Molecular phylogeny of basal gobioid fishes: Rhyacichthyidae, Odontobutidae, Xenisthmidae, Eleotridae (Teleostei: Perciformes: Gobioidei)

Morphological character analyses indicate that Rhyacichthyidae, Odontobutidae, Eleotridae, and Xenisthmidae are the basal families within the perciform suborder Gobioidei. This study uses DNA sequence data to infer the relationships of genera within these families, as well as determine the placement of more derived gobioids (family Gobiidae) and the identity of the outgroup to Gobioidei. Complete sequences of the mitochondrial ND1, ND2, COI, and cyt b genes (4397 base pairs) are analyzed for representatives of 27 gobioid genera and a variety of perciform and scorpaeniform outgroup candidates; the phylogeny is rooted with a beryciform as a distal outgroup. The single most parsimonious tree that results indicates that, of the outgroups sampled, the perciform family Apogonidae is most closely related to Gobioidei. Gobioidei is monophyletic, and Rhyacichthys aspro is the most basal taxon. The remainder of Gobioidei is resolved into clades corresponding to the families Odontobutidae (plus Milyeringa) and Eleotridae+Xenisthmidae+Gobiidae. Within Eleotridae, the subfamily Butinae (minus Milyeringa) is paraphyletic with respect to Gobiidae, and Eleotrinae is paraphyletic with respect to Xenisthmidae. Other than these groupings, the primary disagreement with the current morphology-based classification is that the molecular data indicate that the troglodytic Milyeringa should be placed in Odontobutidae, not Butinae, although support for this placement is weak. The most basal lineage of Gobioidei is known from the freshwaters of the Indo-Pacific, with marine-dwelling lineages arising several times independently in the group. The phylogeny also indicates that different gobioid lineages are distributed in Asia, Africa, Madagascar and the Neotropics. Five sister pairs of basal gobioid species inhabit Atlantic and Pacific drainages of Panama, with widely varying divergences.     

Evolutionary aspects of gobioid fishes based upon a phylogenetic analysis of mitochondrial cytochrome B genes

The Gobioidei is a large suborder in the order Perciformes and consists of more than 2000 species belonging to about 270 genera. The vast number of species and their morphological specialization adapted to diverse habits and habitats makes the classification of the gobioid fishes very difficult.A comprehensive estimation of the evolutionary scenario of all gobioid fishes using only morphological information is difficult for two major reasons: first, in addition to wide ecological diversification, there is a trend towards specialization and degeneration of morphological characters among these species; second, an appropriate outgroup of gobioid fishes has not been recognized.Based upon nucleotide sequence comparisons of gobioid mitochondrial cytochrome b genes, we established the phylogenetic relationships of their differentiation into many groups of morphological and ecological diversity. The phylogenetic trees obtained show that most species examined have diverged from each other almost simultaneously or during an extremely short period of time.     

A standardized reanalysis of molecular phylogenetic hypotheses of Gobioidei

Gobioidei is a suborder of perciform fishes with about 2000 species distributed worldwide. Despite the evolutionary and ecological importance of gobioids, their phylogenetic inter- and intrarelationships are still poorly understood. Only a few studies (either morphological or molecular) have tackled the phylogeny of Gobioidei as a whole. Of these, only six studies thus far have addressed gobioid intrarelationships based on molecular data (each using different taxon sampling, genes, outgroups and method of phylogenetic inference), yielding contrasting results regarding the phylogenetic relationships among major lineages. In this study, we have reanalysed data from four of these molecular phylogenetic studies of Gobioidei under standardization criteria (same outgroup and methods of phylogenetic inference) in order to assess the robustness of their results, as well as to identify which parts of the gobioid tree are least resolved. Results from all datasets reanalysed in this study are generally similar to those of the respective original studies, and suggest broad patterns of phylogenetic relationships among gobioid lineages. However, there are numerous topological discrepancies among the four studies, support is low for many phylogenetic relationships and topology tests are unable to reject the vast majority of alternative topologies tested. The concatenation of datasets yields a relatively robust phylogeny of major lineages of Gobioidei, but there are some issues of overlap and missing data, which are ameliorated with the inclusion of additional homologous sequences from GenBank that increase dataset completeness. Because both monophyly of major gobioid groups and phylogenetic relationships among them cannot be fully resolved, it is clear that further phylogenetic research is needed, and this should be accompanied by a major taxonomic revision of the Gobioidei. Nevertheless, even with the relatively unstable nature of the available molecular phylogenies, there are some monophyletic units that can be identified, and a basic structure of the gobioid tree appears evident.     

