropods. We show that tribe-level analyses calibrated solely with the COI clock recover extremely old dates that conflict with published estimates for two well-studied New Zealand subclades within Cicadettini. Additional subclade analyses suggest that COI relaxed-clock rates and maximum-likelihood branch lengths become inflated relative to EF-1α intron and exon rates and branch lengths as clade age increases. We present corrected estimates derived from (1) an extrapolated EF-1α exon clock derived from COI-calibrated analysis within the largest New Zealand subclade, (2) post-hoc scaling of the tribe-level chronogram using results from subclade analyses, and (3) exploitation of a geological calibration point associated with New Caledonia. We caution that considerable uncertainty is generated due to dependence of substitution estimates on both the taxon sample and the choice of model, including gamma category number and the choice of empirical versus estimated base frequencies. Our results suggest that diversification of the tribe Cicadettini commenced in the early- to mid-Cenozoic and continued with the development of open, arid habitats in Australia and worldwide. We find that Cicadettini is a rare example of a global terrestrial animal group with an Australasian origin, with all non-Australasian genera belonging to two distal clades. Within Australia, we show that Cicadettini is more widely distributed than any other cicada tribe, diverse in temperate, arid and monsoonal habitats, and nearly absent from rainforests. We comment on the taxonomic implications of our findings for thirteen cicada genera.

opencc-zeroDec 2011View details →

Data from: Molecular phylogenetics and the evolution of fruit and leaf morphology of Dichaea (Orchidaceae: Zygopetalinae)

BACKGROUND AND AIMS: The orchid genus Dichaea, with over 100 species found throughout the neotropics, is easily recognized by distichous leaves on long stems without pseudobulbs and flowers with infrastigmatic ligules. The genus has previously been divided into four sections based primarily on presence of ovary bristles and a foliar abscission layer. The aim of this work is to use DNA sequence data to estimate phylogenetic relationships within Dichaea and map the distribution of major morphological characters that have been used to delimit subgenera/sections. METHODS: Sequence data for the nuclear ribosomal internal transcribed spacers and plastid matK, trnL intron, trnL-F spacer and ycf1 for 67 ingroup and seven outgroup operational taxonomic units were used to estimate phylogenetic relationships within Dichaea. Taxa from each of the four sections were sampled, with the greatest representation from section Dichaea, the most diverse and taxonomically puzzling group. KEY RESULTS: Molecular data and morphology support monophyly of Dichaea. Results indicate that section Dichaeopsis is polyphyletic and based on symplesiomorphies, including deciduous leaves and smooth ovaries that are widespread in Zygopetalinae. There are at least three well-supported clades within section Dichaeopsis. Section Pseudodichaea is monophyletic and defined by setose ovaries and leaves with an abscission layer. Sections Dichaea and Dichaeastrum are monophyletic and defined by pendent habit and persistent leaves. Section Dichaeastrum, distinguished from section Dichaea primarily by a glabrous ovary, is potentially polyphyletic. CONCLUSIONS: The leaf abscission layer was lost once, occurring only in the derived sections Dichaea and Dichaeastrum. The setose fruit is a more homoplasious character with several losses and gains within the genus. We propose an informal division of the genus based upon five well-supported clades.

opencc-zeroDec 2012View details →

Data from: Molecular phylogenetics of Gobioidei and phylogenetic placement of European gobies

