Monophyletic groups within 'higher land birds'– comparison of morphological and molecular data

The relationships within the ‘higher land birds’ and putatively related taxa are analysed in a study using 89 morphological characters and DNA sequences of three nuclear, protein‐coding genes, c‐myc, RAG‐1, and myoglobin intron II. Separate analyses of the different data sets and a ‘total evidence’ analysis in which the data sets of the morphological and molecular analyses were combined are compared. All three analyses support the hitherto disputed sister group relationship between Pici (Ramphastidae, Indicatoridae and Picidae) and Galbulae (Galbulidae and Bucconidae). Previously unrecognized osteological synapomorphies of this clade are presented. All analyses further resulted in monophyly of the taxon [Aegothelidae + (Apodidae/Hemiprocnidae + Trochilidae)]. Analysis of the morphological data and of the combined data set also supported monophyly of the taxon [Strigiformes + (Falconidae + Accipitridae)]. The morphological data further support monophyly of the taxon (Upupidae + Bucerotidae). Other placements in the three analyses received either no or only weak bootstrap support.     

The phylogenetic relationships of the early Tertiary Primoscenidae and Sylphornithidae and the sister taxon of crown group piciform birds

The phylogenetic relationships of the early Tertiary Primoscenidae and Sylphornithidae are, for the first time, evaluated in a cladistic context. Both taxa include small arboreal birds with a permanently (Primoscenidae) or facultatively (Sylphornithidae) retroverted fourth toe. Primoscenidae were hitherto considered to be most closely related to either woodpeckers and allies (Piciformes) or to songbirds (Passeriformes), whereas the Sylphornithidae were classified into the roller-kingfisher-hornbill assemblage (Coraciiformes). Analysis of 56 morphological characters supports monophyly of a clade including Sylphornithidae and crown group Piciformes and results in sister group relationship between Passeriformes and a clade including Primoscenidae and the early Miocene Zygodactylidae. However, an analysis in which the search was constrained to trees supporting piciform affinities of the Primoscenidae resulted in trees that were only five steps longer than those from the primary analysis. The character evidence for each hypothesis is discussed. The systematic position of the Primoscenidae appears to be connected to the identity of the sister taxon of crown group Piciformes, as the primary search indicated Upupiformes (hoopoes and wood-hoopoes) and Bucerotiformes (hornbills) as sister taxa of Piciformes, whereas the constrained search resulted in sister group relationship between Coliiformes (mousebirds) and Piciformes. Songbirds do not show the slightest indication of a zygodactyl foot but in these birds the hindtoe is greatly elongated, an alternative strategy to increase the grasping capabilities of the foot. If Passeriformes are indeed the sister group of the clade (Primoscenidae + Zygodactylidae), these birds would be an example that, in closely related taxa, selection towards the same functional demands can result in entirely different morphological specializations.Communicated by F. Bairlein     

Clades within the ‘higher land birds’, evaluated by nuclear DNA sequences

In this study we investigated the phylogenetic relationships within the ‘higher land birds’ by parsimony analysis of nucleotide DNA sequences obtained from the two nuclear, protein-coding genes, c- myc and RAG-1. Nuclear genes have not previously been used to address this phylogenetic question. The results include high jackknife support for a monophyletic Apodiformes (including the Trochilidae). This arrangement was further supported by the observation of an insertion of four amino acids in the c- myc gene in all apodiform taxa. Monophyly was also inferred for each of the two piciform groups Galbulae and Pici. Within Pici, the Capitonidae was found to be paraphyletic, with the New World barbets more closely related to the Ramphastidae than to the Old World barbets. Another clade with high jackknife support consists of the Upupidae, Phoeniculidae and Bucerotidae. The families Momotidae and Todidae, and Coraciidae and Brachypteraciidae, respectively, also form well supported monophyletic clades. The results are inconclusive regarding the monophyly of the orders Coraciiformes and Piciformes, respectively.     