Species and shape diversification are inversely correlated among gobies and cardinalfishes (Teleostei: Gobiiformes)

Gobies and their relatives are significant components of nearshore marine, estuarine, and freshwater fish faunas in both tropical and temperate habitats worldwide. They are remarkable for their ability to adapt to and diversify in a wide range of environments. Among gobiiform clades, species diversities vary widely, ranging from two species in Kurtidae to more than 1,000 species in Gobiidae. There is also great variation in head and body shape and in environmental preferences (fresh, brackish, or marine habitats). In this study, I used a time-calibrated molecular phylogeny, coupled with morphometric and comparative analyses, to examine evolutionary rates of both speciation and morphological diversification among gobiiform lineages. Projection of the phylogeny onto a shape-derived morphospace shows that Gobioidei is morphometrically distinct from its sister taxon Apogonoidei, but that families within Gobioidei overlap in morphospace. Analysis of species diversification rates indicates that three rate shifts have occurred over the evolutionary history of Gobiiformes. Relative to the other lineages, Kurtidae has exhibited a slowdown in speciation, whereas both Apogonidae and Gobiidae?+?Gobionellidae have experienced an increase in diversification. Comparative analyses show that in Apogonidae and Gobiidae?+?Gobionellidae, increased speciation is correlated with diminished rates of morphological diversification, differently manifested in either clade and among the various sublineages. The elevation in speciation rates and diminishment in rates of morphological change in both Apogonidae and the clade Gobiidae?+?Gobionellidae are correlated with shifts to oceanic habitats from freshwater. This pattern is the complement to that seen across the global radiation of acanthomorph fishes in which a decrease in species diversification is associated with an increase in morphological disparity.     

A phylogenetic supertree of the bats (Mammalia: Chiroptera)

We present the first estimate of the phylogenetic relationships among all 916 extant and nine recently extinct species of bats Mammalia: Chiroptera), a group that accounts for almost one-quarter of extant mammalian diversity. This phylogeny was derived by combining 105 estimates of bat phylogenetic relationships published since 1970 using the supertree construction technique of Matrix Representation with Parsimony (MRP). Despite the explosive growth in the number of phylogenetic studies of bats since 1990, phylogenetic relationships in the order have been studied non-randomly. For example, over one-third of all bat systematic studies to date have locused on relationships within Phyllostomidae, whereas relationships within clades such as Kerivoulinae and Murinae have never been studied using cladistic methods. Resolution in the supertree similarly differs among clades: overall resolution is poor (46.4%, of a fully bifurcating solution) but reaches 100% in some groups (e.g. relationships within Mormoopidae). The supertree analysis does not support a recent proposal that Microchiroptera is paraphyletic with respect to Megachiroptera, as the majority of source topologies support microbat monophyly. Although it is not a substitute for comprehensive phylogenetic analyses of primary molecular and morphological data, the bat supertree provides a useful tool for future phylogenetic comparative and macroevolutionary studies. Additionally, it identifies clades that have been little studied, highlights groups within which relationships are controversial, and like all phylogenetic studies, provides preliminary hypotheses that can form starting points for future phylogenetic studies of bats.     

Morphological phylogenetics of the sea spiders (Arthropoda: Pycnogonida)

Pycnogonids or sea spiders are a group of marine arthropods whose relations to the chelicerates have been an issue of controversy. Higher-level phylogenetic relationships among the lineages of sea spiders are investigated using 36 morphological characters from 37 species from all extant families and a Devonian pycnogonid fossil. This is one of the first attempts to analyze the higher-level relationships of the Pycnogonida using cladistic techniques. Character homoplasy (implied weights) is taken into account to construct a polytomous, most-parsimonious tree in which two major clades within Pycnogonida are obtained. Clade A includes Ammotheidae paraphyletic with Colossendeidae, Austrodecidae and Rhynchothoracidae, and clade B is formed by Nymphonidae, Callipallenidae (apparently paraphyletic), Pycnogonidae and Phoxichilidiidae. The analysis of equally weighted data is presented and helps to identify those characters less consistent. The reduction of the chelifores, palps and ovigers — shown independently within each of the clades as parallel evolution events — challenges the assumption of a gradual mode of reduction within the group, according to analysis of unordered vs ordered characters. Most of the phylogenetic affinities proposed here are compatible with traditional classifications. However, traditional taxonomic characters need to be complemented by sets of anatomical, molecular and developmental data, among others, to produce more robust phylogenetic hypotheses on the higher- and lower-level relationships of the sea spiders.     