Gobioidei is one of the largest suborders of teleost fishes, with nearly 2000 extant species currently recognized. They have a worldwide distribution and show a spectacular variety in morphology, ecology, and behavior. Despite their importance, phylogenetic relationships among many groups of gobioids (including some of the major lineages) still remain poorly understood. In this study, we analyze sequence data of five molecular markers (two mitochondrial and three nuclear) averaging 6000 bp for 222 species of gobioids. Our study is the first to include both multiple nuclear and mitochondrial genes to reconstruct a comprehensive multilocus phylogeny of gobioids encompassing most major lineages representing the overall diversity of one of the most speciose vertebrate lineages. Two separate datasets are produced and used to specifically address the phylogenetic placement of Rhyacichthyidae and Odontobutidae, and the phylogenetic relationships among the lineages of Gobioidei. Our results strongly support that the initial split in the gobioid tree separated a clade containing Rhyacichthyidae + Odontobutidae as the sister group of all other lineages. The family Eleotrididae branches off the gobioid tree after the Rhyacichthyidae + Odontobutidae clade, followed by the Butidae as sister to the Gobiidae. Additionally, several major monophyletic groups are confidently identified within the two major Gobiidae subclades, the gobiine-like gobiids and the gobionelline-like gobiids. Robustness of the phylogenetic trees inferred here is significantly higher than that of previous studies, hence our results provide the most compelling molecular phylogenetic hypothesis of Gobioidei thus far. For the first time, we provide a comprehensive sampling of European gobies that traditionally have been divided into "transverse" and "sand gobies". We show that the European gobies cluster in three distinct lineages, the Pomatoschistus-, Aphia-, and Gobius-lineages. The former resolved within the gobionelline-like gobiids and the latter two within the gobiine-like gobiids. These findings have significant implications for our understanding of the phylogeographic origin of European gobies in the light of the closure of the Paratethys. A rogue taxon analysis identified Kraemeria as an unstable taxon decreasing support at the base of the gobiine-like gobiids. Removal of this rogue taxon significantly increased phylogenetic resolution in that part of the tree and revealed additional insights into early bursts of cladogenesis of the gobiine-like gobiids.

opencc-zeroDec 2012View details →

Data from: Molecular phylogenetics of Maxillaria and related genera (Orchidaceae: Cymbidieae) based on combined molecular data sets

The orchid genus Maxillaria is one of the largest and most common of neotropical orchid genera, but its current generic boundaries and relationships have long been regarded as artificial. Phylogenetic relationships within subtribe Maxillariinae sensu Dressler (1993) with emphasis on Maxillaria s.l. were inferred using parsimony analyses of individual and combined DNA sequence data. We analyzed a combined matrix of nrITS DNA, the plastid matK gene and flanking trnK intron, and the plastid atpB-rbcL intergenic spacer for 619 individuals representing ca. 354 species. The plastid rpoC1 gene (ca. 2600 bp) was sequenced for 84 selected species and combined in a more limited analysis with the other data sets to provide greater resolution. In a well-resolved, supported consensus, most clades were present in more than one individual analysis. All the currently recognized minor genera of "core" Maxillariinae (Anthosiphon, Chrysocycnis, Cryptocentrum, Cyrtidiorchis, Mormolyca, Pityphyllum, and Trigonidium) are embedded within a polyphyletic Maxillaria s.l. Our results support the recognition of a more restricted Maxillaria, of some previously published segregate genera (Brasiliorchis, Camaridium, Christensonella, Heterotaxis, Ornithidium, Sauvetrea), and of several novel clades at the generic level. These revised monophyletic generic concepts should minimize further nomenclatural changes, encourage monographic studies, and facilitate more focused analyses of character evolution within Maxillariinae.

opencc-zeroDec 2013View details →

Data from: Molecular phylogenetic evidence corroborates morphology but not chemistry in the Lepraria neglecta group

The Lepraria neglecta group is a distinctive entity within the sterile, asexually reproducing lichen genus Lepraria whose constituent populations are united by their occurrence in exposed habitats and the development of a pseudocortex on the granules of the thallus. Previous studies have concluded that the group represents a monophyletic entity; however the question of how to classify the chemical variability exhibited within the group has remained unresolved. A phylogeny was inferred from ITS1, 5.8S, and ITS2 sequence data generated from a geographically and chemically broad sampling of populations within the L. neglecta group. While the inferred phylogeny recovered the core L. neglecta group as a strongly supported and monophyletic, the chemotypes within L. neglecta s.l. (i.e., the core-neglecta group excluding L. granulata) were not recovered as monophyletic and relationships within the group largely remain poorly resolved. Based on these results, a pragmatic circumscription for the group is proposed that emphasizes the strong correlation between morphological, ecological, and molecular characters over the lack of resolution between chemical and molecular characters. The names applied to members of the group are placed in synonymy with L. neglecta (these are L. alpina (basionym Crocynia alpina), L. alpina var. zeorinica, L. angardiana, L. borealis, L. caerulescens, L. caesioalba (basionym Crocynia caesioalba), L. caesioalba var. groenlandica, L. gelida, L. svalbardensis, and L. zonata). The results of these molecular phylogenetic analyses also 1) did not support the distinction of L. salazinica from L. elobata, thus that name is placed in synonymy here, and 2) elucidated the occurrence of L. humida in North America.