A tiny stem group representative of Pici (Aves, Piciformes) from the early Oligocene of the Czech Republic

We describe a new stem group representative of Pici (woodpeckers, honeyguides, barbets, and allies) from the early Oligocene (Rupelian) of the Czech Republic. The holotype of Picavus litencicensis, gen. et sp. nov. is a postcranial skeleton with well-preserved feather remains. The new species is distinguished from crown group Pici in several plesiomorphic features and is assigned to the new taxon Picavidae, fam. nov. The absence of an elongated accessory trochlea for the reversed fourth toe shows P. litencicensis to be the most basal representative of Pici, and concerning the morphology of the distal tarsometatarsus the species represents a morphological link between Pici and their sister taxon, the Galbulae. Like all other early Oligocene piciform birds, P. litencicensis is a tiny bird, the size of the smallest extant Pici. Because all Palaeogene Pici were found in Europe and some of these are outside the crown group, an Old World origin of Pici is likely. With definitive crown group representatives of Pici being unknown before the late Oligocene/early Miocene, the fossil record does not support earlier molecular calibrations, which resulted in a late Cretaceous divergence of crown group Pici.     

New specimens of the Eocene Messelirrisoridae (Aves: Bucerotes), with comments on the preservation of uropygial gland waxes in fossil birds from Messel and the phylogenetic affinities of Bucerotes

Exceptionally well-preserved new specimens of the Messelirrisoridae (Aves: Bucerotes), which show previously unknown features of the osteology and feathering of these tiny birds, are described from the Middle Eocene of Messel in Germany. Most notably in one of the new specimens the wing and tail feathers are excellently preserved and even show the former color pattern of the tail. A cream-colored substance in some specimens most likely constitutes fossilized uropygial gland waxes. For the first time, the phylogenetic affinities of the Messelirrisoridae are evaluated in a cladistic analysis, based on 122 characters and 34 extant and fossil taxa. The results of this analysis support the earlier hypothesis that Messelirrisoridae are stem lineage Upupiformes, i.e. the sister taxon of the clade including extant hoopoes (Upupidae) and woodhoopoes (Phoeniculidae). The analysis further supports sister group relationship between Bucerotes (Upupiformes + Bucerotidae [hornbills]) and Piciformes (woodpeckers and allies), although it is detailed that one of the recently proposed apomorphies of the clade (Bucerotes + Piciformes) is absent in the Messelirrisoridae.     

Higher-order phylogeny of modern birds (Theropoda, Aves: Neornithes) based on comparative anatomy. II. Analysis and discussion