姬缘蝽科系统发育初探：（异翅亚目：缘蝽总科）

本文通过对姬缘蝽科１４属的比较形态学研究,以支序分析方法探讨了各类间的系统发育关系,３其结果证明姬缘蝽科为一明显单系群,并支持Ｃｈｏｐｒａ（１９６７）系统中大部分族的划分意见,但因支序图中玛缘蝽族和姬缘蝽亚科为并系群,从而对Ｃｈｏｐｒａ系统中亚科的划分及玛缘蝽族是否成立提出疑问,并认为已有系统中的“红缘蝽亚科”应降为族级。文中还将支序分析结果与经前作者的系统发育意见相比较,认为本文所提出的关于该科     

Phylogenetic analysis of the Hsp70 sequences reveals the monophyly of Metazoa and specific phylogenetic relationships between animals and fungi

To understand the early evolution of the Metazoa, it is necessary to determine the correct phylogenetic status of diploblastic animals. Despite cladistic studies of morphological characters and recent molecular phylogenetic studies, it remains uncertain whether diploblasts are monophyletic or paraphyletic, and how the phyla of diploblasts are phylogenetically related. The heat shock protein 70 (Hsp70) sequences, because of their ubiquity and high degree of conservation, could provide a useful model for phylogenetic analysis. We have sequenced almost the entire nucleic acid sequence of cytoplasmic Hsp70 from eight diploblastic species. Our data support the monophyly of diploblastic animals. However, the phylogenetic relationships of the diploblast groups were not significantly resolved. Our phylogenetic trees also support the monophyly of Metazoa with high bootstrap values, indicating that animals form an extremely robust clade.      

Phylogenetic analysis of the Brachyura (Crustacea, Decapoda) based on characters of the foregut with establishment of a new taxon

The Brachyura, within the decapod crustaceans, is one of the most species-rich taxa with up to 10 000 species. However, its phylogenetic history, evolution and fossil record remain subjects of controversy. In our study, we examined the phylogenetic relationships of the Brachyura based on morphological characters of the foregut. The cladistic analysis supports a monophyletic Brachyura including the Dromiidae and Raninidae. A clade comprising Dromiidae and Dynomenidae forms the most basal assemblage within the Brachyura, followed by the Homolidae and Latreilliidae. As a result, neither Podotremata nor Archaeobrachyura form a clade. In contrast, foregut data suggest that the classical taxon Oxystomata, comprising Calappidae, Parthenopidae, Dorippidae, Leucosiidae, Cymonomidae and Raninidae, is monophyletic. This makes the Heterotremata paraphyletic or polyphyletic. A newly established taxon, Neobrachyura, embraces some representatives of the Heterotremata and the monophyletic Thoracotremata.     

基于形态学证据的长足虻科系统发育研究(双翅目,短角亚目)