opencc-zeroDec 2013View details →

Data from: Molecular phylogenetics and microsatellite analysis reveals cryptic species of speckled dace (Cyprinidae: Rhinichthys osculus) in Oregon's Great Basin

Speckled dace (Rhinichthys osculus) is a small cyprinid that occurs throughout western North America and is the most commonly occurring fish in Oregon. Because of the high genetic and morphological variation in this species across its range, it has been referred to as a species complex; however, no revision to its taxonomy has occurred since 1984. Here, the phylogenetics and population genetics of speckled dace are examined throughout Oregon's Great Basin to describe genetic variation and infer the geographic boundaries between distinct taxonomic entities and populations. We tested the validity of a putative subspecies, Foskett Spring speckled dace, that occurs in a single spring within Warner Valley in Southeast Oregon and is listed Federally as threatened. Dace were collected from Foskett Spring and all surrounding basins containing speckled dace (Warner, Goose Lake, Lake Abert, Silver Lake, and Malheur), as well as Stinking Lake Spring (located within Malheur), created phylogenetic trees from mitochondrial ND2 and nuclear S7 sequence data, and genotyped eight microsatellite loci for population-level analyses. Three highly divergent clades warrant species-level status: Malheur stream dace, Stinking Lake Spring dace, and dace from the other four basins combined. Although Foskett Spring dace were not monophyletic, substantial population structure occurs at the basin-level and separates Foskett Spring dace from other dace in the surrounding Warner Valley. Thus, we recommend ESU status for the isolated population of speckled dace in Foskett Spring. The high, previously unrecognized, taxonomic diversity within this region indicates a need for a range-wide phylogeographic study of speckled dace and an investigation of the morphological distinctiveness of the putative new species.

opencc-zeroDec 2011View details →

Data from: Molecular phylogenetics unveils the ancient evolutionary origins of the enigmatic fairy armadillos

Fairy armadillos or pichiciegos (Xenarthra, Dasypodidae) are among the most elusive mammals. Due to their subterranean and nocturnal lifestyle, their basic biology and evolutionary history remain virtually unknown. Two distinct species with allopatric distributions are recognized: Chlamyphorus truncatus is restricted to central Argentina, while Calyptophractus retusus occurs in the Gran Chaco of Argentina, Paraguay, and Bolivia. To test their monophyly and resolve their phylogenetic affinities within armadillos, we obtained sequence data from modern and museum specimens for two mitochondrial genes (12S RNA [MT-RNR1] and NADH dehydrogenase 1 [MT-ND1]) and two nuclear exons (breast cancer 1 early onset exon 11 [BRCA1] and von Willebrand factor exon 28 [VWF]). Phylogenetic analyses provided a reference phylogeny and timescale for living xenarthran genera. Our results reveal monophyletic pichiciegos as members of a major armadillo subfamily (Chlamyphorinae). Their strictly fossorial lifestyle probably evolved as a response to the Oligocene aridification that occurred in South America after their divergence from Tolypeutinae around 32 million years ago (Mya). The ancient divergence date (∼17 Mya) for separation between the two species supports their taxonomic classification into distinct genera. The synchronicity with Middle Miocene marine incursions along the Paraná river basin suggests a vicariant origin for pichiciegos by the disruption of their ancestral range. Their phylogenetic distinctiveness and rarity in the wild argue in favor of high conservation priority.

opencc-zeroDec 2010View details →

Data from: The phylogenetic relationship of geographically separated "Flectonotus" (Anura: Hemiphractidae), as revealed by molecular, behavioral, and morphological data

Phylogenetic analyses of data derived from one mitochondrial gene and one nuclear gene show that the five species of small marsupial frogs currently recognized as Flectonotus are in fact two distinct and not closely related lineages. This conclusion is strongly supported by reproductive behavior and morphological characters. Thus, we recognize the genus Fritziana Mello-Leitão for the three species in southeastern Brazil and Flectonotus Miranda-Ribeiro for the two species in northern South America.

opennotspecifiedDec 2007View details →

FIGURE 3. Phylogenetic relationships among 67 in The limits of polymorphism in Liolaemus rothi: Molecular and phenotypic evidence for a new species of the Liolaemus boulengeri clade (Iguanidae, Liolaemini) from boreal Patagonia of Chile

FIGURE 3. Phylogenetic relationships among 67 Liolaemini taxa based on maximum parsimony analysis of 1710 aligned positions of DNA sequence data (length = 5810 steps). Strict consensus of five equally most parsimonious trees. Bootstrap values are presented above branches and decay indices are shown in bold below branches on the cladogram.