In recent years, avian systematics has been characterized by a diminished reliance on morphological cladistics of modern taxa, intensive palaeornithogical research stimulated by new discoveries and an inundation by analyses based on DNA sequences. Unfortunately, in contrast to significant insights into basal origins, the broad picture of neornithine phylogeny remains largely unresolved. Morphological studies have emphasized characters of use in palaeontological contexts. Molecular studies, following disillusionment with the pioneering, but non-cladistic, work of Sibley and Ahlquist, have differed markedly from each other and from morphological works in both methods and findings. Consequently, at the turn of the millennium, points of robust agreement among schools concerning higher-order neornithine phylogeny have been limited to the two basalmost and several mid-level, primary groups. This paper describes a phylogenetic (cladistic) analysis of 150 taxa of Neornithes, including exemplars from all non-passeriform families, and subordinal representatives of Passeriformes. Thirty-five outgroup taxa encompassing Crocodylia, predominately theropod Dinosauria, and selected Mesozoic birds were used to root the trees. Based on study of specimens and the literature, 2954 morphological characters were defined; these characters have been described in a companion work, approximately one-third of which were multistate (i.e. comprised at least three states), and states within more than one-half of these multistate characters were ordered for analysis. Complete heuristic searches using 10 000 random-addition replicates recovered a total solution set of 97 well-resolved, most-parsimonious trees (MPTs). The set of MPTs was confirmed by an expanded heuristic search based on 10 000 random-addition replicates and a full ratchet-augmented exploration to ascertain global optima. A strict consensus tree of MPTs included only six trichotomies, i.e. nodes differing topologically among MPTs. Bootstrapping (based on 10 000 replicates) percentages and ratchet-minimized support (Bremer) indices indicated most nodes to be robust. Several fossil Neornithes (e.g. Dinornithiformes, Aepyornithiformes) were placed within the ingroup a posteriori either through unconstrained, heursitic searches based on the complete matrix augmented by these taxa separately or using backbone-constraints. Analysis confirmed the topology among outgroup Theropoda and achieved robust resolution at virtually all levels of the Neornithes. Findings included monophyly of the palaeognathous birds, comprising the sister taxa Tinamiformes and ratites, respectively, and the Anseriformes and Galliformes as monophyletic sister-groups, together forming the sister-group to other Neornithes exclusive of the Palaeognathae (Neoaves). Noteworthy inferences include: (i) the sister-group to remaining Neoaves comprises a diversity of marine and wading birds; (ii) Podicipedidae are the sister-group of Gaviidae, and not closely related to the Phoenicopteridae, as recently suggested; (iii) the traditional Pelecaniformes, including the shoebill (Balaeniceps rex) as sister-taxon to other members, are monophyletic; (iv) traditional Ciconiiformes are monophyletic; (v) Strigiformes and Falconiformes are sister-groups; (vi) Cathartidae is the sister-group of the remaining Falconiformes; (vii) Ralliformes (Rallidae and Heliornithidae) are the sister-group to the monophyletic Charadriiformes, with the traditionally composed Gruiformes and Turniciformes (Turnicidae and Mesitornithidae) sequentially paraphyletic to the entire foregoing clade; (viii) Opisthocomus hoazin is the sister-taxon to the Cuculiformes (including the Musophagidae); (ix) traditional Caprimulgiformes are monophyletic and the sister-group of the Apodiformes; (x) Trogoniformes are the sister-group of Coliiformes; (xi) Coraciiformes, Piciformes and Passeriformes are mutually monophyletic and closely related; and (xii) the Galbulae are retained within the Piciformes. Unresolved portions of the Neornithes (nodes having more than one most-parsimonious solution) comprised three parts of the tree: (a) several interfamilial nodes within the Charadriiformes; (b) a trichotomy comprising the (i) Psittaciformes, (ii) Columbiformes and (iii) Trogonomorphae (Trogoniformes, Coliiformes) + Passerimorphae (Coraciiformes, Piciformes, Passeriformes); and (c) a trichotomy comprising the Coraciiformes, Piciformes and Passeriformes. The remaining polytomies were among outgroups, although several of the highest-order nodes were only marginally supported; however, the majority of nodes were resolved and met or surpassed conventional standards of support. Quantitative comparisons with alternative hypotheses, examination of highly supportive and diagnostic characters for higher taxa, correspondences with prior studies, complementarity and philosophical differences with palaeontological phylogenetics, promises and challenges of palaeogeography and calibration of evolutionary rates of birds, and classes of promising evidence and future directions of study are reviewed. Homology, as applied to avian examples of apparent homologues, is considered in terms of recent theory, and a revised annotated classification of higher-order taxa of Neornithes and other closely related Theropoda is proposed. (c) 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 149, 1-95.     

Phylogenetic relationships of North American garter snakes (Thamnophis) based on four mitochondrial genes: how much DNA sequence is enough?

The clade of garter snakes (Thamnophis) includes some of the most abundant and well-studied snakes in North America. However, phylogenetic relationships within this group have been little studied. We used DNA sequences of four mitochondrial genes (cytochrome b and NADH dehydrogenase subunits 1, 2, and 4) to estimate relationships among 29 of the 31 recognized species of Thamnophis plus the related species Adelophis foxi. Both maximum parsimony (MP) and maximum-likelihood (ML) analyses of all these genes combined produced well-resolved trees with moderate (70-89%) to strong (90-100%) bootstrap support for most clades. MP and ML trees were very similar, with no strongly supported conflict between the two analyses. These analyses identify a clade of 12 species largely restricted to México (the "Mexican clade"), and a clade containing 15 species that collectively range from Central America to southern Canada (the "widespread clade"). These two groups are identified as sister taxa in both MP and ML analyses. A clade consisting of the ribbon snakes (T. sauritus and T. proximus) and the common garter snake (T. sirtalis) is placed as the sister group to all other Thamnophis (i.e., the Mexican + widespread clades) in our analyses. High bootstrap proportions at several levels in the tree support the inclusion of both Thamnophis validus, which has traditionally been placed in the genus Nerodia, and the poorly known species Adelophis foxi within Thamnophis. We used randomly sampled characters (i.e., standard bootstrapping) and randomly sampled contiguous blocks of characters to examine the effect of number of characters on resolution of and support for relationships within Thamnophis using MP. In general, these analyses indicate that we have reached a point of strongly diminishing returns with respect to the effect of adding mtDNA sequence characters for the current set of taxa; our sample of 3809 mtDNA characters is apparently "enough." The next steps to improve the phylogenetic estimate may be to add nuclear DNA sequences, morphology, or behavior, or to sequence additional mtDNA lineages within species.     