试图根据成虫形态学证据探讨长足虻科各亚科之间的系统关系,同时检验各个亚科的单系性.在比较形态学研究基础上,同时参考前人有关长足虻科高阶元分类的研究结果,筛选出42个来自头部、胸部(包括足和翅)、腹部、雌性和雄性外生殖器在亚科水平的分类特征,为了考察亚科的单系性,也包括亚科的自有衍征;运用支序分类的方法,首次分析并讨论了世界长足虻科17个亚科之间的系统发育关系.结果表明,长足虻科是一个严格的单系群,其支持的共同衍征为体色金绿,亚前缘脉端部与第1径脉中部愈合,前缘脉接近肩横脉处有1个缺刻,第2基室与盘室愈合,臀室短小、终止于径脉分叉点之前,雄性外生殖器明显向下或向前弯折,生殖背板具生殖孔,下生殖板与第9背板愈合.金长足虻亚科Sciapodinae腋瓣发达,中脉分叉,为最基部的支系,是最原始的亚科;而长足虻科的其他亚科构成一单系群,其共同衍征为腋瓣不明显,中脉不分叉.斜脉长足虻亚科Plagioneurinae也比较原始,是靠基部的支系,支持其单系性的特征为腹部第7～8节膜质化,生殖孔基位.异长足虻亚科Diaphorinae和锥长足虻亚科Rhaphiinae以及斯长足虻亚科Stolidosomatinae和合长足虻亚科Sympycninae分别构成姊妹群关系,斯长足虻亚科Stolidosomatinae的两个属Pseudosympycnus和Stolidosoma系统地位还有待进一步研究.此外,巴长足虻亚科Babindellinae、聚脉长足虻亚科Medeterinae和寇长足虻亚科Kowmunginae构成单系群,其共同衍征为臀脉短或不明显,无后顶鬃.研究所用标本大部分保存在中国农业大学昆虫标本馆,包括与美国史密森研究院和澳大利亚博物馆交换而来的标本,部分标本保存在比利时皇家科学院.     

Molecular phylogenetic relationships of neotropical salamanders of the genus Pseudoeurycea

Pseudoeurycea, with 34 described species, is one of the most diversified groups of neotropical salamanders. I generated a phylogenetic hypothesis of relationships for Pseudoeurycea and related taxa, based on DNA sequences of 16S, Cyt b, and ND4 mitochondrial genes. The analyses include 27 species of Pseudoeurycea and samples from the monotypic Lineatriton, Ixalotriton, and Parvimolge. All phylogenetic analyses resulted in a paraphyletic Pseudoeurycea. Ixalotriton and Pseudoeurycea parva always form a monophyletic group. P. parva is transferred to Ixalotriton based on morphological and molecular grounds. The phylogenetic position of the newly defined Ixalotriton clade is uncertain since it is part of an unresolved basal polytomy. Parvimolge is closely related to Pseudoeurycea, and it is also part of the basal polytomy. Lineatriton, a highly specialized taxon, is deeply nested within Pseudoeurycea. In order to provide a taxonomic arrangement consistent with the monophyly of the different units that reflects both evolutionary history and morphological specialization, Pseudoeurycea should be split into several taxonomic units.     

Conflicting phylogenetic hypotheses for the parasitic platyhelminths tested by partial sequencing of 18S ribosomal RNA

Partial sequencing of the 18S ribosomal RNA in nine parasitic and one free-living species of platyhelminth was used to test hypotheses on the phylogenetic relationships among the major groups. The eucestodes, amphilinideans, gyrocotylideans and monopisthocotylideans appeared as a monophyletic assemblage in a cladistic analysis of the data, with a very close association between the gyrocotylideans and monopisthocotylideans. The polyopisthocotylidean monogeneans were paraphyletic to the monopisthocotylideans. The digeneans appeared to be a sister group to the monogeneans and eucestodes, while the temnocephalidean was closely related to the free-living polyclad.     

Complete mitochondrial genome of spined sleeper Eleotris oxycephala (Perciformes,Eleotridae) and phylogenetic consideration

The complete mitochondrial genome of Eleotris oxycephala was determined to be 16,527 bp in length with (A + T) content of 53%, and it consists of 13 protein-coding genes, 22 tRNAs, 2 ribosomal RNAs, and a control region. The gene composition and the structural arrangement of the E. oxycephala complete mtDNA were identical to most of other vertebrates. Phylogenetic analysis based on different sequences of species of the Gobioidei suborder and different methods showed that E. oxycephala formed a cluster with Eleotris acanthopoma and Eleotridae were divided into two clades. Furthermore, extensive taxon sampling and more molecular information are needed to confirm the phylogenetic relationships among the Gobioidei.     