FIGURE 5 in A new species of Liolaemus from Añelo sand dunes, northern Patagonia, Neuquén, Argentina, and molecular phylogenetic relationships of the Liolaemus wiegmannii species group (Squamata, Iguania, Liolaemini)

FIGURE 5. Phylogenetic relationships of Liolaemus cuyumhue with other species of the wiegmannii group as shown by the consensus Bayesian tree. Posterior probabilities and maximum parsimony bootstrap values are shown above and below branches.

FIGURE 3 in A new species of Liolaemus from Añelo sand dunes, northern Patagonia, Neuquén, Argentina, and molecular phylogenetic relationships of the Liolaemus wiegmannii species group (Squamata, Iguania, Liolaemini)

FIGURE 3. Known distribution of wiegmannii species group. Large red star: type locality of Liolaemus cuyumhue. Red squares, L. azarai; orange squares: L. multimaculatus; green squares: L. salinicola; green circles: L. lutzae; yellow circles: L.scapularis; red circles: L. arambarensis; pink circles: L. occipitalis; blue circles: L.wiegmannii; black stars: L. riojanus; yellow square: L. rabinoi. Inset: satellite image of the Añelo basin, a red star mark the type locality.

FIGURE 1 in A new species of Liolaemus from Añelo sand dunes, northern Patagonia, Neuquén, Argentina, and molecular phylogenetic relationships of the Liolaemus wiegmannii species group (Squamata, Iguania, Liolaemini)

FIGURE 1. Liolaemus cuyumhue in life, lateral and ventral view of holotype (MACN 38981), adult male 51.2 mm in SVL.

FIGURE 2 in A new species of Liolaemus from Añelo sand dunes, northern Patagonia, Neuquén, Argentina, and molecular phylogenetic relationships of the Liolaemus wiegmannii species group (Squamata, Iguania, Liolaemini)

FIGURE 2. Dorsal and ventral color variation in the type series of Liolaemus cuyumhue (museum numbers are in diagnosis).

FIGURES 8–11 in Kakadudessus tomweiri, a new genus and species of diving beetle from tropical northern Australia, based on molecular phylogenetic and morphological data (Coleoptera, Dytiscidae, Bidessini)

FIGURES 8–11. Kakadudessus tomweiri sp.n. 8) Gungurul lookout in Kakadu National Park (locality 11, 1996), the white arrow marks the small rest pool near the bank; 9) Bowerbird Creek at Mary River Roadhouse near main road; 10–11) Small rest pool in the almost dry river bed of the Bowerbird Creek, 200 m upstream from main road (locality 15a, 2006). All photos by Lars Hendrich.

FIGURE 7 in Kakadudessus tomweiri, a new genus and species of diving beetle from tropical northern Australia, based on molecular phylogenetic and morphological data (Coleoptera, Dytiscidae, Bidessini)

FIGURE 7. Phylogram of the tree obtained in both MrBayes runs, numbers above branches are posterior probabilities (if>0.5, x100), numbers below branches are maximum likelihood boostrap values obtained from GARLI (if>50%). Note: Clypeodytes migrator will be transferred to Leiodytes by Hendrich & Wang in a forthcoming generic review.

FIGURES 2–5 in Kakadudessus tomweiri, a new genus and species of diving beetle from tropical northern Australia, based on molecular phylogenetic and morphological data (Coleoptera, Dytiscidae, Bidessini)

FIGURES 2–5. Kakadudessus tomweiri sp.n., male genitalia: 2) median lobe lateral aspect, 3) median lobe ventral aspect, 4) left paramere, 5) right paramere (scale bar 0.4 mm).