中国薄叶卷柏复合群的物种划分

卷柏属(Selaginella)是石松类植物中最大的属, 也是分类难度较大的类群之一。该属的物种划分主要基于形态特征, 但许多近缘种在形态上很难区分。近年来, 已有大量分子证据被用于各植物类群的分类学研究, 但目前未发现一套适合卷柏属物种鉴定的分子标记。薄叶卷柏复合群(S. delicatula group)是卷柏属下鉴定较为困难的类群, 包括了薄叶卷柏(S. delicatula)、黑顶卷柏(S. picta)和瓦氏卷柏(S. wallichii) 3个物种, 主要分布于亚洲的热带和亚热带地区。为了探讨薄叶卷柏复合群内物种的亲缘关系和评估不同分子标记在卷柏属分类学研究中的应用价值, 本研究对该复合群物种进行广泛取样, 共收集到73个个体, 并选取3个叶绿体基因(rbcL, psbA和atpI)和2个核基因(26S nrDNA和pgiC)片段进行系统树的构建及叶绿体单倍型分析。研究发现, 基于叶绿体和核基因构建的系统发生关系存在冲突: 叶绿体基因树上薄叶卷柏个体分为两个分支(A和B), 薄叶卷柏B分支与薄叶卷柏A-S. picta分支呈姐妹关系, 并且rbcL单倍型分析结果也表明薄叶卷柏A和B两个分支存在明显分化; 而核基因结果则支持该复合群3个物种各自的单系性, 其中, S. delicatula分支与S. picta分支为姐妹群, S. wallichii与S. delicatula-S. picta分支为姐妹关系。在对复合群分布区大量标本的观察以及野外群体调查的基础上, 评估了植株茎和枝的分枝方式、孢子叶、营养叶(侧叶、中叶和腋叶)和孢子表面纹饰等形态性状的分类学价值。结果表明, 薄叶卷柏A和B分支的样本仅在植株分枝方式和大孢子表面纹饰上存在差异, 但无法依靠小孢子表面纹饰、孢子叶穗和营养叶形态等特征进行区分。基于现有证据, 薄叶卷柏复合群至少可划分为薄叶卷柏、黑顶卷柏和瓦氏卷柏3种, 但彻底澄清该复合群的物种划分还需要获取模式标本产地的材料和细胞学证据。最后, 建议在未来卷柏属的分类学研究集中于该属分类复杂的复合群, 结合使用形态学、细胞学、分子生物学(同时使用核基因和叶绿体分子标记)及地理分布等整合证据来进行物种划分。     

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.     

The deep divergences of neornithine birds: a phylogenetic analysis of morphological characters