雪雀属系统发育关系的研究（雀形目：文鸟科)

雷雀属Montifringilla7种36个形态特征作为分类单元,进行支序分析。以麻雀属Passer、石雀属Petronia部分种类作为比较外群,讨论雪雀属的分类地位及其与近缘属麻雀属、石雀属系统发育关系;分析了雪雀属内种间的系统发育。支序分析的结果表明雪雀属为单系群,建议将雪雀属划分成两个亚属,讨论了雪雀属种类在进货上的位置,在3个近缘属的系统发育关系中,麻雀属类群较原始,雪雀属类群较进化,石雀属在进货中介于二之间。     

Phylogenetic relationships of the monozoic tapeworms (Eucestoda: Caryophyllidea) inferred from morphological characters

Phylogenetic relationships of all genera of the order Caryophyllidea, possibly the earliest branching group of true tapeworms (Platyhelminthes: Eucestoda) and the only one that is monozoic, have been assessed for the first time. Results of this cladistic analysis, inferred from 30 unweighted morphological characters, are only partly congruent with the existing classification, which consists of four families based on the position of the inner longitudinal muscles in relation to the internal genital organs. Whereas all but five genera of the Caryophyllaeidae form a monophyletic clade, members of the Capingentidae are split, occurring within six unrelated groups. The Lytocestidae is also paraphyletic, as some genera appear in four unrelated clades. Archigetes appears in a derived clade, indicating that its direct (monoxenous) life-cycle involving only tubificid oligochaetes is secondarily derived and not plesiomorphic among the Eucestoda, as postulated by some authors.     

Root causes of phylogenetic incongruence observed within basal sauropodomorph interrelationships

The relationships among basal sauropodomorphs are controversial. Results of cladistic analyses vary from a fully paraphyletic assemblage to a monophyletic core‐prosauropod. We apply the comparative cladistics method to three published cladistic analyses of sauropodomorph dinosaurs, in order to identify root causes for differences between phylogenetic results. Except for three taxa (Saturnalia, Thecodontosaurus, and Efraasia) and one clade (Gravisauria), the remaining genera are recovered with conflicting positions. The comparative method is based on indices that allow for the quantification of the degree of similarity in characters and character states among analyses. A comparison of primary data, character selection, and scoring highlights significant discrepancies in data sets. Our results suggest that one character out of two varies from one analysis to the other. These are the root causes for the phylogenetic incongruence observed. The hurdle of the phylogenetic definition of the clade Sauropoda, which has been defined in four different ways, is also treated. We concur with several recent papers following the first node‐based definition of Sauropoda. © 2015 The Linnean Society of London     

Anatomical variation in Cactaceae and relatives: Trait lability and evolutionary innovation

The cacti have undergone extensive specialization in their evolutionary history, providing an excellent system in which to address large-scale questions of morphological and physiological adaptation. Recent molecular phylogenetic studies suggest that (1) Pereskia, the leafy genus long interpreted as the sister group of all other cacti, is likely paraphyletic, and (2) Cactaceae are nested within a paraphyletic Portulacaceae as a member of the "ACPT" clade (Anacampseroteae, Cactaceae, Portulaca, and Talinum). We collected new data on the vegetative anatomy of the ACPT clade and relatives to evaluate whether patterns in the distributions of traits may provide insight into early events in the evolutionary transition to the cactus life form. Many traits had high levels of homoplasy and were mostly equivocal with regard to infraclade relationships of ACPT, although several characters do lend further support to a paraphyletic Pereskia. These include a thick stem cuticle, prominent stem mucilage cells, and hypodermal calcium oxalate druses, all of which are likely to be important traits for stem water storage and photosynthesis. We hypothesize that high lability of many putative "precursor" traits may have been critical in generating the organismal context necessary for the evolution of an efficient and integrated photosynthetic stem.     

Phylogenetic relationships within a patagonian clade of reptiles (Liolaemidae: Phymaturus) based on DNA sequences and morphology

Phymaturus is a clade of lizards that occurs at moderate to high elevations in western Argentina and the adjacent central region of Chile, as well as in various volcanic plateaus of the Patagonian region of Argentina. This genus had previously been divided into two groups: the patagonicus and the palluma groups. In this study, we analyzed relationships within the patagonicus group. The data set was built for 23 species plus nine other terminal taxa of undetermined taxonomic status. In total, 10,631 bp (ND4, Cytb, 12S, COI, five protein coding nuclear genes and seven anonymous nuclear loci) and 254 morphological characters were analyzed in a combined data set for 35 ingroup taxa and nine outgroups. We also ran separate DNA sequence and morphological data sets. We identified four main clades, and revealed congruencies and incongruences with previous studies. The indistinctus clade is recovered as the most basal within the patagonicus group in the strict parsimony analysis, while the somuncurensis clade is the most basal under Bayesian inference. The previously recovered calcogaster clade resulted paraphyletic in both analyses and part of their species are included in a redefined somuncurensis clade. We found low support at basal nodes provoked in part by contradictory evidence shown by rogue taxa. We show the phylogenetic information given by each partition/marker and how they contribute to relationships found in the total evidence analysis. We discuss the phylogenetic position of Phymaturus manuelae, Phymaturus tenebrosus, and Phymaturus patagonicus.     