Consensus is elusive regarding the phylogenetic relationships among neornithine (crown clade) birds. The ongoing debate over their deep divergences is despite recent increases in available molecular sequence data and the publication of several larger morphological data sets. In the present study, the phylogenetic relationships among 43 neornithine higher taxa are addressed using a data set of 148 osteological and soft tissue characters, which is one of the largest to date. The Mesozoic non‐neornithine birds Apsaravis, Hesperornis, and Ichthyornis are used as outgroup taxa for this analysis. Thus, for the first time, a broad array of morphological characters (including both cranial and postcranial characters) are analyzed for an ingroup densely sampling Neornithes, with crown clade outgroups used to polarize these characters. The strict consensus cladogram of two most parsimonious trees resultant from 1000 replicate heuristic searches (random stepwise addition, tree‐bisection‐reconnection) recovered several previously identified clades; the at‐one‐time contentious clades Galloanseres (waterfowl, fowl, and allies) and Palaeognathae were supported. Most notably, our analysis recovered monophyly of Neoaves, i.e., all neognathous birds to the exclusion of the Galloanseres, although this clade was weakly supported. The recently proposed sister taxon relationship between Steatornithidae (oilbird) and Trogonidae (trogons) was recovered. The traditional taxon “Falconiformes” (Cathartidae, Sagittariidae, Accipitridae, and Falconidae) was not found to be monophyletic, as Strigiformes (owls) are placed as the sister taxon of (Falconidae + Accipitridae). Monophyly of the traditional “Gruiformes” (cranes and allies) and ”Ciconiiformes” (storks and allies) was also not recovered. The primary analysis resulted in support for a sister group relationship between Gaviidae (loons) and Podicipedidae (grebes)—foot‐propelled diving birds that share many features of the pelvis and hind limb. Exclusion of Gaviidae and reanalysis of the data set, however, recovered the sister group relationship between Phoenicopteridae (flamingos) and grebes recently proposed from molecular sequence data.     

PHYLOGENETIC RELATIONSHIPS IN SEED PLANTS

Abstract— The phylogenetic relationships of nineteen extant and fossil seed plants are considered. Analysis of 31 characters produced ten topologically similar and equally parsimonious cladograms. A strict consensus tree derived from these cladograms places Lyginopteris as the sister taxon to the other seed plants included. Within this clade all the taxa considered, except medullosans and cycads, form a single monophyletic group defined by the presence of flattened seeds and saccate pollen ("platy-sperms"). Relationships between medullosans, cycads, and "platysperms" were not resolved, but within the "platysperm" clade conifers and cordaites ( Cordaixylon, Mesoxylon ) + Ginkgo form a monophyletic group ("coniferophytes"). The "higher platysperms" (glossopterids, Caytonia , corystosperms, Bennettitales, Pentoxylon , Gnetales, and angiosperms) are also monophyletic, but their relationship to "coniferophytes," peltasperms, and Callistophyton is unresolved. Pentoxylon is placed as sister taxon to the Bennettitales, and together they form the sister group to a clade in which Gnetales and angiosperm are sister taxa. The Bennettitales + Pentoxylon + Gnetales + angiosperms ("anthophytes") form a monophyletic sister group to the corystosperms. This analysis is compared with current classifications of seed plants. It does not support a close relationship between Bennettitales and cycads, it provides no evidence for seed plant polyphyly, and it strongly suggests that the current concept of seed ferns has little value in a phylogenetic context.     

Molecular phylogeny and biogeography of the Neotropical cichlid fish tribe Cichlasomatini (Teleostei: Cichlidae: Cichlasomatinae)

We have conducted the first comprehensive molecular phylogeny of the tribe Cichlasomatini including all valid genera as well as important species of questionable generic status. To recover the relationships among cichlasomatine genera and to test their monophyly we analyzed sequences from two mitochondrial (16S rRNA, cytochrome b) and one nuclear marker (first intron of S7 ribosomal gene) totalling 2236 bp. Our data suggest that all genera except Aequidens are monophyletic, but we found important disagreements between the traditional morphological relationships and the phylogeny based on our molecular data. Our analyses support the following conclusions: (a) Aequidens sensu stricto is paraphyletic, including also Cichlasoma (CA clade); (b) Krobia is not closely related to Bujurquina and includes also the Guyanan Aequidens species A. potaroensis and probably A. paloemeuensis (KA clade). (c) Bujurquina and Tahuantinsuyoa are sister groups, closely related to an undescribed genus formed by the 'Aequidens'pulcher-'Aequidens'rivulatus groups (BTA clade). (d) Nannacara (plus Ivanacara) and Cleithracara are found as sister groups (NIC clade). Acaronia is most probably the sister group of the BTA clade, and Laetacara may be the sister group of this clade. Estimation of divergence times suggests that the divergence of Cichlasomatini started around 44Mya with the vicariance between coastal rivers of the Guyanas (KA and NIC clades) and remaining cis-andean South America, followed by evolution of the Acaronia-Laetacara-BTA clade in Western Amazon, and the CA clade in the Eastern Amazon. Vicariant divergence has played importantly in evolution of cichlasomatine genera, with dispersal limited to later range extension of species within genera.     

Phylogeny of the tribe Colletieae, Rhamnaceae

A cladistic analysis based on 63 morphological characters was carried out on the tribe Colletieae including two presumed closely related genera, Geanothus and Noltea as outgroupS. In addition to a parsimony analysis of the equally weighted characters, analyses investigating the effects of character weighting, removal of a presumed hybrid species as well as the impact of uncertainly scored characters were undertaken. In all analyses Noltea was placed as sister group to a well supported monophyletic Colletieae. Nineteen different in group topologies were found, with the additional analyses mainly supporting two of them. Within the Colletieae a basal dichotomy divides Trevoa and Retanilla from the remainder of the tribe. While the Trevoa-Retanilla clade is fully resolved, the second lacks detailed resolution. Within this clade the Colletia species from a well supported monophyletic group, while monophyly of the disjunct genus Discaria could not be confirmed.     

Molecular and morphological evidence for a new grass genus,Dupontiopsis (Poaceae tribe Poeae subtribe Poinae s.l.), endemic to alpine Japan,and implications for the reticulate origin of Dupontia and Arctophila within Poinae s.l.

Phylogenetic analyses within Poaceae tribe Poeae subtribes Puccinellinae (=Coleanthinae), Phleinae, Poinae s.l. (including Alopecurinae), and Miliinae (PPAM clade), revealed that one species formerly placed in Poa represents a new monotypic genus belonging to subtribe Poinae s.l., Dupontiopsis gen. nov., D. hayachinensis comb. nov. (based on Poa hayachinensis), endemic to wet, gravelly, serpentine, alpine habitats in northern Japan. This genus forms a strongly supported clade (DAD) with two circumarctic Poinae genera, Arctophila and Dupontia, in phylogenetic analyses of plastid and nuclear ribosomal DNA sequence data. Both morphology and DNA sequence analyses provide support for D. hayachinensis as a lineage distinct from either Arctophila or Dupontia, with moderate DNA support for a position as sister to these two genera. Dupontiopsis resembles these other monotypic genera in its several-flowered spikelets, lemmas usually 3-nerved, with frequently awned attenuate scarious apices (as in Dupontia) and calluses with a crown of hairs around the base of the lemma, but differs in its keeled lemmas, scabrous palea keels, glumes shorter than the first lemma. Our investigation suggests that the most recent shared ancestor of the DAD clade evolved from a single hybridization event, as a hexaploid, probably in western Beringia. The probable parentage of the ancestor is considered to be within the Poinae–Alopecurinae clade excluding Poa. We provide evidence for possible secondary hybridization and introgression of duodecaploid Dupontia fisheri with Puccinellia. A key to perennial genera of PPAM with hairy calluses, and a supplemental table of morphological characters in the genera accepted in PPAM are provided.     

Phylogenetic relationships of fantails (Aves: Rhipiduridae)

We explore the phylogenetic relationships of fantails (Aves: Rhipiduridae) using molecular characters derived from two nuclear introns and two mitochondrial genes. Our results indicate that Rhipidura hypoxantha is not a true fantail, but rather a member of the Stenostiridae clade that is morphologically and behaviourally convergent with fantails. Within the true Rhipiduridae, we identified six distinct clades; however, phylogenetic relationships among these groups were unresolved. The only well-supported sister relationship was between members of the grey and the rufous fantail complexes. Clades recovered through our model-based phylogenetic analyses generally correspond to previously proposed fantail complexes based on morphological characters. The phylogenetic position of R. atra and R. diluta remain unclear, as sister relationships varied between analyses for the prior whereas the latter was placed as sister to the New Guinea thicket fantails, R. leucothorax and R. threnothorax ; yet significant node support was not recovered for either taxa. Biogeographically, fantails appear to have radiated rapidly and the six clades are not geographically restricted, but instead span South-east Asia, New Guinea, Australia and Pacific Islands.     