DNA barcoding of xeniid soft corals (Octocorallia: Alcyonacea: Xeniidae) from Indonesia: species richness and phylogenetic relationships

We conducted the first ever survey of xeniid octocorals in the Indonesian Archipelago, centre of the highly biodiverse Coral Triangle region of the Indo-Pacific. Among 48 xeniid specimens collected from Lembeh Strait, North Sulawesi, we identified 26 morphospecies belonging to six genera based on assessment of the morphological characters traditionally used for xeniid taxonomy. Multilocus DNA barcodes obtained from 23 morphospecies clustered into 21 molecular operational taxonomic units (MOTUs) separated by average genetic distance values >0.3%. The overall concordance between morphospecies and MOTUs was 91%; just one pair and one trio of morphospecies were not distinguished by the DNA barcodes. A molecular phylogenetic reconstruction of family Xeniidae based on four loci (COI, mtMutS, ND2, 28S rDNA) supported the distinction of Anthelia and Cespitularia+Efflatounaria from all other xeniid genera. Although the remaining genera for which molecular data were available (Asterospicularia, Heteroxenia, Ovabunda, Sansibia, Sarcothelia, Sympodium, Xenia) belonged to a single, well-supported clade, the phylogenetic relationships among them were poorly resolved. Species of Xenia were distributed among three different sub-clades within which they were paraphyletic with Ovabunda (clade X1), Heteroxenia (clade X2) and Sansibia plus Sarcothelia (clade X3). No morphological characters have yet been identified that differentiate these three phylogenetically distinct clades of Xenia. Use of molecular barcodes to discriminate species will facilitate future ecological studies of Xeniidae, a group that has been shown to opportunistically monopolize disturbed reef habitat.     

Interrelationships of the Gastrotricha and their place among the Metazoa inferred from 18S rRNA genes

The phylum Gastrotricha includes about 700 species. They are small worm‐like organisms abundant among marine and freshwater meiobenthos. In spite of their ubiquity, diversity and relative abundance, phylogenetic relationships of these animals remain enigmatic due to the conflicting results of morphological and molecular cladistic analyses. Also unclear are the alliances within the phylum. In order to best estimate the position of Gastrotricha among the Metazoa and to shed some light on the ingroup phylogenetic relationships, small subunit (SSU) ribosomal DNA (rDNA) from 15 species of Chaetonotida (eight genera) and 28 species of Macrodasyida (26 genera) were included in an alignment of 50 metazoan taxa representing 26 phyla. Of the gastrotrich SSU rDNA sequences, eight are new and, along with published sequences represent eight families, including the five marine most speciose. Gastrotricha were resolved within a monophyletic Lophotrochozoa as part of a clade including Micrognathozoa, Rotifera and Cycliophora. The Gnathostomulida were sister to this clade. Nodal support was low for all of these relationships except the grouping of the Micrognathozoa, Rotifera and Cycliophora. Bayesian inference resolved the Gastrotricha as monophyletic with weak nodal support; the Macrodasyida were resolved as paraphyletic with many basal nodes poorly supported. Within the Chaetonotida, the monotypic Multitubulatina Neodasys was found in alliance with the macrodasyidan Urodasys while all the Paucitubulatina were found to form a single, well‐supported clade, with Musellifer as the most basal member. Among the more densely sampled Macrodasyida the Lepidodasyidae and Macrodasyidae were each found to be polyphyletic while monophyly was well supported for the Turbanellidae and Thaumastodermatidae. The congruence of our results with those of the cladistic analysis based on morphological traits provides confidence about the value of each dataset, and calls for widening of the research to include additional taxa of particular phylogenetic significance such as the Dactylopodolidae, Diuronotus, Heteroxenotrichula and Draculiciteria. The study highlights the problems in working with small species, the need for voucher specimens and the confused taxonomic status and membership of various gastrotrich families.