Convergent evolution and character correlation in burrowing reptiles: towards a resolution of squamate relationships

The affinities of three problematic groups of elongate, burrowing reptiles (amphisbaenians, dibamids and snakes) are reassessed through a phylogenetic analysis of all the major groups of squamates, including the important fossil taxa Sineoamphisbaena, mosasauroids and Pachyrhachis; 230 phylogenetically informative osteological characters were evaluated in 22 taxa. Snakes (including Pachyrhachis) are anguimorphs, being related firstly to large marine mosasauroids, and secondly to monitor lizards (varanids). Scincids and cordylids are not related to lacertiforms as previously thought, but to anguimorphs. Amphisbaenians and dibamids are closely related, and Sineoamphisbaena is the sister group to this clade. The amphisbaenian-dibamid-Sineoamphisbaena clade, in turn, is related to gekkotans and xantusiids. When the fossil taxa are ignored, snakes, amphisbaenians and dibamids form an apparently well-corroborated clade nested within anguimorphs. However, nearly all of the characters supporting this arrangement are correlated with head-first burrowing (miniaturization, cranial consolidation, body elongation, limb reduction), and invariably co-occur in other tetrapods with similar habits. These characters are potentially very misleading because of their sheer number and because they largely represent reductions or losses. It takes very drastic downweighting of these linked characters to alter tree topology: if fossils are excluded from the analysis, a (probably spurious) clade consisting of elongate, fossorial taxa almost always results. These results underscore the importance of including all relevant taxa in phylogenetic analyses. Inferring squamate phylogeny depends critically on the inclusion of certain (fossil) taxa with combinations of character states that demonstrate convergent evolution of the elongate, fossorial ecomorph in amphisbaenians and dibamids, and in snakes. In the all-taxon analysis, the position of snakes within anguimorphs is more strongly-corroborated than the association of amphisbaenians and dibamids with gekkotans. When the critical fossil taxa are deleted, snakes ‘attract’ the amphisbaenian-dibamid clade on the basis of a suite of correlated characters. While snakes remain anchored in anguimorphs, the amphisbaenian-dibamid clade moves away from gekkotans to join them. Regardless of the varying positions of the three elongate burrowing taxa, the interrelationships between the remaining limbed squamates (‘lizards’) are constant; thus, the heterodox affinities of scincids, cordylids, and xantusiids identified in this analysis appear to be robust. Finally, the position of Pachyrhachis as a basal snake rather than (as recently suggested) a derived snake is supported on both phylogenetic and evolutionary grounds.     

A phylogenetic analysis of the tropidurine lizards (Squamata: Tropiduridae), including new characters of squamation and epidermal microstructure

Characters of scale surface microstructure are combined with 'traditional'morphological characters in a phylogenetic analysis of the Tropidurini. Tropidurid lizards show variation in types of coarse and fine scale surface microstructure, in the anatomical distribution of different scale surface features, and in scale organ morphology and distribution. The morphology of the inner surface zone of scales is here described for the first time using scanning electron microscopy. Our phylogeny differs considerably from those proposed in earlier studies. New characters and frequency coding of polymorphic characters help resolve the problematic relationships of several species. Statistical confidence supports recognition of one large cis-Andean and one large trans-Andean clade of species. Based on our results, we synonymize Plesiomicrolophus with Microlophus and Uranoscodon with Tropidurus. The phylogenetic relationships of newly discovered Tropidurus are resolved: T. caltathelys is the sister species of T. melanopleurus; T. xanthochilus is the sister species of T. spinulosus. Tropidurus spinulosus is found to be more closely related to T. strobilurus and a clade of Amazonian species than to T. melanopleurus. The species previously placed in Uracentron are more closely related to species previously placed in Plica than to 77 strobilurus as previously thought.     

Molecular phylogenetics of the giant genus Croton and tribe Crotoneae (Euphorbiaceae sensu stricto) using ITS and TRNL-TRNF DNA sequence data

Parsimony, likelihood, and Bayesian analyses of nuclear ITS and plastid trnL-F DNA sequence data are presented for the giant genus Croton (Euphorbiaceae s.s.) and related taxa. Sampling comprises 88 taxa, including 78 of the estimated 1223 species and 29 of the 40 sections previously recognized of Croton. It also includes the satellite genus Moacroton and genera formerly placed in tribe Crotoneae. Croton and all sampled segregate genera form a monophyletic group sister to Brasiliocroton, with the exception of Croton sect. Astraea, which is reinstated to the genus Astraea. A small clade including Moacroton, Croton alabamensis, and C. olivaceus is sister to all other Croton species sampled. The remaining Croton species fall into three major clades. One of these is entirely New World, corresponding to sections Cyclostigma, Cascarilla, and Velamea sensu Webster. The second is entirely Old World and is sister to a third, also entirely New World clade, which is composed of at least 13 of Webster's sections of Croton. This study establishes a phylogenetic framework for future studies in the hyper-diverse genus Croton, indicates a New World origin for the genus, and will soon be used to evaluate wood anatomical, cytological, and morphological data in the Crotoneae tribe.     

A molecular systematic revision of two historically problematic songbird clades: Aimophila and Pipilo

The emberizid genera Aimophila and Pipilo represent longstanding taxonomic conundrums. Each is comprised of sub-clades whose members appear to share diagnostic morphological and behavioral characters; however, relationships among sub-clades within each of these genera remain unclear, and numerous authors have suggested that either one or both of these genera may be polyphyletic. We addressed this taxonomic problem by sequencing and analyzing complete mitochondrial cytochrome- b and NADH dehydrogenase subunit 2 genes for all members of Aimophila and Pipilo along with 33 species representing 17 additional emberizid genera. Our maximum likelihood and Bayesian analyses indicate that both Aimophila and Pipilo are polyphyletic. Aimophila is divided into a minimum of three distinct groups. The forms notosticta, ruficeps , and rufescens are part of a well-supported clade that includes all members of Melozone and some members of Pipilo . Aimophila quinquestriata is placed within Amphispiza , and the remaining members of Aimophila are placed within a clade that includes all members of Arremonops and some members of Ammodramus . Within Pipilo , the "rufous-sided" and "brown" towhee groups do not form sister groups. Rather, the former are most closely related to the tropical genus Atlapetes whereas the latter are placed nearest Melozone and some Aimophila . Our analyses reject traditional taxonomic arrangements for both genera, and we present suggestions for a revised taxonomy for all members of Aimophila and Pipilo . These results provide further evidence of discordance among phylogenetic hypotheses based on morphological and molecular characters for groups of birds with generally conserved morphology.     

Phylogenetic studies on the Thamnocalamus group and its allies (Gramineae: Bambusoideae) based on its sequence data.

Phylogenetic analyses, using the parsimony method and the neighbor-joining method, of 31 species of the Thamnocalamus group and its allies based on internal transcribed spacer (ITS) sequences in nuclear ribosomal DNA are presented. Two species from Arundinaria and Acidosasa were used as outgroups. The ITS phylogeny strongly supports the monophyly of the Thamnocalamus group and its allies, which have pachymorph rhizomes and semelauctant synflorescences with three stamens. Within this clade, Chimonocalamus pallens was resolved in the basal position. The Thamnocalamus group, including species placed in Thamnocalamus, Fargesia (Sinarundinaria, Borinda), and Yushania, may be polyphyletic/paraphyletic according to the ITS phylogeny, but internal support was relatively low. All three sampled species of Ampelocalamus were resolved as a monophyletic group and may be related to Drepanostachyum hookerianum. Two taxa of Thamnocalamus and the species Gaoligongshania megalothyrsa were resolved as monophyletic despite their different morphological characters, but again with a low bootstrap support. Within the Fargesia yunnanensis subclade, the sister relationship of Fargesia fungosa and Fargesia edulis was supported. Another subclade, the Fargesia communis clade, was also weakly supported as monophyletic. However, further resolution within the Thamnocalamus group has not been provided by this sequence data. The results indicate that reevaluation of relationships within this group is necessary.